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Kababji AM, Butt H, Mahfouz M. Synthetic directed evolution for targeted engineering of plant traits. FRONTIERS IN PLANT SCIENCE 2024; 15:1449579. [PMID: 39286837 PMCID: PMC11402689 DOI: 10.3389/fpls.2024.1449579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 08/12/2024] [Indexed: 09/19/2024]
Abstract
Improving crop traits requires genetic diversity, which allows breeders to select advantageous alleles of key genes. In species or loci that lack sufficient genetic diversity, synthetic directed evolution (SDE) can supplement natural variation, thus expanding the possibilities for trait engineering. In this review, we explore recent advances and applications of SDE for crop improvement, highlighting potential targets (coding sequences and cis-regulatory elements) and computational tools to enhance crop resilience and performance across diverse environments. Recent advancements in SDE approaches have streamlined the generation of variants and the selection processes; by leveraging these advanced technologies and principles, we can minimize concerns about host fitness and unintended effects, thus opening promising avenues for effectively enhancing crop traits.
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Affiliation(s)
- Ahad Moussa Kababji
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Nazir MF, Lou J, Wang Y, Zou S, Huang H. Kiwifruit in the Omics Age: Advances in Genomics, Breeding, and Beyond. PLANTS (BASEL, SWITZERLAND) 2024; 13:2156. [PMID: 39124274 PMCID: PMC11313697 DOI: 10.3390/plants13152156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024]
Abstract
The kiwifruit, Actinidia genus, has emerged as a nutritionally rich and economically significant crop with a history rooted in China. This review paper examines the global journey of the kiwifruit, its genetic diversity, and the role of advanced breeding techniques in its cultivation and improvement. The expansion of kiwifruit cultivation from China to New Zealand, Italy, Chile and beyond, driven by the development of new cultivars and improved agricultural practices, is discussed, highlighting the fruit's high content of vitamins C, E, and K. The genetic resources within the Actinidia genus are reviewed, with emphasis on the potential of this diversity in breeding programs. The review provides extensive coverage to the application of modern omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, which have revolutionized the understanding of the biology of kiwifruit and facilitated targeted breeding efforts. It examines both conventional breeding methods and modern approaches, like marker-assisted selection, genomic selection, mutation breeding, and the potential of CRISPR-Cas9 technology for precise trait enhancement. Special attention is paid to interspecific hybridization and cisgenesis as strategies for incorporating beneficial traits and developing superior kiwifruit varieties. This comprehensive synthesis not only sheds light on the current state of kiwifruit research and breeding, but also outlines the future directions and challenges in the field, underscoring the importance of integrating traditional and omics-based approaches to meet the demands of a changing global climate and market preferences.
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Affiliation(s)
- Mian Faisal Nazir
- Key Laboratory of Ex Situ Plant Conservation and Utilization of Jiangxi Province, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 330022, China; (M.F.N.)
| | - Jinpeng Lou
- Key Laboratory of Ex Situ Plant Conservation and Utilization of Jiangxi Province, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 330022, China; (M.F.N.)
| | - Yu Wang
- Key Laboratory of Ex Situ Plant Conservation and Utilization of Jiangxi Province, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 330022, China; (M.F.N.)
| | - Shuaiyu Zou
- Key Laboratory of Ex Situ Plant Conservation and Utilization of Jiangxi Province, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 330022, China; (M.F.N.)
| | - Hongwen Huang
- Key Laboratory of Ex Situ Plant Conservation and Utilization of Jiangxi Province, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 330022, China; (M.F.N.)
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Shelake RM, Pramanik D, Kim JY. CRISPR base editor-based targeted random mutagenesis (BE-TRM) toolbox for directed evolution. BMB Rep 2024; 57:30-39. [PMID: 38053292 PMCID: PMC10828429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/26/2023] [Accepted: 08/16/2023] [Indexed: 12/07/2023] Open
Abstract
Directed evolution (DE) of desired locus by targeted random mutagenesis (TRM) tools is a powerful approach for generating genetic variations with novel or improved functions, particularly in complex genomes. TRM-based DE involves developing a mutant library of targeted DNA sequences and screening the variants for the desired properties. However, DE methods have for a long time been confined to bacteria and yeasts. Lately, CRISPR/Cas and DNA deaminase-based tools that circumvent enduring barriers such as longer life cycle, small library sizes, and low mutation rates have been developed to facilitate DE in native genetic environments of multicellular organisms. Notably, deaminase-based base editing-TRM (BE-TRM) tools have greatly expanded the scope and efficiency of DE schemes by enabling base substitutions and randomization of targeted DNA sequences. BE-TRM tools provide a robust platform for the continuous molecular evolution of desired proteins, metabolic pathway engineering, creation of a mutant library of desired locus to evolve novel functions, and other applications, such as predicting mutants conferring antibiotic resistance. This review provides timely updates on the recent advances in BE-TRM tools for DE, their applications in biology, and future directions for further improvements. [BMB Reports 2024; 57(1): 30-39].
