Progress in lactic acid bacterial phage research

Abstract

Research on lactic acid bacteria (LAB) has advanced significantly over the past number of decades and these developments have been driven by the parallel advances in technologies such as genomics, bioinformatics, protein expression systems and structural biology, combined with the ever increasing commercial relevance of this group of microorganisms. Some of the more significant and impressive outputs have been in the domain of bacteriophage-host interactions which provides a prime example of the cutting-edge model systems represented by LAB research. Here, we present a retrospective overview of the key advances in LAB phage research including phage-host interactions and co-evolution. We describe how in many instances this knowledge can be pivotal in creating real improvements in the application of LAB cultures in commercial practice.

Figure 1

Schematic representation of the known morphotypes of phages infecting LAB. 1A represents the prolate-headed Siphoviridae while 1B represents the isometric-headed Siphoviridae phages. Members of the Siphoviridae family possess long non-contractile tails. 1C displays the long contractile tail typical of Myoviridae phages. 1D is a schematic highlighting the short non-contractile tails of the Podoviridae phages.

Figure 2

Pan-virome analysis of the P335 and 936 phage species. 2A) Heatmap showing the hierarchical clustering analysis conducted on the P335 and 936 data sets. The separation achieved between the two species is indicated by a vertical red line, while the 936 common genes (core genome) area is indicated by a horizontal green line. B & C) Accumulated number of P335 (b) or 936 (c) pan-virome genes, respectively, plotted against the number of P335 (b) or 936-species (c) phage genomes added. The deduced mathematical function is also indicated.

Figure 3

Figure adapted from Chapot-Chartier et al., 2010 [51] and Farenc et al., 2014 [53] highlighting the structure of the cell wall polysaccharide of L. lactis SMQ388, 3107 and MG1363. The relatively conserved rightmost trisaccharide coloured in green, red and purple represents the proposed receptor for the lactococcal phages infecting these host strains i.e. 1358, TP901-1 and p2, respectively.

Figure 4

The crystal structure of the "heads-down" conformations of L. lactis phage p2 baseplate. (A) Side view in ribbon representation of the "heads-down" conformations of L. lactis phage p2 baseplate. (B) View from top (ORF15, green; ORF16, pink; ORF18 (RBP), blue). (C) Superposition of the rings formed by the N-terminal domains of ORF15. ORF18 (RBP) trimers have undergone a 200° rotation downwards [63]. This figure has been taken from Sciara et al., 2010 with permission [63].

Figure 5

Structure of the L. lactis phage TP901-1 baseplate (i.e., host adsorption machinery). This figure is adapted from Veesler et al., 2012 with permission [64]. (Left) Negatively-stained electron micrograph of a TP901-1 virion. (Right) Close-up view of the phage baseplate X-ray structure fitted in the adsorption device three-dimensional electron microscopy reconstruction (the region is highlighted by a black square on the micrograph). The baseplate is formed by 18 copies of BppU (red) arranged around a central Dit hexamer (green) and holding eighteen trimeric RBPs (receptor-binding proteins, blue). The baseplate is permanently observed in the RBP downward-facing or "infection-ready" orientation.