1
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Imai S, Hirozawa H, Sugahara S, Ishizaki C, Higuchi M, Matsushita Y, Suzuki T, Mochizuki N, Nagatani A, Ueguchi C. The CRK14 gene encoding a cysteine-rich receptor-like kinase is implicated in the regulation of global proliferative arrest in Arabidopsis thaliana. Genes Cells 2024; 29:735-745. [PMID: 38938200 DOI: 10.1111/gtc.13139] [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: 05/23/2024] [Revised: 06/14/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024]
Abstract
Global proliferative arrest (GPA) is a phenomenon in monocarpic plants in which the activity of all aboveground meristems generally ceases in a nearly coordinated manner after the formation of a certain number of fruits. Despite the fact that GPA is a biologically and agriculturally important event, the underlying molecular mechanisms are not well understood. In this study, we attempted to elucidate the molecular mechanism of GPA regulation by identifying the gene responsible for the Arabidopsis mutant fireworks (fiw), causing an early GPA phenotype. Map-based cloning revealed that the fiw gene encodes CYSTEIN-RICH RECEPTOR-LIKE KINASE 14 (CRK14). Genetic analysis suggested that fiw is a missense, gain-of-function allele of CRK14. Since overexpression of the extracellular domain of CRK14 resulted in delayed GPA in the wild-type background, we concluded that CRK14 is involved in GPA regulation. Analysis of double mutants revealed that fiw acts downstream of or independently of the FRUITFULL-APETALA2 (AP2)/AP2-like pathway, which was previously reported as an age-dependent default pathway in GPA regulation. In addition, fiw is epistatic to clv with respect to GPA control. Furthermore, we found a negative effect on WUSCHEL expression in the fiw mutants. These results thus suggest the existence of a novel CRK14-dependent signaling pathway involved in GPA regulation.
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Affiliation(s)
- Sho Imai
- Laboratory of Plant Cell Function, Graduate school of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hikaru Hirozawa
- Laboratory of Plant Cell Function, Graduate school of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Shingo Sugahara
- Laboratory of Plant Cell Function, Graduate school of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Chisato Ishizaki
- Laboratory of Plant Cell Function, Graduate school of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mayu Higuchi
- Laboratory of Plant Cell Function, Graduate school of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yuma Matsushita
- Laboratory of Plant Cell Function, Graduate school of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Nobuyoshi Mochizuki
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Akira Nagatani
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Chiharu Ueguchi
- Laboratory of Plant Cell Function, Graduate school of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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2
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Gehrke F, Wolf S, Puchta H. Protocol to efficiently induce CRISPR-Kill-mediated cell ablation in Arabidopsis thaliana. STAR Protoc 2024; 5:103072. [PMID: 38768032 PMCID: PMC11134856 DOI: 10.1016/j.xpro.2024.103072] [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: 02/13/2024] [Revised: 04/08/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024] Open
Abstract
The CRISPR-Kill system enables targeted cell ablation by inducing multiple double-strand breaks in evolutionarily conserved repetitive genomic regions. Here, we present a protocol for the application of the CRISPR-Kill system to analyze the systemic and cellular effects of targeted cell death in Arabidopsis. We describe steps for generating constitutive and inducible CRISPR-Kill lines, chemically inducing CRISPR-Cas9-mediated genome elimination, and monitoring of cell death in shoot and root apical meristems. This enables the investigation of a wide range of questions in developmental plant biology. For complete details on the use and execution of this protocol, please refer to Gehrke et al.1.
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Affiliation(s)
- Fabienne Gehrke
- Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP) - Molecular Biology, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Sebastian Wolf
- Centre for Plant Molecular Biology (ZMBP), Plant Biochemistry, Eberhard-Karls-University Tübingen, 72076 Tübingen, Germany
| | - Holger Puchta
- Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP) - Molecular Biology, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany.
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3
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Schmidt-Marcec S, Parish A, Smertenko T, Hickey M, Piette BMAG, Smertenko A. The microtubule-nucleating factor MACERATOR tethers AUGMIN7 to microtubules and governs phragmoplast architecture. THE PLANT CELL 2024; 36:1072-1097. [PMID: 38079222 PMCID: PMC11181950 DOI: 10.1093/plcell/koad304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/08/2023] [Indexed: 04/02/2024]
Abstract
The plant cytokinetic microtubule array, called the phragmoplast, exhibits higher microtubule dynamics in its center (midzone) than at the periphery (distal zone). This behavior is known as the axial asymmetry. Despite being a major characteristic of the phragmoplast, little is known about regulators of this phenomenon. Here we address the role of microtubule nucleation in axial asymmetry by characterizing MACERATOR (MACET) proteins in Arabidopsis thaliana and Nicotiana benthamiana with a combination of genetic, biochemical, and live-cell imaging assays, using photo-convertible microtubule probes, and modeling. MACET paralogs accumulate at the shrinking microtubule ends and decrease the tubulin OFF rate. Loss of MACET4 and MACET5 function abrogates axial asymmetry by suppressing microtubule dynamicity in the midzone. MACET4 also narrows the microtubule nucleation angle at the phragmoplast leading edge and functions as a microtubule tethering factor for AUGMIN COMPLEX SUBUNIT 7 (AUG7). The macet4 macet5 double mutant shows diminished clustering of AUG7 in the phragmoplast distal zone. Knockout of AUG7 does not affect MACET4 localization, axial asymmetry, or microtubule nucleation angle, but increases phragmoplast length and slows down phragmoplast expansion. The mce4-1 mce5 aug7-1 triple knockout is not viable. Experimental data and modeling demonstrate that microtubule nucleation factors regulate phragmoplast architecture and axial asymmetry directly by generating new microtubules and indirectly by modulating the abundance of free tubulin.
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Affiliation(s)
- Sharol Schmidt-Marcec
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
| | - Alyssa Parish
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
| | - Tetyana Smertenko
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
| | - Matthew Hickey
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
| | | | - Andrei Smertenko
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
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4
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Puchta H, Houben A. Plant chromosome engineering - past, present and future. THE NEW PHYTOLOGIST 2024; 241:541-552. [PMID: 37984056 DOI: 10.1111/nph.19414] [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: 09/06/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023]
Abstract
Spontaneous chromosomal rearrangements (CRs) play an essential role in speciation, genome evolution and crop domestication. To be able to use the potential of CRs for breeding, plant chromosome engineering was initiated by fragmenting chromosomes by X-ray irradiation. With the rise of the CRISPR/Cas system, it became possible to induce double-strand breaks (DSBs) in a highly efficient manner at will at any chromosomal position. This has enabled a completely new level of predesigned chromosome engineering. The genetic linkage between specific genes can be broken by inducing chromosomal translocations. Natural inversions, which suppress genetic exchange, can be reverted for breeding. In addition, various approaches for constructing minichromosomes by downsizing regular standard A or supernumerary B chromosomes, which could serve as future vectors in plant biotechnology, have been developed. Recently, a functional synthetic centromere could be constructed. Also, different ways of genome haploidization have been set up, some based on centromere manipulations. In the future, we expect to see even more complex rearrangements, which can be combined with previously developed engineering technologies such as recombinases. Chromosome engineering might help to redefine genetic linkage groups, change the number of chromosomes, stack beneficial genes on mini cargo chromosomes, or set up genetic isolation to avoid outcrossing.
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Affiliation(s)
- Holger Puchta
- Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP) - Molecular Biology, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
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Martín-Valmaseda M, Devin SR, Ortuño-Hernández G, Pérez-Caselles C, Mahdavi SME, Bujdoso G, Salazar JA, Martínez-Gómez P, Alburquerque N. CRISPR/Cas as a Genome-Editing Technique in Fruit Tree Breeding. Int J Mol Sci 2023; 24:16656. [PMID: 38068981 PMCID: PMC10705926 DOI: 10.3390/ijms242316656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
CRISPR (short for "Clustered Regularly Interspaced Short Palindromic Repeats") is a technology that research scientists use to selectively modify the DNA of living organisms. CRISPR was adapted for use in the laboratory from the naturally occurring genome-editing systems found in bacteria. In this work, we reviewed the methods used to introduce CRISPR/Cas-mediated genome editing into fruit species, as well as the impacts of the application of this technology to activate and knock out target genes in different fruit tree species, including on tree development, yield, fruit quality, and tolerance to biotic and abiotic stresses. The application of this gene-editing technology could allow the development of new generations of fruit crops with improved traits by targeting different genetic segments or even could facilitate the introduction of traits into elite cultivars without changing other traits. However, currently, the scarcity of efficient regeneration and transformation protocols in some species, the fact that many of those procedures are genotype-dependent, and the convenience of segregating the transgenic parts of the CRISPR system represent the main handicaps limiting the potential of genetic editing techniques for fruit trees. Finally, the latest news on the legislation and regulations about the use of plants modified using CRISPR/Cas systems has been also discussed.
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Affiliation(s)
- Marina Martín-Valmaseda
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
| | - Sama Rahimi Devin
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.R.D.); (S.M.E.M.)
| | - Germán Ortuño-Hernández
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Cristian Pérez-Caselles
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
| | - Sayyed Mohammad Ehsan Mahdavi
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.R.D.); (S.M.E.M.)
| | - Geza Bujdoso
- Research Centre for Fruit Growing, Hungarian University of Agriculture and Life Sciences, 1223 Budapest, Hungary;
| | - Juan Alfonso Salazar
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Pedro Martínez-Gómez
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Nuria Alburquerque
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
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6
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Yang TH, Che´telat A, Kurenda A, Farmer EE. Mechanosensation in leaf veins. SCIENCE ADVANCES 2023; 9:eadh5078. [PMID: 37729418 PMCID: PMC10511200 DOI: 10.1126/sciadv.adh5078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023]
Abstract
Whether the plant vasculature has the capacity to sense touch is unknown. We developed a quantitative assay to investigate touch-response electrical signals in the leaves and veins of Arabidopsis thaliana. Mechanostimulated electrical signaling in leaves displayed strong diel regulation. Signals of full amplitude could be generated by repeated stimulation at the same site after approximately 90 minutes. However, the signals showed intermediate amplitudes when repeatedly stimulated in shorter timeframes. Using intracellular electrodes, we detected touch-response membrane depolarizations in the phloem. On the basis of this, we mutated multiple Arabidopsis H+-ATPase (AHA) genes expressed in companion cells. We found that aha1 aha3 double mutants attenuated touch-responses, and this was coupled to growth rate reduction. Moreover, propagating membrane depolarizations could be triggered by mechanostimulating the exposed primary vasculature of wild-type plants but not of aha1 aha3 mutants. Primary veins have autonomous mechanosensory properties which depend on P-type proton pumps.
