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Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation

Nature Microbiologyvolume 4pages177186 (2019) | Download Citation


CRISPR–Cas systems provide prokaryotes with sequence-specific immunity against viruses and plasmids based on DNA acquired from these invaders, known as spacers. Surprisingly, many archaea possess spacers that match chromosomal genes of related species, including those encoding core housekeeping genes. By sequencing genomes of environmental archaea isolated from a single site, we demonstrate that inter-species spacers are common. We show experimentally, by mating Haloferax volcanii and Haloferax mediterranei, that spacers are indeed acquired chromosome-wide, although a preference for integrated mobile elements and nearby regions of the chromosome exists. Inter-species mating induces increased spacer acquisition and may result in interactions between the acquisition machinery of the two species. Surprisingly, many of the spacers acquired following inter-species mating target self-replicons along with those originating from the mating partner, indicating that the acquisition machinery cannot distinguish self from non-self under these conditions. Engineering the chromosome of one species to be targeted by the other’s CRISPR–Cas reduces gene exchange between them substantially. Thus, spacers acquired during inter-species mating could limit future gene transfer, resulting in a role for CRISPR–Cas systems in microbial speciation.

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The authors thank R. Sorek and A. Herskovits for their helpful comments and insights, and H. Xiang for providing sequence data and provirus annotations. The authors thank S. Green of the University of Illinois at Chicago for his continued expert help in challenging sequencing projects and E. Koonin (NIH) for helpful discussions. Funding was provided by Deutsche Forschungsgemeinschaft (MA1538/16-2), the Israel Science Foundation (535/15), the Binational Science Foundation (2013061) with partial support by the Constantiner Institute, European Research Council (grant ERC-AdG 787514).

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Author notes

    • Adit Naor

    Present address: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA


  1. Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel

    • Israela Turgeman-Grott
    • , Shirley Joseph
    • , Sam Marton
    • , Kim Eizenshtein
    • , Adit Naor
    • , Yarden Shalev
    • , Mor Zarkor
    • , Leah Reshef
    • , Neta Altman-Price
    •  & Uri Gophna
  2. Department of Biological Sciences, Dartmouth College, Hanover, NH, USA

    • Shannon M. Soucy
  3. Department of Biology II, Ulm University, Ulm, Germany

    • Aris-Edda Stachler
    •  & Anita Marchfelder


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U.G. and I.T.-G. conceived the study. U.G., I.T.-G. and A.M. designed the experiments. S.S. assembled and annotated genome sequences. I.T.-G., A.N. and N.A.-P. designed and constructed strains. I.T.-G., S.J., K.E., Y.S., A.-E.S. and M.Z. performed experiments. L.R., S.M., I.T.G. and U.G. analysed data. U.G. and I.T.-G. wrote the manuscript. L.R., S.S. and A.M. commented and made critical revisions to the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Uri Gophna.

Supplementary information

  1. Supplementary Information

    Supplementary Figures 1–10, Supplementary Tables 1–12, Supplementary References.

  2. Reporting Summary

  3. Supplementary Table 13

    Complete spacer acquisition data from H. volcanii arrays obtained following three independent inter-species mating experiments.

  4. Supplementary Table 14

    Complete spacer acquisition data from H. mediterranei arrays obtained following three independent inter-species mating experiments.

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