RNA-Independent DNA Cleavage Activities of Cas9 and Cas12a

Abstract

CRISPR-Cas systems provide bacteria and archaea with sequence-specific protection against invading mobile genetic elements. In the presence of divalent metal ions, Cas9 and Cas12a (formerly Cpf1) proteins target and cleave DNA that is complementary to a cognate guide RNA. The recognition of a protospacer adjacent motif (PAM) sequence in the target DNA by Cas9 and Cas12a is essential for cleavage. This RNA-guided DNA targeting is widely used for gene-editing methods. Here, we show that Francisella tularensis novicida (Fno) Cas12a, FnoCas9, and Streptococcus pyogenes Cas9 (SpyCas9) cleave DNA without a guide RNA in the presence of Mn²⁺ ions. Substrate requirements for the RNA-independent activity vary. FnoCas9 preferentially nicks double-stranded plasmid, SpyCas9 degrades single-stranded plasmid, and FnoCas12a cleaves both substrates. These observations suggest that the identities and levels of intracellular metals, along with the Cas9/Cas12a ortholog employed, could have significant impacts in genome editing applications.

Keywords: CRISPR; Cas12a; Cas9 endonucleases; Cpf1; FnoCas12a; FnoCas9; Francisella tularensis novicida; Mn(2+)-specific CRISPR activity; RNA-independent DNA cleavage; SpyCas9.

Figure 1. FnoCas9 and FnoCas12a Possess RNA-Independent dsDNA Nickase Activity while SpyCas9 and FnoCas12a Possess RNA-Independent ssDNA Degradation in the Presence of Mn²⁺

(A) dsDNA cleavage by FnoCas12a. (B) dsDNA cleavage by FnoCas9. (C) dsDNA cleavage by SpyCas9. FnoCas9 and FnoCas12a nicked pUC19 (ds plasmid) in the presence of Mn²⁺. There is limited linearization of the plasmid by FnoCas12a. For comparison, pUC19 was digested with EcoRI (linearizes [L]) or Nt.BspQI (nicks [N]). SpyCas9 does not nick or linearize pUC19. (D) ssDNA cleavage by SpyCas9 and FnoCas9. (E) ssDNA cleavage by FnoCas12a. M13mp18 circular (Cr) ssDNA was degraded by SpyCas9 and FnoCas12a in the presence of Mn²⁺. In comparison, FnoCas9 has limited ssDNA degradation. D, degradation; C, control condition with no protein; None, condition with protein but no external metal or EDTA; SC, supercoiled. See also Figures S1–S3, S6, and S7.

Figure 2. Time Course Assay to Quantify the RNA-Independent DNA Cleavage Activity

(A) Activity of FnoCas12a on pUC19 plasmid. The major product is the nicked band. The linearization of the plasmid is incomplete after an overnight incubation. (B) Activity of FnoCas9 on pUC19 plasmid. The linearization of the plasmid is minimal compared to FnoCas12a. (C) Activity of FnoCas12a on M13mp18 circular DNA. The DNA is degraded, and there is no accumulation of lower molecular weight species except for the smaller degradation products. (D) Activity of SpyCas9 on M13mp18 circular DNA. The DNA is degraded during the reaction. The graphs represent the average formation of nicked DNA for ds plasmid substrate or the amount of circular DNA left for circular ssDNA substrate. The graphs (mean ± SEM) indicate activity based on quantification of DNA bands (Schneider et al., 2012), and error bars are from three replications performed using proteins from different protein preparations. (E) Time to reach 50% activity for all activities. The error bars are represented as SEM and were calculated using the formula $\mathit{\text{SEM}}=\mathit{\text{SD}}/\sqrt{n}$, where n represents the number of replications (see Experimental Procedures). SD was calculated using the formula $\mathit{\text{SD}}=\sqrt{\frac{\sum {(P-P_{\mathit{\text{AV}}})}^2}{(n-1)}}$. C, control with no protein; N, nicked; L, linear; SC, supercoiled; Cr, circular ssDNA; D, degradation.

Figure 3. Active Sites Responsible for the RNA-Independent DNA Cleavage Activity

(A) ds nicking activity in FnoCas9 is performed by the HNH domain. (B) ssDNA cleavage is performed by the RuvC domain in SpyCas9. (C) Coordinated activity of both the RuvC and the Nuc domains is essential for RNA-independent dsDNA nicking in FnoCas12a. (D) Both RuvC and Nuc active sites are required for ssDNA degradation in FnoCas12a. C, control with no protein; WT, wild-type; M, mutant; DM, double mutant (both endonuclease sites inactivated); N, nicked; SC, supercoiled; Cr, circular ssDNA; D, degradation; None, condition with protein but no external metal or EDTA. See also Figure S5.