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Affiliation(s)
- Tsu-Hao Yang
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Aurore Che´telat
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Edward E. Farmer
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
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7
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Bekalu ZE, Panting M, Bæksted Holme I, Brinch-Pedersen H. Opportunities and Challenges of In Vitro Tissue Culture Systems in the Era of Crop Genome Editing. Int J Mol Sci 2023; 24:11920. [PMID: 37569295 PMCID: PMC10419073 DOI: 10.3390/ijms241511920] [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: 06/21/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Currently, the development of genome editing (GE) tools has provided a wide platform for targeted modification of plant genomes. However, the lack of versatile DNA delivery systems for a large variety of crop species has been the main bottleneck for improving crops with beneficial traits. Currently, the generation of plants with heritable mutations induced by GE tools mostly goes through tissue culture. Unfortunately, current tissue culture systems restrict successful results to only a limited number of plant species and genotypes. In order to release the full potential of the GE tools, procedures need to be species and genotype independent. This review provides an in-depth summary and insights into the various in vitro tissue culture systems used for GE in the economically important crops barley, wheat, rice, sorghum, soybean, maize, potatoes, cassava, and millet and uncovers new opportunities and challenges of already-established tissue culture platforms for GE in the crops.
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8
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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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9
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Mackon E, Mackon GCJDE, Guo Y, Ma Y, Yao Y, Liu P. Development and Application of CRISPR/Cas9 to Improve Anthocyanin Pigmentation in Plants: Opportunities and Perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023:111746. [PMID: 37230190 DOI: 10.1016/j.plantsci.2023.111746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/22/2023] [Accepted: 05/21/2023] [Indexed: 05/27/2023]
Abstract
Since its discovery in 2012, the novel technology of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) has greatly contributed to revolutionizing molecular biology. It has been demonstrated to be an effective approach for identifying gene function and improving some important traits. Anthocyanins are secondary metabolites responsible for a wide spectrum of aesthetic coloration in various plant organs and are beneficial for health. As such, increasing anthocyanin content in plants, especially the edible tissue and organs, is always a main goal for plant breeding. Recently, CRISPR/Cas9 technology has been highly desired to enhance the amount of anthocyanin in vegetables, fruits, cereals, and other attractive plants with more precision. Here we reviewed the recent knowledge concerning CRISPR/Cas9-mediated anthocyanin enhancement in plants. In addition, we addressed the future avenues of promising potential target genes that could be helpful for achieving the same goal using CRISPR/Cas9 in several plants. Thus, molecular biologists, genetic engineers, agricultural scientists, plant geneticists, and physiologists may benefit from CRISPR technology to boost the biosynthesis and accumulation of anthocyanins in fresh fruits, vegetables, grains, roots, and ornamental plants.
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Affiliation(s)
- Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University.
| | | | - Yongqiang Guo
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Yafei Ma
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Yuhang Yao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Piqing Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
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10
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Wu J, Tao Y, Deng D, Meng Z, Zhao Y. The applications of CRISPR/Cas-mediated genome editing in genetic hearing loss. Cell Biosci 2023; 13:93. [PMID: 37210555 DOI: 10.1186/s13578-023-01021-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/25/2023] [Indexed: 05/22/2023] Open
Abstract
Hearing loss (HL) can be caused by a number of different genetic factors. Non-syndromic HL refers that HL occurs as an isolated symptom in an individual, whereas syndromic HL refers that HL is associated with other symptoms or abnormalities. To date, more than 140 genes have been identified as being associated with non-syndromic HL, and approximately 400 genetic syndromes can include HL as one of the clinical symptoms. However, no gene therapeutic approaches are currently available to restore or improve hearing. Therefore, there is an urgent necessity to elucidate the possible pathogenesis of specific mutations in HL-associated genes and to investigate the promising therapeutic strategies for genetic HL. The development of the CRISPR/Cas system has revolutionized the field of genome engineering, which has become an efficacious and cost-effective tool to foster genetic HL research. Moreover, several in vivo studies have demonstrated the therapeutic efficacy of the CRISPR/Cas-mediated treatments for specific genetic HL. In this review, we briefly introduce the progress in CRISPR/Cas technique as well as the understanding of genetic HL, and then we detail the recent achievements of CRISPR/Cas technique in disease modeling and therapeutic strategies for genetic HL. Furthermore, we discuss the challenges for the application of CRISPR/Cas technique in future clinical treatments.
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Affiliation(s)
- Junhao Wu
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Yong Tao
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Di Deng
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Zhaoli Meng
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China.
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China.
| | - Yu Zhao
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China.
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China.
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11
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Zhang F, Neik TX, Thomas WJW, Batley J. CRISPR-Based Genome Editing Tools: An Accelerator in Crop Breeding for a Changing Future. Int J Mol Sci 2023; 24:8623. [PMID: 37239967 PMCID: PMC10218198 DOI: 10.3390/ijms24108623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Genome editing is an important strategy to maintain global food security and achieve sustainable agricultural development. Among all genome editing tools, CRISPR-Cas is currently the most prevalent and offers the most promise. In this review, we summarize the development of CRISPR-Cas systems, outline their classification and distinctive features, delineate their natural mechanisms in plant genome editing and exemplify the applications in plant research. Both classical and recently discovered CRISPR-Cas systems are included, detailing the class, type, structures and functions of each. We conclude by highlighting the challenges that come with CRISPR-Cas and offer suggestions on how to tackle them. We believe the gene editing toolbox will be greatly enriched, providing new avenues for a more efficient and precise breeding of climate-resilient crops.
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Affiliation(s)
- Fangning Zhang
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Ting Xiang Neik
- School of Biosciences, University of Nottingham Malaysia, Semenyih 43500, Malaysia
| | - William J. W. Thomas
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
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12
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Reimann TM, Müdsam C, Schachtler C, Ince S, Sticht H, Herrmann C, Stürzl M, Kost B. The large GTPase AtGBPL3 links nuclear envelope formation and morphogenesis to transcriptional repression. NATURE PLANTS 2023; 9:766-784. [PMID: 37095224 DOI: 10.1038/s41477-023-01400-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Guanylate binding proteins (GBPs) are prominent regulators of immunity not known to be required for nuclear envelope formation and morphogenesis. Here we identify the Arabidopsis GBP orthologue AtGBPL3 as a lamina component with essential functions in mitotic nuclear envelope reformation, nuclear morphogenesis and transcriptional repression during interphase. AtGBPL3 is preferentially expressed in mitotically active root tips, accumulates at the nuclear envelope and interacts with centromeric chromatin as well as with lamina components transcriptionally repressing pericentromeric chromatin. Reduced expression of AtGBPL3 or associated lamina components similarly altered nuclear morphology and caused overlapping transcriptional deregulation. Investigating the dynamics of AtGBPL3-GFP and other nuclear markers during mitosis (1) revealed that AtGBPL3 accumulation on the surface of daughter nuclei precedes nuclear envelope reformation and (2) uncovered defects in this process in roots of AtGBPL3 mutants, which cause programmed cell death and impair growth. AtGBPL3 functions established by these observations are unique among dynamin-family large GTPases.
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Affiliation(s)
- Theresa Maria Reimann
- Cell Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christina Müdsam
- Cell Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christina Schachtler
- Cell Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Semra Ince
- Physical and Biophysical Chemistry, Department of Physical Chemistry 1, Ruhr-Universität Bochum (RUB), Bochum, Germany
| | - Heinrich Sticht
- Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christian Herrmann
- Physical and Biophysical Chemistry, Department of Physical Chemistry 1, Ruhr-Universität Bochum (RUB), Bochum, Germany
| | - Michael Stürzl
- Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Benedikt Kost
- Cell Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
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13
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Illa-Berenguer E, LaFayette PR, Parrott WA. Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice. Front Genome Ed 2023; 5:1074641. [PMID: 37032710 PMCID: PMC10080323 DOI: 10.3389/fgeed.2023.1074641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest remains challenging in many cases. To assess target site flexibility, we tested five different Cas9/Cas12a endonucleases (SpCas9, SaCas9, St1Cas9, Mb3Cas12a, and AsCas12a) in embryogenic rice calli from Taipei 309 at 37°C (optimal temperature for most Cas9/Cas12a proteins) and 27°C (optimal temperature for tissue culture) and measured their editing rates under regular tissue culture conditions using Illumina sequencing. StCas9 and AsCas12 were not functional as tested, regardless of the temperature used. SpCas9 was the most efficient endonuclease at either temperature, regardless of whether monoallelic or biallelic edits were considered. Mb3Cas12a at 37°C was the next most efficient endonuclease. Monoallelic edits prevailed for both SaCas9 and Mb3Cas12a at 27°C, but biallelic edits prevailed at 37°C. Overall, the use of other Cas9 orthologs, the use of Cas12a endonucleases, and the optimal temperature can expand the range of targetable sequences.
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Affiliation(s)
- Eudald Illa-Berenguer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- *Correspondence: Eudald Illa-Berenguer,
| | - Peter R. LaFayette
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Wayne A. Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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14
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Adeyinka OS, Tabassum B, Koloko BL, Ogungbe IV. Enhancing the quality of staple food crops through CRISPR/Cas-mediated site-directed mutagenesis. PLANTA 2023; 257:78. [PMID: 36913066 DOI: 10.1007/s00425-023-04110-6] [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: 11/20/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The enhancement of CRISPR-Cas gene editing with robust nuclease activity promotes genetic modification of desirable agronomic traits, such as resistance to pathogens, drought tolerance, nutritional value, and yield-related traits in crops. The genetic diversity of food crops has reduced tremendously over the past twelve millennia due to plant domestication. This reduction presents significant challenges for the future especially considering the risks posed by global climate change to food production. While crops with improved phenotypes have been generated through crossbreeding, mutation breeding, and transgenic breeding over the years, improving phenotypic traits through precise genetic diversification has been challenging. The challenges are broadly associated with the randomness of genetic recombination and conventional mutagenesis. This review highlights how emerging gene-editing technologies reduce the burden and time necessary for developing desired traits in plants. Our focus is to provide readers with an overview of the advances in CRISPR-Cas-based genome editing for crop improvement. The use of CRISPR-Cas systems in generating genetic diversity to enhance the quality and nutritional value of staple food crops is discussed. We also outlined recent applications of CRISPR-Cas in developing pest-resistant crops and removing unwanted traits, such as allergenicity from crops. Genome editing tools continue to evolve and present unprecedented opportunities to enhance crop germplasm via precise mutations at the desired loci of the plant genome.
