Phage-inducible islands in the Gram-positive cocci

Abstract

The SaPIs are a cohesive sub-family of extremely common phage-inducible chromosomal islands (PICIs) that reside quiescently at specific att sites in the staphylococcal chromosome and are induced by helper phages to excise and replicate. They are usually packaged in small capsids composed of phage virion proteins, giving rise to very high transfer frequencies, which they enhance by interfering with helper phage reproduction. As the SaPIs represent a highly successful biological strategy, with many natural Staphylococcus aureus strains containing two or more, we assumed that similar elements would be widespread in the Gram-positive cocci. On the basis of resemblance to the paradigmatic SaPI genome, we have readily identified large cohesive families of similar elements in the lactococci and pneumococci/streptococci plus a few such elements in Enterococcus faecalis. Based on extensive ortholog analyses, we find that the PICI elements in the four different genera all represent distinct but parallel lineages, suggesting that they represent convergent evolution towards a highly successful life style. We have characterized in depth the enterococcal element, EfCIV583, and have shown that it very closely resembles the SaPIs in functionality as well as in genome organization, setting the stage for expansion of the study of elements of this type. In summary, our findings greatly broaden the PICI family to include elements from at least three genera of cocci.

Assembly-free single-molecule nanopore sequencing recovers complete virus genomes from natural microbial communities

“…Further, the concatemeric whole number repeat copies and read lengths we observed were consistent with predicted PICI-like DNA synthesis and packaging strategies. Previously, these unique mobile phage parasites have been identified mainly in cultures of gram-positive and gram-negative bacteria (Chen and Novick 2009;Martinez-Rubio et al 2017;Fillol-Salom et al 2018). To the best of our knowledge, these results represent some of the first observations of concatemeric PICIs packaged in phage particles from natural samples.…”

“…Concatemers of PICI DNA reproduce postexcision by rolling circle replication and are believed to be packaged "by the headful" into the hijacked, infectious temperate phage capsids, replacing the native phage DNA (Penades and Christie 2015) with their own. By virtue of this phage hijacking, PICI mobile elements can increase their rates of horizontal transfer by as much as five orders of magnitude (Penades and Christie 2015;Martinez-Rubio et al 2017;Fillol-Salom et al 2018). The gene content, repeat size, and overall length support the hypothesis that the concatemeric reads discovered here by our nanopore sequencing method represent PICIs packaged into phage particles.…”

Staphylococcal pathogenicity islands — movers and shakers in the genomic firmament

“…Although there is clearly an ancestral relation, we consider it very distant for the following reasons: i) the SaPIs are a coherent family, within which the similarities between SaPI genes are much greater than similarities between SaPI and phage genes or genes of other genetic elements [2, 4]; ii) they possess genes that are shared among SaPIs but are not found elsewhere, especially the hypothetical genes, and the interference genes, of which the latter are all located in the same region of the island, a region that has probably been imported [2, 4]; iii) they share a rare (though not absolutely unique) biological functionality – the property of being induced by prophage anti-repressor genes; iv) they occupy unique SaPI-specific att sites that are conserved throughout the staphylococci and are never occupied by other elements; v) they carry certain accessory genes that are not found on other genetic elements.…”

“…Some carry identifiable accessory genes, especially fusidic acid resistance in S. epidermidis [34]. Similarly, large families of SaPI-like elements have been identified in the genomes of lactococci, pneumococci, and streptococci [2, 4] [35]; functionality has yet to be demonstrated for any of those in lactococci and pneumococci. Enterococcus faecalis strain V583 possesses the only SaPI-like-like element, EfCIV583, outside of the staphylococci whose SaPI-like functionality has been demonstrated [33] [2]: it is induced by a helper phage (Φ1) whose xis gene is the de-repressor, is packaged in small particles, is transferred at high frequency, and interferes with its helper phage.…”

“…The SaPIs are extremely common in S. aureus , with an average of one per strain, some strains having 3 or more. They are also common in non- aureus staphylococci and similar elements have been identified by sequence analysis in streptococci and lactococci [2], though these elements have not been found to carry virulence genes, nor has their functionality been demonstrated as yet.…”