Expanded base editing in rice and wheat using a Cas9-adenosine deaminase fusion

The CRISPR (clustered regularly interspaced short palindromic repeat) system has been used to edit a variety of plant species [1]. CRISPR/Cas9 and CRISPR/Cpf1 typically produce double strand breaks (DSBs) that result in mutant plants with either gene knock-outs (via non-homologous end joining (NHEJ)) or gene replacements and insertions (via homology-directed repair (HDR)) [2, 3]. Base editing is a unique genome editing system that creates precise and highly predictable nucleotide substitutions at genomic targets without requiring DSBs, or donor DNA templates, or depending on NHEJ and HDR [4]. Base editing is more efficient than HDR-mediated base pair substitution, and produces fewer undesirable mutations in the target locus [5]. The most commonly used base editing systems, such as BE3 [6], BE4 [7], Targeted-AID [8], and dCpf1-BE [9], use Cas9 or Cpf1 variants to recruit cytidine deaminases that exploit DNA mismatch repair pathways and generate specific C to T substitutions. This base-editing technology has already been used in a wide variety of cell lines and organisms [4, 5]. Recently, adenine base editors (ABE), developed by fusing an evolved tRNA adenosine deaminase with SpCas9 nickase (D10A), were shown to generate A•T to G•C conversions when directed by single guide RNAs (sgRNAs) to genomic targets in human cells [10].

In this report, we adapted this method and optimized an ABE for application in plant systems, demonstrating its high efficiency in creating targeted point mutations at multiple endogenous loci in rice and wheat.

We used ABE7.10, a fusion of an adenosine deaminase (ecTadA-ecTadA*) with nCas9 (D10A), which base edits A•T to G•C accurately in human cells [10]. To develop an efficient ABE for plant cells, we constructed seven ABE fusion proteins. The seven proteins, named PABE-1 to PABE-7, varied in the position of the adenosine deaminase and the number and locations of nuclear localization sequences (NLSs; Fig. 1a; Additional file 1: Sequences). All the PABE constructs were codon-optimized for cereal plants, and placed under control of the maize Ubiquitin-1 promoter (Ubi-1).

Editing efficiencies of the PABE constructs were first tested using a green fluorescent protein (GFP) reporter that contained a mutation within the expression cassette converting the Gln-69 codon (CAG) for GFP into a stop codon (TAG) (Fig. 1b). This mutated gene, termed mGFP, produces active GFP when the stop codon is corrected by a T to C single nucleotide substitution (TAG to CAG), thus allowing mutagenesis efficiency to be measured as the frequency of GFP-expressing cells (Fig. 1b). We designed an sgRNA-mGFP with the desired T at position 6 (T₆) of the protospacer, counting from the distal end to the protospacer-adjacent motif (PAM), based on the ABE7.10 deamination window in human cells [10] (Fig. 1b; Additional file 2: Table S1). Each PABE construct was co-transfected with sgRNA-mGFP and Ubi-mGFP into rice protoplasts by PEG-mediated transformation [11].

At 24 h post-transfection, GFP fluorescence was reliably detected in cells treated with the following five of the seven test constructs: PABE-1, PABE-2, PABE-3, PABE-6, and PABE-7 (Fig. 1c). Flow cytometry (FCM) analyses showed that the percentages of fluorescent cells ranged from 0.1 to 32.8% (Fig. 1d). Three copies of the NLS at the C-terminus of nCas9 (PABE-7) gave the highest yield of GFP-expressing cells, higher than PABE-2, which was similar to the construct used in human cells [10] and the other PABE constructs (Fig. 1c, d). These results also showed that putting ecTadA-ecTadA* adenosine deaminase at the C-terminus of nCas9 (PABE-4 and PABE-5) renders the plant ABE system ineffective (Fig. 1c, d).

To further compare the editing efficiency of PABE-2 and PABE-7, we targeted 16 rice endogenous genomic sites (Fig. 1e; Additional file 2: Table S1). A to G base editing of the respective genes in protoplasts was assessed by next-generation sequencing (100,000–220,000 reads per locus). PABE-7 was identified to offer modestly higher base editing efficiency, about 1.1-fold average increase in A•T to G•C conversion at each site over PABE-2 (Fig. 1e; Additional file 2: Table S3). Taken together, these results demonstrate that the plant ABE system can induce A to G conversions in rice, and that the presence of three NLS at the C-terminus of nCas9 maximizes editing efficiency.

