With a Little Help from Their Friends

by Merry & Elio

EM of phage 80α particles and a SaPI1
particle with a smaller head (arrow).
31,500×. Source

Genomic islands are long stretches of chromosomal DNA that look suspiciously foreign in origin and are found in many pathogenic and non-pathogenic bacteria alike. Some of them, called pathogenicity islands, encode toxins or other factors that contribute to the virulence of the pathogenic ones. It is suspected that they arrived by horizontal transfer, perhaps with the help of a phage. A story has turned up that makes the connection between pathogenicity islands and phages even more plausible.

One in five isolates of Staphylococcus aureus produces TSST-1, a potent superantigen that causes the toxic shock syndrome. The TSST-1 gene is on a mobile pathogenicity island called a SaPI. Such islands are extremely common in this species, with at least one of them found in all but one of the S. aureus genomes sequenced as of 2007. SaPIs share characteristics that set them apart from your run-of-the-mill pathogenicity island.

They are typically 15- to 17 kb long and encode at least one superantigen, often two or more. But it is their overall genome organization that is intriguingly reminiscent of temperate phages; they carry a gene for integrase (int) and direct repeats at the ends, but they lack genes for capsid proteins. SaPIs transfer from host to host at extremely high frequencies—provided they have some help from the right temperate phage.

A SaPI doesn't need any help in order to locate its particular site in the host chromosome and to integrate there via the classical Campbell mechanism. Its own integrase can handle that. However, many SaPIs don't encode a mechanism for their own excision (e.g., they have no ORF resembling xis of phage lambda) and thus they cannot excise spontaneously. For that step, they rely on temperate generalized transducing phages. If the host cell is a lysogen for the appropriate phage, prophage induction excises the SaPI, as well. After excision, the linear SaPI DNA replicates, yielding typically more than 120 copies per cell.

Then what? The host cell is lysed releasing both plaque-forming virus particles and infectious SaPI particles. Researchers looked at the particles in the lysate under the electron microscope. They found that the infectious SaPI particles looked just like the phage particles, only smaller. This suggested that, in the presence of the SaPI, a portion of the pool of capsid proteins assembles into smaller capsids which are then filled with SaPI DNA. Since the small particles are about 1/3 the volume of the large, and the SaPI genome is about 1/3 the size of the phage genome, it is most likely that one SaPI chromosome is packaged per particle.

This capsid proteoklepty (as we have chosen to call it) was elegantly confirmed. Researchers created lysogens that carried a SaPI and a prophage with a mutation that prevented its DNA from packaging. Induction of these cells yielded a cell lysate in which all of the particles were SaPI particles. The proteins in those particles were all phage-encoded, including all of the phage structural proteins.

Still this leaves some questions. Given that these phage "pro-heads" are built from just one protein and that they are pre-assembled before filling, what determines whether they will become small or large pro-heads? A partial answer is that most of the known SaPIs contain 3 conserved ORFs that are required for the assembly of the small capsids. These proteins are not included in the finished SaPI particle. One SaPI lacks one of those genes, but no matter. Its 27 kb genome—too large to fit in the small heads—is routinely packaged into the large ones.

This system works very well for the SaPI. It results in extremely high transfer frequencies, reduces the number of ORFs the SaPI has to carry around, and ensures that the SaPI replicates only when there is a suitable phage present, ready to provide it with capsid proteins. For us as observers, it also blurs the line between phages and pathogencity islands even further.

Which aspect of this story seems more exciting—the near identity of pathogenicity islands with phages or the morphogenetic choice between two structural assemblies? We cannot decide.

Comments

[Merry]

Thanks for your thoughtful comment, Paul. Especially interesting was your observation that the SaPIs could be considered to be parasites exploiting the phage. Indeed, they do decrease the phage burst size, presumably by being efficient at assembling the phage capsid proteins into the small SaPI capsids. (Also, a point that was not included in the post, the SaPIs encode one subunit of the phage terminase. It combines with a phage-encoded subunit to yield a terminase that selectively processes the SaPI DNA for packaging.) This 3-way interaction appears to be stable, which from my point of view seems to suggest that it works for all the members. Our language, which offers us words such as parasitic, symbiotic, and mutualistic, cannot convey the complexities of such relationships.

I also find myself thinking about the factors that came together to make this particular interaction work with these particular players. For example, this particular capsid protein can be assembled into a smaller capsid which can accommodate most SaPI genomes. In any event, it adds another dot to my imaginary dot plot of the different strategies used by nucleic acids to replicate and get around.

Merry

[Paul Orwin]

As someone who used to dabble in that area (in the halcyon days of graduate school), I'm glad to see that interest persists, and spreads from the clinical aspects to the more fundamental. I like your neologism as well. The massive superantigen amplification (SAg for short) that seems to have occurred in S. aureus is an interesting phenomenon, and the SaPIs seem a reasonable mechanism for the formation of all of these proteins by recombination, phage replication, and integration events. I wish I had more insight into the mechanics (I haven't read all the Novick group papers - they've been very active!) of the process. Is it sensible to consider SaPIs to be parasites of bacteriophages? If I have more constructive thoughts i'll add them...