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
- Division of Life Science, Gyeongsang National University, Jinju 52828, Korea
- R&D Center, Nulla Bio Inc., Jinju 52828, Korea
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Oliveira-Filho ER, Voiniciuc C, Hanson AD. Adapting enzymes to improve their functionality in plants: why and how. Biochem Soc Trans 2023; 51:1957-1966. [PMID: 37787016 PMCID: PMC10657173 DOI: 10.1042/bst20230532] [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: 09/06/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
Synthetic biology creates new metabolic processes and improves existing ones using engineered or natural enzymes. These enzymes are often sourced from cells that differ from those in the target plant organ with respect to, e.g. redox potential, effector levels, or proteostasis machinery. Non-native enzymes may thus need to be adapted to work well in their new plant context ('plantized') even if their specificity and kinetics in vitro are adequate. Hence there are two distinct ways in which an enzyme destined for use in plants can require improvement: In catalytic properties such as substrate and product specificity, kcat, and KM; and in general compatibility with the milieu of cells that express the enzyme. Continuous directed evolution systems can deliver both types of improvement and are so far the most broadly effective way to deliver the second type. Accordingly, in this review we provide a short account of continuous evolution methods, emphasizing the yeast OrthoRep system because of its suitability for plant applications. We then cover the down-to-earth and increasingly urgent issues of which enzymes and enzyme properties can - or cannot - be improved in theory, and which in practice are the best to target for crop improvement, i.e. those that are realistically improvable and important enough to warrant deploying continuous directed evolution. We take horticultural crops as examples because of the opportunities they present and to sharpen the focus.
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Affiliation(s)
| | - Cătălin Voiniciuc
- Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A
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Ahmad N, Fatima S, Mehmood MA, Zaman QU, Atif RM, Zhou W, Rahman MU, Gill RA. Targeted genome editing in polyploids: lessons from Brassica. FRONTIERS IN PLANT SCIENCE 2023; 14:1152468. [PMID: 37409308 PMCID: PMC10318174 DOI: 10.3389/fpls.2023.1152468] [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: 01/27/2023] [Accepted: 04/11/2023] [Indexed: 07/07/2023]
Abstract
CRISPR-mediated genome editing has emerged as a powerful tool for creating targeted mutations in the genome for various applications, including studying gene functions, engineering resilience against biotic and abiotic stresses, and increasing yield and quality. However, its utilization is limited to model crops for which well-annotated genome sequences are available. Many crops of dietary and economic importance, such as wheat, cotton, rapeseed-mustard, and potato, are polyploids with complex genomes. Therefore, progress in these crops has been hampered due to genome complexity. Excellent work has been conducted on some species of Brassica for its improvement through genome editing. Although excellent work has been conducted on some species of Brassica for genome improvement through editing, work on polyploid crops, including U's triangle species, holds numerous implications for improving other polyploid crops. In this review, we summarize key examples from genome editing work done on Brassica and discuss important considerations for deploying CRISPR-mediated genome editing more efficiently in other polyploid crops for improvement.
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Affiliation(s)
- Niaz Ahmad
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Samia Fatima
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Aamer Mehmood
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Qamar U. Zaman
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Rana Muhammad Atif
- National Center of Genome Editing, Center of Advanced Studies, Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Weijun Zhou
- Ministry of Agriculture and Rural Affairs Key Lab of Spectroscopy Sensing, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Mehboob-ur Rahman
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Rafaqat Ali Gill
- Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Yasmeen E, Wang J, Riaz M, Zhang L, Zuo K. Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants. PLANT COMMUNICATIONS 2023:100558. [PMID: 36760129 PMCID: PMC10363483 DOI: 10.1016/j.xplc.2023.100558] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of native promoters in controlling gene expression, artificial promoter design aims to synthesize short, inducible, and conditionally controlled promoters to coordinate the expression of multiple genes in diverse plant metabolic and signaling pathways. Synthetic promoters are versatile and can drive gene expression accurately with smart responses; they show potential for enhancing desirable traits in crops, thereby improving crop yield, nutritional quality, and food security. This review first illustrates the importance of synthetic promoters, then introduces promoter architecture and thoroughly summarizes advances in synthetic promoter construction. Restrictions to the development of synthetic promoters and future applications of such promoters in synthetic plant biology and crop improvement are also discussed.
