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Vats S, Kumar J, Sonah H, Zhang F, Deshmukh R. Prime editing in plants: prospects and challenges. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5344-5356. [PMID: 38366636 DOI: 10.1093/jxb/erae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/08/2024] [Indexed: 02/18/2024]
Abstract
Prime editors are reverse transcriptase (RT)-based genome-editing tools that utilize double-strand break (DSB)-free mechanisms to decrease off-target editing in genomes and enhance the efficiency of targeted insertions. The multiple prime editors that have been developed within a short span of time are a testament to the potential of this technique for targeted insertions. This is mainly because of the possibility of generation of all types of mutations including deletions, insertions, transitions, and transversions. Prime editing reverses several bottlenecks of gene editing technologies that limit the biotechnological applicability to produce designer crops. This review evaluates the status and evolution of the prime editing technique in terms of the types of editors available up to prime editor 5 and twin prime editors, and considers the developments in plants in a systematic manner. The various factors affecting prime editing efficiency in plants are discussed in detail, including the effects of temperature, the prime editing guide (peg)RNA, and RT template amongst others. We discuss the current obstructions, key challenges, and available resolutions associated with the technique, and consider future directions and further improvements that are feasible to elevate the efficiency in plants.
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Affiliation(s)
- Sanskriti Vats
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
- Regional Centre for Biotechnology, Faridabad, Haryana (NCR Delhi), India
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jitesh Kumar
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Feng Zhang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Rupesh Deshmukh
- Department of Biotechnology, Central University of Haryana, Mahendragarh, Haryana, 123031, India
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2
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Lu P, Zuo E, Yan J. Developing a multi-modular assembled prime editing (mPE) system improved precise multi-base insertion efficiency in dicots. J Adv Res 2024:S2090-1232(24)00259-5. [PMID: 38942381 DOI: 10.1016/j.jare.2024.06.021] [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: 02/19/2024] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024] Open
Abstract
INTRODUCTION The Prime Editing (PE) system is a precise and versatile genome editing tool with great potential in plant breeding and plant synthetic biology. However, low PE efficiency severely restricts its application, especially in dicots. PE can introduce small tags to trace target protein or cis-element to regulate gene transcription which is an expertise superior to other gene editing tools. Owing to low efficiency, PE adaption in stably transformed Arabidopsis is lacking. OBJECTIVES This study aimed to investigate the issue of low PE efficiency in dicots and develop systematic solutions to improve it. Currently, PE in dicots is undetectable and inconsistent, and this study seeks to address it. Split PE into several parts showed better performance in some target sites in mammal cells. We plan to discover the optimal split PE combination in dicot. METHODS We conducted large-scale transformation experiments in dicot model plants Arabidopsis thaliana (At) and Nicotiana benthamiana (Nb) by Agrobacterium-mediated transformation with deep amplicon sequencing (0.2-0.5 million clean total reads). RESULTS The editing efficiency decreased upon using a fused reverse transcriptase (RT) or an extended pegRNA separately and further decreased dramatically when these were used together. With the help of the pol II strategy to express PE gRNA (pegRNA), we named the most effective split PE combination as a multi-modular assembled prime editing system (mPE). mPE exhibited improved precise editing efficiency on most gene sites with various editing types, ranging from 1.3-fold to 1288.5-fold and achieved PE on some sites that could not be edited by original PE2. Especially, mPE showed superiority for multi-base insertion with an average improvement of 197.9-fold. CONCLUSION The original PE architecture strongly inhibited the cleavage activity of Cas9. Split PE improved PE efficiency extensively and was in favor of introducing small insertions in dicot plants, indicating that different PE variants might have their own expertise.
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Affiliation(s)
- Pengjun Lu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Erwei Zuo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
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Singh PK, Devanna BN, Dubey H, Singh P, Joshi G, Kumar R. The potential of genome editing to create novel alleles of resistance genes in rice. Front Genome Ed 2024; 6:1415244. [PMID: 38933684 PMCID: PMC11201548 DOI: 10.3389/fgeed.2024.1415244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Rice, a staple food for a significant portion of the global population, faces persistent threats from various pathogens and pests, necessitating the development of resilient crop varieties. Deployment of resistance genes in rice is the best practice to manage diseases and reduce environmental damage by reducing the application of agro-chemicals. Genome editing technologies, such as CRISPR-Cas, have revolutionized the field of molecular biology, offering precise and efficient tools for targeted modifications within the rice genome. This study delves into the application of these tools to engineer novel alleles of resistance genes in rice, aiming to enhance the plant's innate ability to combat evolving threats. By harnessing the power of genome editing, researchers can introduce tailored genetic modifications that bolster the plant's defense mechanisms without compromising its essential characteristics. In this study, we synthesize recent advancements in genome editing methodologies applicable to rice and discuss the ethical considerations and regulatory frameworks surrounding the creation of genetically modified crops. Additionally, it explores potential challenges and future prospects for deploying edited rice varieties in agricultural landscapes. In summary, this study highlights the promise of genome editing in reshaping the genetic landscape of rice to confront emerging challenges, contributing to global food security and sustainable agriculture practices.
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Affiliation(s)
- Pankaj Kumar Singh
- Department of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali, Punjab, India
| | | | - Himanshu Dubey
- Seri-Biotech Research Laboratory, Central Silk Board, Bangalore, India
| | - Prabhakar Singh
- Botany Department, Banaras Hindu University, Varanasi, India
| | - Gaurav Joshi
- Department of Pharmaceutical Sciences, Hemvati Nandan Bahuguna Garhwal (A Central University), Tehri Garhwal, Uttarakhand, India
| | - Roshan Kumar
- Department of Microbiology, Central University of Punjab, Bathinda, Punjab, India
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Li P, Li X, Wang F, Gao M, Bai Y, Zhang Z, Wei Z. Enrichment of prime-edited mammalian cells with surrogate Puro R reporters. Int J Biol Macromol 2024; 271:132474. [PMID: 38777019 DOI: 10.1016/j.ijbiomac.2024.132474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/01/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
Prime editing is a programmable genetic method that can precisely generate any desired small-scale variations in cells without requiring double-strand breaks and DNA donors. However, higher editing efficiency is greatly desirable for wide practical applications. In this study, we developed a target-specific prime editing reporter (tsPER) and a universal prime editing reporter (UPER) to facilitate rapid selection of desired edited cells through puromycin screening. The modification efficiency of HEK3_i1CTT_d5G in HEK293T cells improved from 36.37 % to 64.84 % with the incorporation of tsPER. The target sequence of interested genes could be custom inserted into a selection cassette in tsPER to establish personalized reporters. The UPER demonstrated PE3 editing efficiency up to 74.49 % on HEK3_i1CTT_d5G and 73.52 % on HEK3_i1His6, achieved through co-selection with an additional pegRNA (puro) to repair the mutant PuroR cassette. Overall, tsPER and UPER robustly improved the efficiency of prime editing. Both of these approaches expand enrichment strategies for genomically modified cells and accelerate the generation of genetically modified models.
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Affiliation(s)
- Pengcheng Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Yazhouwan National Laboratory, Sanya 572024, China
| | - Xinyi Li
- Division of Cardiovascular Medicine, Department of Medicin Solna(MedS), Karolinska institutet, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Fang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Mengyu Gao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yichun Bai
- School of Public Health, Xinxiang Medical University, Xinxiang 453000, China
| | - Zhiying Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Zehui Wei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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Yang Y, Wheatley M, Meakem V, Galarneau E, Gutierrez B, Zhong G. Editing VvDXS1 for the creation of muscat flavour in Vitis vinifera cv. Scarlet Royal. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1610-1621. [PMID: 38243882 PMCID: PMC11123410 DOI: 10.1111/pbi.14290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/01/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024]
Abstract
Muscat flavour represents a group of unique aromatic attributes in some grape varieties. Biochemically, grape berries with muscat flavour produce high levels of monoterpenes. Monoterpene biosynthesis is mainly through the DOXP/MEP pathway, and VvDXS1 encodes the first enzyme in this plastidial pathway of terpene biosynthesis in grapevine. A single-point mutation resulting in the substitution of a lysine with an asparagine at position 284 in the VvDXS1 protein has previously been identified as the major cause for producing muscat flavour in grapes. In this study, the same substitution in the VvDXS1 protein was successfully created through prime editing in the table grape Vitis vinifera cv. 'Scarlet Royal'. The targeted point mutation was detected in most of the transgenic vines, with varying editing efficiencies. No unintended mutations were detected in the edited alleles, either by PCR Sanger sequencing or by amplicon sequencing. More than a dozen edited vines were identified with an editing efficiency of more than 50%, indicating that these vines were likely derived from single cells in which one allele was edited. These vines had much higher levels of monoterpenes in their leaves than the control, similar to what was found in leaf samples between field-grown muscat and non-muscat grapes.
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Affiliation(s)
- Yingzhen Yang
- USDA‐Agricultural Research ServiceGrape Genetics Research UnitGenevaNew YorkUSA
| | - Matthew Wheatley
- USDA‐Agricultural Research ServiceGrape Genetics Research UnitGenevaNew YorkUSA
| | - Victoria Meakem
- USDA‐Agricultural Research ServicePlant Genetic Resources UnitGenevaNew YorkUSA
| | - Erin Galarneau
- USDA‐Agricultural Research ServicePlant Genetic Resources UnitGenevaNew YorkUSA
| | - Benjamin Gutierrez
- USDA‐Agricultural Research ServicePlant Genetic Resources UnitGenevaNew YorkUSA
| | - Gan‐Yuan Zhong
- USDA‐Agricultural Research ServiceGrape Genetics Research UnitGenevaNew YorkUSA
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Hwarari D, Radani Y, Ke Y, Chen J, Yang L. CRISPR/Cas genome editing in plants: mechanisms, applications, and overcoming bottlenecks. Funct Integr Genomics 2024; 24:50. [PMID: 38441816 DOI: 10.1007/s10142-024-01314-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
The CRISPR/Cas systems have emerged as transformative tools for precisely manipulating plant genomes and enhancement. It has provided unparalleled applications from modifying the plant genomes to resistant enhancement. This review manuscript summarises the mechanism, application, and current challenges in the CRISPR/Cas genome editing technology. It addresses the molecular mechanisms of different Cas genes, elucidating their applications in various plants through crop improvement, disease resistance, and trait improvement. The advent of the CRISPR/Cas systems has enabled researchers to precisely modify plant genomes through gene knockouts, knock-ins, and gene expression modulation. Despite these successes, the CRISPR/Cas technology faces challenges, including off-target effects, Cas toxicity, and efficiency. In this manuscript, we also discuss these challenges and outline ongoing strategies employed to overcome these challenges, including the development of novel CRISPR/Cas variants with improved specificity and specific delivery methods for different plant species. The manuscript will conclude by addressing the future perspectives of the CRISPR/Cas technology in plants. Although this review manuscript is not conclusive, it aims to provide immense insights into the current state and future potential of CRISPR/Cas in sustainable and secure plant production.
