PhieABEs: a PAM‐less/free high‐efficiency adenine base editor toolbox with wide target scope in plants
Open accessAbstract
Adenine base editors (ABEs), which are generally engineered adenosine deaminases and Cas variants, introduce site-specific A-to-G mutations for agronomic trait improvement. However, notably varying editing efficiencies, restrictive requirements for protospacer-adjacent motifs (PAMs) and a narrow editing window greatly limit their application. Here, we developed a robust high-efficiency ABE (PhieABE) toolbox for plants by fusing an evolved, highly active form of the adenosine deaminase TadA8e and a single-stranded DNA-binding domain (DBD), based on PAM-less/free Streptococcus pyogenes Cas9 (SpCas9) nickase variants that recognize the PAM NGN (for SpCas9n-NG and SpGn) or NNN (for SpRYn). By targeting 29 representative targets in rice and assessing the results, we demonstrate that PhieABEs have significantly improved base-editing activity, expanded target range and broader editing windows compared to the ABE7.10 and general ABE8e systems. Among these PhieABEs, hyper ABE8e-DBD-SpRYn (hyABE8e-SpRY) showed nearly 100% editing efficiency at some tested sites, with a high proportion of homozygous base substitutions in the editing windows and no single guide RNA (sgRNA)-dependent off-target changes. The original sgRNA was more compatible with PhieABEs than the evolved sgRNA. In conclusion, the DBD fusion effectively promotes base-editing efficiency, and this novel PhieABE toolbox should have wide applications in plant functional genomics and crop improvement.
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Bio-mimicking is achieved through gene silencing or gene knockout via induced mutation within gene sequence and its replacement within the cultivated species, and through induction of mutations within allele and promoter region of the gene.
“It is being achieved through gene silencing or gene knockout via induced mutation within gene sequence and its replacement within the cultivated species, induction of mutations within allele as well as promoter region of the gene (Tan et al., 2022).”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Tan et al., 2022
The Introduction (page unavailable) says CRISPR editing can produce knockout mutants and base editing can change specific bases in plant genes. The Results and discussion (page unavailable) report induced bi-allelic mutations and mention editing regulatory elements. The paper does not establish the broader bio-mimicking process described in the claim, including gene silencing, gene replacement within cultivated species, or mutations specifically in promoters. (LLM, conf=0.85)
Experimental — accuracy not yet measuredBio-mimicking offers introduction of mutation instead of the whole gene using CRISPR, wherein the target gene sequence is converted into a desirable gene sequence that has a specific trait.
“It offers the introduction of mutation instead of the whole gene using CRISPR, wherein the sequence of the target gene is converted into a desirable gene sequence that has a specific trait.”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Tan et al., 2022
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Emerging applications of gene editing technologies for the development of climate-resilient crops
Chavhan, R. L., Jaybhaye, S. G., Hinge, V. R., Deshmukh, A. S., Shaikh, U. S., Jadhav, P. K., Kadam, U. S., & Hong, J. C. (2025) · Frontiers in Genome Editing · doi:10.3389/fgeed.2025.1524767 · Cited by 43 · see citing works
- Authors
- Tan, J., Zeng, D., Zhao, Y., Wang, Y., Liu, T., Li, S., Xue, Y., Luo, Y., Xie, X., Chen, L., Liu, Y., & Zhu, Q.
- Affiliations
- South China Agricultural University (CN)
- Corresponding author
- Zhu, Qinlong
- ORCID
- Venue
- Plant Biotechnology Journal
- Publisher
- Wiley
- Published
- 2022-01-17
- Volume
- 20
- Issue
- 5
- Pages
- 934-943
- ISSN
- 1467-7644 (ISSN-L)
- 1467-7652
- PMC
- PMC9055815
- OpenAlex
- W4205661453
- Cited by
- 80
- References
- 35
- Citations by year
- 2026: 10 · 2025: 17 · 2024: 16 · 2023: 22 · 2022: 14 · 2012: 1
- FWCI
- 5.63
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Plant Biotechnology Journal (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (31991222, 31971915)
- China Postdoctoral Science Foundation (2020M682728, 2020M682729)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Genetic and Mutation Studies
- Keywords
- adenine base editors, rice, single guide RNA, off-target mutagenesis, crop improvement, plant functional genomics
- MeSH terms
- Gene Editing, CRISPR-Associated Protein 9, Adenine, Genome, Plant, CRISPR-Cas Systems
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