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Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages
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 m...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7744054/ https://www.ncbi.nlm.nih.gov/pubmed/33275597 http://dx.doi.org/10.1371/journal.pcbi.1008482 |
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author | Khan, Amjad Burmeister, Alita R. Wahl, Lindi M. |
author_facet | Khan, Amjad Burmeister, Alita R. Wahl, Lindi M. |
author_sort | Khan, Amjad |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7744054 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-77440542020-12-31 Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages Khan, Amjad Burmeister, Alita R. Wahl, Lindi M. PLoS Comput Biol Research Article 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. Public Library of Science 2020-12-04 /pmc/articles/PMC7744054/ /pubmed/33275597 http://dx.doi.org/10.1371/journal.pcbi.1008482 Text en © 2020 Khan et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Khan, Amjad Burmeister, Alita R. Wahl, Lindi M. Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages |
title | Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages |
title_full | Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages |
title_fullStr | Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages |
title_full_unstemmed | Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages |
title_short | Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages |
title_sort | evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7744054/ https://www.ncbi.nlm.nih.gov/pubmed/33275597 http://dx.doi.org/10.1371/journal.pcbi.1008482 |
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