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Li P, Zheng T, Domingues DS, Liu Y, Ahmad S. Editorial: Low-temperature stress in plants: molecular responses, tolerance mechanisms, plant biodesign and breeding applications. Front Plant Sci 2024; 15:1411636. [PMID: 38774222 PMCID: PMC11107426 DOI: 10.3389/fpls.2024.1411636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 04/30/2024] [Indexed: 05/24/2024]
Affiliation(s)
- Ping Li
- College of Forestry and College of Landscape and Tourism, Agricultural University of Hebei, Baoding, China
| | - Tangchun Zheng
- School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Douglas S. Domingues
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
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2
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El Nahas R, Al-Aghbar MA, Herrero L, van Panhuys N, Espino-Guarch M. Applications of Genome-Editing Technologies for Type 1 Diabetes. Int J Mol Sci 2023; 25:344. [PMID: 38203514 PMCID: PMC10778854 DOI: 10.3390/ijms25010344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
Type 1 diabetes (T1D) is a chronic autoimmune disease characterized by the destruction of insulin-producing pancreatic β-cells by the immune system. Although conventional therapeutic modalities, such as insulin injection, remain a mainstay, recent years have witnessed the emergence of novel treatment approaches encompassing immunomodulatory therapies, such as stem cell and β-cell transplantation, along with revolutionary gene-editing techniques. Notably, recent research endeavors have enabled the reshaping of the T-cell repertoire, leading to the prevention of T1D development. Furthermore, CRISPR-Cas9 technology has demonstrated remarkable potential in targeting endogenous gene activation, ushering in a promising avenue for the precise guidance of mesenchymal stem cells (MSCs) toward differentiation into insulin-producing cells. This innovative approach holds substantial promise for the treatment of T1D. In this review, we focus on studies that have developed T1D models and treatments using gene-editing systems.
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Affiliation(s)
- Rana El Nahas
- Laboratory of Immunoregulation, Translational Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar; (R.E.N.); (M.A.A.-A.)
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institute of Biomedicine of the University of Barcelona (IBUB), 08028 Barcelona, Spain;
| | - Mohammad Ameen Al-Aghbar
- Laboratory of Immunoregulation, Translational Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar; (R.E.N.); (M.A.A.-A.)
| | - Laura Herrero
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institute of Biomedicine of the University of Barcelona (IBUB), 08028 Barcelona, Spain;
| | - Nicholas van Panhuys
- Laboratory of Immunoregulation, Translational Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar; (R.E.N.); (M.A.A.-A.)
| | - Meritxell Espino-Guarch
- Laboratory of Immunoregulation, Translational Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar; (R.E.N.); (M.A.A.-A.)
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3
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Watanabe Y, Katsumura E, Domon T, Ishikawa Y, Oguri R, Takashima M, Meng Q, Kinoshita M, Hashimoto H, Hitomi K. Establishment of transgenic epithelium-specific Cre-recombinase driving medaka (Oryzias latipes) by homology repair mediated knock-in. Biosci Biotechnol Biochem 2023; 87:1285-1294. [PMID: 37607777 DOI: 10.1093/bbb/zbad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/17/2023] [Indexed: 08/24/2023]
Abstract
Deletion of gene expression in the target tissues and cells is an effective strategy for elucidating the physiological functions of the protein of interest. For tissue-specific and/or inducible gene deletion, the Cre-loxP system has been widely used in various model organisms including medaka (Oryzias latipes). The epithelium is the key tissue, locating at the outermost area and playing a role in barrier to external stimuli. Despite a large genetic toolbox developed in medaka, there is no available Cre-driver line that works in an epithelium-specific manner. Here, we established epithelium-specific Cre-driver lines in medaka using a homology-directed repair mediated knock-in approach with CRISPR/Cas9, targeting each of periplakin and keratin genes. We show that Cre-recombinase is expressed exclusively in the epithelium in the knock-in lines and that it efficiently and specifically induces recombination in the tissues. These Cre-driver lines are useful for studying the functions of proteins expressed in the epithelium.