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Affiliation(s)
- Olawale Samuel Adeyinka
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA.
| | - Bushra Tabassum
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Ifedayo Victor Ogungbe
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA
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15
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Sukegawa S, Nureki O, Toki S, Saika H. Genome editing in rice mediated by miniature size Cas nuclease SpCas12f. Front Genome Ed 2023; 5:1138843. [PMID: 36992681 PMCID: PMC10040665 DOI: 10.3389/fgeed.2023.1138843] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/28/2023] [Indexed: 03/14/2023] Open
Abstract
Cas9 derived from Streptococcus pyogenes (SpCas9) is used widely in genome editing using the CRISPR-Cas system due to its high activity, but is a relatively large molecule (1,368 amino acid (a.a.) residues). Recently, targeted mutagenesis in human cells and maize using Cas12f derived from Syntrophomonas palmitatica (SpCas12f)—a very small Cas of 497 a.a, which is a more suitable size for virus vectors—was reported. However, there are no reports of genome editing using SpCas12f in crops other than maize. In this study, we applied SpCas12f to genome editing in rice—one of the most important staple crops in the world. An expression vector encoding rice codon-optimized SpCas12f and sgRNA for OsTubulin as a target was introduced into rice calli by Agrobacterium-mediated transformation. Molecular analysis of SpCas12f-transformed calli showed that mutations were introduced successfully into the target region. Detailed analysis by amplicon sequencing revealed estimated mutation frequencies (a ratio of the number of mutated calli to that of SpCas12f-transformed calli) of 28.8% and 55.6% in two targets. Most mutation patterns were deletions, but base substitutions and insertions were also confirmed at low frequency. Moreover, off-target mutations by SpCas12f were not found. Furthermore, mutant plants were regenerated successfully from the mutated calli. It was confirmed that the mutations in the regenerated plants were inherited to the next-generation. In the previous report in maize, mutations were introduced by treatment with heat shock at 45°C for 4 h per day for 3 days; no mutations were introduced under normal growth conditions at 28°C. Surprisingly, however, mutations can be introduced without heat-shock treatment in rice. This might be due to the culture conditions, with relatively higher temperature (30°C or higher) and constant light during callus proliferation. Taken together, we demonstrated that SpCas12f can be used to achieve targeted mutagenesis in rice. SpCas12f is thus a useful tool for genome editing in rice and is suitable for virus vector-mediated genome editing due to its very small size.
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Affiliation(s)
- Satoru Sukegawa
- Division of Crop Genome Editing Research, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Seiichi Toki
- Division of Crop Genome Editing Research, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
- *Correspondence: Seiichi Toki, ; Hiroaki Saika,
| | - Hiroaki Saika
- Division of Crop Genome Editing Research, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
- *Correspondence: Seiichi Toki, ; Hiroaki Saika,
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16
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Guzmán-Benito I, Achkar NP, Bologna N, Ursache R. CRISPR/Cas-mediated inplanta gene targeting: current advances and challenges. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad072. [PMID: 36861321 DOI: 10.1093/jxb/erad072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Indexed: 06/18/2023]
Abstract
We can use gene targeting (GT) to make modifications at a specific region in a plant's genome and create high-precision tools for plant biotechnology and breeding. However, its low efficiency is a major barrier to its use in plants. The discovery of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas-based site-specific nucleases capable of inducing double-strand breaks in desired loci resulted in the development of novel approaches for plant GT. Several studies have recently demonstrated improvements in GT efficiency through cell-type-specific expression of Cas nucleases, the use of self-amplified GT-vector DNA, or manipulation of RNA silencing and DNA repair pathways. In this review, we summarize recent advances in CRISPR/Cas-mediated GT in plants and discuss potential efficiency improvements. Increasing the efficiency of GT technology will help us pave the way for increased crop yields and food safety in environmentally friendly agriculture.
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Affiliation(s)
- Irene Guzmán-Benito
- The Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Natalia Patricia Achkar
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
| | - Nicolas Bologna
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
| | - Robertas Ursache
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
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17
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Wang Y, Zafar N, Ali Q, Manghwar H, Wang G, Yu L, Ding X, Ding F, Hong N, Wang G, Jin S. CRISPR/Cas Genome Editing Technologies for Plant Improvement against Biotic and Abiotic Stresses: Advances, Limitations, and Future Perspectives. Cells 2022; 11:3928. [PMID: 36497186 PMCID: PMC9736268 DOI: 10.3390/cells11233928] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Crossbreeding, mutation breeding, and traditional transgenic breeding take much time to improve desirable characters/traits. CRISPR/Cas-mediated genome editing (GE) is a game-changing tool that can create variation in desired traits, such as biotic and abiotic resistance, increase quality and yield in less time with easy applications, high efficiency, and low cost in producing the targeted edits for rapid improvement of crop plants. Plant pathogens and the severe environment cause considerable crop losses worldwide. GE approaches have emerged and opened new doors for breeding multiple-resistance crop varieties. Here, we have summarized recent advances in CRISPR/Cas-mediated GE for resistance against biotic and abiotic stresses in a crop molecular breeding program that includes the modification and improvement of genes response to biotic stresses induced by fungus, virus, and bacterial pathogens. We also discussed in depth the application of CRISPR/Cas for abiotic stresses (herbicide, drought, heat, and cold) in plants. In addition, we discussed the limitations and future challenges faced by breeders using GE tools for crop improvement and suggested directions for future improvements in GE for agricultural applications, providing novel ideas to create super cultivars with broad resistance to biotic and abiotic stress.
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Affiliation(s)
- Yaxin Wang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Naeem Zafar
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qurban Ali
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hakim Manghwar
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guanying Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Yu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao Ding
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Ding
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ni Hong
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoping Wang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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18
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Rahman MU, Zulfiqar S, Raza MA, Ahmad N, Zhang B. Engineering Abiotic Stress Tolerance in Crop Plants through CRISPR Genome Editing. Cells 2022; 11:3590. [PMID: 36429019 PMCID: PMC9688763 DOI: 10.3390/cells11223590] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental abiotic stresses challenge food security by depressing crop yields often exceeding 50% of their annual production. Different methods, including conventional as well as genomic-assisted breeding, mutagenesis, and genetic engineering have been utilized to enhance stress resilience in several crop species. Plant breeding has been partly successful in developing crop varieties against abiotic stresses owning to the complex genetics of the traits as well as the narrow genetic base in the germplasm. Irrespective of the fact that genetic engineering can transfer gene(s) from any organism(s), transgenic crops have become controversial mainly due to the potential risk of transgene-outcrossing. Consequently, the cultivation of transgenic crops is banned in certain countries, particularly in European countries. In this scenario, the discovery of the CRISPR tool provides a platform for producing transgene-free genetically edited plants-similar to the mutagenized crops that are not extensively regulated such as genetically modified organisms (GMOs). Thus, the genome-edited plants without a transgene would likely go into the field without any restriction. Here, we focused on the deployment of CRISPR for the successful development of abiotic stress-tolerant crop plants for sustaining crop productivity under changing environments.
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Affiliation(s)
- Mehboob-ur Rahman
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Sana Zulfiqar
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Muhammad Ahmad Raza
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Niaz Ahmad
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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19
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Rönspies M, Schmidt C, Schindele P, Lieberman-Lazarovich M, Houben A, Puchta H. Massive crossover suppression by CRISPR-Cas-mediated plant chromosome engineering. NATURE PLANTS 2022; 8:1153-1159. [PMID: 36109610 DOI: 10.1038/s41477-022-01238-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/02/2022] [Indexed: 05/06/2023]
Abstract
Recent studies have demonstrated that not only genes but also entire chromosomes can be engineered using clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPER-associated protein 9 (Cas9)1-5. A major objective of applying chromosome restructuring in plant breeding is the manipulation of genetic exchange6. Here we show that meiotic recombination can be suppressed in nearly the entire chromosome using chromosome restructuring. We were able to induce a heritable inversion of a >17 Mb-long chromosome fragment that contained the centromere and covered most of chromosome 2 of the Arabidopsis ecotype Col-0. Only the 2 and 0.5 Mb-long telomeric ends remained in their original orientation. In single-nucleotide polymorphism marker analysis of the offspring of crosses with the ecotype Ler-1, we detected a massive reduction of crossovers within the inverted chromosome region, coupled with a shift of crossovers to the telomeric ends. The few genetic exchanges detected within the inversion all originated from double crossovers. This not only indicates that heritable genetic exchange can occur by interstitial chromosome pairing, but also that it is restricted to the production of viable progeny.
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Affiliation(s)
- Michelle Rönspies
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Carla Schmidt
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Schindele
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Department of Vegetable and Field Crops, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion, Israel
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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20
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Dhakate P, Sehgal D, Vaishnavi S, Chandra A, Singh A, Raina SN, Rajpal VR. Comprehending the evolution of gene editing platforms for crop trait improvement. Front Genet 2022; 13:876987. [PMID: 36082000 PMCID: PMC9445674 DOI: 10.3389/fgene.2022.876987] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR-associated) system was initially discovered as an underlying mechanism for conferring adaptive immunity to bacteria and archaea against viruses. Over the past decade, this has been repurposed as a genome-editing tool. Numerous gene editing-based crop improvement technologies involving CRISPR/Cas platforms individually or in combination with next-generation sequencing methods have been developed that have revolutionized plant genome-editing methodologies. Initially, CRISPR/Cas nucleases replaced the earlier used sequence-specific nucleases (SSNs), such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), to address the problem of associated off-targets. The adaptation of this platform led to the development of concepts such as epigenome editing, base editing, and prime editing. Epigenome editing employed epi-effectors to manipulate chromatin structure, while base editing uses base editors to engineer precise changes for trait improvement. Newer technologies such as prime editing have now been developed as a "search-and-replace" tool to engineer all possible single-base changes. Owing to the availability of these, the field of genome editing has evolved rapidly to develop crop plants with improved traits. In this review, we present the evolution of the CRISPR/Cas system into new-age methods of genome engineering across various plant species and the impact they have had on tweaking plant genomes and associated outcomes on crop improvement initiatives.
