Abstract
Integrated into their bacterial hosts’ genomes, prophage sequences exhibit a wide diversity of length and gene content, from highly degraded cryptic sequences to intact, functional prophages that retain a full complement of lytic-function genes. We apply three approaches—bioinformatics, analytical modelling and computational simulation—to understand the diverse gene content of prophages. In the bioinformatics work, we examine the distributions of over 50,000 annotated prophage genes identified in 1384 prophage sequences, comparing the gene repertoires of intact and incomplete prophages. These data indicate that genes involved in the replication, packaging, and release of phage particles have been preferentially lost in incomplete prophages, while tail fiber, transposase and integrase genes are significantly enriched. Consistent with these results, our mathematical and computational approaches predict that genes involved in phage lytic function are preferentially lost, resulting in shorter prophages that often retain genes that benefit the host. Informed by these models, we offer novel hypotheses for the enrichment of integrase and transposase genes in cryptic prophages. Overall, we demonstrate that functional and cryptic prophages represent a diversity of genetic sequences that evolve along a parasitism-mutualism continuum.
Highlights
Bacteriophages (‘phages’), viruses that infect bacteria, are the most prevalent life form on the planet, vastly outnumbering both their bacterial hosts and all other life forms combined [1,2,3].Many phages alternate between lytic and temperate life cycles
Prophages exhibit tremendous variation in both length and gene content, but little is understood about the gene repertoires of intact or degraded prophage sequences
By comparing large datasets of annotated prophage genes, we offer evidence for both the enrichment and loss of genes of specific function, resulting in various
Summary
Bacteriophages (‘phages’), viruses that infect bacteria, are the most prevalent life form on the planet, vastly outnumbering both their bacterial hosts and all other life forms combined [1,2,3].Many phages alternate between lytic and temperate life cycles. The phage genome ( termed a “prophage”) quiescently integrates into the bacterial genome, leaving the host largely unharmed (assuming prophage integration did not inactivate beneficial host genes) and potentially contributing beneficial genes to the host cell. These two life cycles represent the extremes of parasitism and mutualism within a single phage genotype, but these life cycles can evolve along a phage lineage. While integrated in the bacterial genome, prophage sequences are subject to selection, mutation, and horizontal gene transfer (HGT).
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
