C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

Abstract

The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated genes (Cas) adaptive immune system defends microbes against foreign genetic elements via DNA or RNA-DNA interference. We characterize the class 2 type VI CRISPR-Cas effector C2c2 and demonstrate its RNA-guided ribonuclease function. C2c2 from the bacterium Leptotrichia shahii provides interference against RNA phage. In vitro biochemical analysis shows that C2c2 is guided by a single CRISPR RNA and can be programmed to cleave single-stranded RNA targets carrying complementary protospacers. In bacteria, C2c2 can be programmed to knock down specific mRNAs. Cleavage is mediated by catalytic residues in the two conserved Higher Eukaryotes and Prokaryotes Nucleotide-binding (HEPN) domains, mutations of which generate catalytically inactive RNA-binding proteins. These results broaden our understanding of CRISPR-Cas systems and suggest that C2c2 can be used to develop new RNA-targeting tools.

Figure 1. Heterologous expression of the Leptotrichia shahii C2c2 locus mediates robust interference of RNA phage in Escherichia coli

A) Schematic for the MS2 bacteriophage interference screen. A library consisting of spacers targeting all possible sequences in the MS2 RNA genome was cloned into the LshC2c2 CRISPR array. Cells transformed with the MS2-targeting spacer library were then treated with phage and plated, and surviving cells were harvested. The frequency of spacers was compared to an untreated control (no phage), and enriched spacers from the phage-treated condition were used for the generation of PFS preference logos. B) Box plot showing the distribution of normalized crRNA frequencies for the phage-treated conditions and control screen (no phage) biological replicates (n = 3). The box extends from the first to third quartile with whiskers denoting 1.5 times the interquartile range. The mean is indicated by the red horizontal bar. The 10⁻¹ and 10⁻³ phage dilution distributions are significantly different than each of the control replicates (****, p < 0.0001 by ANOVA with multiple hypothesis correction). C) Sequence logo generated from sequences flanking the 3’ end of protospacers corresponding to enriched spacers in the 10⁻¹ phage dilution condition, revealing the presence of a 3’ H PFS (not G). D) Plaque assay used to validate the functional significance of the H PFS in MS2 interference. All protospacers flanked by non-G PFSs exhibited robust phage interference. Spacer were designed to target the MS2 mat gene and their sequences are shown above the plaque images; the spacer used in the non-targeting control is not complementary to any sequence in either the E. coli or MS2 genome. Phage spots were applied as series of half-log dilutions. E) Quantitation of MS2 plaque assay validating the H (non-G) PFS preference. 4 MS2-targeting spacers were designed for each PFS. Each point on the scatter plot represents the average of three biological replicates and corresponds to a single spacer. Bars indicate the mean of 4 spacers for each PFS and standard error (s.e.m).

Figure 2. LshC2c2 and crRNA mediate RNA-guided ssRNA cleavage

A) Schematic of the ssRNA substrate being targeted by the crRNA. The protospacer region is highlighted in blue and the PFS is indicated by the magenta bar. B) A denaturing gel demonstrating crRNA-mediated ssRNA cleavage by LshC2c2 after 1 hour of incubation. The ssRNA target is either 5’ labeled with IRDye 800 or 3’ labeled with Cy5. Cleavage requires the presence of the crRNA and is abolished by addition of EDTA. Four cleavage sites are observed. Reported band lengths are matched from RNA sequencing. C) A denaturing gel demonstrating the requirement for an H PFS (not G) after 3 hours of incubation. Four ssRNA substrates that are identical except for the PFS (indicated by the magenta X in the schematic) were used for the in vitro cleavage reactions. ssRNA cleavage activity is dependent on the nucleotide immediately 3’ of the target site. Reported band lengths are matched from RNA sequencing. D) Schematic showing five protospacers for each PFS on the ssRNA target (top). Denaturing gel showing crRNA-guided ssRNA cleavage activity after 1 hour of incubation. crRNAs correspond to protospacer numbering. Reported band lengths are matched from RNA sequencing.

Figure 3. C2c2 cleavage sites are determined by secondary structure and sequence of the target RNA

A) Denaturing gel showing C2c2-crRNA-mediated cleavage after 3 hours of incubation of three non-homopolymeric ssRNA targets (1, 4, 5; black, blue and green on figs 3B–C and S12A–D respectively) that share the same protospacer but are flanked by different sequences. Despite identical protospacers, different flanking sequences resulted in different cleavage patterns. Reported band lengths are matched from RNA sequencing. B) The cleavage sites of non-homopolymer ssRNA target 1 were mapped with RNA-sequencing of the cleavage products. The frequency of cleavage at each base is colored according to the z-score and shown on the predicted crRNA-ssRNA co-fold secondary structure. Fragments used to generate the frequency analysis contained the complete 5’ end. The 5’ and 3’ end of the ssRNA target are indicated by blue and red outlines, on the ssRNA and secondary structure, respectively. The 5’ and 3’ end of the spacer (outlined in yellow) is indicated by the blue and orange residues highlighted respectively. The crRNA nucleotides are highlighted in orange. C) Plot of the frequencies of cleavage sites for each position of ssRNA target 1 for all reads that begin at the 5’ end. The protospacer is indicated by the blue highlighted region. D) Schematic of a modified ssRNA 1 target showing sites (red) of single U to A flips (left). Denaturing gel showing C2c2-crRNA mediated cleavage of each of these single nucleotide variants after 3 hours of incubation (right). Reported band lengths are matched from RNA sequencing.