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Affiliation(s)
- Yuko Watanabe
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Eri Katsumura
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Tatsuki Domon
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Yuta Ishikawa
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Rina Oguri
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Minami Takashima
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Qi Meng
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | | | | | - Kiyotaka Hitomi
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
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4
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Chen BC, Chen YZ, Lin HY. An Introduced RNA-Only Approach for Plasmid Curing via the CRISPR-Cpf1 System in Saccharomyces cerevisiae. Biomolecules 2023; 13:1561. [PMID: 37892243 PMCID: PMC10604987 DOI: 10.3390/biom13101561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
The CRISPR-Cas system has been widely used for genome editing due to its convenience, simplicity and flexibility. Using a plasmid-carrying Cas protein and crRNA or sgRNA expression cassettes is an efficient strategy in the CRISPR-Cas genome editing system. However, the plasmid remains in the cells after genome editing. Development of general plasmid-curing strategies is necessary. Based on our previous CRISPR-Cpf1 genome-editing system in Saccharomyces cerevisiae, the crRNA, designed for the replication origin of the CRISPR-Cpf1 plasmid, and the ssDNA, as a template for homologous recombination, were introduced for plasmid curing. The efficiency of the plasmid curing was 96 ± 4%. In addition, we further simplified the plasmid curing system by transforming only one crRNA into S. cerevisiae, and the curing efficiency was about 70%. In summary, we have developed a CRISPR-mediated plasmid-curing system. The RNA-only plasmid curing system is fast and easy. This plasmid curing strategy can be applied in broad hosts by designing crRNA specific for the replication origin of the plasmid. The plasmid curing system via CRISPR-Cas editing technology can be applied to produce traceless products without foreign genes and to perform iterative processes in multiple rounds of genome editing.
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Affiliation(s)
- Bo-Chou Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan;
| | - Yu-Zhen Chen
- Department of Food Science and Technology, Hungkuang University, Taichung 433, Taiwan;
| | - Huan-Yu Lin
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan;
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5
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Kumar KRR. Lost in the bloom: DNA-PKcs in green plants. Front Plant Sci 2023; 14:1231678. [PMID: 37575944 PMCID: PMC10419180 DOI: 10.3389/fpls.2023.1231678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023]
Abstract
The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a protein encoded by the PRKDC gene in humans and plays a crucial role in repairing DNA double-strand breaks (DSBs). Recent studies have revealed that DNA-PKcs has additional functions in the cell beyond DSB repair, including transcriptional regulation, telomere protection and capping, preserving chromosomal integrity, and regulating senescence, apoptosis, and autophagy. Moreover, DNA-PKcs has also been implicated in regulating the innate immune response, and dysregulation of DNA-PKcs has been commonly observed in various types of cancers. Until recently it was believed that DNA-PKcs is not present in plants in general. However, DNA-PKcs is conserved in green plants ranging from microscopic green algae such as Ostreococcus of the chlorophytes to the tallest living trees on earth, Sequoia of the gymnosperms. Interestingly, DNA-PKcs has not been detected in angiosperms, or in basal angiosperms which are considered sister groups to all other flowering plants. The long polypeptide and gene length of DNA-PKcs coupled with errors in genome assembly, annotation, and gene prediction, have contributed to the challenges in detecting and extracting DNA-PKcs sequences in plant lineages. Sequence alignment showed that several amino acids throughout the length of DNA-PKcs are conserved between plants and human, and all the typical domains identified in human DNA-PKcs are also found in DNA-PKcs from green plants suggesting possible structural and functional conservation. Given the highly conserved nature of DNA repair pathways between mammals and plants further highlights the potential significance of DNA-PKcs in plant biology.
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Eckerstorfer MF, Dolezel M, Engelhard M, Giovannelli V, Grabowski M, Heissenberger A, Lener M, Reichenbecher W, Simon S, Staiano G, Wüst Saucy AG, Zünd J, Lüthi C. Recommendations for the Assessment of Potential Environmental Effects of Genome-Editing Applications in Plants in the EU. Plants (Basel) 2023; 12:plants12091764. [PMID: 37176822 PMCID: PMC10180588 DOI: 10.3390/plants12091764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/11/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
The current initiative of the European Commission (EC) concerning plants produced using certain new genomic techniques, in particular, targeted mutagenesis and cisgenesis, underlines that a high level of protection for human and animal health and the environment needs to be maintained when using such applications. The current EU biosafety regulation framework ensures a high level of protection with a mandatory environmental risk assessment (ERA) of genetically modified (GM) products prior to the authorization of individual GMOs for environmental release or marketing. However, the guidance available from the European Food Safety Authority (EFSA) for conducting such an ERA is not specific enough regarding the techniques under discussion and needs to be further developed to support the policy goals towards ERA, i.e., a case-by-case assessment approach proportionate to the respective risks, currently put forward by the EC. This review identifies important elements for the case-by-case approach for the ERA that need to be taken into account in the framework for a risk-oriented regulatory approach. We also discuss that the comparison of genome-edited plants with plants developed using conventional breeding methods should be conducted at the level of a scientific case-by-case assessment of individual applications rather than at a general, technology-based level. Our considerations aim to support the development of further specific guidance for the ERA of genome-edited plants.
