Genetic and functional characterisation of the lactococcal P335 phage-host interactions

Abstract

BackgroundDespite continuous research efforts, bacterio(phages) infecting Lactococcus lactis starter strains persist as a major threat to dairy fermentations. The lactococcal P335 phages, which are currently classified into four sub-groups (I-IV), are the second most frequently isolated phage group in an industrial dairy context.ResultsThe current work describes the isolation and comparative genomic analysis of 17 novel P335 group phages. Detailed analysis of the genomic region of P335 phages encoding the so-called “baseplate”, which includes the receptor binding protein (RBP) was combined with a functional characterization of the RBP of sub-group III and IV phages. Additionally, calcium-dependence assays revealed a specific requirement for calcium by sub-group IV phages while host range analysis highlighted a higher number of strains with CWPS type A (11 of 39 strains) are infected by the P335 phages assessed in this study than those with a C (five strains), B (three of 39 strains) or unknown (one of 39 strains) CWPS type.ConclusionsThese analyses revealed significant divergence among RBP sequences, apparently reflecting their unique interactions with the host and particularly for strains with a type A CWPS. The implications of the genomic architecture of lactococcal P335 phages on serving as a general model for Siphoviridae phages are discussed.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3537-5) contains supplementary material, which is available to authorized users.

A Decade of Streptococcus thermophilus Phage Evolution in an Irish Dairy Plant

“…Dit proteins are designated either "classical," i.e., with a short sequence, or "evolved," i.e., bearing carbohydrate-binding domains (CBDs) (11,40). The phages in this study all encode evolved Dit proteins, since they harbor a CBD that shares structural similarity (HHpred score, 99.9%) with the CBD of the evolved Dit from Lactobacillus casei phage J-1 (40).…”

“…Phage biodiversity surveys in dairy fermentation facilities are widely reported for lactococcal phages (11)(12)(13)(14)(15)(16)(17)(18), while studies on S. thermophilus phage biodiversity are comparatively limited (9,10,(19)(20)(21). While these studies have considerable merit in identifying the biodiversity of phages at a given time point, they do not provide temporal insights into the prevalence, maintenance, evolution, and diversification of genetic lineages of phages within the industrial setting.…”

Evolved distal tail carbohydrate binding modules of Lactobacillus phage J‐1: a novel type of anti‐receptor widespread among lactic acid bacteria phages

“…a). Other examples of insertions in Dit have been reported in the lactococcal phage group P335 (Mahony et al ., ) (e.g., phage C4143) (Fig. b).…”

“…a. Dit protein from phage PhiM1127 belonging to lactococcal group 936 . b. Dit protein from phage C4143 belonging to lactococcal group P335 (Mahony et al, 2017).…”

Genomics of tailless bacteriophages in a complex lactic acid bacteria starter culture

“…All L. lactis phages described are members of the Caudovirales order and possess a double-stranded DNA genome and a noncontractile tail. The vast majority of lactococcal phages belong to one of the three main groups within Siphoviridae family: 936, c2, or P335 (Mahony et al, 2017). Groups 936 and c2 consist of only virulent phages, while P335 group consists of both temperate and virulent phages (Chmielewska-Jeznach et al, 2018).…”