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Affiliation(s)
- Delight Hwarari
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Yasmina Radani
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Yongchao Ke
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinhui Chen
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
| | - Liming Yang
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
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Pacesa M, Pelea O, Jinek M. Past, present, and future of CRISPR genome editing technologies. Cell 2024; 187:1076-1100. [PMID: 38428389 DOI: 10.1016/j.cell.2024.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Genome editing has been a transformative force in the life sciences and human medicine, offering unprecedented opportunities to dissect complex biological processes and treat the underlying causes of many genetic diseases. CRISPR-based technologies, with their remarkable efficiency and easy programmability, stand at the forefront of this revolution. In this Review, we discuss the current state of CRISPR gene editing technologies in both research and therapy, highlighting limitations that constrain them and the technological innovations that have been developed in recent years to address them. Additionally, we examine and summarize the current landscape of gene editing applications in the context of human health and therapeutics. Finally, we outline potential future developments that could shape gene editing technologies and their applications in the coming years.
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Affiliation(s)
- Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Station 19, CH-1015 Lausanne, Switzerland
| | - Oana Pelea
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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8
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Chen Y, Luo X, Kang R, Cui K, Ou J, Zhang X, Liang P. Current therapies for osteoarthritis and prospects of CRISPR-based genome, epigenome, and RNA editing in osteoarthritis treatment. J Genet Genomics 2024; 51:159-183. [PMID: 37516348 DOI: 10.1016/j.jgg.2023.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/31/2023]
Abstract
Osteoarthritis (OA) is one of the most common degenerative joint diseases worldwide, causing pain, disability, and decreased quality of life. The balance between regeneration and inflammation-induced degradation results in multiple etiologies and complex pathogenesis of OA. Currently, there is a lack of effective therapeutic strategies for OA treatment. With the development of CRISPR-based genome, epigenome, and RNA editing tools, OA treatment has been improved by targeting genetic risk factors, activating chondrogenic elements, and modulating inflammatory regulators. Supported by cell therapy and in vivo delivery vectors, genome, epigenome, and RNA editing tools may provide a promising approach for personalized OA therapy. This review summarizes CRISPR-based genome, epigenome, and RNA editing tools that can be applied to the treatment of OA and provides insights into the development of CRISPR-based therapeutics for OA treatment. Moreover, in-depth evaluations of the efficacy and safety of these tools in human OA treatment are needed.
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Affiliation(s)
- Yuxi Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xiao Luo
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Rui Kang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Kaixin Cui
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jianping Ou
- Center for Reproductive Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Xiya Zhang
- Center for Reproductive Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong 510630, China.
| | - Puping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
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Hong C, Han JH, Hwang GH, Bae S, Seo PJ. Genome-wide in-locus epitope tagging of Arabidopsis proteins using prime editors. BMB Rep 2024; 57:66-70. [PMID: 38053291 PMCID: PMC10828436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/05/2023] [Accepted: 06/19/2023] [Indexed: 12/07/2023] Open
Abstract
Prime editors (PEs), which are CRISPR-Cas9 nickase (H840A)-reverse transcriptase fusion proteins programmed with prime editing guide RNAs (pegRNAs), can not only edit bases but also install transversions, insertions, or deletions without both donor DNA and double-strand breaks at the target DNA. As the demand for in-locus tagging is increasing, to reflect gene expression dynamics influenced by endogenous genomic contexts, we demonstrated that PEs can be used to introduce the hemagglutinin (HA) epitope tag to a target gene locus, enabling molecular and biochemical studies using in-locus tagged plants. To promote genome-wide in-locus tagging, we also implemented a publicly available database that designs pegRNAs for in-locus tagging of all the Arabidopsis genes. [BMB Reports 2024; 57(1): 66-70].
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Affiliation(s)
- Cheljong Hong
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jun Hee Han
- Department of Chemistry, Hanyang University, Seoul 04673, Korea
| | - Gue-Ho Hwang
- Medical Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Sangsu Bae
- Medical Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
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Vu TV, Nguyen NT, Kim J, Hong JC, Kim J. Prime editing: Mechanism insight and recent applications in plants. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:19-36. [PMID: 37794706 PMCID: PMC10754014 DOI: 10.1111/pbi.14188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
Prime editing (PE) technology utilizes an extended prime editing guide RNA (pegRNA) to direct a fusion peptide consisting of nCas9 (H840) and reverse transcriptase (RT) to a specific location in the genome. This enables the installation of base changes at the targeted site using the extended portion of the pegRNA through RT activity. The resulting product of the RT reaction forms a 3' flap, which can be incorporated into the genomic site through a series of biochemical steps involving DNA repair and synthesis pathways. PE has demonstrated its effectiveness in achieving almost all forms of precise gene editing, such as base conversions (all types), DNA sequence insertions and deletions, chromosomal translocation and inversion and long DNA sequence insertion at safe harbour sites within the genome. In plant science, PE could serve as a groundbreaking tool for precise gene editing, allowing the creation of desired alleles to improve crop varieties. Nevertheless, its application has encountered limitations due to efficiency constraints, particularly in dicotyledonous plants. In this review, we discuss the step-by-step mechanism of PE, shedding light on the critical aspects of each step while suggesting possible solutions to enhance its efficiency. Additionally, we present an overview of recent advancements and future perspectives in PE research specifically focused on plants, examining the key technical considerations of its applications.
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Affiliation(s)
- Tien V. Vu
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Ngan Thi Nguyen
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jong Chan Hong
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
- Division of Life ScienceGyeongsang National UniversityJinjuKorea
- Nulla Bio Inc.JinjuKorea
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11
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Yu X, Huo G, Yu J, Li H, Li J. Prime editing: Its systematic optimization and current applications in disease treatment and agricultural breeding. Int J Biol Macromol 2023; 253:127025. [PMID: 37769783 DOI: 10.1016/j.ijbiomac.2023.127025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/03/2023]
Abstract
CRISPR/Cas-mediated genome-editing technology has accelerated the development of the life sciences. Prime editing has raised genome editing to a new level because it allows for all 12 types of base substitutions, targeted insertions and deletions, large DNA fragment integration, and even combinations of these edits without generating DNA double-strand breaks. This versatile and game-changing technology has successfully been applied to human cells and plants, and it currently plays important roles in basic research, gene therapy, and crop breeding. Although prime editing has substantially expanded the range of possibilities for genome editing, its efficiency requires improvement. In this review, we briefly introduce prime editing and highlight recent optimizations that have improved the efficiency of prime editors. We also describe how the dual-pegRNA strategy has expanded current editing capabilities, and we summarize the potential of prime editing in treating mammalian diseases and improving crop breeding. Finally, we discuss the limitations of current prime editors and future prospects for optimizing these editors.
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Affiliation(s)
- Xiaoxiao Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, China; Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Guanzhong Huo
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, China; Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Jintai Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, China; College of Modern Science and Technology, Hebei Agricultural University, Baoding, China
| | - Huiyuan Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Jun Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, China; Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.
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12
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Bhuyan SJ, Kumar M, Ramrao Devde P, Rai AC, Mishra AK, Singh PK, Siddique KHM. Progress in gene editing tools, implications and success in plants: a review. Front Genome Ed 2023; 5:1272678. [PMID: 38144710 PMCID: PMC10744593 DOI: 10.3389/fgeed.2023.1272678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/13/2023] [Indexed: 12/26/2023] Open
Abstract
Genetic modifications are made through diverse mutagenesis techniques for crop improvement programs. Among these mutagenesis tools, the traditional methods involve chemical and radiation-induced mutagenesis, resulting in off-target and unintended mutations in the genome. However, recent advances have introduced site-directed nucleases (SDNs) for gene editing, significantly reducing off-target changes in the genome compared to induced mutagenesis and naturally occurring mutations in breeding populations. SDNs have revolutionized genetic engineering, enabling precise gene editing in recent decades. One widely used method, homology-directed repair (HDR), has been effective for accurate base substitution and gene alterations in some plant species. However, its application has been limited due to the inefficiency of HDR in plant cells and the prevalence of the error-prone repair pathway known as non-homologous end joining (NHEJ). The discovery of CRISPR-Cas has been a game-changer in this field. This system induces mutations by creating double-strand breaks (DSBs) in the genome and repairing them through associated repair pathways like NHEJ. As a result, the CRISPR-Cas system has been extensively used to transform plants for gene function analysis and to enhance desirable traits. Researchers have made significant progress in genetic engineering in recent years, particularly in understanding the CRISPR-Cas mechanism. This has led to various CRISPR-Cas variants, including CRISPR-Cas13, CRISPR interference, CRISPR activation, base editors, primes editors, and CRASPASE, a new CRISPR-Cas system for genetic engineering that cleaves proteins. Moreover, gene editing technologies like the prime editor and base editor approaches offer excellent opportunities for plant genome engineering. These cutting-edge tools have opened up new avenues for rapidly manipulating plant genomes. This review article provides a comprehensive overview of the current state of plant genetic engineering, focusing on recently developed tools for gene alteration and their potential applications in plant research.
