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Zhang R, Chai N, Liu T, Zheng Z, Lin Q, Xie X, Wen J, Yang Z, Liu YG, Zhu Q. The type V effectors for CRISPR/Cas-mediated genome engineering in plants. Biotechnol Adv 2024; 74:108382. [PMID: 38801866 DOI: 10.1016/j.biotechadv.2024.108382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/07/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
A plethora of CRISPR effectors, such as Cas3, Cas9, and Cas12a, are commonly employed as gene editing tools. Among these, Cas12 effectors developed based on Class II type V proteins exhibit distinct characteristics compared to Class II type VI and type II effectors, such as their ability to generate non-allelic DNA double-strand breaks, their compact structures, and the presence of a single RuvC-like nuclease domain. Capitalizing on these advantages, Cas12 family proteins have been increasingly explored and utilized in recent years. However, the characteristics and applications of different subfamilies within the type V protein family have not been systematically summarized. In this review, we focus on the characteristics of type V effector (CRISPR/Cas12) proteins and the current methods used to discover new effector proteins. We also summarize recent modifications based on engineering of type V effectors. In addition, we introduce the applications of type V effectors for gene editing in animals and plants, including the development of base editors, tools for regulating gene expression, methods for gene targeting, and biosensors. We emphasize the prospects for development and application of CRISPR/Cas12 effectors with the goal of better utilizing toolkits based on this protein family for crop improvement and enhanced agricultural production.
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Affiliation(s)
- Ruixiang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Nan Chai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Taoli Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhiye Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qiupeng Lin
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jun Wen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zi Yang
- College of Natural & Agricultural Sciences, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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Li B, Sun C, Li J, Gao C. Targeted genome-modification tools and their advanced applications in crop breeding. Nat Rev Genet 2024:10.1038/s41576-024-00720-2. [PMID: 38658741 DOI: 10.1038/s41576-024-00720-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2024] [Indexed: 04/26/2024]
Abstract
Crop improvement by genome editing involves the targeted alteration of genes to improve plant traits, such as stress tolerance, disease resistance or nutritional content. Techniques for the targeted modification of genomes have evolved from generating random mutations to precise base substitutions, followed by insertions, substitutions and deletions of small DNA fragments, and are finally starting to achieve precision manipulation of large DNA segments. Recent developments in base editing, prime editing and other CRISPR-associated systems have laid a solid technological foundation to enable plant basic research and precise molecular breeding. In this Review, we systematically outline the technological principles underlying precise and targeted genome-modification methods. We also review methods for the delivery of genome-editing reagents in plants and outline emerging crop-breeding strategies based on targeted genome modification. Finally, we consider potential future developments in precise genome-editing technologies, delivery methods and crop-breeding approaches, as well as regulatory policies for genome-editing products.
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Affiliation(s)
- Boshu Li
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chao Sun
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiayang Li
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Caixia Gao
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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Tian Y, Li X, Xie J, Zheng Z, Shen R, Cao X, Wang M, Dong C, Zhu JK. Targeted G-to-T base editing for generation of novel herbicide-resistance gene alleles in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38578176 DOI: 10.1111/jipb.13657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/15/2024] [Indexed: 04/06/2024]
Affiliation(s)
- Yifu Tian
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Hainan Seed Industry Laboratory, Sanya, 572024, China
| | - Xinbo Li
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Hainan Seed Industry Laboratory, Sanya, 572024, China
| | - Jiyong Xie
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zai Zheng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Hainan Seed Industry Laboratory, Sanya, 572024, China
| | - Rundong Shen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Hainan Seed Industry Laboratory, Sanya, 572024, China
| | - Xuesong Cao
- Institute of Advanced Biotechnology, and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Mugui Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Chao Dong
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Hainan Seed Industry Laboratory, Sanya, 572024, China
| | - Jian-Kang Zhu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Institute of Advanced Biotechnology, and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
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Bai M, Lin W, Peng C, Song P, Kuang H, Lin J, Zhang J, Wang J, Chen B, Li H, Kong F, Jia G, Guan Y. Expressing a human RNA demethylase as an assister improves gene-editing efficiency in plants. MOLECULAR PLANT 2024; 17:363-366. [PMID: 38368507 DOI: 10.1016/j.molp.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/03/2024] [Accepted: 02/14/2024] [Indexed: 02/19/2024]
Affiliation(s)
- Mengyan Bai
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Wenxin Lin
- College of Agronomy, China Agricultural University, Beijing 100193, China
| | - Chunyan Peng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Huaqin Kuang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jieni Lin
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jieping Zhang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jiyao Wang
- Kingagroot Co., Ltd., Qingdao, Shandong 266000, China
| | - Bo Chen
- Kingagroot Co., Ltd., Qingdao, Shandong 266000, China
| | - Huarong Li
- Kingagroot Co., Ltd., Qingdao, Shandong 266000, China
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100871, China.