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Affiliation(s)
- Michael F Eckerstorfer
- Umweltbundesamt-Environment Agency Austria (EAA), Landuse and Biosafety Unit, Spittelauer Lände 5, 1090 Vienna, Austria
| | - Marion Dolezel
- Umweltbundesamt-Environment Agency Austria (EAA), Landuse and Biosafety Unit, Spittelauer Lände 5, 1090 Vienna, Austria
| | - Margret Engelhard
- Federal Agency for Nature Conservation, Division of Assessment of GMOs/Enforcement of Genetic Engineering Act, Konstantinstr. 110, 53179 Bonn, Germany
| | - Valeria Giovannelli
- ISPRA (Italian Institute for Environmental Protection and Research), Department for Environmental Monitoring and Protection and for Biodiversity Conservation, Via Vitaliano Brancati, 48, 00144 Rome, Italy
| | - Marcin Grabowski
- Ministry of Climate and Environment, Department Nature Conservation, GMO Unit, Wawelska 52/54, 00-922 Warsaw, Poland
| | - Andreas Heissenberger
- Umweltbundesamt-Environment Agency Austria (EAA), Landuse and Biosafety Unit, Spittelauer Lände 5, 1090 Vienna, Austria
| | - Matteo Lener
- ISPRA (Italian Institute for Environmental Protection and Research), Department for Environmental Monitoring and Protection and for Biodiversity Conservation, Via Vitaliano Brancati, 48, 00144 Rome, Italy
| | - Wolfram Reichenbecher
- Federal Agency for Nature Conservation, Division of Assessment of GMOs/Enforcement of Genetic Engineering Act, Konstantinstr. 110, 53179 Bonn, Germany
| | - Samson Simon
- Federal Agency for Nature Conservation, Division of Assessment of GMOs/Enforcement of Genetic Engineering Act, Konstantinstr. 110, 53179 Bonn, Germany
| | - Giovanni Staiano
- ISPRA (Italian Institute for Environmental Protection and Research), Department for Environmental Monitoring and Protection and for Biodiversity Conservation, Via Vitaliano Brancati, 48, 00144 Rome, Italy
| | - Anne Gabrielle Wüst Saucy
- Federal Office for the Environment (FOEN), Biotechnology Section, Soil and Biotechnology Division, 3003 Bern, Switzerland
| | - Jan Zünd
- Federal Office for the Environment (FOEN), Biotechnology Section, Soil and Biotechnology Division, 3003 Bern, Switzerland
| | - Christoph Lüthi
- Federal Office for the Environment (FOEN), Biotechnology Section, Soil and Biotechnology Division, 3003 Bern, Switzerland
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Kong Q, Li J, Wang S, Feng X, Shou H. Combination of Hairy Root and Whole-Plant Transformation Protocols to Achieve Efficient CRISPR/Cas9 Genome Editing in Soybean. Plants (Basel) 2023; 12:1017. [PMID: 36903878 PMCID: PMC10005656 DOI: 10.3390/plants12051017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
The new gene-editing technology CRISPR/Cas system has been widely used for genome engineering in various organisms. Since the CRISPR/Cas gene-editing system has a certain possibility of low efficiency and the whole plant transformation of soybean is time-consuming and laborious, it is important to evaluate the editing efficiency of designed CRISPR constructs before the stable whole plant transformation process starts. Here, we provide a modified protocol for generating transgenic hairy soybean roots to assess the efficiency of guide RNA (gRNA) sequences of the CRISPR/Cas constructs within 14 days. The cost- and space-effective protocol was first tested in transgenic soybean harboring the GUS reporter gene for the efficiency of different gRNA sequences. Targeted DNA mutations were detected in 71.43-97.62% of the transgenic hairy roots analyzed as evident by GUS staining and DNA sequencing of the target region. Among the four designed gene-editing sites, the highest editing efficiency occurred at the 3' terminal of the GUS gene. In addition to the reporter gene, the protocol was tested for the gene-editing of 26 soybean genes. Among the gRNAs selected for stable transformation, the editing efficiency of hairy root transformation and stable transformation ranged from 5% to 88.8% and 2.7% to 80%, respectively. The editing efficiencies of stable transformation were positively correlated with those of hairy root transformation with a Pearson correlation coefficient (r) of 0.83. Our results demonstrated that soybean hairy root transformation could rapidly assess the efficiency of designed gRNA sequences on genome editing. This method can not only be directly applied to the functional study of root-specific genes, but more importantly, it can be applied to the pre-screening of gRNA in CRISPR/Cas gene editing.