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Affiliation(s)
- Priyanka Dhakate
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), México-Veracruz, Mexico
| | | | - Atika Chandra
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Apekshita Singh
- Amity Institute of Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
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21
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Jedličková V, Mácová K, Štefková M, Butula J, Staveníková J, Sedláček M, Robert HS. Hairy root transformation system as a tool for CRISPR/Cas9-directed genome editing in oilseed rape ( Brassica napus). FRONTIERS IN PLANT SCIENCE 2022; 13:919290. [PMID: 35991410 PMCID: PMC9386449 DOI: 10.3389/fpls.2022.919290] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Our study examined the mutation efficiency of the CRISPR/Cas9 method for tryptophan aminotransferase BnaTAA1 genes involved in the auxin biosynthesis pathway. We made nine CRISPR/Cas9 constructs with various promoters driving the expression of a Cas9 from Staphylococcus aureus (SaCas9) or a plant-codon-optimized Streptococcus pyogenes Cas9 (pcoCas9). We developed a fast and efficient system for evaluating the variety and frequency of mutations caused by each construct using Brassica napus hairy roots. We showed that pcoCas9 is more efficient in mutating the targeted loci than SaCas9 and the presence of the NLS signal enhanced the chance of mutagenesis by 25%. The mutations were studied further in regenerated lines, and we determined the BnaTAA1 gene expression and heritability of the gene modifications in transgenic plants. Hairy root transformation combined with CRISPR/Cas9-mediated gene editing represents a fast and straightforward system for studying target gene function in the important oilseed crop B. napus.
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Affiliation(s)
- Veronika Jedličková
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Kateřina Mácová
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Marie Štefková
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Jan Butula
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jana Staveníková
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Marek Sedláček
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Hélène S. Robert
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
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22
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Touzdjian Pinheiro Kohlrausch Távora F, de Assis dos Santos Diniz F, de Moraes Rêgo-Machado C, Chagas Freitas N, Barbosa Monteiro Arraes F, Chumbinho de Andrade E, Furtado LL, Osiro KO, Lima de Sousa N, Cardoso TB, Márcia Mertz Henning L, Abrão de Oliveira Molinari P, Feingold SE, Hunter WB, Fátima Grossi de Sá M, Kobayashi AK, Lima Nepomuceno A, Santiago TR, Correa Molinari HB. CRISPR/Cas- and Topical RNAi-Based Technologies for Crop Management and Improvement: Reviewing the Risk Assessment and Challenges Towards a More Sustainable Agriculture. Front Bioeng Biotechnol 2022; 10:913728. [PMID: 35837551 PMCID: PMC9274005 DOI: 10.3389/fbioe.2022.913728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated gene (Cas) system and RNA interference (RNAi)-based non-transgenic approaches are powerful technologies capable of revolutionizing plant research and breeding. In recent years, the use of these modern technologies has been explored in various sectors of agriculture, introducing or improving important agronomic traits in plant crops, such as increased yield, nutritional quality, abiotic- and, mostly, biotic-stress resistance. However, the limitations of each technique, public perception, and regulatory aspects are hindering its wide adoption for the development of new crop varieties or products. In an attempt to reverse these mishaps, scientists have been researching alternatives to increase the specificity, uptake, and stability of the CRISPR and RNAi system components in the target organism, as well as to reduce the chance of toxicity in nontarget organisms to minimize environmental risk, health problems, and regulatory issues. In this review, we discuss several aspects related to risk assessment, toxicity, and advances in the use of CRISPR/Cas and topical RNAi-based technologies in crop management and breeding. The present study also highlights the advantages and possible drawbacks of each technology, provides a brief overview of how to circumvent the off-target occurrence, the strategies to increase on-target specificity, the harm/benefits of association with nanotechnology, the public perception of the available techniques, worldwide regulatory frameworks regarding topical RNAi and CRISPR technologies, and, lastly, presents successful case studies of biotechnological solutions derived from both technologies, raising potential challenges to reach the market and being social and environmentally safe.
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Affiliation(s)
| | | | | | | | | | | | | | - Karen Ofuji Osiro
- Department of Phytopathology, University of Brasília, Brasília, Brazil
- Embrapa Agroenergy, Brasília, Brazil
| | | | | | | | | | | | - Wayne B. Hunter
- USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL, United States
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23
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Uranga M, Daròs JA. Tools and targets: The dual role of plant viruses in CRISPR-Cas genome editing. THE PLANT GENOME 2022:e20220. [PMID: 35698891 DOI: 10.1002/tpg2.20220] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
The recent emergence of tools based on the clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins have revolutionized targeted genome editing, thus holding great promise to both basic plant science and precision crop breeding. Conventional approaches for the delivery of editing components rely on transformation technologies or transient delivery to protoplasts, both of which are time-consuming, laborious, and can raise legal concerns. Alternatively, plant RNA viruses can be used as transient delivery vectors of CRISPR-Cas reaction components, following the so-called virus-induced genome editing (VIGE). During the last years, researchers have been able to engineer viral vectors for the delivery of CRISPR guide RNAs and Cas nucleases. Considering that each viral vector is limited to its molecular biology properties and a specific host range, here we review recent advances for improving the VIGE toolbox with a special focus on strategies to achieve tissue-culture-free editing in plants. We also explore the utility of CRISPR-Cas technology to enhance biotic resistance with a special focus on plant virus diseases. This can be achieved by either targeting the viral genome or modifying essential host susceptibility genes that mediate in the infection process. Finally, we discuss the challenges and potential that VIGE holds in future breeding technologies.
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Affiliation(s)
- Mireia Uranga
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - University. Politècnica de València, Valencia, 46022, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - University. Politècnica de València, Valencia, 46022, Spain
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Negi C, Vasistha NK, Singh D, Vyas P, Dhaliwal HS. Application of CRISPR-Mediated Gene Editing for Crop Improvement. Mol Biotechnol 2022; 64:1198-1217. [PMID: 35672603 DOI: 10.1007/s12033-022-00507-y] [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: 12/08/2021] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
Abstract
Plant gene editing has become an important molecular tool to revolutionize modern breeding of crops. Over the past years, remarkable advancement has been made in developing robust and efficient editing methods for plants. Despite a variety of available genome editing methods, the discovery of most recent system of clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) has been one of the biggest advancement in this path, with being the most efficient approach for genome manipulation. Until recently, genetic manipulations were confined to methods, like Agrobacterium-mediated transformations, zinc-finger nucleases, and TAL effector nucleases. However this technology supersedes all other methods for genetic modification. This RNA-guided CRISPR-Cas system is being rapidly developed with enhanced functionalities for better use and greater possibilities in biological research. In this review, we discuss and sum up the application of this simple yet powerful tool of CRISPR-Cas system for crop improvement with recent advancement in this technology.
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Affiliation(s)
- Chandranandani Negi
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, India
| | - Neeraj Kumar Vasistha
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, India
| | | | - Pritesh Vyas
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, India.
| | - H S Dhaliwal
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, India
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25
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Kouhen M, García-Caparrós P, Twyman RM, Abdelly C, Mahmoudi H, Schillberg S, Debez A. Improving environmental stress resilience in crops by genome editing: insights from extremophile plants. Crit Rev Biotechnol 2022; 43:559-574. [PMID: 35606905 DOI: 10.1080/07388551.2022.2042481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In basic and applied sciences, genome editing has become an indispensable tool, especially the versatile and adaptable CRISPR/Cas9 system. Using CRISPR/Cas9 in plants has enabled modifications of many valuable traits, including environmental stress tolerance, an essential aspect when it comes to ensuring food security under climate change pressure. The CRISPR toolbox enables faster and more precise plant breeding by facilitating: multiplex gene editing, gene pyramiding, and de novo domestication. In this paper, we discuss the most recent advances in CRISPR/Cas9 and alternative CRISPR-based systems, along with the technical challenges that remain to be overcome. A revision of the latest proof-of-concept and functional characterization studies has indeed provided more insight into the quantitative traits affecting crop yield and stress tolerance. Additionally, we focus on the applications of CRISPR/Cas9 technology in regard to extremophile plants, due to their significance on: industrial, ecological and economic levels. These still unexplored genetic resources could provide the means to harden our crops against the threat of climate change, thus ensuring food security over the next century.
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Affiliation(s)
- Mohamed Kouhen
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia.,Department of Biosciences and Territory, University of Molise, Pesche, Italy
| | - Pedro García-Caparrós
- Agronomy Department of Superior School Engineering, University of Almeria, CIAIMBITAL, Almería, Spain
| | | | - Chedly Abdelly
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia
| | - Henda Mahmoudi
- International Center for Biosaline Agriculture, Academic City, Near Zayed University, Dubai, United Arab Emirates
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Ahmed Debez
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia
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Rönspies M, Schindele P, Wetzel R, Puchta H. CRISPR-Cas9-mediated chromosome engineering in Arabidopsis thaliana. Nat Protoc 2022; 17:1332-1358. [PMID: 35388178 DOI: 10.1038/s41596-022-00686-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/11/2022] [Indexed: 11/09/2022]
Abstract
The rise of the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) system has made it possible to induce double-strand breaks at almost any desired target site in the genome. In plant somatic cells, double-strand breaks are predominantly repaired by the error-prone nonhomologous end-joining pathway, which can lead to mutations at the break site upon repair. So far, it had only been possible to induce genomic changes of up to a few hundred kilobases in plants utilizing this mechanism. However, by combining the highly efficient Staphylococcus aureus Cas9 (SaCas9) with an egg-cell-specific promoter to facilitate heritable mutations, chromosomal rearrangements in the Mb range, such as inversion and translocations, were obtained in Arabidopsis thaliana recently. Here we describe the chromosome-engineering protocol used to generate these heritable chromosomal rearrangements in A. thaliana. The protocol is based on Agrobacterium-mediated transformation of A. thaliana with transfer DNA constructs containing SaCas9, which is driven by an egg-cell-specific promoter, and two guide RNAs that have been preselected based on their cutting efficiency. In the T1 generation, primary transformants are selected and, if required, analyzed by Droplet Digital PCR and propagated. In the following generations, junction-specific PCR screenings are carried out until plants that carry the rearrangement homozygously are identified. Using this protocol, overall rearrangement frequencies range between 0.03% and 0.5%, depending on the type of rearrangement. In total, it takes about 1 year to establish homozygous lines.