To identify the optimal form of sgRNA for PABE-7 activity, various sgRNA modifications were tested over a broad range of endogenous loci. Previous work has shown that modifications to the sgRNA sequence (known as sgRNA^(F + E), enhanced sgRNA, or esgRNA) [12] or tRNA-sgRNA expression system [13, 14] can enhance CRISPR/Cas9 genome editing. We therefore compared the base editing activities of the three sgRNA forms (native sgRNA, esgRNA, tRNA-sgRNA) at ten and three endogenous genomic target sites in rice and wheat, respectively (Fig. 2a; Additional file 2: Figure S1 and Table S1). The protospacers targeting these endogenous genes were individually cloned into the three sgRNA structures and co-transformed with PABE-7 into either rice or wheat protoplasts. Wild-type Cas9 (WT Cas9) was used as a control to produce deletion and/or insertion mutations (indels). A to G conversion was observed at all 13 target sites for each combination of PABE-7 and sgRNA expression system, with effective editing frequency spanning positions 4 to 8 within the protospacer (Fig. 2a). Of the three sgRNA constructs, esgRNA showed the highest base editing efficiency in a large majority of the tests ranging from 0.1–7.5% in both rice and wheat (Fig. 2a). The average efficiency of esgRNA for the 13 target sites was about twofold higher than that of the native sgRNA, and threefold higher than that of the tRNA-sgRNA (Fig. 2b), which is consistent with the observation that esgRNA increases the stability and promotes complexing with the Cas9 protein [12]. We observed only A to G conversions, with no evidence of undesired editing at any of the rice and wheat genomic on-target loci (< 0.02%; Additional file 2: Figures S2 and S3), and a much lower frequency of indels (< 0.1%) than with WT Cas9 (3.3–31.6%) (Fig. 2c). To summarize, the PABE-7 base editing construct, together with the esgRNA, induces A to G substitutions efficiently and with high fidelity at multiple loci in rice and wheat.

We also tested the effect of spacer length of the esgRNA on base editing efficiency by targeting OsEV and OsOD, and found that the esgRNAs with canonical 20-nucleotide spacers showed the highest conversion efficiency (Fig. 2d; Additional file 2: Table S3). At both target sites, esgRNAs with spacer lengths ranging from 14 to 19 nucleotides showed substantially decreased or undetectable A to G base editing activities (< 0.9%) compared with the esgRNAs with canonical 20-nucleotide spacers (< 4.5%) (Fig. 2d). In addition, the WT Cas9 with 14- to 19-nucleotide spacer lengths of esgRNAs also gave much lower frequencies of indels (0.3–12.6%) than with 20-nucleotide esgRNA (10.8–22.4%) at these two sites (Additional file 2: Figure S4). These results suggest that the 20-nucleotide spacer of esgRNA is essential for the plant ABE system with no tolerance for shorter lengths.

Herbicide resistance is an important goal in modern crop breeding as it will reduce the time cost for weeding. In turn, this makes a significant contribution to increasing food productivity and reducing soil degradation. Herbicides often target specific enzymes in metabolic pathways, and mutations in an enzyme can be selected that confer herbicide resistance through a substitution in a single amino acid [15]. Acetyl-coenzyme A carboxylase (ACC) is a key enzyme in lipid biosynthesis and it has been shown that a T to C replacement (C2088R) in Lolium rigidum could endow plants with resistance to the herbicides across the aryloxyphenoxypropionate (APP), cyclohexanedione (CHD), and phenylpyrazoline (PPZ) chemical groups [16]. The point mutation C2088R in Lolium rigidum corresponds to C2186R in rice (Oryza sativa), which is our target site OsACC-T1. Examination of 160 pH-PABE-7-esgRNA-transformed lines revealed that 33 harbored at least one T to C substitution in the target region (mutation efficiency of 20.6%) (Table 1; Additional file 2: Table S1). One of the mutant lines contained a homozygous substitution (T₄T₇ > C₄C₇), whereas the remaining 32 contained heterozygous substitutions: 20 with double-base substitutions (T₄T₇ > C₄C₇), ten with T₄ > C₄ single-base substitutions, and two that contained single-base substitutions providing the desired C2186R amino acid substitution at one of the alleles (T₇ > C₇; T0–7 and T0–13) (Fig. 2e; Table 1; Additional file 2: Figure S5b). We did not detect mutations in the potential off-target regions among all OsACC-T1 mutant lines (Additional file 2: Tables S2 and S3). We then assessed the herbicide resistance of the T0–13 mutant carrying the heterozygous C2186R substitution. After one week of growth on the regeneration medium supplemented with 0.086 ppm haloxyfop-R-methyl, the mutant plant had normal phenotypes with no symptoms of damage whereas wild-type (WT) plants displayed severe stunting and withered leaves (Fig. 2e). To the best of our knowledge, this is the first report of producing C2186R substitution of resistant rice plants using genome editing tools.

