Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity - PubMed (original) (raw)

Review

Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity

Emmanuelle Charpentier et al. FEMS Microbiol Rev. 2015 May.

Abstract

CRISPR-Cas is an RNA-mediated adaptive immune system that defends bacteria and archaea against mobile genetic elements. Short mature CRISPR RNAs (crRNAs) are key elements in the interference step of the immune pathway. A CRISPR array composed of a series of repeats interspaced by spacer sequences acquired from invading mobile genomes is transcribed as a precursor crRNA (pre-crRNA) molecule. This pre-crRNA undergoes one or two maturation steps to generate the mature crRNAs that guide CRISPR-associated (Cas) protein(s) to cognate invading genomes for their destruction. Different types of CRISPR-Cas systems have evolved distinct crRNA biogenesis pathways that implicate highly sophisticated processing mechanisms. In Types I and III CRISPR-Cas systems, a specific endoribonuclease of the Cas6 family, either standalone or in a complex with other Cas proteins, cleaves the pre-crRNA within the repeat regions. In Type II systems, the trans-acting small RNA (tracrRNA) base pairs with each repeat of the pre-crRNA to form a dual-RNA that is cleaved by the housekeeping RNase III in the presence of the protein Cas9. In this review, we present a detailed comparative analysis of pre-crRNA recognition and cleavage mechanisms involved in the biogenesis of guide crRNAs in the three CRISPR-Cas types.

Keywords: Cas5d; Cas6; Cas9; RNase III; crRNA biogenesis; tracrRNA.

© FEMS 2015.

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Figures

Figure 1.

Figure 1.

cas gene composition of the CRISPR-Cas systems. Loci from Types I-A to I-F, Types II-A to II-C and Types III-A and II-B CRISPR-Cas systems are represented. The CRISPR arrays are composed of a series of repeats (black diamonds) interspaced by invading genome-targeting spacers (colored diamonds). An operon of cas genes is located in the close vicinity of the CRISPR array. The Cas proteins involved in the crRNA biogenesis in Types I-A, I-B, I-D, I-E and I-F and Types III-A and III-B belong to the Cas6 family. An exception is the gene product Cas5d responsible for the processing of pre-crRNA in Type I-C. In Type II systems, tracrRNA, and the proteins Cas9 and RNase III are the three components responsible for pre-crRNA maturation.

Figure 2.

Figure 2.

crRNA processing pathways in Type I CRISPR-Cas systems. In Type I systems, the palindromic repeats in the pre-crRNA are either unstructured (Cascade/I-A, Cascade/I-B) or form hairpin structures (Cascade/I-C, Cascade/I-D, Cascade/I-E, Cascade/I-F) that are recognized by the nuclease Cas6 (Cas6a, Cascade/I-A; Cas6b, Cascade/I-B; Cas6d, Cascade/I-D; Cas6e, Cascade/I-E; Cas6f, Cascade/I-F) or Cas5 (Cas5d, Cascade/I-C). After cleavage, the crRNA hairpin remains associated with Cas6 or Cas5 whilst other subunits bind the 5′ handle and spacer, which is used for the recognition of cognate genetic element sequences by the respective Cascade complexes.

Figure 3.

Figure 3.

crRNA processing pathways in Type II CRISPR-Cas systems. In Type II systems, the precursor transcript of the CRISPR repeat-spacer array forms duplexes with the _trans_-activating tracrRNA through pre-crRNA repeat:tracrRNA anti-repeat interactions. The duplex RNAs stabilized by the protein Cas9 are recognized and cleaved by the bacterial endoribonuclease III (RNase III). A second processing by unknown nucleases (trimming by an exonuclease and/or cleavage by an endoribonuclease) generates the mature crRNAs. An alternative pathway for the production of mature crRNAs was described in a Type II-C of N. meningitidis. Here, the transcription of short crRNAs occurs directly from promoters contained within the repeats of the array, and thus independently of cleavage by RNase III. The mature dual tracrRNA:crRNAs complexed with the protein Cas9 form the interference complex that target and cleave site specifically double-stranded DNA.

Figure 4.

Figure 4.

crRNA processing pathways in Type III CRISPR-Cas systems. In Type III-A and III-B systems, the standalone Cas6 endonuclease binds unstructured pre-crRNA and cleaves within each repeat to generate intermediate crRNAs with 5′ and 3′ repeat-derived termini. The crRNAs are loaded into the Csm (Type III-A) or Cmr (Type III-B) complex and undergo further maturation through trimming of the 3′ repeat-derived sequence by nucleases that are yet to be identified.

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References

    1. Anders C, Niewoehner O, Duerst A, et al. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature. 2014;513:569–73. - PMC - PubMed
    1. Baranova N, Nikaido H. The baeSR two-component regulatory system activates transcription of the yegMNOB (mdtABCD) transporter gene cluster in Escherichia coli and increases its resistance to novobiocin and deoxycholate. J Bacteriol. 2002;184:4168–76. - PMC - PubMed
    1. Barrangou R, Fremaux C, Deveau H, et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007;315:1709–12. - PubMed
    1. Beloglazova N, Petit P, Flick R, et al. Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. EMBO J. 2011;30:4616–27. - PMC - PubMed
    1. Briner AE, Donohoue PD, Gomaa AA, et al. Guide RNA functional modules direct Cas9 activity and orthogonality. Mol Cell. 2014;56:333–9. - PubMed

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