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

Abstract

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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Fig. 1: Simplified representation of perfect inter-species matches between CRISPR spacers and DNA sequences in the genomes of environmental Atlit isolates.
Fig. 2: Number of spacers acquired during mating between H. volcanii and H. mediterranei.
Fig. 3: Spacers acquired from the H. mediterranei chromosome by either H. volcanii or H. mediterranei CRISPR–Cas.
Fig. 4: PAM preference for each of the species against different replicons.
Fig. 5: Inter-species mating is reduced by CRISPR–Cas targeting.

Data availability

Haloarchaeal environmental isolates genomes are available at GenBank under accession numbers PSYS00000000, PSYT00000000, PSYU00000000, PSYV00000000, PSYW00000000, PSYX00000000, PSYY00000000, QEQI00000000, QEQJ00000000, QPLN00000000, QPLO00000000, QPLP00000000, QPLQ00000000, QPLR00000000, QPLS00000000, QPLT00000000, QPLU00000000, QXIJ00000000, QXIK00000000 and QPLV00000000.

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Acknowledgements

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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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.

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Correspondence to Uri Gophna.

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

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Supplementary Table 13

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

Supplementary Table 14

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

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Turgeman-Grott, I., Joseph, S., Marton, S. et al. Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation. Nat Microbiol 4, 177–186 (2019). https://doi.org/10.1038/s41564-018-0302-8

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