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Affiliation(s)
- Suman Jyoti Bhuyan
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | - Manoj Kumar
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Pandurang Ramrao Devde
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | - Avinash Chandra Rai
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | | | - Prashant Kumar Singh
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
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Zhang J, Zhang L, Zhang C, Yang Y, Liu H, Li L, Zhang S, Li X, Liu X, Liu Y, Wang J, Yang G, Xia Q, Wang W, Yang J. Developing an efficient and visible prime editing system to restore tobacco 8-hydroxy-copalyl diphosphate gene for labdane diterpene Z-abienol biosynthesis. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2910-2921. [PMID: 37460713 DOI: 10.1007/s11427-022-2396-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/30/2023] [Indexed: 12/18/2023]
Abstract
Prime editing (PE) is a versatile CRISPR-Cas based precise genome-editing platform widely used to introduce a range of possible base conversions in various organisms. However, no PE systems have been shown to induce heritable mutations in tobacco, nor in any other dicot. In this study, we generated an efficient PE system in tobacco that not only introduced heritable mutations, but also enabled anthocyanin-based reporter selection of transgene-free T1 plants. This system was used to confer Z-abienol biosynthesis in the allotetraploid tobacco cultivar HHDJY by restoring a G>T conversion in the NtCPS2 gene. High levels of Z-abienol were detected in the leaves of homozygous T1 plants at two weeks after topping. This study describes an advance in PE systems and expands genome-editing toolbox in tobacco, even in dicots, for use in basic research and molecular breeding. And restoring biosynthesis of Z-abienol in tobacco might provide an efficient way to obtain Z-abienol in plants.
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Affiliation(s)
- Jianduo Zhang
- Yunnan Key Laboratory of Tobacco, Yunnan Academy of Tobacco Science, Kunming, 650231, China
| | - Lu Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100089, China
| | - Chengwei Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100089, China
| | - Yongxing Yang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100089, China
| | - Huayin Liu
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Yunnan Minzu University, Kunming, 650031, China
| | - Lu Li
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100089, China
| | | | - Xianggan Li
- Cropedit Biotechnology Co. Ltd., Beijing, 102206, China
| | - Xinxiang Liu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100089, China
| | - Ya Liu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100089, China
| | - Jin Wang
- Yunnan Key Laboratory of Tobacco, Yunnan Academy of Tobacco Science, Kunming, 650231, China
| | - Guangyu Yang
- Yunnan Key Laboratory of Tobacco, Yunnan Academy of Tobacco Science, Kunming, 650231, China
| | - Qingyou Xia
- Biological Science Research Center, Southwest University, Chongqing, 400716, China.
| | - Weiguang Wang
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Yunnan Minzu University, Kunming, 650031, China.
| | - Jinxiao Yang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100089, China.
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14
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Li Y, Huang B, Chen J, Huang L, Xu J, Wang Y, Cui G, Zhao H, Xin B, Song W, Zhu J, Lai J. Targeted large fragment deletion in plants using paired crRNAs with type I CRISPR system. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2196-2208. [PMID: 37641539 PMCID: PMC10579709 DOI: 10.1111/pbi.14122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/19/2023] [Accepted: 06/25/2023] [Indexed: 08/31/2023]
Abstract
The CRISPR-Cas systems have been widely used as genome editing tools, with type II and V systems typically introducing small indels, and type I system mediating long-range deletions. However, the precision of type I systems for large fragment deletion is still remained to be optimized. Here, we developed a compact Cascade-Cas3 Dvu I-C system with Cas11c for plant genome editing. The Dvu I-C system was efficient to introduce controllable large fragment deletion up to at least 20 kb using paired crRNAs. The paired-crRNAs design also improved the controllability of deletions for the type I-E system. Dvu I-C system was sensitive to spacer length and mismatch, which was benefit for target specificity. In addition, we showed that the Dvu I-C system was efficient for generating stable transgenic lines in maize and rice with the editing efficiency up to 86.67%. Overall, Dvu I-C system we developed here is powerful for achieving controllable large fragment deletions.
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Affiliation(s)
- Yingnan Li
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Boyu Huang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jian Chen
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Liangliang Huang
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jianghai Xu
- College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yingying Wang
- College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Guanghui Cui
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Haiming Zhao
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Beibei Xin
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Weibin Song
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jian‐Kang Zhu
- Institute of Advanced Biotechnology and School of Life SciencesSouthern University of Science and TechnologyShenzhenChina
- Center for Advanced Bioindustry TechnologiesChinese Academy of Agricultural SciencesBeijingChina
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
- Frontiers Science Center for Molecular Design BreedingChina Agricultural UniversityBeijingChina
- Center for Crop Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
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15
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Shi L, Su J, Cho MJ, Song H, Dong X, Liang Y, Zhang Z. Promoter editing for the genetic improvement of crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4349-4366. [PMID: 37204916 DOI: 10.1093/jxb/erad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/06/2023] [Indexed: 05/21/2023]
Abstract
Gene expression plays a fundamental role in the regulation of agronomically important traits in crop plants. The genetic manipulation of plant promoters through genome editing has emerged as an effective strategy to create favorable traits in crops by altering the expression pattern of the pertinent genes. Promoter editing can be applied in a directed manner, where nucleotide sequences associated with favorable traits are precisely generated. Alternatively, promoter editing can also be exploited as a random mutagenic approach to generate novel genetic variations within a designated promoter, from which elite alleles are selected based on their phenotypic effects. Pioneering studies have demonstrated the potential of promoter editing in engineering agronomically important traits as well as in mining novel promoter alleles valuable for plant breeding. In this review, we provide an update on the application of promoter editing in crops for increased yield, enhanced tolerance to biotic and abiotic stresses, and improved quality. We also discuss several remaining technical bottlenecks and how this strategy may be better employed for the genetic improvement of crops in the future.
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Affiliation(s)
- Lu Shi
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jing Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94704, USA
| | - Hao Song
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoou Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Ying Liang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhiyong Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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16
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Liang Z, Wu Y, Guo Y, Wei S. Addition of the T5 exonuclease increases the prime editing efficiency in plants. J Genet Genomics 2023; 50:582-588. [PMID: 36958601 DOI: 10.1016/j.jgg.2023.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/25/2023]
Abstract
Prime editing (PE) is a versatile genome editing tool without the need for double-stranded DNA breaks or donor DNA templates, but is limited by low editing efficiency. We previously fused the M-MLV reverse transcriptase to the Cas9 nickase, generating the PE2 (v1) system, but the editing efficiency of this system is still low. Here we develop different versions of PE2 by adding the 5'-to-3' exonuclease at different positions of the nCas9-M-MLV RT fusion protein. PE2 (v2), in which the T5 exonuclease fused to the N-terminus of the nCas9-MMLV fusion protein enhances prime editing efficiency of base substitutions, deletions, and insertions at several genomic sites by 1.7- to 2.9-fold in plant cells compared to PE2 (v1). The improved editing efficiency of PE2 (v2) is further confirmed by generating increased heritable prime edits in stable transgenic plants compared to the previously established PE-P1, PE-P2, and PPE systems. Using PE2 (v2), we generate herbicide-resistant rice by simultaneously introducing mutations causing amino acid substitutions at two target sites. The PE efficiency is further improved by combining PE2 (v2) and dual-pegRNAs. Taken together, the increased genome editing efficiency of PE2 (v2) developed in this study may enhance the applications of PE in plants.
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Affiliation(s)
- Zhen Liang
- School of Life Science, Shanxi University, Taiyuan, Shanxi 030006, China.
| | - Yuqing Wu
- School of Life Science, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Yingjie Guo
- Research Institute of Big Data Science and Industry, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Sha Wei
- School of Life Science, Shanxi University, Taiyuan, Shanxi 030006, China
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17
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Singh C, Kumar R, Sehgal H, Bhati S, Singhal T, Gayacharan, Nimmy MS, Yadav R, Gupta SK, Abdallah NA, Hamwieh A, Kumar R. Unclasping potentials of genomics and gene editing in chickpea to fight climate change and global hunger threat. Front Genet 2023; 14:1085024. [PMID: 37144131 PMCID: PMC10153629 DOI: 10.3389/fgene.2023.1085024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/24/2023] [Indexed: 09/09/2023] Open
Abstract
Genomics and genome editing promise enormous opportunities for crop improvement and elementary research. Precise modification in the specific targeted location of a genome has profited over the unplanned insertional events which are generally accomplished employing unadventurous means of genetic modifications. The advent of new genome editing procedures viz; zinc finger nucleases (ZFNs), homing endonucleases, transcription activator like effector nucleases (TALENs), Base Editors (BEs), and Primer Editors (PEs) enable molecular scientists to modulate gene expressions or create novel genes with high precision and efficiency. However, all these techniques are exorbitant and tedious since their prerequisites are difficult processes that necessitate protein engineering. Contrary to first generation genome modifying methods, CRISPR/Cas9 is simple to construct, and clones can hypothetically target several locations in the genome with different guide RNAs. Following the model of the application in crop with the help of the CRISPR/Cas9 module, various customized Cas9 cassettes have been cast off to advance mark discrimination and diminish random cuts. The present study discusses the progression in genome editing apparatuses, and their applications in chickpea crop development, scientific limitations, and future perspectives for biofortifying cytokinin dehydrogenase, nitrate reductase, superoxide dismutase to induce drought resistance, heat tolerance and higher yield in chickpea to encounter global climate change, hunger and nutritional threats.
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Affiliation(s)
- Charul Singh
- USBT, Guru Govind Singh Indraprastha University, Delhi, India
| | - Ramesh Kumar
- Department of Biochemistry, University of Allahabad Prayagraj, Prayagraj, India
| | - Hansa Sehgal
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani, India
| | - Sharmista Bhati
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Tripti Singhal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Gayacharan
- Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - M. S. Nimmy
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | | | | | - Aladdin Hamwieh
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Cairo, Egypt
| | - Rajendra Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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18
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Hernandes-Lopes J, Yassitepe JEDCT, Koltun A, Pauwels L, da Silva VCH, Dante RA, Gerhardt IR, Arruda P. Genome editing in maize: Toward improving complex traits in a global crop. Genet Mol Biol 2023; 46:e20220217. [PMID: 36880696 PMCID: PMC9990078 DOI: 10.1590/1678-4685-gmb-2022-0217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/23/2022] [Indexed: 03/08/2023] Open
Abstract
Recent advances in genome editing have enormously enhanced the effort to develop biotechnology crops for more sustainable food production. CRISPR/Cas, the most versatile genome-editing tool, has shown the potential to create genome modifications that range from gene knockout and gene expression pattern modulations to allele-specific changes in order to design superior genotypes harboring multiple improved agronomic traits. However, a frequent bottleneck is the delivery of CRISPR/Cas to crops that are less amenable to transformation and regeneration. Several technologies have recently been proposed to overcome transformation recalcitrance, including HI-Edit/IMGE and ectopic/transient expression of genes encoding morphogenic regulators. These technologies allow the eroding of the barriers that make crops inaccessible for genome editing. In this review, we discuss the advances in genome editing in crops with a particular focus on the use of technologies to improve complex traits such as water use efficiency, drought stress, and yield in maize.
