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RNA-targeting CRISPR–Cas systems

Abstract

CRISPR–Cas is a widespread adaptive immune system in bacteria and archaea that protects against viral infection by targeting specific invading nucleic acid sequences. Whereas some CRISPR–Cas systems sense and cleave viral DNA, type III and type VI CRISPR–Cas systems sense RNA that results from viral transcription and perhaps invasion by RNA viruses. The sequence-specific detection of viral RNA evokes a cell-wide response that typically involves global damage to halt the infection. How can one make sense of an immune strategy that encompasses broad, collateral effects rather than specific, targeted destruction? In this Review, we summarize the current understanding of RNA-targeting CRISPR–Cas systems. We detail the composition and properties of type III and type VI systems, outline the cellular defence processes that are instigated upon viral RNA sensing and describe the biological rationale behind the broad RNA-activated immune responses as an effective strategy to combat viral infection.

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Fig. 1: DNA-targeting and RNA-targeting host defence systems and viral evasion strategies.
Fig. 2: Type III CRISPR–Cas immunity.
Fig. 3: Type VI CRISPR–Cas immunity.
Fig. 4: Model of the dormancy strategy used by type III and type VI CRISPR–Cas systems.
Fig. 5: Blindfolded self/non-self discrimination.

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Acknowledgements

S.J.J.B. is supported by the Netherlands Organization for Scientific Research (VICI grant no. VI.C.182.027) and has received funding from the European Research Council Consolidator Grant programme under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 101003229). The authors thank members of the Brouns laboratory for helpful discussions.

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S.P.B.v.B., J.S., A.R.-M. and S.J.J.B. researched data for the article and contributed substantially to discussion of the content. S.P.B.v.B. wrote the manuscript. S.P.B.v.B. and A.R.-M. designed figures. S.P.B.v.B. and S.J.J.B. reviewed and edited the manuscript before submission.

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Correspondence to Sam P. B. van Beljouw or Stan J. J. Brouns.

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Glossary

Mobile genetic elements

(MGEs). Simple genetic organisms (such as phages, plasmids, conjugative elements, transposons, introns and phage-inducible chromosomal islands) capable of horizontal transfer within or between genomes.

Dormancy

A non-replicating cellular state defined by low or inactive metabolism that promotes survival during stressful conditions.

Protospacer adjacent motif

(PAM). A small DNA sequence which serves as a recognition motif for various CRISPR–Cas nucleases, positioned next to a target sequence in an invading DNA-based mobile genetic element but absent from the host genome, allowing the discrimination between self and non-self.

Protospacer flanking site

(PFS). A small RNA sequence positioned next to a target sequence in RNA which needs to be non-complementary to the repeat-derived portion of the CRISPR RNA for the type III and type VI CRISPR–Cas effectors to become active, thereby preventing activation by a self-transcript.

CRISPR adaptation

The process by which a sequence of an invading mobile genetic element is extracted and stored in the CRISPR array.

Palm domain

A domain in the Cas10 subunit of various type III CRISPR–Cas effectors with structural similarity to nucleotidyl cyclases and nucleotide polymerases, catalysing the synthesis of cyclic oligoadenylate molecules from ATP.

Cyclic oligonucleotide-based antiphage signalling system

A family of defence systems in bacteria and archaea related to animal cGAS–STING immunity in which a cyclase generates cyclic oligonucleotides to activate a cell death effector protein in response to viral infection.

Restriction–modification systems

Genetic compositions encoding nucleases and methylases in which specific methylation patterns generated by the methylases prevent or facilitate cleavage by the nucleases, presenting a means for discriminating self from non-self.

Membrane depolarization

The process by which the basal electrochemical potential across cellular membranes changes from a negative state to a positive state.

Toxin–antitoxin systems

Genetic compositions encoding at least a toxin and a counteracting antitoxin whereby the toxin component becomes active when the antitoxin is absent.

Kin selection

A theory of natural selection describing behaviour that favours the fitness of closely related kin over the fitness of the individual enacting the behaviour.

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van Beljouw, S.P.B., Sanders, J., Rodríguez-Molina, A. et al. RNA-targeting CRISPR–Cas systems. Nat Rev Microbiol (2022). https://doi.org/10.1038/s41579-022-00793-y

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