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Anti-cas spacers in orphan CRISPR4 arrays prevent uptake of active CRISPR–Cas I-F systems

Nature Microbiology volume 1, Article number: 16081 (2016) Cite this article

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Abstract

Archaea and bacteria harbour clustered regularly interspaced short palindromic repeats (CRISPR) loci. These arrays encode RNA molecules (crRNA), each containing a sequence of a single repeat–intervening spacer. The crRNAs guide CRISPR-associated (Cas) proteins to cleave nucleic acids complementary to the crRNA spacer, thus interfering with targeted foreign elements. Notably, pre-existing spacers may trigger the acquisition of new spacers from the target molecule by means of a primed adaptation mechanism. Here, we show that naturally occurring orphan CRISPR arrays that contain spacers matching sequences of the cognate (absent) cas genes are able to elicit both primed adaptation and direct interference against genetic elements carrying those genes. Our findings show the existence of an anti-cas mechanism that prevents the transfer of a fully equipped CRISPR–Cas system. Hence, they suggest that CRISPR immunity may be undesired by particular prokaryotes, potentially because they could limit possibilities for gaining favourable sequences by lateral transfer.

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Figure 1: Diversity of CRISPR4.1–2 in E. coli.
Figure 2: Plasmid loss assays in BL21 AI.
Figure 3: Coverage of spacers acquired in BL21 AI + pCas1–3 + pCas5–8 grown without antibiotic selection.
Figure 4: Coverage of spacers acquired under antibiotic selection.

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Acknowledgements

This work was supported by the Ministerio de Economía y Competitividad (BIO2011-24417 and BIO2014-53029-P) and the Consellería D'Educació, Cultura i Esport, Generalitat Valenciana (ACOMP/2014/135). The authors thank E. Denamur (INSERM U722-Université Paris Diderot, France) for E. coli strain ED1a.

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Authors and Affiliations

  1. Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain

    Cristóbal Almendros, Noemí M. Guzmán, Jesús García-Martínez & Francisco J. M. Mojica

  2. Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’, Universidad de Alicante, Alicante, Spain

    Francisco J. M. Mojica

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  1. Cristóbal Almendros
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Contributions

C.A. and N.M.G. performed the experiments. C.A., J.G.-M. and F.J.M.M. conceived and designed the experiments. C.A. and F.J.M.M. analysed the data and wrote the paper, with comments from the co-authors.

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Correspondence to Cristóbal Almendros or Francisco J. M. Mojica.

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Almendros, C., Guzmán, N., García-Martínez, J. et al. Anti-cas spacers in orphan CRISPR4 arrays prevent uptake of active CRISPR–Cas I-F systems. Nat Microbiol 1, 16081 (2016). https://doi.org/10.1038/nmicrobiol.2016.81

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