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Affiliation(s)
- José Hernandes-Lopes
- Universidade Estadual de Campinas, Genomics for Climate Change Research Center (GCCRC), Campinas, SP, Brazil
- Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Campinas, SP, Brazil
| | - Juliana Erika de Carvalho Teixeira Yassitepe
- Universidade Estadual de Campinas, Genomics for Climate Change Research Center (GCCRC), Campinas, SP, Brazil
- Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Campinas, SP, Brazil
- Embrapa Agricultura Digital, Campinas, SP, Brazil
| | - Alessandra Koltun
- Universidade Estadual de Campinas, Genomics for Climate Change Research Center (GCCRC), Campinas, SP, Brazil
- Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Campinas, SP, Brazil
| | - Laurens Pauwels
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB, Center for Plant Systems Biology, Ghent, Belgium
| | - Viviane Cristina Heinzen da Silva
- Universidade Estadual de Campinas, Genomics for Climate Change Research Center (GCCRC), Campinas, SP, Brazil
- Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Campinas, SP, Brazil
| | - Ricardo Augusto Dante
- Universidade Estadual de Campinas, Genomics for Climate Change Research Center (GCCRC), Campinas, SP, Brazil
- Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Campinas, SP, Brazil
- Embrapa Agricultura Digital, Campinas, SP, Brazil
| | - Isabel Rodrigues Gerhardt
- Universidade Estadual de Campinas, Genomics for Climate Change Research Center (GCCRC), Campinas, SP, Brazil
- Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Campinas, SP, Brazil
- Embrapa Agricultura Digital, Campinas, SP, Brazil
| | - Paulo Arruda
- Universidade Estadual de Campinas, Genomics for Climate Change Research Center (GCCRC), Campinas, SP, Brazil
- Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Campinas, SP, Brazil
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia e Evolução, Campinas, SP, Brazil
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19
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Jin S, Lin Q, Gao Q, Gao C. Optimized prime editing in monocot plants using PlantPegDesigner and engineered plant prime editors (ePPEs). Nat Protoc 2023; 18:831-853. [PMID: 36434096 DOI: 10.1038/s41596-022-00773-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/16/2022] [Indexed: 11/27/2022]
Abstract
Prime editors (PEs), which can install desired base edits without donor DNA or double-strand breaks, have been used in plants and can, in principle, accelerate crop improvement and breeding. However, their editing efficiency in plants is generally low. Optimizing the prime editing guide RNA (pegRNA) by designing the sequence on the basis of melting temperature, using dual-pegRNAs and engineering PEs have all been shown to enhance PE efficiency. In addition, an automated pegRNA design platform, PlantPegDesigner, has been developed on the basis of rice prime editing experimental data. In this protocol, we present detailed protocols for designing and optimizing pegRNAs using PlantPegDesigner, constructing engineered plant PE vectors with enhanced editing efficiency for prime editing, evaluating prime editing efficiencies using a reporter system and comparing the effectiveness and byproducts of PEs by deep amplicon sequencing. Using this protocol, researchers can construct optimized pegRNAs for prime editing in 4-7 d and obtain prime-edited rice or wheat plants within 3 months.
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Affiliation(s)
- Shuai Jin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Qiupeng Lin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Qiang Gao
- Qi Biodesign, Life Science Park, Beijing, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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20
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Mahmood MA, Naqvi RZ, Rahman SU, Amin I, Mansoor S. Plant Virus-Derived Vectors for Plant Genome Engineering. Viruses 2023; 15:v15020531. [PMID: 36851743 PMCID: PMC9958682 DOI: 10.3390/v15020531] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/25/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Advances in genome engineering (GE) tools based on sequence-specific programmable nucleases have revolutionized precise genome editing in plants. However, only the traditional approaches are used to deliver these GE reagents, which mostly rely on Agrobacterium-mediated transformation or particle bombardment. These techniques have been successfully used for the past decades for the genetic engineering of plants with some limitations relating to lengthy time-taking protocols and transgenes integration-related regulatory concerns. Nevertheless, in the era of climate change, we require certain faster protocols for developing climate-smart resilient crops through GE to deal with global food security. Therefore, some alternative approaches are needed to robustly deliver the GE reagents. In this case, the plant viral vectors could be an excellent option for the delivery of GE reagents because they are efficient, effective, and precise. Additionally, these are autonomously replicating and considered as natural specialists for transient delivery. In the present review, we have discussed the potential use of these plant viral vectors for the efficient delivery of GE reagents. We have further described the different plant viral vectors, such as DNA and RNA viruses, which have been used as efficient gene targeting systems in model plants, and in other important crops including potato, tomato, wheat, and rice. The achievements gained so far in the use of viral vectors as a carrier for GE reagent delivery are depicted along with the benefits and limitations of each viral vector. Moreover, recent advances have been explored in employing viral vectors for GE and adapting this technology for future research.
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Affiliation(s)
- Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
- Department of Biological Sciences, University of Sialkot, Sialkot 51310, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Saleem Ur Rahman
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi 74000, Pakistan
- Correspondence:
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21
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Li J, Zhang C, He Y, Li S, Yan L, Li Y, Zhu Z, Xia L. Plant base editing and prime editing: The current status and future perspectives. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:444-467. [PMID: 36479615 DOI: 10.1111/jipb.13425] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Precise replacement of an allele with an elite allele controlling an important agronomic trait in a predefined manner by gene editing technologies is highly desirable in crop improvement. Base editing and prime editing are two newly developed precision gene editing systems which can introduce the substitution of a single base and install the desired short indels to the target loci in the absence of double-strand breaks and donor repair templates, respectively. Since their discoveries, various strategies have been attempted to optimize both base editor (BE) and prime editor (PE) in order to improve the precise editing efficacy, specificity, and expand the targeting scopes. Here, we summarize the latest development of various BEs and PEs, as well as their applications in plants. Based on these progresses, we recommend the appropriate BEs and PEs for both basic plant research and crop improvement. Moreover, we propose the perspectives for further optimization of these two editors. We envision that both BEs and PEs will become the routine and customized precise gene editing tools for both plant biological research and crop improvement in the near future.
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Affiliation(s)
- Jingying Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
| | - Chen Zhang
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yubing He
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
| | - Shaoya Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
| | - Lei Yan
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yucai Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Ziwei Zhu
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Lanqin Xia
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
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22
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Richardson C, Kelsh RN, J. Richardson R. New advances in CRISPR/Cas-mediated precise gene-editing techniques. Dis Model Mech 2023; 16:dmm049874. [PMID: 36847161 PMCID: PMC10003097 DOI: 10.1242/dmm.049874] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Over the past decade, CRISPR/Cas-based gene editing has become a powerful tool for generating mutations in a variety of model organisms, from Escherichia coli to zebrafish, rodents and large mammals. CRISPR/Cas-based gene editing effectively generates insertions or deletions (indels), which allow for rapid gene disruption. However, a large proportion of human genetic diseases are caused by single-base-pair substitutions, which result in more subtle alterations to protein function, and which require more complex and precise editing to recreate in model systems. Precise genome editing (PGE) methods, however, typically have efficiencies of less than a tenth of those that generate less-specific indels, and so there has been a great deal of effort to improve PGE efficiency. Such optimisations include optimal guide RNA and mutation-bearing donor DNA template design, modulation of DNA repair pathways that underpin how edits result from Cas-induced cuts, and the development of Cas9 fusion proteins that introduce edits via alternative mechanisms. In this Review, we provide an overview of the recent progress in optimising PGE methods and their potential for generating models of human genetic disease.
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Affiliation(s)
- Chris Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Robert N. Kelsh
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Rebecca J. Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
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Vu TV, Nguyen NT, Kim J, Das S, Lee J, Kim JY. The Obstacles and Potential Solution Clues of Prime Editing Applications in Tomato. BIODESIGN RESEARCH 2022; 2022:0001. [PMID: 37905201 PMCID: PMC10593121 DOI: 10.34133/bdr.0001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/16/2022] [Indexed: 11/02/2023] Open
Abstract
Precision genome editing is highly desired for crop improvement. The recently emerged CRISPR/Cas technology offers great potential applications in precision plant genome engineering. A prime editing (PE) approach combining a reverse transcriptase (RT) with a Cas9 nickase and a "priming" extended guide RNA (gRNA) has shown a high frequency for precise genome modification in mammalian cells and several plant species. Nevertheless, the applications of the PE approach in dicot plants are still limited and inefficient. We designed and tested prime editors for precision editing of a synthetic sequence in a transient assay and for desirable alleles of 10 loci in tomato by stable transformation. Our data obtained by targeted deep sequencing also revealed only low PE efficiencies in both the tobacco and tomato systems. Further assessment of the activities of the PE components uncovered that the fusion of RT to Cas9 and the structure of PE gRNAs (pegRNAs) negatively affected the cleaving activity of the Cas9 nuclease. The self-complementarity between the primer binding sequences (PBSs) and spacer sequence might pose risks to the activity of the Cas9 complex. However, modifying the pegRNA sequences by shortening or introducing mismatches to the PBSs to reduce their melting temperatures did not enhance the PE efficiency at the MADS-box protein (SlMBP21), alcobaca (SlALC), and acetolactate synthase 1 (SlALS1) loci. Our data show challenges of the PE approach in tomato, indicating that a further improvement of the PE system for successful applications is demanded, such as the use of improved expression systems for enriching active PE complexes.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Km 02, Pham Van Dong Road, Co Nhue 1, Bac Tu Liem, Hanoi 11917, Vietnam
| | - Ngan Thi Nguyen
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Swati Das
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jinsu Lee
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea
- Nulla Bio Inc., 501 Jinju-daero, Jinju 660-701, Republic of Korea
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24
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Li J, Chen L, Liang J, Xu R, Jiang Y, Li Y, Ding J, Li M, Qin R, Wei P. Development of a highly efficient prime editor 2 system in plants. Genome Biol 2022; 23:161. [PMID: 35879771 PMCID: PMC9310484 DOI: 10.1186/s13059-022-02730-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractLow efficiency has seriously restricted the application of prime editing (PE) systems in plants. In this study, we develop an enhanced plant prime editor 2 system, enpPE2, by stacking various optimization strategies, including updating the PE architecture to PEmax and expressing engineered pegRNA with a structured motif under the control of a composite promoter. In T0 rice plants, enpPE2 exhibits editing frequencies of 64.58% to 77.08%, which are much higher than the frequencies with unmodified pPE2. Our results indicate that the enpPE2 system provides a robust and powerful tool for the precise modification of plant genomes.