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Affiliation(s)
- Michelle Rönspies
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Patrick Schindele
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Rebecca Wetzel
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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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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Schindele A, Gehrke F, Schmidt C, Röhrig S, Dorn A, Puchta H. Using CRISPR-Kill for organ specific cell elimination by cleavage of tandem repeats. Nat Commun 2022; 13:1502. [PMID: 35314679 PMCID: PMC8938420 DOI: 10.1038/s41467-022-29130-w] [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: 05/19/2021] [Accepted: 02/28/2022] [Indexed: 11/12/2022] Open
Abstract
CRISPR/Cas has been mainly used for mutagenesis through the induction of double strand breaks (DSBs) within unique protein-coding genes. Using the SaCas9 nuclease to induce multiple DSBs in functional repetitive DNA of Arabidopsis thaliana, we can now show that cell death can be induced in a controlled way. This approach, named CRISPR-Kill, can be used as tool for tissue engineering. By simply exchanging the constitutive promoter of SaCas9 with cell type-specific promoters, it is possible to block organogenesis in Arabidopsis. By AP1-specific expression of CRISPR-Kill, we are able to restore the apetala1 phenotype and to specifically eliminate petals. In addition, by expressing CRISPR-Kill in root-specific pericycle cells, we are able to dramatically reduce the number and the length of lateral roots. In the future, the application of CRISPR-Kill may not only help to control development but could also be used to change the biochemical properties of plants. How double strand breaks (DSBs) are repaired within the plant 45S rDNA repeats is unclear. Here, the authors show that Cas9-mediated DSBs in 45S rDNA are mainly repaired by cNHEJ and describe CRISPR-Kill as a tool for organ-specific cell elimination by targeting functional repetitive DNA in Arabidopsis.
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Abstract
Genome engineering technologies enable targeted mutations to be induced at almost any location in plant genomes. In particular, Cas9 nucleases use easily recoded RNA guides to target user-defined sequences and generate double-stranded breaks (DSB) that are then repaired by the cell's endogenous repair mechanisms. Incorrect repair results in mutations at the target. When the targets are in coding sequences, this often results in loss-of-function mutations. In this chapter, we describe a method to rapidly design and assemble RNA-guided Cas9 constructs for plants and test their ability to induce mutations at their intended targets in rapid assays using both Agrobacterium-mediated transient expression and PEG-mediated DNA delivery to protoplasts, the latter of which can be adapted to a wide range of plant species. We describe a PCR-based method for detecting mutagenesis and outline the steps required to segregate the Cas9 transgene from the targeted mutation to enable the production of transgene-free mutated plants. These techniques are amenable to a range of plant species and should accelerate the application of Cas-9-mediated genome engineering for basic plant science as well as crop development.
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Hacker L, Capdeville N, Feller L, Enderle-Kukla J, Dorn A, Puchta H. The DNA-dependent protease AtWSS1A suppresses persistent double strand break formation during replication. THE NEW PHYTOLOGIST 2022; 233:1172-1187. [PMID: 34761387 DOI: 10.1111/nph.17848] [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: 09/16/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
The protease WSS1A is an important factor in the repair of DNA-protein crosslinks in plants. Here we show that the loss of WSS1A leads to a reduction of 45S rDNA repeats and chromosomal fragmentation in Arabidopsis. Moreover, in the absence of any factor of the RTR (RECQ4A/TOP3α/RMI1/2) complex, which is involved in the dissolution of DNA replication intermediates, WSS1A becomes essential for viability. If WSS1A loss is combined with loss of the classical (c) or alternative (a) nonhomologous end joining (NHEJ) pathways of double-strand break (DSB) repair, the resulting mutants show proliferation defects and enhanced chromosome fragmentation, which is especially aggravated in the absence of aNHEJ. This indicates that WSS1A is involved either in the suppression of DSB formation or in DSB repair itself. To test the latter we induced DSB by CRISPR/Cas9 at different loci in wild-type and mutant cells and analyzed their repair by deep sequencing. However, no change in the quality of the repair events and only a slight increase in their quantity was found. Thus, by removing complex DNA-protein structures, WSS1A seems to be required for the repair of replication intermediates which would otherwise be resolved into persistent DSB leading to genome instability.
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Affiliation(s)
- Leonie Hacker
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Niklas Capdeville
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Laura Feller
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Janina Enderle-Kukla
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
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31
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Xu R, Qin R, Xie H, Li J, Liu X, Zhu M, Sun Y, Yu Y, Lu P, Wei P. Genome editing with type II-C CRISPR-Cas9 systems from Neisseria meningitidis in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:350-359. [PMID: 34582079 PMCID: PMC8753361 DOI: 10.1111/pbi.13716] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 05/05/2023]
Abstract
Two type II-C Cas9 orthologs (Nm1Cas9 and Nm2Cas9) were recently identified from Neisseria meningitidis and have been extensively used in mammalian cells, but whether these NmCas9 orthologs or other type II-C Cas9 proteins can mediate genome editing in plants remains unclear. In this study, we developed and optimized targeted mutagenesis systems from NmCas9s for plants. Efficient genome editing at the target with N4 GATT and N4 CC protospacer adjacent motifs (PAMs) was achieved with Nm1Cas9 and Nm2Cas9 respectively. These results indicated that a highly active editing system could be developed from type II-C Cas9s with distinct PAM preferences, thus providing a reliable strategy to extend the scope of genome editing in plants. Base editors (BEs) were further developed from the NmCas9s. The editing efficiency of adenine BEs (ABEs) of TadA*-7.10 and cytosine BEs (CBEs) of rat APOBEC1 (rAPO1) or human APOBEC3a (hA3A) were extremely limited, whereas ABEs of TadA-8e and CBEs of Petromyzon marinus cytidine deaminase 1 (PmCDA1) exhibited markedly improved performance on the same targets. In addition, we found that fusion of a single-stranded DNA-binding domain from the human Rad51 protein enhanced the base editing capability of rAPO1-CBEs of NmCas9s. Together, our results suggest that the engineering of NmCas9s or other type II-C Cas9s can provide useful alternatives for crop genome editing.
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Affiliation(s)
- Rongfang Xu
- College of AgronomyAnhui Agricultural UniversityHefeiChina
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Ruiying Qin
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Hongjun Xie
- Key Laboratory of Indica Rice Genetics and Breeding in the middle and Lower Reaches of Yangtze River ValleyMinistry of AgricultureHunan Rice Research InstituteChangshaChina
| | - Juan Li
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Xiaoshuang Liu
- College of AgronomyAnhui Agricultural UniversityHefeiChina
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Mingdong Zhu
- Key Laboratory of Indica Rice Genetics and Breeding in the middle and Lower Reaches of Yangtze River ValleyMinistry of AgricultureHunan Rice Research InstituteChangshaChina
| | - Yang Sun
- State Key Laboratory of Crop Stress Adaptation and ImprovementKey Laboratory of Plant Stress BiologySchool of Life SciencesHenan UniversityKaifengChina
| | - Yinghong Yu
- Key Laboratory of Indica Rice Genetics and Breeding in the middle and Lower Reaches of Yangtze River ValleyMinistry of AgricultureHunan Rice Research InstituteChangshaChina
| | - Pingli Lu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major DiseasesCollege of Life SciencesAnhui Normal UniversityWuhuChina
| | - Pengcheng Wei
- College of AgronomyAnhui Agricultural UniversityHefeiChina
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
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Hacker L, Dorn A, Enderle J, Puchta H. The repair of topoisomerase 2 cleavage complexes in Arabidopsis. THE PLANT CELL 2022; 34:287-301. [PMID: 34524446 PMCID: PMC8773952 DOI: 10.1093/plcell/koab228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/08/2021] [Indexed: 05/04/2023]
Abstract
DNA-protein crosslinks (DPCs) and DNA double-stranded breaks (DSBs), including those produced by stalled topoisomerase 2 cleavage complexes (TOP2ccs), must be repaired to ensure genome stability. The basic mechanisms of TOP2cc repair have been characterized in other eukaryotes, but we lack information for plants. Using CRISPR/Cas-induced mutants, we show that Arabidopsis thaliana has two main TOP2cc repair pathways: one is defined by TYROSYL-DNA-PHOSPHODIESTERASE 2 (TDP2), which hydrolyzes TOP2-DNA linkages, the other by the DNA-dependent protease WSS1A (a homolog of human SPARTAN/yeast weak suppressor of smt3 [Wss1]), which also functions in DPC repair. TDP1 and TDP2 function nonredundantly in TOP1cc repair, indicating that they act specifically on their respective stalled cleavage complexes. The nuclease METHYL METHANESULFONATE AND UV-SENSITIVE PROTEIN 81 (MUS81) plays a major role in global DPC repair and a minor role in TOP2cc repair. DSBs arise as intermediates of TOP2cc repair and are repaired by classical and alternative nonhomologous end joining (NHEJ) pathways. Double-mutant analysis indicates that "clean" DNA ends caused by TDP2 hydrolysis are mainly religated by classical NHEJ, which helps avoid mutation. In contrast, the mutagenic alternative NHEJ pathway mainly processes nonligateable DNA ends. Thus, TDP2 promotes maintenance of plant genome integrity by error-free repair of TOP2cc.
