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CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids

View ORCID ProfileRafael Pinilla-Redondo, View ORCID ProfileJakob Russel, View ORCID ProfileDavid Mayo-Muñoz, Shiraz A. Shah, Roger A. Garrett, Joseph Nesme, Jonas S. Madsen, View ORCID ProfilePeter C. Fineran, View ORCID ProfileSøren J. Sørensen
doi: https://doi.org/10.1101/2021.06.04.447074
Rafael Pinilla-Redondo
1Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
2Department of Technological Educations, University College Copenhagen, Sigurdsgade 26, 2200 Copenhagen, Denmark
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  • For correspondence: rafapinillaredondo@gmail.com
Jakob Russel
1Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
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David Mayo-Muñoz
1Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
3Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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Shiraz A. Shah
4Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
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Roger A. Garrett
5Danish Archaea Centre, Department of Biology, University of Copenhagen, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
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Joseph Nesme
1Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
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Jonas S. Madsen
1Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
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Peter C. Fineran
3Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
6Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand
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Søren J. Sørensen
1Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
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  • For correspondence: rafapinillaredondo@gmail.com
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ABSTRACT

Many prokaryotes encode CRISPR-Cas systems as immune protection against mobile genetic elements (MGEs), yet, a number of MGEs also harbor CRISPR-Cas components. With a few exceptions, CRISPR-Cas loci encoded on MGEs are uncharted and a comprehensive analysis of their distribution, prevalence, diversity, and function is lacking. Here, we systematically investigated CRISPR-Cas loci across the largest curated collection of natural bacterial and archaeal plasmids. CRISPR-Cas loci are widely but heterogeneously distributed across plasmids and, in comparison to host chromosomes, their mean prevalence per Mbp is higher and their distribution is markedly distinct. Furthermore, the spacer content of plasmid CRISPRs exhibits a strong targeting bias towards other plasmids, while chromosomal arrays are enriched with virus-targeting spacers. These contrasting targeting preferences dominate across the diversity of CRISPR-Cas subtypes and host taxa, highlighting the genetic independence of plasmids and suggesting a major role of CRISPR-Cas for mediating plasmid-plasmid conflicts. Altogether, CRISPR-Cas are frequent accessory components of many plasmids, which is an overlooked phenomenon that possibly facilitates their dissemination across microbiomes.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted June 04, 2021.
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CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids
Rafael Pinilla-Redondo, Jakob Russel, David Mayo-Muñoz, Shiraz A. Shah, Roger A. Garrett, Joseph Nesme, Jonas S. Madsen, Peter C. Fineran, Søren J. Sørensen
bioRxiv 2021.06.04.447074; doi: https://doi.org/10.1101/2021.06.04.447074
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CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids
Rafael Pinilla-Redondo, Jakob Russel, David Mayo-Muñoz, Shiraz A. Shah, Roger A. Garrett, Joseph Nesme, Jonas S. Madsen, Peter C. Fineran, Søren J. Sørensen
bioRxiv 2021.06.04.447074; doi: https://doi.org/10.1101/2021.06.04.447074

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