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Affiliation(s)
- Qihui Kong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Lab, Hangzhou 310012, China
| | - Jie Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shoudong Wang
- Zhejiang Lab, Hangzhou 310012, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xianzhong Feng
- Zhejiang Lab, Hangzhou 310012, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Lab, Hangzhou 310012, China
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Tachikawa M, Matsuo M. Divergence and convergence in international regulatory policies regarding genome-edited food: How to find a middle ground. Front Plant Sci 2023; 14:1105426. [PMID: 36794228 PMCID: PMC9923018 DOI: 10.3389/fpls.2023.1105426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Regulations for organisms and products to which genome-editing technologies are applied are increasing in diversity, with the path-dependent effect of previous regulations for genetically modified organisms. Regulations for genome-editing technologies are a patchwork of international regulations that are difficult to harmonize. However, if the approaches are arranged in chronological order and the overall trend is examined, the regulation of genome-edited organisms and GM food products has recently been trending toward a middle ground which can be characterized as "limited convergence." There is a trend toward the adoption of two approaches: one that considers GMOs but tries to apply simplified regulations and another that excludes them from the scope of regulations as non-GMOs but requires confirmation. In this paper, we discuss why there is a tendency toward convergence of these two approaches and examine the challenges and implications of these two approaches for the governance of the agricultural and food sectors.
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Affiliation(s)
- Masashi Tachikawa
- Graduate School of Environmental Studies, Nagoya University, Nagoya, Japan
| | - Makiko Matsuo
- Graduate School of Public Policy, The University of Tokyo, Tokyo, Japan
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Miranda S, Piazza S, Nuzzo F, Li M, Lagrèze J, Mithöfer A, Cestaro A, Tarkowska D, Espley R, Dare A, Malnoy M, Martens S. CRISPR/Cas9 genome-editing applied to MdPGT1 in apple results in reduced foliar phloridzin without impacting plant growth. Plant J 2023; 113:92-105. [PMID: 36401738 DOI: 10.1111/tpj.16036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 11/05/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Phloridzin is the most abundant polyphenolic compound in apple (Malus × domestica Borkh.), which results from the action of a key phloretin-specific UDP-2'-O-glucosyltransferase (MdPGT1). Here, we simultaneously assessed the effects of targeting MdPGT1 by conventional transgenesis and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated genome editing. To this end, we conducted transcriptomic and metabolic analyses of MdPGT1 RNA interference knockdown and genome-edited lines. Knockdown lines exhibited characteristic impairment of plant growth and leaf morphology, whereas genome-edited lines exhibited normal growth despite reduced foliar phloridzin. RNA-sequencing analysis identified a common core of regulated genes, involved in phenylpropanoid and flavonoid pathways. However, we identified genes and processes differentially modulated in stunted and genome-edited lines, including key transcription factors and genes involved in phytohormone signalling. Therefore, we conducted a phytohormone profiling to obtain insight into their role in the phenotypes observed. We found that salicylic and jasmonic acid were increased in dwarf lines, whereas auxin and ABA showed no correlation with the growth phenotype. Furthermore, bioactive brassinosteroids were commonly up-regulated, whereas gibberellin GA4 was distinctively altered, showing a sharp decrease in RNA interference knockdown lines. Expression analysis by reverse transcriptase-quantitative polymerase chain reaction expression analysis further confirmed transcriptional regulation of key factors involved in brassinosteroid and gibberellin interaction. These findings suggest that a differential modulation of phytohormones may be involved in the contrasting effects on growth following phloridzin reduction. The present study also illustrates how CRISPR/Cas9 genome editing can be applied to dissect the contribution of genes involved in phloridzin biosynthesis in apple.