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Affiliation(s)
- Erum Yasmeen
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Riaz
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lida Zhang
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Liu X, Zhang P, Zhao Q, Huang AC. Making small molecules in plants: A chassis for synthetic biology-based production of plant natural products. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:417-443. [PMID: 35852486 DOI: 10.1111/jipb.13330] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Plant natural products have been extensively exploited in food, medicine, flavor, cosmetic, renewable fuel, and other industrial sectors. Synthetic biology has recently emerged as a promising means for the cost-effective and sustainable production of natural products. Compared with engineering microbes for the production of plant natural products, the potential of plants as chassis for producing these compounds is underestimated, largely due to challenges encountered in engineering plants. Knowledge in plant engineering is instrumental for enabling the effective and efficient production of valuable phytochemicals in plants, and also paves the way for a more sustainable future agriculture. In this manuscript, we briefly recap the biosynthesis of plant natural products, focusing primarily on industrially important terpenoids, alkaloids, and phenylpropanoids. We further summarize the plant hosts and strategies that have been used to engineer the production of natural products. The challenges and opportunities of using plant synthetic biology to achieve rapid and scalable production of high-value plant natural products are also discussed.
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Affiliation(s)
- Xinyu Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Peijun Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qiao Zhao
- Shenzhen Institutes of Advanced Technology (SIAT), the Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ancheng C Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
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Leong BJ, Hanson AD. Continuous Directed Evolution of a Feedback-Resistant Arabidopsis Arogenate Dehydratase in Plantized Escherichia coli. ACS Synth Biol 2023; 12:43-50. [PMID: 36534785 PMCID: PMC9872817 DOI: 10.1021/acssynbio.2c00511] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Indexed: 12/24/2022]
Abstract
Continuous directed evolution (CDE) is a powerful tool for enzyme engineering due to the depth and scale of evolutionary search that it enables. If suitably controlled and calibrated, CDE could be widely applied in plant breeding and biotechnology to improve plant enzymes ex planta. We tested this concept by evolving Arabidopsis arogenate dehydratase (AtADT2) for resistance to feedback inhibition. We used an Escherichia coli platform with a phenylalanine biosynthesis pathway reconfigured ("plantized") to mimic the plant pathway, a T7RNA polymerase-base deaminase hypermutation system (eMutaT7), and 4-fluorophenylalanine as selective agent. Selection schemes were prevalidated using a known feedback-resistant AtADT2 variant. We obtained variants that had 4-fluorophenylalanine resistance at least matching the known variant and that carried mutations in the ACT domain responsible for feedback inhibition. We conclude that ex planta CDE of plant enzymes in a microbial platform is a viable way to tailor characteristics that involve interaction with small molecules.
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Affiliation(s)
- Bryan J. Leong
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
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Sánchez E, Ali Z, Islam T, Mahfouz M. A CRISPR-based lateral flow assay for plant genotyping and pathogen diagnostics. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2418-2429. [PMID: 36072993 PMCID: PMC9674313 DOI: 10.1111/pbi.13924] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/14/2022] [Accepted: 08/28/2022] [Indexed: 05/27/2023]
Abstract
Efficient pathogen diagnostics and genotyping methods enable effective disease management and breeding, improve crop productivity and ensure food security. However, current germplasm selection and pathogen detection techniques are laborious, time-consuming, expensive and not easy to mass-scale application in the field. Here, we optimized a field-deployable lateral flow assay, Bio-SCAN, as a highly sensitive tool to precisely identify elite germplasm and detect mutations, transgenes and phytopathogens in <1 h, starting from sample isolation to result output using lateral flow strips. As a proof of concept, we genotyped various wheat germplasms for the Lr34 and Lr67 alleles conferring broad-spectrum resistance to stripe rust, confirmed the presence of synthetically produced herbicide-resistant alleles in the rice genome and screened for the presence of transgenic elements in the genome of transgenic tobacco and rice plants with 100% specificity. We also successfully applied this new assay to the detection of phytopathogens, including viruses and bacterial pathogens in Nicotiana benthamiana, and two destructive fungal pathogens (Puccinia striiformis f. sp. tritici and Magnaporthe oryzae Triticum) in wheat. Our results illustrate the power of Bio-SCAN in crop breeding, genetic engineering and pathogen diagnostics to enhance food security. The high sensitivity, simplicity, versatility and in-field deployability make the Bio-SCAN as an attractive molecular diagnostic tool for diverse applications in agriculture.