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Maharajan T, Krishna TPA, Rakkammal K, Ceasar SA, Ramesh M. Application of CRISPR/Cas system in cereal improvement for biotic and abiotic stress tolerance. PLANTA 2022; 256:106. [PMID: 36326904 DOI: 10.1007/s00425-022-04023-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Application of the recently developed CRISPR/Cas tools might help enhance cereals' growth and yield under biotic and abiotic stresses. Cereals are the most important food crops for human life and an essential source of nutrients for people in developed and developing countries. The growth and yield of all major cereals are affected by both biotic and abiotic stresses. To date, molecular breeding and functional genomic studies have contributed to the understanding and improving cereals' growth and yield under biotic and abiotic stresses. Clustered, regularly inter-spaced, short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been predicted to play a major role in precision plant breeding and developing non-transgenic cereals that can tolerate adverse effects of climate change. Variants of next-generation CRISPR/Cas tools, such as prime editor, base editor, CRISPR activator and repressor, chromatin imager, Cas12a, and Cas12b, are currently used in various fields, including plant science. However, few studies have been reported on applying the CRISPR/Cas system to understand the mechanism of biotic and abiotic stress tolerance in cereals. Rice is the only plant used frequently for such studies. Genes responsible for biotic and abiotic stress tolerance have not yet been studied by CRISPR/Cas system in other major cereals (sorghum, barley, maize and small millets). Examining the role of genes that respond to biotic and abiotic stresses using the CRISPR/Cas system may help enhance cereals' growth and yield under biotic and abiotic stresses. It will help to develop new and improved cultivars with biotic- and abiotic-tolerant traits for better yields to strengthen food security. This review provides information for cereal researchers on the current status of the CRISPR/Cas system for improving biotic and abiotic stress tolerance in cereals.
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Affiliation(s)
- Theivanayagam Maharajan
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683104, India
| | - T P Ajeesh Krishna
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683104, India
| | - Kasinathan Rakkammal
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, 630003, India
| | - Stanislaus Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683104, India.
| | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, 630003, India
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26
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Tan J, Forner J, Karcher D, Bock R. DNA base editing in nuclear and organellar genomes. Trends Genet 2022; 38:1147-1169. [PMID: 35853769 DOI: 10.1016/j.tig.2022.06.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/12/2022] [Accepted: 06/24/2022] [Indexed: 01/24/2023]
Abstract
Genome editing continues to revolutionize biological research. Due to its simplicity and flexibility, CRISPR/Cas-based editing has become the preferred technology in most systems. Cas nucleases tolerate fusion to large protein domains, thus allowing combination of their DNA recognition properties with new enzymatic activities. Fusion to nucleoside deaminase or reverse transcriptase domains has produced base editors and prime editors that, instead of generating double-strand breaks in the target sequence, induce site-specific alterations of single (or a few adjacent) nucleotides. The availability of protein-only genome editing reagents based on transcription activator-like effectors has enabled the extension of base editing to the genomes of chloroplasts and mitochondria. In this review, we summarize currently available base editing methods for nuclear and organellar genomes. We highlight recent advances with improving precision, specificity, and efficiency and discuss current limitations and future challenges. We also provide a brief overview of applications in agricultural biotechnology and gene therapy.
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Affiliation(s)
- Junjie Tan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Innovation Center for Genome Editing and Engineering, Nanjing Agricultural University, Nanjing, 210095, China
| | - Joachim Forner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Karcher
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany.
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27
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Hassan MM, Yuan G, Liu Y, Alam M, Eckert CA, Tuskan GA, Golz JF, Yang X. Precision genome editing in plants using gene targeting and prime editing: existing and emerging strategies. Biotechnol J 2022; 17:e2100673. [PMID: 35766313 DOI: 10.1002/biot.202100673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 11/08/2022]
Abstract
Precise modification of plant genomes, such as seamless insertion, deletion, or replacement of DNA sequences at a predefined site, is a challenging task. Gene targeting (GT) and prime editing are currently the best approaches for this purpose. However, these techniques are inefficient in plants, which limits their applications for crop breeding programs. Recently, substantial developments have been made to improve the efficiency of these techniques in plants. Several strategies, such as RNA donor templating, chemically modified donor DNA template, and tandem-repeat homology-directed repair, are aimed at improving GT. Additionally, improved prime editing gRNA design, use of engineered reverse transcriptase enzymes, and splitting prime editing components have improved the efficacy of prime editing in plants. These emerging strategies and existing technologies are reviewed along with various perspectives on their future improvement and the development of robust precision genome editing technologies for plants.
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Affiliation(s)
- Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Mobashwer Alam
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Nambour, Queensland, Australia
| | - Carrie A Eckert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - John F Golz
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria, 3010, Australia
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
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28
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Li Z, Ma R, Liu D, Wang M, Zhu T, Deng Y. A straightforward plant prime editing system enabled highly efficient precise editing of rice Waxy gene. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111400. [PMID: 35905895 DOI: 10.1016/j.plantsci.2022.111400] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/19/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
CRISPR Cas9-mediated genome editing is highly efficient at targeted site-specific gene knock-out through NHEJ (Non-Homology End Joining), but ineffective for specific DNA integration through HDR (Homology Directed Repair) for precise gene editing. Base editors can make limited base substitutions but only within restricted small windows of the protospacer. Prime editing has been applied in plants with various degrees of success. However, several questions such as low and inconsistent editing efficiencies across different target sites need to be addressed. We compared two prime editing approaches PE3 and PE2 at two neighboring target sites within rice Waxy gene to partially address those questions. A straightforward PE2 plant prime editing system retrofitted from a regular CRISPR-Cas9 editing system can deliver highly efficient up to 66.7% precise gene editing. Various forms of precise editing including base substitutions, small deletions and insertions can be accurately achieved. The secondary structure variations of different pegRNAs may be the primary reason for inconsistent editing across different target sites and should be the optimization focus to further improve plant prime editing.
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Affiliation(s)
- Zhongsen Li
- Beidahuang Kenfeng Seed, 380 Changjiang Road, Nangang District, Harbin, Heilongjiang, PR China.
| | - Rui Ma
- Beidahuang Kenfeng Seed, 380 Changjiang Road, Nangang District, Harbin, Heilongjiang, PR China
| | - Dan Liu
- Beidahuang Kenfeng Seed, 380 Changjiang Road, Nangang District, Harbin, Heilongjiang, PR China
| | - Mingyue Wang
- Beidahuang Kenfeng Seed, 380 Changjiang Road, Nangang District, Harbin, Heilongjiang, PR China
| | - Ting Zhu
- Beidahuang Kenfeng Seed, 380 Changjiang Road, Nangang District, Harbin, Heilongjiang, PR China
| | - Yanxue Deng
- Beidahuang Kenfeng Seed, 380 Changjiang Road, Nangang District, Harbin, Heilongjiang, PR China
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29
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Biswas S, Bridgeland A, Irum S, Thomson MJ, Septiningsih EM. Optimization of Prime Editing in Rice, Peanut, Chickpea, and Cowpea Protoplasts by Restoration of GFP Activity. Int J Mol Sci 2022; 23:9809. [PMID: 36077206 PMCID: PMC9456013 DOI: 10.3390/ijms23179809] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/19/2022] [Accepted: 08/26/2022] [Indexed: 01/23/2023] Open
Abstract
Precise editing of the plant genome has long been desired for functional genomic research and crop breeding. Prime editing is a newly developed precise editing technology based on CRISPR-Cas9, which uses an engineered reverse transcriptase (RT), a catalytically impaired Cas9 endonuclease (nCas9), and a prime editing guide RNA (pegRNA). In addition, prime editing has a wider range of editing types than base editing and can produce nearly all types of edits. Although prime editing was first established in human cells, it has recently been applied to plants. As a relatively new technique, optimization will be needed to increase the editing efficiency in different crops. In this study, we successfully edited a mutant GFP in rice, peanut, chickpea, and cowpea protoplasts. In rice, up to 16 times higher editing efficiency was achieved with a dual pegRNA than the single pegRNA containing vectors. Edited-mutant GFP protoplasts have also been obtained in peanut, chickpea, and cowpea after transformation with the dual pegRNA vectors, albeit with much lower editing efficiency than in rice, ranging from 0.2% to 0.5%. These initial results promise to expedite the application of prime editing in legume breeding programs to accelerate crop improvement.