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Affiliation(s)
- Simón Miranda
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
- C3A Center Agriculture Food Environment, University of Trento, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
- The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland, 1025, New Zealand
| | - Stefano Piazza
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
| | - Floriana Nuzzo
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
| | - Mingai Li
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
| | - Jorge Lagrèze
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
- C3A Center Agriculture Food Environment, University of Trento, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
| | - Axel Mithöfer
- Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena, 07745, Germany
| | - Alessandro Cestaro
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
| | - Danuše Tarkowska
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences and Palacky University, Slechtitelu 19, Olomouc, CZ-783 71, Czech Republic
| | - Richard Espley
- The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland, 1025, New Zealand
| | - Andrew Dare
- The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland, 1025, New Zealand
| | - Mickael Malnoy
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
| | - Stefan Martens
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
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Narushima J, Kimata S, Shiwa Y, Gondo T, Akimoto S, Soga K, Yoshiba S, Nakamura K, Shibata N, Kondo K. Unbiased prediction of off-target sites in genome-edited rice using SITE-Seq analysis on a web-based platform. Genes Cells 2022; 27:706-718. [PMID: 36181413 DOI: 10.1111/gtc.12985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 12/13/2022]
Abstract
Genome-editing using the CRISPR-Cas9 system has the potential to substantially accelerate crop breeding. Since off-target editing is one of problems, a reliable method for comprehensively detecting off-target sites is needed. A number of in silico methods based on homology to on-target sequence have been developed, however the prediction without false negative is still under discussion. In this study, we performed a SITE-Seq analysis to predict potential off-target sites. SITE-Seq analysis is a comprehensive method that can detect double-strand breaks in vitro. Furthermore, we developed a systematic method using SITE-Seq in combination with web-based Galaxy system (Galaxy for Cut Site Detection), which can perform reproducible analyses without command line operations. We conducted a SITE-Seq analysis of a rice genome targeted by OsFH15 gRNA-Cas9 as a model, and found 41 candidate off-target sites in the annotated regions. Detailed amplicon-sequencing revealed mutations at one off-target site in actual genome-edited rice. Since this off-target site has an uncommon protospacer adjacent motif, it is difficult to predict using in silico methods alone. Therefore, we propose a novel off-target assessment scheme for genome-edited crops that combines the prediction of off-target candidates by SITE-Seq and in silico programs and the validation of off-target sites by amplicon-sequencing.
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Affiliation(s)
- Jumpei Narushima
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Shinya Kimata
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Tokyo, Japan
| | - Takahiro Gondo
- Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Satoshi Akimoto
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Keisuke Soga
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Satoko Yoshiba
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Kosuke Nakamura
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Norihito Shibata
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Kazunari Kondo
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
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Meng Q, Watanabe Y, Tatsukawa H, Hashimoto H, Hitomi K. Biochemical characterization of medaka (Oryzias latipes) fibrinogen gamma and its gene disruption resulting in anemia as a model fish. J Biochem 2022; 172:293-302. [PMID: 35997167 DOI: 10.1093/jb/mvac065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
At the final stages of blood coagulation, fibrinogen is processed into insoluble fibrin by thrombin resulting in fibril-like structure formation. Via further cross-linking reactions between the fibrin gamma subunit by the catalytic action of blood transglutaminase (Factor XIII), this molecule gains further physical stability. Meanwhile, since fibrinogen is expressed in various cells and tissues, this molecule can exhibit other functions apart from its role in blood coagulation. To create a system studying on aberrant coagulation and investigate the physiological functions, using a model fish medaka (Oryzias latipes), we established gene-deficient mutants of fibrinogen gamma subunit protein in parallel with its biochemical analysis, such as tissue distribution pattern and substrate properties. By genetic deletion via genome-editing, two distinct mutants displayed retardation of blood coagulation. The mutants showed lower hematocrit with aberrant erythrocyte maturation indicating that fibrin deficiency caused severe anemia, and also appeared as a model for investigation of the fibrin function.
