Specificity of staphylococcal phage and SaPI DNA packaging as revealed by integrase and terminase mutations

Abstract

SaPI1 and SaPIbov1 are chromosomal pathogenicity islands in S. aureus that carry tst and other superantigen genes. They are induced to excise and replicate by certain phages, are efficiently encapsidated in SaPI-specific small particles composed of phage virion proteins and are transferred at very high frequencies. In this study, we have analyzed 3 SaPI genes that are important for the phage-SaPI interaction, int (integrase) terS (phage terminase small subunit homolog), and pif (phage interference function). SaPI1 int is required for SaPI excision, replication and packaging in a donor strain, and is required for integration in a recipient. A SaPI1 int mutant, following phage induction, produces small SaPI-specific capsids which are filled with partial phage genomes. SaPIbov1 DNA is efficiently packaged into full-sized phage heads as well as into SaPI-specific small ones, whereas SaPI1 DNA is found almost exclusively in the small capsids. TerS, however, determines DNA packaging specificity but not the choice of large vs. small capsids. This choice is influenced by SaPIbov1 gene 12, which prevents phage DNA packaging into small capsids, and which is also primarily responsible for interference by SaPIbov1 with phage reproduction.

Staphylococcal pathogenicity island interference with helper phage reproduction is a paradigm of molecular parasitism

“…However, in the presence of SaPI1 or SaPI2, most of the particle DNA migrates as an 18-kb band, corresponding to monomeric SaPI DNA from small-headed particles, and only a tiny fraction migrates as 45-kb DNA from large-headed particles, accounting for the observed reduction in phage titer. We have previously shown by Southern blotting of such a gel that both of these bands contain both phage and SaPI DNA, and that most of the phage DNA migrates with the SaPI monomers (9). As also shown in Fig.…”

“…1A; note that interference is assessed as a reduction in phage titer or as a reduction in plaque size or number, and that these two parameters do not always match precisely). An earlier study hinted that gene 12 of the closely related 15-kb SaPIbov1 might be involved in phage interference (9). We originally designated this gene pif (phage interference function) (9), but because pif had been used previously (14), we now use ppi for phage packaging interference (see below) and add a subscript to indicate its origin, e.g., ppi spb2 denotes the SaPIbov2 version.…”

“…Phage and SaPI both use the phage-encoded large (TerL) subunit, and this is complexed with a phage-or SaPI-encoded small subunit (TerS P or TerS S , respectively), which determines packaging specificity (9,12). It therefore seemed likely that TerS P would be the target of Ppi spb2 inhibition.…”

“…Upon superinfection by certain phages or upon SOS induction of a resident prophage, SaPIs use specific nonessential phage proteins to lift the repression, enabling the expression of their integrase and excision genes (3)(4)(5); following excision, they initiate replication at a SaPI-specific replication origin using SaPI-coded initiator and primase, and continue replication using the host cell replication machinery (6,7). SaPIs reorganize the phage virion proteins to form small capsids commensurate with their genomes (usually about one-third the size of the phage genome), and they use a SaPI-coded terminase small subunit to package their DNA preferentially (8,9). This process results in the efficient production of SaPI-specific infectious particles by means of which they are spread not only among staphylococci but also to other bacteria, such as Listeria monocytogenes (10), at very high frequency.…”

Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn't Kill You Makes You Stronger

“…[18] There can also be biases in the DNA that is transferred, since in some cases other mobile genetic elements such as pathogenicity islands are disproportionately mobilized by transduction relative to the genome as a whole. [19] This may be because mobile elements have adapted to hijack transduction for their own transmission.…”