We also used the plant ABE system to generate base-edited plants in wheat by targeting TaDEP1 and TaGW2 genes. PABE-7 and pTaU6-esgRNA constructs (Additional file 2: Figure S1e and Table S1) were delivered into immature wheat embryos by particle bombardment, and plants regenerated without herbicide selection, as previously described [17]. Through T7E1 and Sanger sequencing, we obtained five A₈ to G₈ heterozygous TaDEP1 mutant plants regenerated from 460 bombarded immature embryos (Table 1; Additional file 2: Figure S6a), with four mutants heterozygous for TaDEP1-A (tadep1-AaBBDD) and one mutant heterozygous for TaDEP1-B (tadep1-AABbDD) (Table 1; Additional file 2: Figure S6a). For the TaGW2 target site, two heterozygous mutants were identified. Both harbored an A to G substitution at position 5 for TaGW2-B (tagw2-AABbDD) (Table 1; Additional file 2: Figure S6b). Again, no indels were observed in the target region of all mutant plants. Furthermore, PCR screening with six primer sets, specific for PABE-7 and pTaU6-esgRNA (Additional file 2: Figure S7a and Table S3), confirmed that three of five TaDEP1 mutants and two TaGW2 mutants did not carry the transgene vectors (Additional file 2: Figure S7b). Taken together, these results support that the plant ABE system is effective in inducing specific point mutations in rice and wheat in a highly specific and precise manner without causing other genomic modifications.

Despite the newly developed high efficiency of cytidine deaminase mediated C to T substitution exhibiting a great potential for disease therapeutic and agronomic traits engineering [4], additional base editing tools are needed for expanding editing more DNA nucleotides. Here, we adapted and optimized a plant ABE system (fusion of an evolved tRNA adenosine deaminase with nuclease-inactivated CRISPR/Cas9) to efficiently and specifically achieve targeted conversion of adenine to guanine in crop plants. To our knowledge, this is the first report of achieving wheat A to G base-edited plants and herbicide-resistant rice plants with the plant ABE system. High base-editing efficiency, low indels, and high purity products make this plant ABE system outperform HDR-mediated genome editing.

Based on the ABE7.10 architectures for human cells, we optimized the system for crop plants from two perspectives. One was by optimizing the position of the tRNA adenosine deaminase relative to the nCas9, and the number and locations of NLSs. Our observation shows that placing the ecTadA-ecTadA* adenosine deaminase at the N-terminus of nCas9 and the presence of three NLSs at the C-terminus (PABE-7) maximizes editing efficiency, probably because this configuration maximizes fusion protein folding and nuclear importing. The other improvement to the plant ABE system was based on comparing three forms of sgRNA (native sgRNA, esgRNA, and tRNA-sgRNA). We found that the esgRNA showed a higher editing efficiency than the native sgRNA and the tRNA-sgRNA in both protoplasts and regenerated plants, indicating that the esgRNA has a higher expression level and better binding activity with Cas9 [12]. With our most effective combination, PABE-7 plus esgRNA, we obtained base-edited rice and wheat plants in the T0 generation. The herbicide-resistant rice plants harboring the C2186R substitution in OsACC was also obtained, indicating this plant ABE system is a reliable tool for achieving targeted base editing in crop plants.

There are still opportunities for extending and optimizing the plant ABE system. One could use engineered Cas9 variants with different protospacer-adjacent motif (PAM) specificities (xCas9, SpCas9-VQR, SpCas9-VRER, SaCas9, and SaCas9-KKH), or Cpf1 [9, 18, 19], to expand the number of sites that can be targeted. The plant ABE system combined with the plant C to T base editing system by ligating sgRNA with different aptamers (MS2, PP7, COM, and boxB) [20, 21] could achieve simultaneous A to G and C to T changes, and could be used to correct point mutations related to important agronomic traits. It could also provide a novel forward genetics tool to screen gain-of-function and partial loss-of-function genetic variants at the resolution of single bases. Furthermore, plant ABE ribonucleoproteins (RNPs) could be delivered to create transgene-free mutant plants, which could avoid inserting recombinant DNA into host genomes, and would have a good chance of being commercialized [17, 22].

We describe here an efficient plant base-editing system that induces precise A•T to G•C substitutions across a broad range of endogenous genomic loci. The effective deamination window of this plant ABE system extends from positions 4 to 8 of the protospacer and produces high-fidelity substitutions at the targeted loci with low indels. These findings, together with previously described plant substitution systems [23–26], extend the application of base editing to the majority of codons and now provides feasible opportunities for significant in vivo mutagenesis studies and trait improvement in plants.