| | - Yuefeng Guan
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
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Zhong D, Pan H, Li K, Zhou Y, Zhao F, Ye L, Ruan S, Deng Q, Xu J, Lu Y. Targeted A-to-T and A-to-C base replacement in maize using an optimized adenine base editor. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:541-543. [PMID: 38102813 PMCID: PMC10893946 DOI: 10.1111/pbi.14256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/30/2023] [Accepted: 11/18/2023] [Indexed: 12/17/2023]
Affiliation(s)
- Dating Zhong
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Hong Pan
- WIMI Biotechnology Co., LtdChangzhouChina
| | - Kai Li
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ying Zhou
- Xishuangbanna Institute of Agricultural Science, Yunnan Academy of Agricultural SciencesKunmingChina
| | | | - Lu Ye
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | | | - Qi Deng
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Jieting Xu
- WIMI Biotechnology Co., LtdChangzhouChina
| | - Yuming Lu
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
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Li X, Xie J, Dong C, Zheng Z, Shen R, Cao X, Chen X, Wang M, Zhu JK, Tian Y. Efficient and heritable A-to-K base editing in rice and tomato. HORTICULTURE RESEARCH 2024; 11:uhad250. [PMID: 38269296 PMCID: PMC10807703 DOI: 10.1093/hr/uhad250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/15/2023] [Indexed: 01/26/2024]
Abstract
Cytosine and adenosine base editors (CBE and ABE) have been widely used in plants, greatly accelerating gene function research and crop breeding. Current base editors can achieve efficient A-to-G and C-to-T/G/A editing. However, efficient and heritable A-to-Y (A-to-T/C) editing remains to be developed in plants. In this study, a series of A-to-K base editor (AKBE) systems were constructed for monocot and dicot plants. Furthermore, nSpCas9 was replaced with the PAM-less Cas9 variant (nSpRY) to expand the target range of the AKBEs. Analysis of 228 T0 rice plants and 121 T0 tomato plants edited using AKBEs at 18 endogenous loci revealed that, in addition to highly efficient A-to-G substitution (41.0% on average), the plant AKBEs can achieve A-to-T conversion with efficiencies of up to 25.9 and 10.5% in rice and tomato, respectively. Moreover, the rice-optimized AKBE generates A-to-C conversion in rice, with an average efficiency of 1.8%, revealing the significant value of plant-optimized AKBE in creating genetic diversity. Although most of the A-to-T and A-to-C edits were chimeric, desired editing types could be transmitted to the T1 offspring, similar to the edits generated by the traditional ABE8e. Besides, using AKBEs to target tyrosine (Y, TAT) or cysteine (C, TGT) achieved the introduction of an early stop codon (TAG/TAA/TGA) of target genes, demonstrating its potential use in gene disruption.
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Affiliation(s)
- Xinbo Li
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan 572024, China
| | - Jiyong Xie
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Dong
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan 572024, China
| | - Zai Zheng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan 572024, China
| | - Rundong Shen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan 572024, China
| | - Xuesong Cao
- Institute of Advanced Biotechnology, and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiaoyan Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
| | - Mugui Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
| | - Jian-Kang Zhu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
- Institute of Advanced Biotechnology, and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yifu Tian
- Ministry of Agriculture and Rural Affairs Key Laboratory of Gene Editing Technologies (Hainan), Institute of Crop Sciences and National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan 572024, China
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