Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Kupczok, Anne, Landan, Giddy, Dagan, Tal
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
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
_version_ 1782384204090179584
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
work_keys_str_mv AT kupczokanne thecontributionofgeneticrecombinationtocrisprarrayevolution
AT landangiddy thecontributionofgeneticrecombinationtocrisprarrayevolution
AT dagantal thecontributionofgeneticrecombinationtocrisprarrayevolution
AT kupczokanne contributionofgeneticrecombinationtocrisprarrayevolution
AT landangiddy contributionofgeneticrecombinationtocrisprarrayevolution
AT dagantal contributionofgeneticrecombinationtocrisprarrayevolution