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Affiliation(s)
- Leonie Hacker
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Janina Enderle
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
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33
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Takasugi PR, Wang S, Truong KT, Drage EP, Kanishka SN, Higbee MA, Bamidele N, Ojelabi O, Sontheimer EJ, Gagnon JA. Orthogonal CRISPR-Cas tools for genome editing, inhibition, and CRISPR recording in zebrafish embryos. Genetics 2022; 220:iyab196. [PMID: 34735006 PMCID: PMC8733422 DOI: 10.1093/genetics/iyab196] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 10/26/2021] [Indexed: 11/15/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas universe continues to expand. The type II CRISPR-Cas system from Streptococcus pyogenes (SpyCas9) is the most widely used for genome editing due to its high efficiency in cells and organisms. However, concentrating on a single CRISPR-Cas system imposes limits on target selection and multiplexed genome engineering. We hypothesized that CRISPR-Cas systems originating from different bacterial species could operate simultaneously and independently due to their distinct single-guide RNAs (sgRNAs) or CRISPR-RNAs (crRNAs), and protospacer adjacent motifs (PAMs). Additionally, we hypothesized that CRISPR-Cas activity in zebrafish could be regulated through the expression of inhibitory anti-CRISPR (Acr) proteins. Here, we use a simple mutagenesis approach to demonstrate that CRISPR-Cas systems from S. pyogenes (SpyCas9), Streptococcus aureus (SauCas9), Lachnospiraceae bacterium (LbaCas12a, previously known as LbCpf1) are orthogonal systems capable of operating simultaneously in zebrafish. CRISPR systems from Acidaminococcus sp. (AspCas12a, previously known as AsCpf1) and Neisseria meningitidis (Nme2Cas9) were also active in embryos. We implemented multichannel CRISPR recording using three CRISPR systems and show that LbaCas12a may provide superior information density compared with previous methods. We also demonstrate that type II Acrs (anti-CRISPRs) are effective inhibitors of SpyCas9 in zebrafish. Our results indicate that at least five CRISPR-Cas systems and two anti-CRISPR proteins are functional in zebrafish embryos. These orthogonal CRISPR-Cas systems and Acr proteins will enable combinatorial and intersectional strategies for spatiotemporal control of genome editing and genetic recording in animals.
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Affiliation(s)
- Paige R Takasugi
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Shengzhou Wang
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Kimberly T Truong
- Department of Mathematics, University of Utah, Salt Lake City, UT 84112, USA
| | - Evan P Drage
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Sahar N Kanishka
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Marissa A Higbee
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Nathan Bamidele
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ogooluwa Ojelabi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James A Gagnon
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Henry Eyring Center for Cell & Genome Science, University of Utah, Salt Lake City, UT 84112, USA
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34
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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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35
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Wolter F, Schindele P, Beying N, Scheben A, Puchta H. Different DNA repair pathways are involved in single-strand break-induced genomic changes in plants. THE PLANT CELL 2021; 33:3454-3469. [PMID: 34375428 PMCID: PMC8566284 DOI: 10.1093/plcell/koab204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/04/2021] [Indexed: 05/03/2023]
Abstract
In nature, single-strand breaks (SSBs) in DNA occur more frequently (by orders of magnitude) than double-strand breaks (DSBs). SSBs induced by the CRISPR/Cas9 nickase at a distance of 50-100 bp on opposite strands are highly mutagenic, leading to insertions/deletions (InDels), with insertions mainly occurring as direct tandem duplications. As short tandem repeats are overrepresented in plant genomes, this mechanism seems to be important for genome evolution. We investigated the distance at which paired 5'-overhanging SSBs are mutagenic and which DNA repair pathways are essential for insertion formation in Arabidopsis thaliana. We were able to detect InDel formation up to a distance of 250 bp, although with much reduced efficiency. Surprisingly, the loss of the classical nonhomologous end joining (NHEJ) pathway factors KU70 or DNA ligase 4 completely abolished tandem repeat formation. The microhomology-mediated NHEJ factor POLQ was required only for patch-like insertions, which are well-known from DSB repair as templated insertions from ectopic sites. As SSBs can also be repaired using homology, we furthermore asked whether the classical homologous recombination (HR) pathway is involved in this process in plants. The fact that RAD54 is not required for homology-mediated SSB repair demonstrates that the mechanisms for DSB- and SSB-induced HR differ in plants.
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Affiliation(s)
- Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Patrick Schindele
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Natalja Beying
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Author for correspondence:
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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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Ursache R, Fujita S, Dénervaud Tendon V, Geldner N. Combined fluorescent seed selection and multiplex CRISPR/Cas9 assembly for fast generation of multiple Arabidopsis mutants. PLANT METHODS 2021; 17:111. [PMID: 34717688 PMCID: PMC8556964 DOI: 10.1186/s13007-021-00811-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/16/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND Multiplex CRISPR-Cas9-based genome editing is an efficient method for targeted disruption of gene function in plants. Use of CRISPR-Cas9 has increased rapidly in recent years and is becoming a routine method for generating single and higher order Arabidopsis thaliana mutants. Low entry, reliable assembly of CRISPR/Cas9 vectors and efficient mutagenesis is necessary to enable a maximum of researchers to break through the genetic redundancy within plant multi-gene families and allow for a plethora of gene function studies that have been previously unachievable. It will also allow routine de novo generation of mutations in ever more complex genetic backgrounds that make introgression of pre-existing alleles highly cumbersome. RESULTS To facilitate rapid and efficient use of CRISPR/Cas9 for Arabidopsis research, we developed a CRISPR/Cas9-based toolbox for generating mutations at multiple genomic loci, using two-color fluorescent seed selection. In our system, up-to eight gRNAs can be routinely introduced into a binary vector carrying either a FastRed, FastGreen or FastCyan fluorescent seed selection cassette. FastRed and FastGreen binary vectors can be co-transformed as a cocktail via floral dip to introduce sixteen gRNAs at the same time. The seeds can be screened either for red or green fluorescence, or for the presence of both colors. Importantly, in the second generation after transformation, Cas9 free plants are identified simply by screening the non-fluorescent seeds. Our collection of binary vectors allows to choose between two widely-used promoters to drive Cas enzymes, either the egg cell-specific (pEC1.2) from A. thaliana or the constitutive promoter from Petroselinum crispum (PcUBi4-2). Available enzymes are "classical" Cas9 codon-optimized for A. thaliana and a recently reported, intron-containing version of Cas9 codon-optimized for Zea mays, zCas9i. We observed the highest efficiency in producing knockout phenotypes by using intron-containing zCas9i driven under egg-cell specific pEC1.2 promoter. Finally, we introduced convenient restriction sites flanking promoter, Cas9 and fluorescent selection cassette in some of the T-DNA vectors, thus allowing straightforward swapping of all three elements for further adaptation and improvement of the system. CONCLUSION A rapid, simple and flexible CISPR/Cas9 cloning system was established that allows assembly of multi-guide RNA constructs in a robust and reproducible fashion, by avoiding generation of very big constructs. The system enables a flexible, fast and efficient screening of single or higher order A. thaliana mutants.
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Affiliation(s)
- Robertas Ursache
- Department of Plant Molecular Biology, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Satoshi Fujita
- Department of Plant Molecular Biology, University of Lausanne, 1015, Lausanne, Switzerland
- UMR5546 CNRS, Toulouse-INP, University of Toulouse, 24 Chemin de Borde Rouge, Auzeville Tolosane, 31320, France
| | | | - Niko Geldner
- Department of Plant Molecular Biology, University of Lausanne, 1015, Lausanne, Switzerland.
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Negishi K, Mikami M, Toki S, Endo M. Enhanced FnCas12a-Mediated Targeted Mutagenesis Using crRNA With Altered Target Length in Rice. Front Genome Ed 2021; 2:608563. [PMID: 34713233 PMCID: PMC8525410 DOI: 10.3389/fgeed.2020.608563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/18/2020] [Indexed: 11/25/2022] Open
Abstract
The CRISPR/Cas12a (Cpf1) system utilizes a thymidine-rich protospacer adjacent motif (PAM) and generates DNA ends with a 5′ overhang. These properties differ from those of CRISPR/Cas9, making Cas12a an attractive alternative in the CRISPR toolbox. However, genome editing efficiencies of Cas12a orthologs are generally lower than those of SpCas9 and depend on their target sequences. Here, we report that the efficiency of FnCas12a-mediated targeted mutagenesis varies depending on the length of the crRNA guide sequence. Generally, the crRNA of FnCas12a contains a 24-nt guide sequence; however, some target sites showed higher mutation frequency when using crRNA with an 18-nt or 30-nt guide sequence. We also show that a short crRNA containing an 18-nt guide sequence could induce large deletions compared with middle- (24-nt guide sequence) and long- (30-nt guide sequence) crRNAs. We demonstrate that alteration of crRNA guide sequence length does not change the rate of off-target mutation of FnCas12a. Our results indicate that efficiency and deletion size of FnCas12a-mediated targeted mutagenesis in rice can be fine-tuned using crRNAs with appropriate guide sequences.
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Affiliation(s)
- Katsuya Negishi
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Masafumi Mikami
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan.,Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - Seiichi Toki
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan.,Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Masaki Endo
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan.,Probabilistic Modeling Team, Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Japan
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Karlson CKS, Mohd-Noor SN, Nolte N, Tan BC. CRISPR/dCas9-Based Systems: Mechanisms and Applications in Plant Sciences. PLANTS 2021; 10:plants10102055. [PMID: 34685863 PMCID: PMC8540305 DOI: 10.3390/plants10102055] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022]
Abstract
RNA-guided genomic transcriptional regulation tools, namely clustered regularly interspaced short palindromic repeats interference (CRISPRi) and CRISPR-mediated gene activation (CRISPRa), are a powerful technology for gene functional studies. Deriving from the CRISPR/Cas9 system, both systems consist of a catalytically dead Cas9 (dCas9), a transcriptional effector and a single guide RNA (sgRNA). This type of dCas9 is incapable to cleave DNA but retains its ability to specifically bind to DNA. The binding of the dCas9/sgRNA complex to a target gene results in transcriptional interference. The CRISPR/dCas9 system has been explored as a tool for transcriptional modulation and genome imaging. Despite its potential applications and benefits, the challenges and limitations faced by the CRISPR/dCas9 system include the off-target effects, protospacer adjacent motif (PAM) sequence requirements, efficient delivery methods and the CRISPR/dCas9-interfered crops being labeled as genetically modified organisms in several countries. This review highlights the progression of CRISPR/dCas9 technology as well as its applications and potential challenges in crop improvement.