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Affiliation(s)
- Edith Sánchez
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological SciencesKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological SciencesKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE)Bangabandhu Sheikh Mujibur Rahman Agricultural UniversityGazipurBangladesh
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological SciencesKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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Butt H, Ramirez JLM, Mahfouz M. Synthetic evolution of herbicide resistance using a T7 RNAP-based random DNA base editor. Life Sci Alliance 2022; 5:5/12/e202201538. [PMID: 36171140 PMCID: PMC9526444 DOI: 10.26508/lsa.202201538] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
Abstract
A chimeric fusion of T7 RNAP and deaminase edits the DNA under the T7 promoter in plant cells. It directs the continuous synthetic evolution of OsALS to produce variants with herbicide resistance. Synthetic directed evolution via localized sequence diversification and the simultaneous application of selection pressure is a promising method for producing new, beneficial alleles that affect traits of interest in diverse species; however, this technique has rarely been applied in plants. Here, we designed, built, and tested a chimeric fusion of T7 RNA Polymerase (RNAP) and deaminase to enable the localized sequence diversification of a target sequence of interest. We tested our T7 RNAP–DNA base editor in Nicotiana benthamiana transient assays to target a transgene expressing GFP under the control of the T7 promoter and observed C-to-T conversions. We then targeted the T7 promoter-driven acetolactate synthase sequence that had been stably integrated in the rice genome and generated C-to-T and G-to-A transitions. We used herbicide treatment as selection pressure for the evolution of the acetolactate synthase sequence, resulting in the enrichment of herbicide-responsive residues. We then validated these herbicide-responsive regions in the transgenic rice plants. Thus, our system could be used for the continuous synthetic evolution of gene functions to produce variants with improved herbicide resistance.
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Affiliation(s)
- Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jose Luis Moreno Ramirez
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Jiang W, Sivakrishna Rao G, Aman R, Butt H, Kamel R, Sedeek K, Mahfouz MM. High-efficiency retron-mediated single-stranded DNA production in plants. Synth Biol (Oxf) 2022; 7:ysac025. [PMID: 36452068 PMCID: PMC9700382 DOI: 10.1093/synbio/ysac025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/20/2022] [Accepted: 10/30/2022] [Indexed: 07/29/2023] Open
Abstract
Retrons are a class of retroelements that produce multicopy single-stranded DNA (ssDNA) and participate in anti-phage defenses in bacteria. Retrons have been harnessed for the overproduction of ssDNA, genome engineering and directed evolution in bacteria, yeast and mammalian cells. Retron-mediated ssDNA production in plants could unlock their potential applications in plant biotechnology. For example, ssDNA can be used as a template for homology-directed repair (HDR) in several organisms. However, current gene editing technologies rely on the physical delivery of synthetic ssDNA, which limits their applications. Here, we demonstrated retron-mediated overproduction of ssDNA in Nicotiana benthamiana. Additionally, we tested different retron architectures for improved ssDNA production and identified a new retron architecture that resulted in greater ssDNA abundance. Furthermore, co-expression of the gene encoding the ssDNA-protecting protein VirE2 from Agrobacterium tumefaciens with the retron systems resulted in a 10.7-fold increase in ssDNA production in vivo. We also demonstrated clustered regularly interspaced short palindromic repeats-retron-coupled ssDNA overproduction and targeted HDR in N. benthamiana. Overall, we present an efficient approach for in vivo ssDNA production in plants, which can be harnessed for biotechnological applications. Graphical Abstract.
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Affiliation(s)
| | | | - Rashid Aman
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Radwa Kamel
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Khalid Sedeek
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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The Rice Serine/Arginine Splicing Factor RS33 Regulates Pre-mRNA Splicing during Abiotic Stress Responses. Cells 2022; 11:cells11111796. [PMID: 35681491 PMCID: PMC9180459 DOI: 10.3390/cells11111796] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/27/2022] [Accepted: 05/07/2022] [Indexed: 02/06/2023] Open
Abstract
Abiotic stresses profoundly affect plant growth and development and limit crop productivity. Pre-mRNA splicing is a major form of gene regulation that helps plants cope with various stresses. Serine/arginine (SR)-rich splicing factors play a key role in pre-mRNA splicing to regulate different biological processes under stress conditions. Alternative splicing (AS) of SR transcripts and other transcripts of stress-responsive genes generates multiple splice isoforms that contribute to protein diversity, modulate gene expression, and affect plant stress tolerance. Here, we investigated the function of the plant-specific SR protein RS33 in regulating pre-mRNA splicing and abiotic stress responses in rice. The loss-of-function mutant rs33 showed increased sensitivity to salt and low-temperature stresses. Genome-wide analyses of gene expression and splicing in wild-type and rs33 seedlings subjected to these stresses identified multiple splice isoforms of stress-responsive genes whose AS are regulated by RS33. The number of RS33-regulated genes was much higher under low-temperature stress than under salt stress. Our results suggest that the plant-specific splicing factor RS33 plays a crucial role during plant responses to abiotic stresses.
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