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Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: Insights from a natural arms-race

Amelia C. McKitterick, Kristen N. LeGault, Angus Angermeyer, Muniral Alam, View ORCID ProfileKimberley D. Seed
doi: https://doi.org/10.1101/381962
Amelia C. McKitterick
1Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
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Kristen N. LeGault
1Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
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Angus Angermeyer
1Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
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Muniral Alam
2International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
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Kimberley D. Seed
1Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
3Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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  • ORCID record for Kimberley D. Seed
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Abstract

CRISPR-Cas systems function as adaptive immune systems by acquiring nucleotide sequences called spacers that mediate sequence-specific defense against competitors. Uniquely, the phage ICP1 encodes a Type I-F CRISPR-Cas system that is deployed to target and overcome PLE, a mobile genetic element with anti-phage activity in Vibrio cholerae. Here, we exploit the arms race between ICP1 and PLE to examine spacer acquisition and interference under laboratory conditions to reconcile findings from wild populations. Natural ICP1 isolates encode multiple spacers directed against PLE, but we find that single spacers do not equally interfere with PLE mobilization. High-throughput sequencing to assay spacer acquisition reveals that ICP1 can also acquire spacers that target the V. cholerae chromosome. We find that targeting the V. cholerae chromosome proximal to PLE is sufficient to block PLE and propose a model in which indirect chromosomal spacers are able to circumvent PLE by Cas2-3-mediated processive degradation of the V. cholerae chromosome before PLE mobilization. Generally, laboratory acquired spacers are much more diverse than the subset of spacers maintained by ICP1 in nature, showing how evolutionary pressures can constrain CRISPR-Cas targeting in ways that are often not appreciated through in vitro analyses.

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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-ND 4.0 International license.
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Posted August 01, 2018.
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Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: Insights from a natural arms-race
Amelia C. McKitterick, Kristen N. LeGault, Angus Angermeyer, Muniral Alam, Kimberley D. Seed
bioRxiv 381962; doi: https://doi.org/10.1101/381962
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Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: Insights from a natural arms-race
Amelia C. McKitterick, Kristen N. LeGault, Angus Angermeyer, Muniral Alam, Kimberley D. Seed
bioRxiv 381962; doi: https://doi.org/10.1101/381962

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