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Recombination between phages and CRISPR−cas loci facilitates horizontal gene transfer in staphylococci

Nature Microbiology volume 4, pages 956–963 (2019)Cite this article

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Abstract

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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Fig. 1: Transfer of CRISPR–Cas elements through spacer-mediated transduction.
Fig. 2: Spacer sequences determine the frequency of pCRISPR transduction.
Fig. 3: Spacers that mediate high pCRISPR transduction provide poor immunity to the host.

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Code availability

All codes used in this study are available on request from the corresponding author.

Data availability

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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Acknowledgements

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).

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Authors and Affiliations

  1. Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA

    Andrew Varble & Luciano A. Marraffini

  2. Environment and Sustainability Institute, Centre for Ecology and Conservation, University of Exeter, Biosciences, Penryn, Cornwall, UK

    Sean Meaden & Edze R. Westra

  3. Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA

    Rodolphe Barrangou

  4. Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA

    Luciano A. Marraffini

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Contributions

A.V. and L.A.M. conceived the study. A.V., S.M., R.B., E.R.W. and L.A.M. designed the experiments. A.V. executed the experimental work. S.M. executed the experimental work with P. aeruginosa. A.V., S.M., R.B., E.R.W. and L.A.M. wrote the paper.

Corresponding author

Correspondence to Luciano A. Marraffini.

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Competing interests

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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Supplementary Information

Supplementary Figures 1–9, Supplementary Tables 1 and 2, legend for Supplementary Dataset and Supplementary References.

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Supplementary Data Set 1

Next-generation sequencing data used to generate Fig. 2a and Supplementary Fig. 2a–c.

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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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