by Merry Youle
Troublesome strains of Staphylococcus aureus are often troublesome because they carry genes for superantigens and multiple antibiotic resistance. But don’t blame the bacteria. These genes are hitchhikers that arrived by horizontal gene transfer, embedded within mobile pathogenicity islands known as SaPIs. SaPIs are common; all S. aureus strains investigated so far carry at least one. They have also been found in other staph species and a few other Gram-positive genera. They have garnered much research attention because they rapidly move those clinically-significant genes from host to host. (They received some attention on this blog, too, several years ago.) The typical SaPI is composed of 15-17,000 base pairs of DNA that encode 18-22 proteins. Of those proteins, nine at most are required for the SaPI life cycle. This leaves plenty available to use to benefit or manipulate their host bacterium.
SaPIs resemble temperate phages in that they travel from host to host within a capsid and, upon infection, they choose between two options: they can replicate immediately or they can integrate into a specific site in the host chromosome and assume a quiescent state, held in check by a SaPI-encoded repressor. You might think of them as defective phages because they don’t encode the structural proteins required for their own capsids, relying instead on a “helper phage” to supply them. However, these kleptoparasites (see Fig. 1) are no more defective than every other sophisticated parasite that exploits another life form to provide some essential goods or services. It isn’t simple to be a successful parasite. Let’s consider how SaPIs do it.
One obvious requirement for successful capsid theft is that the SaPI must replicate its genome when capsids are available. This synchronization can be achieved a couple of ways. For one, co-infection by a SAPI and a phage can lead to immediate replication of both. Alternatively, since most S. aureus strains also carry at least one prophage, a SaPI can integrate into the host chromosome and wait until the prophage is induced. Induction of the resident prophage also prompts the SaPI to exit from the chromosome and replicate. This SaPI replication is just in time to take advantage of the synthesis of phage capsid proteins. Synchronization alone does not guarantee capsids for the SaPI. The phage needs to be of the “helpful” sort, and not all are.
A “helpful” phage is one whose capsid assembly and DNA packaging can be exploited by the SaPI. No altruism here. Stuffing a SaPI genome into a phage capsid requires subverting the phage packaging machinery that otherwise would package only phage DNA. Packaging is done by the phage terminase. The small subunit of the terminase (TerS) recognizes the phage DNA, while the large subunit handles the actual packing. SaPIs encode their own TerS protein, one specific for SaPI DNA. Upon induction, SaPI TerS transcription gets underway before the phage’s TerS. Not only does this fill some capsids with SaPI DNA, but these can even be the majority. On the other hand, if you experimentally inactivate the SaPI TerS, all capsids contain only phage DNA.
Many SaPIs also take advantage of their smaller genome size (only one third of the size of the helper phage’s) and assemble smaller, SaPI-size capsids. This architectural sleight-of-hand is possible because two different size icosahedral capsids can be assembled from the same building blocks. The SaPI helper phage assemble 415 copies of their major capsid protein into a 63 nm capsid with T=7 icosahedral symmetry, while the SaPIs build smaller, 46 nm capsids with T=4 symmetry from 240 copies. Assembly of the small capsids does require a SaPI-encoded protein in addition to the phage-encoded building blocks. That SaPI protein is an internal scaffolding protein. Scaffolding proteins function as chaperones; they direct capsid assembly and are then discarded from the capsid when the DNA is packaged. The SaPI scaffold mimics the helper phage’s own, but directs formation of the smaller capsids. These small capsids may ac