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Affiliation(s)
- Chou Khai Soong Karlson
- Center for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Siti Nurfadhlina Mohd-Noor
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia;
| | - Nadja Nolte
- Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands;
| | - Boon Chin Tan
- Center for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia;
- Correspondence: ; Tel.: +60-3-7967-7982
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Venezia M, Creasey Krainer KM. Current Advancements and Limitations of Gene Editing in Orphan Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:742932. [PMID: 34630494 PMCID: PMC8493294 DOI: 10.3389/fpls.2021.742932] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/20/2021] [Indexed: 05/23/2023]
Abstract
Gene editing provides precise, heritable genome mutagenesis without permanent transgenesis, and has been widely demonstrated and applied in planta. In the past decade, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) has revolutionized the application of gene editing in crops, with mechanistic advances expanding its potential, including prime editing and base editing. To date, CRISPR/Cas has been utilized in over a dozen orphan crops with diverse genetic backgrounds, leading to novel alleles and beneficial phenotypes for breeders, growers, and consumers. In conjunction with the adoption of science-based regulatory practices, there is potential for CRISPR/Cas-mediated gene editing in orphan crop improvement programs to solve a plethora of agricultural problems, especially impacting developing countries. Genome sequencing has progressed, becoming more affordable and applicable to orphan crops. Open-access resources allow for target gene identification and guide RNA (gRNA) design and evaluation, with modular cloning systems and enzyme screening methods providing experimental feasibility. While the genomic and mechanistic limitations are being overcome, crop transformation and regeneration continue to be the bottleneck for gene editing applications. International collaboration between all stakeholders involved in crop improvement is vital to provide equitable access and bridge the scientific gap between the world's most economically important crops and the most under-researched crops. This review describes the mechanisms and workflow of CRISPR/Cas in planta and addresses the challenges, current applications, and future prospects in orphan crops.
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Cable J, Ronald PC, Voytas D, Zhang F, Levy AA, Takatsuka A, Arimura SI, Jacobsen SE, Toki S, Toda E, Gao C, Zhu JK, Boch J, Van Eck J, Mahfouz M, Andersson M, Fridman E, Weiss T, Wang K, Qi Y, Jores T, Adams T, Bagchi R. Plant genome engineering from lab to field-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:35-54. [PMID: 34435370 DOI: 10.1111/nyas.14675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 12/30/2022]
Abstract
Facing the challenges of the world's food sources posed by a growing global population and a warming climate will require improvements in plant breeding and technology. Enhancing crop resiliency and yield via genome engineering will undoubtedly be a key part of the solution. The advent of new tools, such as CRIPSR/Cas, has ushered in significant advances in plant genome engineering. However, several serious challenges remain in achieving this goal. Among them are efficient transformation and plant regeneration for most crop species, low frequency of some editing applications, and high attrition rates. On March 8 and 9, 2021, experts in plant genome engineering and breeding from academia and industry met virtually for the Keystone eSymposium "Plant Genome Engineering: From Lab to Field" to discuss advances in genome editing tools, plant transformation, plant breeding, and crop trait development, all vital for transferring the benefits of novel technologies to the field.
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Affiliation(s)
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, and the Joint BioEnergy Institute, Davis, California
| | - Daniel Voytas
- Department of Genetics, Cell Biology and Development; Center for Precision Plant Genomics; and Center for Genome Engineering, University of Minnesota, St. Paul, Minnesota
| | - Feng Zhang
- College of Biological Sciences, University of Minnesota, St. Paul, Minnesota
| | - Avraham A Levy
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ayumu Takatsuka
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shin-Ichi Arimura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Steven E Jacobsen
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; Department of Molecular, Cell and Developmental Biology; and Howard Hughes Medical Institute, University of California, Los Angeles, California
| | - Seiichi Toki
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Erika Toda
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - 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, and College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Joyce Van Eck
- The Boyce Thompson Institute, Ithaca, New York, and Plant Breeding and Genetics Section, Cornell University, Ithaca, New York
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Eyal Fridman
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
| | - Trevor Weiss
- Department of Genetics, Cell Biology and Development; Center for Precision Plant Genomics; and Center for Genome Engineering, University of Minnesota, St. Paul, Minnesota
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, Iowa
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, and Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
| | - Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | | | - Rammyani Bagchi
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, North Carolina
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Dorone Y, Boeynaems S, Flores E, Jin B, Hateley S, Bossi F, Lazarus E, Pennington JG, Michiels E, De Decker M, Vints K, Baatsen P, Bassel GW, Otegui MS, Holehouse AS, Exposito-Alonso M, Sukenik S, Gitler AD, Rhee SY. A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation. Cell 2021; 184:4284-4298.e27. [PMID: 34233164 PMCID: PMC8513799 DOI: 10.1016/j.cell.2021.06.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 03/22/2021] [Accepted: 06/04/2021] [Indexed: 12/22/2022]
Abstract
Many organisms evolved strategies to survive desiccation. Plant seeds protect dehydrated embryos from various stressors and can lay dormant for millennia. Hydration is the key trigger to initiate germination, but the mechanism by which seeds sense water remains unresolved. We identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the embryo to sense water stress. We demonstrate that biophysical states of FLOE1 condensates modulate its biological function in vivo in suppressing seed germination under unfavorable environments. We find intragenic, intraspecific, and interspecific natural variation in FLOE1 expression and phase separation and show that intragenic variation is associated with adaptive germination strategies in natural populations. This combination of molecular, organismal, and ecological studies uncovers FLOE1 as a tunable environmental sensor with direct implications for the design of drought-resistant crops, in the face of climate change.
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Affiliation(s)
- Yanniv Dorone
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eduardo Flores
- Department of Chemistry and Chemical Biology, UC Merced, Merced, CA 95340, USA
| | - Benjamin Jin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Shannon Hateley
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Flavia Bossi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Elena Lazarus
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Janice G Pennington
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA
| | - Emiel Michiels
- EM-platform@VIB Bio Imaging Core and VIB Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Mathias De Decker
- EM-platform@VIB Bio Imaging Core and VIB Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium; KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), 3000 Leuven, Belgium
| | - Katlijn Vints
- EM-platform@VIB Bio Imaging Core and VIB Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium
| | - Pieter Baatsen
- EM-platform@VIB Bio Imaging Core and VIB Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium
| | - George W Bassel
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Marisa S Otegui
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA; Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Shahar Sukenik
- Department of Chemistry and Chemical Biology, UC Merced, Merced, CA 95340, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
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Huang TK, Puchta H. Novel CRISPR/Cas applications in plants: from prime editing to chromosome engineering. Transgenic Res 2021; 30:529-549. [PMID: 33646511 PMCID: PMC8316200 DOI: 10.1007/s11248-021-00238-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/13/2021] [Indexed: 12/26/2022]
Abstract
In the last years, tremendous progress has been made in the development of CRISPR/Cas-mediated genome editing tools. A number of natural CRISPR/Cas nuclease variants have been characterized. Engineered Cas proteins have been developed to minimize PAM restrictions, off-side effects and temperature sensitivity. Both kinds of enzymes have, by now, been applied widely and efficiently in many plant species to generate either single or multiple mutations at the desired loci by multiplexing. In addition to DSB-induced mutagenesis, specifically designed CRISPR/Cas systems allow more precise gene editing, resulting not only in random mutations but also in predefined changes. Applications in plants include gene targeting by homologous recombination, base editing and, more recently, prime editing. We will evaluate these different technologies for their prospects and practical applicability in plants. In addition, we will discuss a novel application of the Cas9 nuclease in plants, enabling the induction of heritable chromosomal rearrangements, such as inversions and translocations. This technique will make it possible to change genetic linkages in a programmed way and add another level of genome engineering to the toolbox of plant breeding. Also, strategies for tissue culture free genome editing were developed, which might be helpful to overcome the transformation bottlenecks in many crops. All in all, the recent advances of CRISPR/Cas technology will help agriculture to address the challenges of the twenty-first century related to global warming, pollution and the resulting food shortage.
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Affiliation(s)
- Teng-Kuei Huang
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany.
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Razzaq A, Kaur P, Akhter N, Wani SH, Saleem F. Next-Generation Breeding Strategies for Climate-Ready Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:620420. [PMID: 34367194 PMCID: PMC8336580 DOI: 10.3389/fpls.2021.620420] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/14/2021] [Indexed: 05/17/2023]
Abstract
Climate change is a threat to global food security due to the reduction of crop productivity around the globe. Food security is a matter of concern for stakeholders and policymakers as the global population is predicted to bypass 10 billion in the coming years. Crop improvement via modern breeding techniques along with efficient agronomic practices innovations in microbiome applications, and exploiting the natural variations in underutilized crops is an excellent way forward to fulfill future food requirements. In this review, we describe the next-generation breeding tools that can be used to increase crop production by developing climate-resilient superior genotypes to cope with the future challenges of global food security. Recent innovations in genomic-assisted breeding (GAB) strategies allow the construction of highly annotated crop pan-genomes to give a snapshot of the full landscape of genetic diversity (GD) and recapture the lost gene repertoire of a species. Pan-genomes provide new platforms to exploit these unique genes or genetic variation for optimizing breeding programs. The advent of next-generation clustered regularly interspaced short palindromic repeat/CRISPR-associated (CRISPR/Cas) systems, such as prime editing, base editing, and de nova domestication, has institutionalized the idea that genome editing is revamped for crop improvement. Also, the availability of versatile Cas orthologs, including Cas9, Cas12, Cas13, and Cas14, improved the editing efficiency. Now, the CRISPR/Cas systems have numerous applications in crop research and successfully edit the major crop to develop resistance against abiotic and biotic stress. By adopting high-throughput phenotyping approaches and big data analytics tools like artificial intelligence (AI) and machine learning (ML), agriculture is heading toward automation or digitalization. The integration of speed breeding with genomic and phenomic tools can allow rapid gene identifications and ultimately accelerate crop improvement programs. In addition, the integration of next-generation multidisciplinary breeding platforms can open exciting avenues to develop climate-ready crops toward global food security.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Naheed Akhter
- College of Allied Health Professional, Faculty of Medical Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
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Abstract
Fruit and vegetable crops are rich in dietary fibre, vitamins and minerals, which are vital to human health. However, many biotic stressors (such as pests and diseases) and abiotic stressors threaten crop growth, quality, and yield. Traditional breeding strategies for improving crop traits include a series of backcrosses and selection to introduce beneficial traits into fine germplasm, this process is slow and resource-intensive. The new breeding technique known as clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 (Cas9) has the potential to improve many traits rapidly and accurately, such as yield, quality, disease resistance, abiotic stress tolerance, and nutritional aspects in crops. Because of its simple operation and high mutation efficiency, this system has been applied to obtain new germplasm resources via gene-directed mutation. With the availability of whole-genome sequencing data, and information about gene function for important traits, CRISPR-Cas9 editing to precisely mutate key genes can rapidly generate new germplasm resources for the improvement of important agronomic traits. In this review, we explore this technology and its application in fruit and vegetable crops. We address the challenges, existing variants and the associated regulatory framework, and consider future applications.
