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Abstract
Analysis of spacer acquisition in Staphylococcus aureus reveals that type II CRISPR–Cas systems exploit viral DNA injection to ensure a successful CRISPR immune response. CRISPR–Cas systems provide anti-viral and plasmid immunity in prokaryotes by acquiring short DNA sequences known as spacers from the infecting agents and using them as templates to cleave the pathogens. This report unveils a new aspect of CRISPR–Cas function by describing the timeline of spacer acquisition during infection. The timeline shows how early acquisition enhances the microbial immune response. Clustered regularly interspaced short palindromic repeats (CRISPR)–Cas systems provide protection against viral1 and plasmid2 infection by capturing short DNA sequences from these invaders and integrating them into the CRISPR locus of the prokaryotic host1. These sequences, known as spacers, are transcribed into short CRISPR RNA guides3,4,5 that specify the cleavage site of Cas nucleases in the genome of the invader6,7,8. It is not known when spacer sequences are acquired during viral infection. Here, to investigate this, we tracked spacer acquisition in Staphylococcus aureus cells harbouring a type II CRISPR–Cas9 system after infection with the staphylococcal bacteriophage ϕ12. We found that new spacers were acquired immediately after infection preferentially from the cos site, the viral free DNA end that is first injected into the cell. Analysis of spacer acquisition after infection with mutant phages demonstrated that most spacers are acquired during DNA injection, but not during other stages of the viral cycle that produce free DNA ends, such as DNA replication or packaging. Finally, we showed that spacers acquired from early-injected genomic regions, which direct Cas9 cleavage of the viral DNA immediately after infection, provide better immunity than spacers acquired from late-injected regions. Our results reveal that CRISPR–Cas systems exploit the phage life cycle to generate a pattern of spacer acquisition that ensures a successful CRISPR immune response.Cite this article
Modell, J., Jiang, W. & Marraffini, L. CRISPR–Cas systems exploit viral DNA injection to establish and maintain adaptive immunity. Nature 544, 101–104 (2017). https://doi.org/10.1038/nature21719 