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Affiliation(s)
- Qi Meng
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yuko Watanabe
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hideki Tatsukawa
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hisashi Hashimoto
- Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Kiyotaka Hitomi
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
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12
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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). Front Plant Sci 2022; 13:919290. [PMID: 35991410 PMCID: PMC9386449 DOI: 10.3389/fpls.2022.919290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Mahto RK, Ambika, Singh C, Chandana BS, Singh RK, Verma S, Gahlaut V, Manohar M, Yadav N, Kumar R. Chickpea Biofortification for Cytokinin Dehydrogenase via Genome Editing to Enhance Abiotic-Biotic Stress Tolerance and Food Security. Front Genet 2022; 13:900324. [PMID: 35669196 PMCID: PMC9164125 DOI: 10.3389/fgene.2022.900324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Globally more than two billion people suffer from micronutrient malnutrition (also known as "hidden hunger"). Further, the pregnant women and children in developing nations are mainly affected by micronutrient deficiencies. One of the most important factors is food insecurity which can be mitigated by improving the nutritional values through biofortification using selective breeding and genetic enhancement techniques. Chickpea is the second most important legume with numerous economic and nutraceutical properties. Therefore, chickpea production needs to be increased from the current level. However, various kind of biotic and abiotic stresses hamper global chickpea production. The emerging popular targets for biofortification in agronomic crops include targeting cytokinin dehydrogenase (CKX). The CKXs play essential roles in both physiological and developmental processes and directly impact several agronomic parameters i.e., growth, development, and yield. Manipulation of CKX genes using genome editing tools in several crop plants reveal that CKXs are involved in regulation yield, shoot and root growth, and minerals nutrition. Therefore, CKXs have become popular targets for yield improvement, their overexpression and mutants can be directly correlated with the increased yield and tolerance to various stresses. Here, we provide detailed information on the different roles of CKX genes in chickpea. In the end, we discuss the utilization of genome editing tool clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) to engineer CKX genes that can facilitate trait improvement. Overall, recent advancements in CKX and their role in plant growth, stresses and nutrient accumulation are highlighted, which could be used for chickpea improvement.
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Affiliation(s)
| | - Ambika
- Department of Genetics and Plant Breeding, UAS, Bangalore, India
| | - Charul Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - B S. Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | - Shruti Verma
- NCoE-SAM, Department of Pediatrics, KSCH, Lady Hardinge Medical College, New Delhi, India
| | - Vijay Gahlaut
- Institute of Himalayan Bioresource Technology (CSIR), Palampur, India
| | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Neelam Yadav
- Centre of Food Technology, University of Allahabad, Prayagraj, India
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
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14
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Bekhite MM, Schulze PC. Human Induced Pluripotent Stem Cell as a Disease Modeling and Drug Development Platform-A Cardiac Perspective. Cells 2021; 10:3483. [PMID: 34943991 DOI: 10.3390/cells10123483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 02/07/2023] Open
Abstract
A comprehensive understanding of the pathophysiology and cellular responses to drugs in human heart disease is limited by species differences between humans and experimental animals. In addition, isolation of human cardiomyocytes (CMs) is complicated because cells obtained by biopsy do not proliferate to provide sufficient numbers of cells for preclinical studies in vitro. Interestingly, the discovery of human-induced pluripotent stem cell (hiPSC) has opened up the possibility of generating and studying heart disease in a culture dish. The combination of reprogramming and genome editing technologies to generate a broad spectrum of human heart diseases in vitro offers a great opportunity to elucidate gene function and mechanisms. However, to exploit the potential applications of hiPSC-derived-CMs for drug testing and studying adult-onset cardiac disease, a full functional characterization of maturation and metabolic traits is required. In this review, we focus on methods to reprogram somatic cells into hiPSC and the solutions for overcome immaturity of the hiPSC-derived-CMs to mimic the structure and physiological properties of the adult human CMs to accurately model disease and test drug safety. Finally, we discuss how to improve the culture, differentiation, and purification of CMs to obtain sufficient numbers of desired types of hiPSC-derived-CMs for disease modeling and drug development platform.