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Affiliation(s)
- Sudip Biswas
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Aya Bridgeland
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Samra Irum
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
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30
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Lu Y, Happi Mbakam C, Song B, Bendavid E, Tremblay JP. Improvements of nuclease and nickase gene modification techniques for the treatment of genetic diseases. Front Genome Ed 2022; 4:892769. [PMID: 35958050 PMCID: PMC9360573 DOI: 10.3389/fgeed.2022.892769] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/08/2022] [Indexed: 12/20/2022] Open
Abstract
Advancements in genome editing make possible to exploit the functions of enzymes for efficient DNA modifications with tremendous potential to treat human genetic diseases. Several nuclease genome editing strategies including Meganucleases (MNs), Zinc Finger Nucleases (ZFNs), Transcription Activator-like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated proteins (CRISPR-Cas) have been developed for the correction of genetic mutations. CRISPR-Cas has further been engineered to create nickase genome editing tools including Base editors and Prime editors with much precision and efficacy. In this review, we summarized recent improvements in nuclease and nickase genome editing approaches for the treatment of genetic diseases. We also highlighted some limitations for the translation of these approaches into clinical applications.
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Affiliation(s)
- Yaoyao Lu
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
| | - Cedric Happi Mbakam
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
| | - Bo Song
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
| | - Eli Bendavid
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
| | - Jacques-P. Tremblay
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
- *Correspondence: Jacques-P. Tremblay,
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31
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Baloglu MC, Celik Altunoglu Y, Baloglu P, Yildiz AB, Türkölmez N, Özden Çiftçi Y. Gene-Editing Technologies and Applications in Legumes: Progress, Evolution, and Future Prospects. Front Genet 2022; 13:859437. [PMID: 35836569 PMCID: PMC9275826 DOI: 10.3389/fgene.2022.859437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/13/2022] [Indexed: 12/22/2022] Open
Abstract
Legumes are rich in protein and phytochemicals and have provided a healthy diet for human beings for thousands of years. In recognition of the important role they play in human nutrition and agricultural production, the researchers have made great efforts to gain new genetic traits in legumes such as yield, stress tolerance, and nutritional quality. In recent years, the significant increase in genomic resources for legume plants has prepared the groundwork for applying cutting-edge breeding technologies, such as transgenic technologies, genome editing, and genomic selection for crop improvement. In addition to the different genome editing technologies including the CRISPR/Cas9-based genome editing system, this review article discusses the recent advances in plant-specific gene-editing methods, as well as problems and potential benefits associated with the improvement of legume crops with important agronomic properties. The genome editing technologies have been effectively used in different legume plants including model legumes like alfalfa and lotus, as well as crops like soybean, cowpea, and chickpea. We also discussed gene-editing methods used in legumes and the improvements of agronomic traits in model and recalcitrant legumes. Despite the immense opportunities genome editing can offer to the breeding of legumes, governmental regulatory restrictions present a major concern. In this context, the comparison of the regulatory framework of genome editing strategies in the European Union and the United States of America was also discussed. Gene-editing technologies have opened up new possibilities for the improvement of significant agronomic traits in legume breeding.
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Affiliation(s)
- Mehmet Cengiz Baloglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Yasemin Celik Altunoglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Pinar Baloglu
- Research and Application Center, Kastamonu University, Kastamonu, Turkey
| | - Ali Burak Yildiz
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
| | - Nil Türkölmez
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
| | - Yelda Özden Çiftçi
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
- Smart Agriculture Research and Application Center, Gebze Technical University, Kocaeli, Turkey
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32
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Li J, Yu X, Zhang C, Li N, Zhao J. The application of CRISPR/Cas technologies to Brassica crops: current progress and future perspectives. ABIOTECH 2022; 3:146-161. [PMID: 36304520 PMCID: PMC9590542 DOI: 10.1007/s42994-022-00076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/20/2022] [Indexed: 12/04/2022]
Abstract
Brassica species are a global source of nutrients and edible vegetable oil for humans. However, all commercially important Brassica crops underwent a whole-genome triplication event, hindering the development of functional genomics and breeding programs. Fortunately, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) technologies, by allowing multiplex and precise genome engineering, have become valuable genome-editing tools and opened up new avenues for biotechnology. Here, we review current progress in the use of CRISPR/Cas technologies with an emphasis on the latest breakthroughs in precise genome editing. We also summarize the application of CRISPR/Cas technologies to Brassica crops for trait improvements. Finally, we discuss the challenges and future directions of these technologies for comprehensive application in Brassica crops. Ongoing advancement in CRISPR/Cas technologies, in combination with other achievements, will play a significant role in the genetic improvement and molecular breeding of Brassica crops.
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Affiliation(s)
- Jun Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, 071001 China
| | - Xiaoxiao Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, 071001 China
| | - Chao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, 071001 China
| | - Na Li
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071001 China
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, 071001 China
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071001 China
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33
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Mattiello L, Rütgers M, Sua-Rojas MF, Tavares R, Soares JS, Begcy K, Menossi M. Molecular and Computational Strategies to Increase the Efficiency of CRISPR-Based Techniques. FRONTIERS IN PLANT SCIENCE 2022; 13:868027. [PMID: 35712599 PMCID: PMC9194676 DOI: 10.3389/fpls.2022.868027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The prokaryote-derived Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas mediated gene editing tools have revolutionized our ability to precisely manipulate specific genome sequences in plants and animals. The simplicity, precision, affordability, and robustness of this technology have allowed a myriad of genomes from a diverse group of plant species to be successfully edited. Even though CRISPR/Cas, base editing, and prime editing technologies have been rapidly adopted and implemented in plants, their editing efficiency rate and specificity varies greatly. In this review, we provide a critical overview of the recent advances in CRISPR/Cas9-derived technologies and their implications on enhancing editing efficiency. We highlight the major efforts of engineering Cas9, Cas12a, Cas12b, and Cas12f proteins aiming to improve their efficiencies. We also provide a perspective on the global future of agriculturally based products using DNA-free CRISPR/Cas techniques. The improvement of CRISPR-based technologies efficiency will enable the implementation of genome editing tools in a variety of crop plants, as well as accelerate progress in basic research and molecular breeding.
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Affiliation(s)
- Lucia Mattiello
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Mark Rütgers
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Maria Fernanda Sua-Rojas
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Rafael Tavares
- Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - José Sérgio Soares
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Kevin Begcy
- Environmental Horticulture Department, University of Florida, Gainesville, FL, United States
| | - Marcelo Menossi
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
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Das D, Singha DL, Paswan RR, Chowdhury N, Sharma M, Reddy PS, Chikkaputtaiah C. Recent advancements in CRISPR/Cas technology for accelerated crop improvement. PLANTA 2022; 255:109. [PMID: 35460444 DOI: 10.1007/s00425-022-03894-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Precise genome engineering approaches could be perceived as a second paradigm for targeted trait improvement in crop plants, with the potential to overcome the constraints imposed by conventional CRISPR/Cas technology. The likelihood of reduced agricultural production due to highly turbulent climatic conditions increases as the global population expands. The second paradigm of stress-resilient crops with enhanced tolerance and increased productivity against various stresses is paramount to support global production and consumption equilibrium. Although traditional breeding approaches have substantially increased crop production and yield, effective strategies are anticipated to restore crop productivity even further in meeting the world's increasing food demands. CRISPR/Cas, which originated in prokaryotes, has surfaced as a coveted genome editing tool in recent decades, reshaping plant molecular biology in unprecedented ways and paving the way for engineering stress-tolerant crops. CRISPR/Cas is distinguished by its efficiency, high target specificity, and modularity, enables precise genetic modification of crop plants, allowing for the creation of allelic variations in the germplasm and the development of novel and more productive agricultural practices. Additionally, a slew of advanced biotechnologies premised on the CRISPR/Cas methodologies have augmented fundamental research and plant synthetic biology toolkits. Here, we describe gene editing tools, including CRISPR/Cas and its imitative tools, such as base and prime editing, multiplex genome editing, chromosome engineering followed by their implications in crop genetic improvement. Further, we comprehensively discuss the latest developments of CRISPR/Cas technology including CRISPR-mediated gene drive, tissue-specific genome editing, dCas9 mediated epigenetic modification and programmed self-elimination of transgenes in plants. Finally, we highlight the applicability and scope of advanced CRISPR-based techniques in crop genetic improvement.
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Affiliation(s)
- Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Dhanawantari L Singha
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Ricky Raj Paswan
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Monica Sharma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Palakolanu Sudhakar Reddy
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India.
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35
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Xiong X, Li Z, Liang J, Liu K, Li C, Li JF. A cytosine base editor toolkit with varying activity windows and target scopes for versatile gene manipulation in plants. Nucleic Acids Res 2022; 50:3565-3580. [PMID: 35286371 PMCID: PMC8989527 DOI: 10.1093/nar/gkac166] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/20/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas-derived base editing tools empower efficient alteration of genomic cytosines or adenines associated with essential genetic traits in plants and animals. Diversified target sequences and customized editing products call for base editors with distinct features regarding the editing window and target scope. Here we developed a toolkit of plant base editors containing AID10, an engineered human AID cytosine deaminase. When fused to the N-terminus or C-terminus of the conventional Cas9 nickase (nSpCas9), AID10 exhibited a broad or narrow activity window at the protospacer adjacent motif (PAM)-distal and -proximal protospacer, respectively, while AID10 fused to both termini conferred an additive activity window. We further replaced nSpCas9 with orthogonal or PAM-relaxed Cas9 variants to widen target scopes. Moreover, we devised dual base editors with AID10 located adjacently or distally to the adenine deaminase ABE8e, leading to juxtaposed or spaced cytosine and adenine co-editing at the same target sequence in plant cells. Furthermore, we expanded the application of this toolkit in plants for tunable knockdown of protein-coding genes via creating upstream open reading frame and for loss-of-function analysis of non-coding genes, such as microRNA sponges. Collectively, this toolkit increases the functional diversity and versatility of base editors in basic and applied plant research.
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Affiliation(s)
- Xiangyu Xiong
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhenxiang Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jieping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kehui Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chenlong Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jian-Feng Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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36
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Hua K, Han P, Zhu JK. Improvement of base editors and prime editors advances precision genome engineering in plants. PLANT PHYSIOLOGY 2022; 188:1795-1810. [PMID: 34962995 PMCID: PMC8968349 DOI: 10.1093/plphys/kiab591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/22/2021] [Indexed: 05/11/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein (Cas)-mediated gene disruption has revolutionized biomedical research as well as plant and animal breeding. However, most disease-causing mutations and agronomically important genetic variations are single base polymorphisms (single-nucleotide polymorphisms) that require precision genome editing tools for correction of the sequences. Although homology-directed repair of double-stranded breaks (DSBs) can introduce precise changes, such repairs are inefficient in differentiated animal and plant cells. Base editing and prime editing are two recently developed genome engineering approaches that can efficiently introduce precise edits into target sites without requirement of DSB formation or donor DNA templates. They have been applied in several plant species with promising results. Here, we review the extensive literature on improving the efficiency, target scope, and specificity of base editors and prime editors in plants. We also highlight recent progress on base editing in plant organellar genomes and discuss how these precision genome editing tools are advancing basic plant research and crop breeding.
