Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR–Cas system

Raymond H. J. Staals, Simon A. Jackson, Ambarish Biswas, Stan J. J. Brouns, Chris M. Brown and Peter C. Fineran ()
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Raymond H. J. Staals: University of Otago
Simon A. Jackson: University of Otago
Ambarish Biswas: University of Otago
Stan J. J. Brouns: Laboratory of Microbiology, Wageningen University
Chris M. Brown: University of Otago
Peter C. Fineran: University of Otago

Nature Communications, 2016, vol. 7, issue 1, 1-13

Abstract: Abstract CRISPR–Cas systems provide bacteria with adaptive immunity against foreign nucleic acids by acquiring short, invader-derived sequences called spacers. Here, we use high-throughput sequencing to analyse millions of spacer acquisition events in wild-type populations of Pectobacterium atrosepticum. Plasmids not previously encountered, or plasmids that had escaped CRISPR–Cas targeting via point mutation, are used to provoke naive or primed spacer acquisition, respectively. The origin, location and order of spacer acquisition show that spacer selection through priming initiates near the site of CRISPR–Cas recognition (the protospacer), but on the displaced strand, and is consistent with 3′–5′ translocation of the Cas1:Cas2-3 acquisition machinery. Newly acquired spacers determine the location and strand specificity of subsequent spacers and demonstrate that interference-driven spacer acquisition (‘targeted acquisition’) is a major contributor to adaptation in type I-F CRISPR–Cas systems. Finally, we show that acquisition of self-targeting spacers is occurring at a constant rate in wild-type cells and can be triggered by foreign DNA with similarity to the bacterial chromosome.

Date: 2016
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DOI: 10.1038/ncomms12853

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