CRISPR (clustered regularly interspaced short palindromic repeats) loci and their associated (cas) genes encode an adaptive immune system that protects prokaryotes from viral1 and plasmid2 invaders. Following viral (phage) infection, a small fraction of the prokaryotic cells are able to integrate a small sequence of the invader’s genome into the CRISPR array1. These sequences, known as spacers, are transcribed and processed into small CRISPR RNA guides3,4,5 that associate with Cas nucleases to specify a viral target for destruction6,7,8,9. Although CRISPR−cas loci are widely distributed throughout microbial genomes and often display hallmarks of horizontal gene transfer10,11,12, the drivers of CRISPR dissemination remain unclear. Here, we show that spacers can recombine with phage target sequences to mediate a form of specialized transduction of CRISPR elements. Phage targets in phage 85, ΦNM1, ΦNM4 and Φ12 can recombine with spacers in either chromosomal or plasmid-borne CRISPR loci in Staphylococcus, leading to either the transfer of CRISPR-adjacent genes or the propagation of acquired immunity to other bacteria in the population, respectively. Our data demonstrate that spacer sequences not only specify the targets of Cas nucleases but also can promote horizontal gene transfer.
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All codes used in this study are available on request from the corresponding author.
All data generated or analysed during this study are included in this published article (and its Supplementary Information files). Raw sequencing data are available on request from the corresponding author.
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We thank J. W. Modell, J. T. Rostol and A. M. Pham for helpful discussion and critical reading of the manuscript. J. W. Modell (The Rockefeller University) also provided the strain pAV293-296. A.V. is supported by the Arnold O. Beckman Postdoctoral Fellowship. L.A.M. is supported by the Rita Allen Scholars Program and an NIH Director’s Pioneer Award (DP1GM128184-01). The work carried out by E.R.W. and S.M. was supported by the Biotechnology and Biological Sciences Research Council (BB/N017412/1) and Natural Environment Research Council (NE/M018350/1).
L.A.M. is a cofounder and Scientific Advisory Board member of Intellia Therapeutics and a cofounder of Eligo Biosciences. R.B. is a cofounder and Scientific Advisory Board member of Intellia Therapeutics, a cofounder of Locus Biosciences, an advisor to Inari Ag and a shareholder of DuPont and Caribou Biosciences. A.V., E.R.W. and S.M. declare no competing interests.
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Varble, A., Meaden, S., Barrangou, R. et al. Recombination between phages and CRISPR−cas loci facilitates horizontal gene transfer in staphylococci. Nat Microbiol 4, 956–963 (2019). https://doi.org/10.1038/s41564-019-0400-2
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