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CRISPR-Cas Systems pp 221–250Cite as

CRISPR-Cas Systems to Probe Ecological Diversity and Host–Viral Interactions

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Abstract

A key feature of the CRISPR-Cas defense system is the ability of the host to rapidly acquire novel spacers from invasive foreign genetic elements such as plasmids, viruses, or transposons. Consequently, host CRISPR loci have the potential to provide time-resolved information about exposure to foreign genetic elements as well as fine-scale ecological diversity. Furthermore, viral genomes can mutate rapidly, allowing viruses to circumvent the host CRISPR-encoded immunity system, which relies on close matches between spacers and incoming nucleic acids. Thus, CRISPR-Cas systems may drive complex, coevolving relationships between bacteria or archaea and viruses. We discuss how ecologically based approaches, in both natural and experimental systems, provide unique insights into host and viral diversity and horizontal gene transfer of CRISPR loci. We critically review recent attempts to model host–viral coevolutionary dynamics in the context of CRISPR loci. Finally, we highlight the future directions in which experimental analyses of host–viral coevolution can be fruitfully combined with theoretical approaches.

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Acknowledgments

NLH and RJW acknowledge support from NSF DEB-0816885. DB and MD acknowledge support from the NSF, The Carnegie Institution of Science and Stanford University. JSW acknowledges the support of a grant from the James S. McDonnell Foundation. JSW holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund.

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Authors and Affiliations

  1. Department of Microbiology, University of Illinois, 601 S. Goodwin Ave., Urbana, IL, 61801, USA

    Nicole L. Held & Rachel J. Whitaker

  2. School of Biology and School of Mathematics, Georgia Institute of Technology, Atlanta, GA, 30332, USA

    Lauren M. Childs

  3. Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA

    Michelle Davison & Devaki Bhaya

  4. School of Biology and School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA

    Joshua S. Weitz

  5. Department of Biology, Stanford University, Stanford, CA, 94305, USA

    Michelle Davison

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  1. Nicole L. Held
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  2. Lauren M. Childs
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  3. Michelle Davison
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  4. Joshua S. Weitz
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  5. Rachel J. Whitaker
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  6. Devaki Bhaya
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Correspondence to Devaki Bhaya .

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  1. DuPont Nutrition and Health, Agriculture Drive 3329, Madison, 53716, Wisconsin, USA

    Rodolphe Barrangou

  2. , Laboratory of Microbiology, University of Wageningen, Dreijenplein 10, Wageningen, 6703 HB, Netherlands

    John van der Oost

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Held, N.L., Childs, L.M., Davison, M., Weitz, J.S., Whitaker, R.J., Bhaya, D. (2013). CRISPR-Cas Systems to Probe Ecological Diversity and Host–Viral Interactions. In: Barrangou, R., van der Oost, J. (eds) CRISPR-Cas Systems. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-34657-6_9

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