Figure 4. The two HEPN domains of C2c2 are necessary for crRNA-guided ssRNA cleavage but not for binding

A) Schematic of the LshC2c2 locus and the domain organization of the LshC2c2 protein, showing conserved residues in HEPN domains (dark blue). B) Quantification of MS2 plaque assay with HEPN catalytic residue mutants. For each mutant, the same crRNA targeting protospacer 35 was used. (n=3 biological replicates, ****, p < 0.0001 compared to pACYC184 by t-test. Bars represent mean ± s.e.m.) C) Denaturing gel showing conserved residues of the HEPN motif, indicated as catalytic residues in panel A, are necessary for crRNA-guided ssRNA target 1 cleavage after 3 hours of incubation. Reported band lengths are matched from RNA sequencing. D) Electrophoretic mobility shift assay (EMSA) evaluating affinity of the wild type LshC2c2-crRNA complex against a targeted (left) and a non-targeted (right) ssRNA substrate. The non-targeted ssRNA substrate is the reverse-complement of the targeted ssRNA 10. EDTA is supplemented to reaction condition to reduce any cleavage activity. E) Electrophoretic mobility shift assay with LshC2c2(R1278A)-crRNA complex against on-target ssRNA 10 and non-targeting ssRNA (same substrate sequences as in D)

Figure 5. RFP mRNA knockdown by retargeting LshC2c2

A) Schematic showing crRNA-guided knockdown of RFP in E. coli heterologously expressing the LshC2c2 locus. Three RFP-targeting spacers were selected for each non-G PFS and each protospacer on the RFP mRNA is numbered. B) RFP mRNA-targeting spacers effected RFP knockdown whereas DNA-targeting spacers (targeting the non-coding strand of the RFP gene on the expression plasmid, indicated as “rc” spacers) did not affect RFP expression. (n=3 biological replicates, ****, p < 0.0001 compared to non-targeting guide by ANOVA with multiple hypothesis correction. Bars represent mean ± s.e.m ) C) Quantification of RFP knockdown in E. coli. Three spacers each targeting C, U, or A PFS-flanking protospacers (9 spacers, numbered 5–13 as indicated in panel (A)) in the RFP mRNA were introduced and RFP expression was measured by flow cytometry. Each point on the scatter plot represents the average of three biological replicates and corresponds to a single spacer. Bars indicate the mean of 3 spacers for each PFS and errors bars are shown as the s.e.m. D) Timeline of E. coli growth assay. E) Effect of RFP mRNA targeting on the growth rate of E. coli transformed with an inducible RFP expression plasmid as well as the LshC2c2 locus with non-targeting, RNA targeting (spacer complementary to the RFP mRNA or RFP gene coding strand), and pACYC control plasmid at different anhydrotetracycline (aTc) concentrations.

Figure 6. crRNA-guided ssRNA cleavage activates non-specific RNase activity of LshC2c2

A) Schematic of the biochemical assay used to detect crRNA-binding-activated non-specific RNase activity on non-crRNA-targeted collateral RNA molecules. The reaction consists of C2c2 protein, unlabeled crRNA, unlabeled target ssRNA, and a second ssRNA with 3’ fluorescent labeling and is incubated for 3 hours. C2c2-crRNA mediates cleavage of the unlabeled target ssRNA as well as the 3’-end-labeled collateral RNA which has no complementarity to the crRNA. B) Denaturing gel showing non-specific RNase activity against non-targeted ssRNA substrates in the presence of target RNA after 3 hours of incubation. The non-targeted ssRNA substrate is not cleaved in the absence of the crRNA-targeted ssRNA substrate.

Figure 7. C2c2 as a putative RNA-targeting prokaryotic immune system

The C2c2-crRNA complex recognizes target RNA via base pairing with the cognate protospacer and cleaves the target RNA. In addition, binding of the target RNA by C2c2-crRNA activates a non-specific RNase activity which may lead to promiscuous cleavage of RNAs without complementarity to the crRNA guide sequence. Through this non-specific RNase activity, C2c2 may also cause abortive infection via programmed cell death or dormancy induction.