Figure 4. RNA-Independent DNA Nicking Activity by FnoCas9 and FnoCas12a Is Non-sequence Specific

(A and B) Restriction enzyme (RE) analysis of the cleavage products produced by FnoCas9 on a native agarose gel (A) and on a denaturing alkaline agarose gel (B). (C and D) RE analysis of the cleavage products produced by FnoCas12a on a native agarose gel (C) and on a denaturing alkaline agarose gel (D). Comparison of native and alkaline gels shows that the nicked band produced by RNA-independent cleavage is converted to the linear product after RE digestion. The absence of specific-sized products compared to the lanes with RNA-dependent cleavage product analysis indicates that RNA-independent activity is non-sequence specific. Identification of sequence- or structure-specific hotspots in the RNA-independent DNA cleavage will require further experiments. pUC19-L, pUC19 treated with EcoRI; pUC19-N, pUC19 treated with Nt.BspQI; ExoIII: nicked pUC19 treated with exonuclease III, Exo III degrades linear DNA; Cas-N, nicked product from the RNA-independent activity of Cas protein (FnoCas9 or FnoCas12a); Cas-L, linear product from the RNA-dependent activity of Cas protein (FnoCas9 or FnoCas12a); L, linearization by RE; Cl, shorter cleavage product produced by sequence-specific digestion by RE; CC, closed circular; kbp, kilo base pairs; kb, kilobases; RI, RNA-independent cleavage; RD, RNA-dependent cleavage.

Figure 5. RNA-Independent DNA Nicking Activity on Linear DNA Substrates

(A and B) M13mp18 digested using EcoRI (one site) was treated with Cas proteins, and the products were analyzed on a native agarose gel (A) and a denaturing alkaline gel (B). Both FnoCas12a and SpyCas9 cleave linear ssDNA, while FnoCas9 has limited activity. The cleavage of M13mp18 with EcoRI is not complete, as seen by the presence of both closed circular (CC) and linear (L) bands on an alkaline gel. Exonuclease III (ExoIII) that degrades linear DNA is included to distinguish CC and L bands. Both CC and L DNA are degraded by FnoCas12a and SpyCas9. (C) 5′-³²P-labeled ss oligo DNA was treated with Cas proteins. Only FnoCas12a cleaves ss oligo substrates. C, control with no protein; none, reaction with protein without added metal; Cr, circular ss M13mp18; D, degradation; kbp, kilo base pairs; kb, kilobases; OI, 60-mer ss oligo; Cl, cleavage products. See also Figure S4.

Figure 6. In the Presence of Either of the RNAs (crRNA or tracrRNA), Mn²⁺ Promotes RNA-Independent Activity by FnoCas9

(A) Activity of FnoCas9 wild-type (WT) and the RuvC-inactive (D11A) mutant. (B) Activity of the FnoCas9 HNH-inactive (H969A) mutant and the double mutant (DM), where both RuvC and HNH are inactivated. While Mg²⁺ promotes RNA-dependent DNA cleavage (linear product) only when both crRNA and tracrRNA are present in the reaction, Mn²⁺ can promote plasmid nicking when either crRNA or tracrRNA is present in the reaction and linearization when both RNAs are present. In the case of D11A, nicking is observed for RNA-dependent (both RNAs present) and RNA-independent activities. The mutants H969A and DM show negligible RNA-independent activity. Control lanes with linear (L) bands produced by EcoRI digestion and nicked plasmids (N) produced by Nt.BspQI digestion are also shown. SC, supercoiled.

Figure 7. Limited Trypsin Proteolysis Suggests Structural Differences between Apo-, RNA-Bound, and DNA-Bound Forms of SpyCas9, FnoCas9, and FnoCas12a

(A) Limited proteolysis of SpyCas9. In the presence of Mn²⁺-DNA, full-length protein is more intact compared to Mg²⁺ (arrows). (B) Limited proteolysis of FnoCas9. There are no visible differences between Mn²⁺ and Mg²⁺ digestion patterns (arrow). (C) Limited proteolysis of FnoCas12a. A distinct pattern with additional bands at 37 kDa (arrow) is present for DNA-bound structures when compared to apo- and RNA-bound FnoCas12a. For all proteins, apo protein is rapidly degraded, while the RNA- and DNA-bound structures appear to be more stable, with distinct banding patterns compared to apo protein digestion. A protein marker (M) is present in each gel. T, trypsin.