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The Contribution of Genetic Recombination to CRISPR Array Evolution
CRISPR (clustered regularly interspaced short palindromic repeats) is a microbial immune system against foreign DNA. Recognition sequences (spacers) encoded within the CRISPR array mediate the immune reaction in a sequence-specific manner. The known mechanisms for the evolution of CRISPR arrays incl...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Oxford University Press
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524480/ https://www.ncbi.nlm.nih.gov/pubmed/26085541 http://dx.doi.org/10.1093/gbe/evv113 |
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author | Kupczok, Anne Landan, Giddy Dagan, Tal |
author_facet | Kupczok, Anne Landan, Giddy Dagan, Tal |
author_sort | Kupczok, Anne |
collection | PubMed |
description | CRISPR (clustered regularly interspaced short palindromic repeats) is a microbial immune system against foreign DNA. Recognition sequences (spacers) encoded within the CRISPR array mediate the immune reaction in a sequence-specific manner. The known mechanisms for the evolution of CRISPR arrays include spacer acquisition from foreign DNA elements at the time of invasion and array erosion through spacer deletion. Here, we consider the contribution of genetic recombination between homologous CRISPR arrays to the evolution of spacer repertoire. Acquisition of spacers from exogenic arrays via recombination may confer the recipient with immunity against unencountered antagonists. For this purpose, we develop a novel method for the detection of recombination in CRISPR arrays by modeling the spacer order in arrays from multiple strains from the same species. Because the evolutionary signal of spacer recombination may be similar to that of pervasive spacer deletions or independent spacer acquisition, our method entails a robustness analysis of the recombination inference by a statistical comparison to resampled and perturbed data sets. We analyze CRISPR data sets from four bacterial species: two Gammaproteobacteria species harboring CRISPR type I and two Streptococcus species harboring CRISPR type II loci. We find that CRISPR array evolution in Escherichia coli and Streptococcus agalactiae can be explained solely by vertical inheritance and differential spacer deletion. In Pseudomonas aeruginosa, we find an excess of single spacers potentially incorporated into the CRISPR locus during independent acquisition events. In Streptococcus thermophilus, evidence for spacer acquisition by recombination is present in 5 out of 70 strains. Genetic recombination has been proposed to accelerate adaptation by combining beneficial mutations that arose in independent lineages. However, for most species under study, we find that CRISPR evolution is shaped mainly by spacer acquisition and loss rather than recombination. Since the evolution of spacer content is characterized by a rapid turnover, it is likely that recombination is not beneficial for improving phage resistance in the strains under study, or that it cannot be detected in the resolution of intraspecies comparisons. |
format | Online Article Text |
id | pubmed-4524480 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-45244802015-08-07 The Contribution of Genetic Recombination to CRISPR Array Evolution Kupczok, Anne Landan, Giddy Dagan, Tal Genome Biol Evol Research Article CRISPR (clustered regularly interspaced short palindromic repeats) is a microbial immune system against foreign DNA. Recognition sequences (spacers) encoded within the CRISPR array mediate the immune reaction in a sequence-specific manner. The known mechanisms for the evolution of CRISPR arrays include spacer acquisition from foreign DNA elements at the time of invasion and array erosion through spacer deletion. Here, we consider the contribution of genetic recombination between homologous CRISPR arrays to the evolution of spacer repertoire. Acquisition of spacers from exogenic arrays via recombination may confer the recipient with immunity against unencountered antagonists. For this purpose, we develop a novel method for the detection of recombination in CRISPR arrays by modeling the spacer order in arrays from multiple strains from the same species. Because the evolutionary signal of spacer recombination may be similar to that of pervasive spacer deletions or independent spacer acquisition, our method entails a robustness analysis of the recombination inference by a statistical comparison to resampled and perturbed data sets. We analyze CRISPR data sets from four bacterial species: two Gammaproteobacteria species harboring CRISPR type I and two Streptococcus species harboring CRISPR type II loci. We find that CRISPR array evolution in Escherichia coli and Streptococcus agalactiae can be explained solely by vertical inheritance and differential spacer deletion. In Pseudomonas aeruginosa, we find an excess of single spacers potentially incorporated into the CRISPR locus during independent acquisition events. In Streptococcus thermophilus, evidence for spacer acquisition by recombination is present in 5 out of 70 strains. Genetic recombination has been proposed to accelerate adaptation by combining beneficial mutations that arose in independent lineages. However, for most species under study, we find that CRISPR evolution is shaped mainly by spacer acquisition and loss rather than recombination. Since the evolution of spacer content is characterized by a rapid turnover, it is likely that recombination is not beneficial for improving phage resistance in the strains under study, or that it cannot be detected in the resolution of intraspecies comparisons. Oxford University Press 2015-06-16 /pmc/articles/PMC4524480/ /pubmed/26085541 http://dx.doi.org/10.1093/gbe/evv113 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Research Article Kupczok, Anne Landan, Giddy Dagan, Tal The Contribution of Genetic Recombination to CRISPR Array Evolution |
title | The Contribution of Genetic Recombination to CRISPR Array Evolution |
title_full | The Contribution of Genetic Recombination to CRISPR Array Evolution |
title_fullStr | The Contribution of Genetic Recombination to CRISPR Array Evolution |
title_full_unstemmed | The Contribution of Genetic Recombination to CRISPR Array Evolution |
title_short | The Contribution of Genetic Recombination to CRISPR Array Evolution |
title_sort | contribution of genetic recombination to crispr array evolution |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524480/ https://www.ncbi.nlm.nih.gov/pubmed/26085541 http://dx.doi.org/10.1093/gbe/evv113 |
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