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Affiliation(s)
- Kai Hua
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Peijin Han
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
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37
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Chen J, Li S, He Y, Li J, Xia L. An update on precision genome editing by homology-directed repair in plants. PLANT PHYSIOLOGY 2022; 188:1780-1794. [PMID: 35238390 PMCID: PMC8968426 DOI: 10.1093/plphys/kiac037] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/20/2022] [Indexed: 05/22/2023]
Abstract
Beneficial alleles derived from local landraces or related species, or even orthologs from other plant species, are often caused by differences of one or several single-nucleotide polymorphisms or indels in either the promoter region or the encoding region of a gene and often account for major differences in agriculturally important traits. Clustered regularly interspaced short palindromic repeats-associated endonuclease Cas9 system (CRISPR/Cas9)-mediated precision genome editing enables targeted allele replacement or insertion of flag or foreign genes at specific loci via homology-directed repair (HDR); however, HDR efficiency is low due to the intrinsic rare occurrence of HDR and insufficient DNA repair template in the proximity of a double-stranded break (DSB). Precise replacement of the targeted gene with elite alleles from landraces or relatives into a commercial variety through genome editing has been a holy grail in the crop genome editing field. In this update, we briefly summarize CRISPR/Cas-mediated HDR in plants. We describe diverse strategies to improve HDR efficiency by manipulating the DNA repair pathway, timing DSB induction, and donor delivery, and so on. Lastly, we outline open questions and challenges in HDR-mediated precision genome editing in both plant biological research and crop improvement.
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Affiliation(s)
- Jilin Chen
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
| | - Shaoya Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Yubing He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingying Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
| | - Lanqin Xia
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
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38
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Lai Z, Huang Z, Sun J, Jing X, Xiang L, Zhao H, Mo C, Hou X. CRISPR/Cas基因组编辑技术及其在农作物品种改良中的应用. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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39
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Ali Q, Yu C, Hussain A, Ali M, Ahmar S, Sohail MA, Riaz M, Ashraf MF, Abdalmegeed D, Wang X, Imran M, Manghwar H, Zhou L. Genome Engineering Technology for Durable Disease Resistance: Recent Progress and Future Outlooks for Sustainable Agriculture. FRONTIERS IN PLANT SCIENCE 2022; 13:860281. [PMID: 35371164 PMCID: PMC8968944 DOI: 10.3389/fpls.2022.860281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/22/2022] [Indexed: 05/15/2023]
Abstract
Crop production worldwide is under pressure from multiple factors, including reductions in available arable land and sources of water, along with the emergence of new pathogens and development of resistance in pre-existing pathogens. In addition, the ever-growing world population has increased the demand for food, which is predicted to increase by more than 100% by 2050. To meet these needs, different techniques have been deployed to produce new cultivars with novel heritable mutations. Although traditional breeding continues to play a vital role in crop improvement, it typically involves long and laborious artificial planting over multiple generations. Recently, the application of innovative genome engineering techniques, particularly CRISPR-Cas9-based systems, has opened up new avenues that offer the prospects of sustainable farming in the modern agricultural industry. In addition, the emergence of novel editing systems has enabled the development of transgene-free non-genetically modified plants, which represent a suitable option for improving desired traits in a range of crop plants. To date, a number of disease-resistant crops have been produced using gene-editing tools, which can make a significant contribution to overcoming disease-related problems. Not only does this directly minimize yield losses but also reduces the reliance on pesticide application, thereby enhancing crop productivity that can meet the globally increasing demand for food. In this review, we describe recent progress in genome engineering techniques, particularly CRISPR-Cas9 systems, in development of disease-resistant crop plants. In addition, we describe the role of CRISPR-Cas9-mediated genome editing in sustainable agriculture.
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Affiliation(s)
- Qurban Ali
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Chenjie Yu
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Amjad Hussain
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mohsin Ali
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology, and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Muhammad Aamir Sohail
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Riaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Muhammad Furqan Ashraf
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Dyaaaldin Abdalmegeed
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
- Department of Botany and Microbiology, Faculty of Science, Tanta University, Tanta, Egypt
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Muhammad Imran
- Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agriculture University, Guangzhou, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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40
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Development and Optimization of CRISPR Prime Editing System in Photoautotrophic Cells. Molecules 2022; 27:molecules27061758. [PMID: 35335122 PMCID: PMC8948812 DOI: 10.3390/molecules27061758] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 12/04/2022] Open
Abstract
Prime editor (PE), a versatile editor that allows the insertion and deletion of arbitrary sequences, and all 12-point mutations without double-strand breaks (DSB) and a donor template, dramatically enhances research capabilities. PE combines nickase Cas9(H840A) and reverse transcriptase (RT), along with prime editing guide RNA (pegRNA). It has been reported in several plant species, but a weak editing efficiency has led to a decrease in applications. This study reports an optimized-prime editor (O-PE) for endogenous gene editing in Arabidopsis thaliana cells, with an average 1.15% editing efficiency, which is 16.4-fold higher than previously reported. Meanwhile, we observed an increase in indels when testing alternative reverse transcriptase and found out that nCas9(H840A) fused to non-functional reverse transcriptase was responsible for the increase. This work develops an efficient prime editor for plant cells and provides a blueprint for applying PE in other photoautotrophic cells, such as microalgae, that have a high industrial value.
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41
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Perroud PF, Guyon-Debast A, Veillet F, Kermarrec MP, Chauvin L, Chauvin JE, Gallois JL, Nogué F. Prime Editing in the model plant Physcomitrium patens and its potential in the tetraploid potato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 316:111162. [PMID: 35151447 DOI: 10.1016/j.plantsci.2021.111162] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/03/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
Since its discovery and first applications for genome editing in plants, the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology has revolutionized plant research and precision crop breeding. Although the classical CRISPR-Cas9 system is a highly efficient tool for disruptive targeted mutagenesis, this system is mostly inefficient for the introduction of precise and predictable nucleotide substitutions. Recently, Prime Editing technology has been developed, allowing the simultaneous generation of nucleotide transitions and transversions but also short defined indels. In this study, we report on the successful use of Prime Editing in two plants of interest: the plant model Physcomitrium patens and the tetraploid and highly heterozygous potato (Solanum tuberosum). In both cases editing rates were lower than with other CRISPR-Cas9 based techniques, but we were able to successfully introduce nucleotide transversions into targeted genes, a unique feature of Prime Editing. Additionally, the analysis of potential off-target mutation sites in P. patens suggested very high targeting fidelity in this organism. The present work paves the way for the use Prime Editing in Physcomitrium patens and potato, however highlighting the limitations that need to be overcome for more efficient precision plant breeding.
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Affiliation(s)
- Pierre-François Perroud
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France.
| | - Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Florian Veillet
- IGEPP, INRAE, Institut Agro, Univ Rennes, 29260, Ploudaniel, France
| | | | - Laura Chauvin
- IGEPP, INRAE, Institut Agro, Univ Rennes, 29260, Ploudaniel, France
| | | | | | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
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42
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Simon DA, Tálas A, Kulcsár PI, Biczók Z, Krausz SL, Várady G, Welker E. PEAR, a flexible fluorescent reporter for the identification and enrichment of successfully prime edited cells. eLife 2022; 11:69504. [PMID: 35196219 PMCID: PMC8865850 DOI: 10.7554/elife.69504] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 02/09/2022] [Indexed: 12/26/2022] Open
Abstract
Prime editing is a recently developed CRISPR/Cas9 based gene engineering tool that allows the introduction of short insertions, deletions, and substitutions into the genome. However, the efficiency of prime editing, which typically achieves editing rates of around 10%–30%, has not matched its versatility. Here, we introduce the prime editor activity reporter (PEAR), a sensitive fluorescent tool for identifying single cells with prime editing activity. PEAR has no background fluorescence and specifically indicates prime editing events. Its design provides apparently unlimited flexibility for sequence variation along the entire length of the spacer sequence, making it uniquely suited for systematic investigation of sequence features that influence prime editing activity. The use of PEAR as an enrichment marker for prime editing can increase the edited population by up to 84%, thus significantly improving the applicability of prime editing for basic research and biotechnological applications.
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Affiliation(s)
- Dorottya Anna Simon
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.,ProteoScientia, Budapest, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.,Biospiral-2006, Szeged, Hungary
| | - Zsuzsanna Biczók
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
| | - Sarah Laura Krausz
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
| | - György Várady
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
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43
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Habib O, Habib G, Hwang GH, Bae S. Comprehensive analysis of prime editing outcomes in human embryonic stem cells. Nucleic Acids Res 2022; 50:1187-1197. [PMID: 35018468 PMCID: PMC8789035 DOI: 10.1093/nar/gkab1295] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 12/26/2022] Open
Abstract
Prime editing is a versatile and precise genome editing technique that can directly copy desired genetic modifications into target DNA sites without the need for donor DNA. This technique holds great promise for the analysis of gene function, disease modeling, and the correction of pathogenic mutations in clinically relevant cells such as human pluripotent stem cells (hPSCs). Here, we comprehensively tested prime editing in hPSCs by generating a doxycycline-inducible prime editing platform. Prime editing successfully induced all types of nucleotide substitutions and small insertions and deletions, similar to observations in other human cell types. Moreover, we compared prime editing and base editing for correcting a disease-related mutation in induced pluripotent stem cells derived form a patient with α 1-antitrypsin (A1AT) deficiency. Finally, whole-genome sequencing showed that, unlike the cytidine deaminase domain of cytosine base editors, the reverse transcriptase domain of a prime editor does not lead to guide RNA-independent off-target mutations in the genome. Our results demonstrate that prime editing in hPSCs has great potential for complementing previously developed CRISPR genome editing tools.