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15
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Ishii M, Ishii T. Proving that a genome-edited organism is not GMO. Trends Biotechnol 2021:S0167-7799(21)00260-2. [PMID: 34893376 DOI: 10.1016/j.tibtech.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 11/23/2022]
Abstract
A genome-edited agricultural product that is proven to contain no exogenous DNA is not subject to genetically modified organism (GMO) regulations in some countries. However, whether such proof is definitive is often disputed. We discuss the approaches to substantially proving that a genome-edited organism is not GMO, while considering social aspects.
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16
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Shojaei Baghini S, Gardanova ZR, Zekiy AO, Shomali N, Tosan F, Jarahian M. Optimizing sgRNA to Improve CRISPR/Cas9 Knockout Efficiency: Special Focus on Human and Animal Cell. Front Bioeng Biotechnol 2021; 9:775309. [PMID: 34869290 PMCID: PMC8640246 DOI: 10.3389/fbioe.2021.775309] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022] Open
Abstract
During recent years, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) technologies have been noticed as a rapidly evolving tool to deliver a possibility for modifying target sequence expression and function. The CRISPR/Cas9 tool is currently being used to treat a myriad of human disorders, ranging from genetic diseases and infections to cancers. Preliminary reports have shown that CRISPR technology could result in valued consequences for the treatment of Duchenne muscular dystrophy (DMD), cystic fibrosis (CF), β-thalassemia, Huntington's diseases (HD), etc. Nonetheless, high rates of off-target effects may hinder its application in clinics. Thereby, recent studies have focused on the finding of the novel strategies to ameliorate these off-target effects and thereby lead to a high rate of fidelity and accuracy in human, animals, prokaryotes, and also plants. Meanwhile, there is clear evidence indicating that the design of the specific sgRNA with high efficiency is of paramount importance. Correspondingly, elucidation of the principal parameters that contributed to determining the sgRNA efficiencies is a prerequisite. Herein, we will deliver an overview regarding the therapeutic application of CRISPR technology to treat human disorders. More importantly, we will discuss the potent influential parameters (e.g., sgRNA structure and feature) implicated in affecting the sgRNA efficacy in CRISPR/Cas9 technology, with special concentration on human and animal studies.
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Affiliation(s)
- Sadegh Shojaei Baghini
- Plant Biotechnology Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Zhanna R. Gardanova
- Department of Psychotherapy, Pirogov Russian National Research Medical University, Moscow, Russia
- Medical Faculty, Russian State Social University, Moscow, Russia
| | - Angelina Olegovna Zekiy
- Department of Prosthetic Dentistry, I. M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Navid Shomali
- Immunology Research Center (IRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Foad Tosan
- Student Research Committee, Semnan University of Medical Sciences, Semnan, Iran
| | - Mostafa Jarahian
- German Cancer Research Center, Toxicology and Chemotherapy Unit (G401), Heidelberg, Germany
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17
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Banjanin B, Schneider RK. Mesenchymal Stromal Cells as a Cellular Target in Myeloid Malignancy: Chances and Challenges in the Genome Editing of Stromal Alterations. Front Genome Ed 2021; 2:618308. [PMID: 34713241 PMCID: PMC8525402 DOI: 10.3389/fgeed.2020.618308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
The contribution of bone marrow stromal cells to the pathogenesis and therapy response of myeloid malignancies has gained significant attention over the last decade. Evidence suggests that the bone marrow stroma should not be neglected in the design of novel, targeted-therapies. In terms of gene-editing, the focus of gene therapies has mainly been on correcting mutations in hematopoietic cells. Here, we outline why alterations in the stroma should also be taken into consideration in the design of novel therapeutic strategies but also outline the challenges in specifically targeting mesenchymal stromal cells in myeloid malignancies caused by somatic and germline mutations.