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46
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Huang T, Armstrong B, Schindele P, Puchta H. Efficient gene targeting in Nicotiana tabacum using CRISPR/SaCas9 and temperature tolerant LbCas12a. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1314-1324. [PMID: 33511745 PMCID: PMC8313123 DOI: 10.1111/pbi.13546] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 05/12/2023]
Abstract
Nicotiana tabacum is a non-food herb that has the potential to be utilized as bio-factory for generating medicines, vaccines or valuable small metabolites. To achieve these goals, the improvement of genetic tools for pre-designed genome modifications is indispensable. The development of CRISPR/Cas nucleases allows the induction of site-specific double-strand breaks to enhance homologous recombination-mediated gene targeting (GT). However, the efficiency of GT is still a challenging obstacle for many crops including tobacco. Recently, studies in several plant species indicated that by replacing SpCas9 with other CRISPR/Cas-based nucleases, GT efficiencies might be enhanced considerably. Therefore, we tested SaCas9 as well as a temperature-insensitive version of LbCas12a (ttLbCas12a) for targeting the tobacco SuRB gene. At the same time, we also optimized the protocol for Agrobacterium-mediated tobacco transformation and tissue culture. In this way, we could improve GT efficiencies to up to a third of the inoculated cotyledons when using ttLbCas12a, which outperformed SaCas9 considerably. In addition, we could show that the conversion tract length of the GT reaction can be up to 606 bp long and in the majority of cases, it is longer than 250 bp. We obtained multiple heritable GT events, mostly heterozygous, but also biallelic GT events and some without T-DNA integration. Thus, we were not only able to obtain CRISPR/Cas-based heritable GT events in allotetraploid Nicotiana tabacum for the first time, but our results also indicate that ttLbCas12a might be a superior alternative for gene editing and GT in tobacco as well as in other crops.
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Affiliation(s)
- Teng‐Kuei Huang
- Botanical Institute IIKarlsruhe Institute of TechnologyKarlsruheGermany
| | | | - Patrick Schindele
- Botanical Institute IIKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Holger Puchta
- Botanical Institute IIKarlsruhe Institute of TechnologyKarlsruheGermany
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Sukegawa S, Saika H, Toki S. Plant genome editing: ever more precise and wide reaching. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1208-1218. [PMID: 33730414 DOI: 10.1111/tpj.15233] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Genome-editing technologies consisting of targeted mutagenesis and gene targeting enable us to modify genes of interest rapidly and precisely. The discovery in 2012 of CRISPR/Cas9 systems and their development as sequence-specific nucleases has brought about a paradigm shift in biology. Initially, CRISPR/Cas9 was applied in targeted mutagenesis to knock out a target gene. Thereafter, advances in genome-editing technologies using CRISPR/Cas9 developed rapidly, with base editing systems for transition substitution using a combination of Cas9 nickase and either cytidine or adenosine deaminase being reported in 2016 and 2017, respectively, and later in 2021 bringing reports of transversion substitution using Cas9 nickase, cytidine deaminase and uracil DNA glycosylase. Moreover, technologies for gene targeting and prime editing systems using DNA or RNA as donors have also been developed in recent years. Besides these precise genome-editing strategies, reports of successful chromosome engineering using CRISPR/Cas9 have been published recently. The application of genome editing to crop breeding has advanced in parallel with the development of these technologies. Genome-editing enzymes can be introduced into plant cells, and there are now many examples of crop breeding using genome-editing technologies. At present, it is no exaggeration to say that we are now in a position to be able to modify a gene precisely and rearrange genomes and chromosomes in a predicted way. In this review, we introduce and discuss recent highlights in the field of precise gene editing, chromosome engineering and genome engineering technology in plants.
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Affiliation(s)
- Satoru Sukegawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Hiroaki Saika
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
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Nitarska D, Boehm R, Debener T, Lucaciu RC, Halbwirth H. First genome edited poinsettias: targeted mutagenesis of flavonoid 3'-hydroxylase using CRISPR/Cas9 results in a colour shift. PLANT CELL, TISSUE AND ORGAN CULTURE 2021; 147:49-60. [PMID: 34776565 PMCID: PMC8550517 DOI: 10.1007/s11240-021-02103-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/07/2021] [Indexed: 06/01/2023]
Abstract
UNLABELLED The CRISPR/Cas9 system is a remarkably promising tool for targeted gene mutagenesis, and becoming ever more popular for modification of ornamental plants. In this study we performed the knockout of flavonoid 3'-hydroxylase (F3'H) with application of CRISPR/Cas9 in the red flowering poinsettia (Euphorbia pulcherrima) cultivar 'Christmas Eve', in order to obtain plants with orange bract colour, which accumulate prevalently pelargonidin. F3'H is an enzyme that is necessary for formation of cyanidin type anthocyanins, which are responsible for the red colour of poinsettia bracts. Even though F3'H was not completely inactivated, the bract colour of transgenic plants changed from vivid red (RHS 45B) to vivid reddish orange (RHS 33A), and cyanidin levels decreased significantly compared with the wild type. In the genetically modified plants, an increased ratio of pelargonidin to cyanidin was observed. By cloning and expression of mutated proteins, the lack of F3'H activity was confirmed. This confirms that a loss of function mutation in the poinsettia F3'H gene is sufficient for obtaining poinsettia with orange bract colour. This is the first report of successful use of CRISPR/Cas9 for genome editing in poinsettia. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11240-021-02103-5.
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Affiliation(s)
- Daria Nitarska
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060 Vienna, Austria
| | | | - Thomas Debener
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Rares Calin Lucaciu
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060 Vienna, Austria
| | - Heidi Halbwirth
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060 Vienna, Austria
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Mushtaq M, Ahmad Dar A, Skalicky M, Tyagi A, Bhagat N, Basu U, Bhat BA, Zaid A, Ali S, Dar TUH, Rai GK, Wani SH, Habib-Ur-Rahman M, Hejnak V, Vachova P, Brestic M, Çığ A, Çığ F, Erman M, EL Sabagh A. CRISPR-Based Genome Editing Tools: Insights into Technological Breakthroughs and Future Challenges. Genes (Basel) 2021; 12:797. [PMID: 34073848 PMCID: PMC8225059 DOI: 10.3390/genes12060797] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
Genome-editing (GE) is having a tremendous influence around the globe in the life science community. Among its versatile uses, the desired modifications of genes, and more importantly the transgene (DNA)-free approach to develop genetically modified organism (GMO), are of special interest. The recent and rapid developments in genome-editing technology have given rise to hopes to achieve global food security in a sustainable manner. We here discuss recent developments in CRISPR-based genome-editing tools for crop improvement concerning adaptation, opportunities, and challenges. Some of the notable advances highlighted here include the development of transgene (DNA)-free genome plants, the availability of compatible nucleases, and the development of safe and effective CRISPR delivery vehicles for plant genome editing, multi-gene targeting and complex genome editing, base editing and prime editing to achieve more complex genetic engineering. Additionally, new avenues that facilitate fine-tuning plant gene regulation have also been addressed. In spite of the tremendous potential of CRISPR and other gene editing tools, major challenges remain. Some of the challenges are related to the practical advances required for the efficient delivery of CRISPR reagents and for precision genome editing, while others come from government policies and public acceptance. This review will therefore be helpful to gain insights into technological advances, its applications, and future challenges for crop improvement.
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Affiliation(s)
- Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Aejaz Ahmad Dar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Anshika Tyagi
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Nancy Bhagat
- School of Biotechnology, University of Jammu, Jammu 180006, India;
| | - Umer Basu
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India;
| | | | - Abbu Zaid
- Plant Physiology and Biochemistry Section, Department of Botany Aligarh Muslim University, Aigarh 202002, India;
| | - Sajad Ali
- Centre of Research for Development, University of Kashmir, Srinagar 190006, India;
| | | | - Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu 192101, India
| | - Muhammad Habib-Ur-Rahman
- Department of Crop Science, Institute of Crop Science and Resource Conservation (INRES), University Bonn, 53115 Bonn, Germany;
| | - Vaclav Hejnak
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Pavla Vachova
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia
| | - Arzu Çığ
- Department of Horticulture, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey;
| | - Fatih Çığ
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
| | - Murat Erman
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
| | - Ayman EL Sabagh
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
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Rönspies M, Dorn A, Schindele P, Puchta H. CRISPR-Cas-mediated chromosome engineering for crop improvement and synthetic biology. NATURE PLANTS 2021; 7:566-573. [PMID: 33958776 DOI: 10.1038/s41477-021-00910-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/31/2021] [Indexed: 05/20/2023]
Abstract
Plant breeding relies on the presence of genetic variation, as well as on the ability to break or stabilize genetic linkages between traits. The development of the genome-editing tool clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) has allowed breeders to induce genetic variability in a controlled and site-specific manner, and to improve traits with high efficiency. However, the presence of genetic linkages is a major obstacle to the transfer of desirable traits from wild species to their cultivated relatives. One way to address this issue is to create mutants with deficiencies in the meiotic recombination machinery, thereby enhancing global crossover frequencies between homologous parental chromosomes. Although this seemed to be a promising approach at first, thus far, no crossover frequencies could be enhanced in recombination-cold regions of the genome. Additionally, this approach can lead to unintended genomic instabilities due to DNA repair defects. Therefore, efforts have been undertaken to obtain predefined crossovers between homologues by inducing site-specific double-strand breaks (DSBs) in meiotic, as well as in somatic plant cells using CRISPR-Cas tools. However, this strategy has not been able to produce a substantial number of heritable homologous recombination-based crossovers. Most recently, heritable chromosomal rearrangements, such as inversions and translocations, have been obtained in a controlled way using CRISPR-Cas in plants. This approach unlocks a completely new way of manipulating genetic linkages, one in which the DSBs are induced in somatic cells, enabling the formation of chromosomal rearrangements in the megabase range, by DSB repair via non-homologous end-joining. This technology might also enable the restructuring of genomes more globally, resulting in not only the obtainment of synthetic plant chromosome, but also of novel plant species.
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Affiliation(s)
- Michelle Rönspies
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Annika Dorn
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Patrick Schindele
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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