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Affiliation(s)
- Omer Habib
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 08826, South Korea
| | - Gizem Habib
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 08826, South Korea
| | - Gue-Ho Hwang
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 08826, South Korea
| | - Sangsu Bae
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 08826, South Korea
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44
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Xu W, Yang Y, Yang B, Krueger CJ, Xiao Q, Zhao S, Zhang L, Kang G, Wang F, Yi H, Ren W, Li L, He X, Zhang C, Zhang B, Zhao J, Yang J. A design optimized prime editor with expanded scope and capability in plants. NATURE PLANTS 2022; 8:45-52. [PMID: 34949802 DOI: 10.1038/s41477-021-01043-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 11/10/2021] [Indexed: 06/14/2023]
Abstract
The ability to manipulate the genome in a programmable manner has illuminated biology and shown promise in plant breeding. Prime editing, a versatile gene-editing approach that directly writes new genetic information into a specified DNA site without requiring double-strand DNA breaks, suffers from low efficiency in plants1-5. In this study, N-terminal reverse transcriptase-Cas9 nickase fusion performed better in rice than the commonly applied C-terminal fusion. In addition, introduction of multiple-nucleotide substitutions in the reverse transcriptase template stimulated prime editing with enhanced efficiency. By using these two methods synergistically, prime editing with an average editing frequency as high as 24.3% at 13 endogenous targets in rice transgenic plants, 6.2% at four targets in maize protoplasts and 12.5% in human cells was achieved, which is two- to threefold higher than the original editor, Prime Editor 3. Therefore, our optimized approach has potential to make more formerly non-editable target sites editable, and expands the scope and capabilities of prime editing in the future.
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Affiliation(s)
- Wen Xu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, People's Republic of China
| | - Yongxing Yang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, People's Republic of China
| | - Biying Yang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Qianlin Xiao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, People's Republic of China
| | - Si Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, People's Republic of China
| | - Lu Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, People's Republic of China
| | - Guiting Kang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, People's Republic of China
| | - Feipeng Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, People's Republic of China
| | - Hongmei Yi
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, People's Republic of China
| | - Wen Ren
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, People's Republic of China
| | - Lu Li
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, People's Republic of China
| | - Xiaoqing He
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, People's Republic of China
| | - Chuanmao Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, People's Republic of China.
| | - Jinxiao Yang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, People's Republic of China.
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45
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Wang Y, Wang H, Jian Y, Luo Z, Shao H, Zhang W. Strategies for optimization of the CRISPR-based genome editing system for enhanced editing specificity. Hum Gene Ther 2021; 33:358-370. [PMID: 34963339 DOI: 10.1089/hum.2021.283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system is inarguably the most valuable gene editing tool ever discovered. Currently, three classes of CRISPR-based genome editing systems have been developed for gene editing, including CRISPR/Cas nucleases, base editors (BEs) and prime editors (PEs). Ever-evolving CRISPR technology plays an important role in medicine; however, the biggest obstacle to its use in clinical practice is the induction of off-target effects (OTEs) during targeted editing. Therefore, continuous improvement and optimization of the CRISPR system for reduction of OTEs is a major focus in the field of CRISPR research. This review aims to provide a comprehensive guide for optimization of the CRISPR-based genome editing system.
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Affiliation(s)
- Yangmin Wang
- Guangdong Pharmaceutical University, 71237, Guangzhou, Guangdong, China;
| | - Haozheng Wang
- Guangdong Pharmaceutical University, 71237, Guangzhou, Guangdong, China;
| | - Yingzhen Jian
- Guangdong Pharmaceutical University, 71237, Guangzhou, Guangdong, China;
| | - Zhongtao Luo
- Guangdong Pharmaceutical University, 71237, Guangzhou, Guangdong, China;
| | - Hongwei Shao
- Guangdong Pharmaceutical University, 71237, Guangzhou, Guangdong, China;
| | - Wenfeng Zhang
- Guangdong Pharmaceutical University, 71237, School of Biosciences and Biopharmaceutics , 28 E. Rd outside the City of Guangzhou University, Guangzhou, China, 510006;
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46
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Liu G, Lin Q, Jin S, Gao C. The CRISPR-Cas toolbox and gene editing technologies. Mol Cell 2021; 82:333-347. [PMID: 34968414 DOI: 10.1016/j.molcel.2021.12.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/04/2021] [Accepted: 12/02/2021] [Indexed: 02/08/2023]
Abstract
The emergence of CRISPR-Cas systems has accelerated the development of gene editing technologies, which are widely used in the life sciences. To improve the performance of these systems, workers have engineered and developed a variety of CRISPR-Cas tools with a broader range of targets, higher efficiency and specificity, and greater precision. Moreover, CRISPR-Cas-related technologies have also been expanded beyond making cuts in DNA by introducing functional elements that permit precise gene modification, control gene expression, make epigenetic changes, and so on. In this review, we introduce and summarize the characteristics and applications of different types of CRISPR-Cas tools. We discuss certain limitations of current approaches and future prospects for optimizing CRISPR-Cas systems.
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Affiliation(s)
- Guanwen Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Qiupeng Lin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shuai Jin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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Recent advances in CRISPR/Cas9 and applications for wheat functional genomics and breeding. ABIOTECH 2021; 2:375-385. [PMID: 36304421 PMCID: PMC9590522 DOI: 10.1007/s42994-021-00042-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/17/2021] [Indexed: 12/21/2022]
Abstract
Common wheat (Triticum aestivum L.) is one of the three major food crops in the world; thus, wheat breeding programs are important for world food security. Characterizing the genes that control important agronomic traits and finding new ways to alter them are necessary to improve wheat breeding. Functional genomics and breeding in polyploid wheat has been greatly accelerated by the advent of several powerful tools, especially CRISPR/Cas9 genome editing technology, which allows multiplex genome engineering. Here, we describe the development of CRISPR/Cas9, which has revolutionized the field of genome editing. In addition, we emphasize technological breakthroughs (e.g., base editing and prime editing) based on CRISPR/Cas9. We also summarize recent applications and advances in the functional annotation and breeding of wheat, and we introduce the production of CRISPR-edited DNA-free wheat. Combined with other achievements, CRISPR and CRISPR-based genome editing will speed progress in wheat biology and promote sustainable agriculture.
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Singh S, Ramakrishna W. Application of CRISPR-Cas9 in plant-plant growth-promoting rhizobacteria interactions for next Green Revolution. 3 Biotech 2021; 11:492. [PMID: 34840925 PMCID: PMC8590643 DOI: 10.1007/s13205-021-03041-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/20/2021] [Indexed: 12/21/2022] Open
Abstract
Agriculture's beginnings resulted in the domestication of numerous plant species as well as the use of natural resources. Food grain production took about 10,000 years to reach a billion tonnes in 1960, however, it took only 40 years to achieve 2 billion tonnes in year 2000. The creation of genetically modified crops, together with the use of enhanced agronomic practices, resulted in this remarkable increase, dubbed the "Green Revolution". Plants and bacteria that interact with each other in nature are co-evolving, according to Red Queen dynamics. Plant microorganisms, also known as plant microbiota, are an essential component of plant life. Plant-microbe (PM) interactions can be beneficial or harmful to hosts, depending on the health impact. The significance of microbiota in plant growth promotion (PGP) and stress resistance is well known. Our understanding of the community composition of the plant microbiome and important driving forces has advanced significantly. As a result, utilising the plant microbiota is a viable strategy for the next Green Revolution for meeting food demand. The utilisation of newer methods to understand essential genetic and molecular components of the multiple PM interactions is required for their application. The use of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) techniques to investigate PM interactions is of tremendous interest. The implementation of GE techniques to boost the ability of microorganisms or plants for agronomic trait development will be enabled by a comprehensive understanding of PM interactions. This review focuses on using GE approaches to investigate the principles of PM interactions, disease resistance, PGP activity, and future implications in agriculture in plants or associated microbiota.
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Affiliation(s)
- Sudiksha Singh
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, Punjab 151401 India
| | - Wusirika Ramakrishna
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, Punjab 151401 India
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Wang T, Zhang C, Zhang H, Zhu H. CRISPR/Cas9-Mediated Gene Editing Revolutionizes the Improvement of Horticulture Food Crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13260-13269. [PMID: 33734711 DOI: 10.1021/acs.jafc.1c00104] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Horticultural food crops are important sources of nutrients for humans. With the increase of the global population, enhanced horticulture food crop production has become a new challenge, and enriching their nutritional content has also been required. Gene editing systems, such as zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9), have accelerated crop improvement through the modification of targeted genomes precisely. Here, we review the development of various gene editors and compare their advantages and shortcomings, especially the newly emerging CRISPR/Cas systems, such as base editing and prime editing. We also summarize their practical applications in crop trait improvement, including yield, nutritional quality, and other consumer traits.
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Affiliation(s)
- Tian Wang
- College of Life Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China
| | - Hongyan Zhang
- College of Life Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
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Hassan MM, Zhang Y, Yuan G, De K, Chen JG, Muchero W, Tuskan GA, Qi Y, Yang X. Construct design for CRISPR/Cas-based genome editing in plants. TRENDS IN PLANT SCIENCE 2021; 26:1133-1152. [PMID: 34340931 DOI: 10.1016/j.tplants.2021.06.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 05/06/2023]
Abstract
CRISPR construct design is a key step in the practice of genome editing, which includes identification of appropriate Cas proteins, design and selection of guide RNAs (gRNAs), and selection of regulatory elements to express gRNAs and Cas proteins. Here, we review the choices of CRISPR-based genome editors suited for different needs in plant genome editing applications. We consider the technical aspects of gRNA design and the associated computational tools. We also discuss strategies for the design of multiplex CRISPR constructs for high-throughput manipulation of complex biological processes or polygenic traits. We provide recommendations for different elements of CRISPR constructs and discuss the remaining challenges of CRISPR construct optimization in plant genome editing.
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Affiliation(s)
- Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali-8602, Bangladesh
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kuntal De
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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