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Affiliation(s)
- Bella Banjanin
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, Netherlands.,Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, Netherlands
| | - Rebekka K Schneider
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, Netherlands.,Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, Netherlands.,Department of Cell Biology, Faculty of Medicine, Institute for Biomedical Engineering, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
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18
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Miyata H, Oyama Y, Kaneda Y, Ikawa M. The motor domain of testis-enriched kinesin KIF9 is essential for its localization in the mouse flagellum. Exp Anim 2021; 71:46-52. [PMID: 34526446 PMCID: PMC8828407 DOI: 10.1538/expanim.21-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Kinesin is a molecular motor that moves along microtubules. Testis-enriched kinesin KIF9 (Kinesin family member 9) is localized in the mouse sperm flagellum and is important for normal sperm motility and male fertility; however, it is unclear if the motor domain of KIF9 is involved in these processes. In this study, we substituted threonine of the ATP binding motif in the KIF9 motor domain to asparagine (T100N) in mice using the CRISPR/Cas9 system, which is known to impair kinesin motor activity. T100N mutant mice exhibit reduced sperm motility and male fertility consistent with Kif9 knockout mice. Further, KIF9 was depleted in the spermatozoa of T100N mutant mice although the amounts of KIF9 were comparable between wild-type and T100N mutant testes. These results indicate that the motor domain of KIF9 is essential for its localization in the sperm flagellum.
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Affiliation(s)
| | - Yuki Oyama
- Research Institute for Microbial Diseases, Osaka University.,Graduate School of Pharmaceutical Sciences, Osaka University
| | - Yuki Kaneda
- Research Institute for Microbial Diseases, Osaka University.,Graduate School of Pharmaceutical Sciences, Osaka University
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University.,Graduate School of Pharmaceutical Sciences, Osaka University.,The Institute of Medical Science, The University of Tokyo
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19
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Dong W, Kantor B. Lentiviral Vectors for Delivery of Gene-Editing Systems Based on CRISPR/Cas: Current State and Perspectives. Viruses 2021; 13:1288. [PMID: 34372494 DOI: 10.3390/v13071288] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/17/2022] Open
Abstract
CRISPR/Cas technology has revolutionized the fields of the genome- and epigenome-editing by supplying unparalleled control over genomic sequences and expression. Lentiviral vector (LV) systems are one of the main delivery vehicles for the CRISPR/Cas systems due to (i) its ability to carry bulky and complex transgenes and (ii) sustain robust and long-term expression in a broad range of dividing and non-dividing cells in vitro and in vivo. It is thus reasonable that substantial effort has been allocated towards the development of the improved and optimized LV systems for effective and accurate gene-to-cell transfer of CRISPR/Cas tools. The main effort on that end has been put towards the improvement and optimization of the vector’s expression, development of integrase-deficient lentiviral vector (IDLV), aiming to minimize the risk of oncogenicity, toxicity, and pathogenicity, and enhancing manufacturing protocols for clinical applications required large-scale production. In this review, we will devote attention to (i) the basic biology of lentiviruses, and (ii) recent advances in the development of safer and more efficient CRISPR/Cas vector systems towards their use in preclinical and clinical applications. In addition, we will discuss in detail the recent progress in the repurposing of CRISPR/Cas systems related to base-editing and prime-editing applications.
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20
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Abstract
Geminiviruses are plant DNA viruses that infect a wide range of plant species and cause significant losses to economically important food and fiber crops. The single-stranded geminiviral genome encodes a small number of proteins which act in an orchestrated manner to infect the host. The fewer proteins encoded by the virus are multifunctional, a mechanism uniquely evolved by the viruses to balance the genome-constraint. The host-mediated resistance against incoming virus includes post-transcriptional gene silencing, transcriptional gene silencing, and expression of defense responsive genes and other cellular regulatory genes. The pathogenicity property of a geminiviral protein is linked to its ability to suppress the host-mediated defense mechanism. This review discusses what is currently known about the targets and mechanism of the viral suppressor AC2/AL2/transcriptional activator protein (TrAP) and explore the biotechnological applications of AC2.
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Affiliation(s)
- Karuppannan Veluthambi
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Sukumaran Sunitha
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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21
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Syombua ED, Zhang Z, Tripathi JN, Ntui VO, Kang M, George OO, Edward NK, Wang K, Yang B, Tripathi L. A CRISPR/Cas9-based genome-editing system for yam (Dioscorea spp.). Plant Biotechnol J 2021; 19:645-647. [PMID: 33222361 PMCID: PMC8051594 DOI: 10.1111/pbi.13515] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/27/2020] [Accepted: 11/06/2020] [Indexed: 05/21/2023]
Affiliation(s)
- Easter D. Syombua
- International Institute of Tropical Agriculture (IITA)NairobiKenya
- Centre for Biotechnology and BioinformaticsUniversity of NairobiNairobiKenya
| | - Zhengzhi Zhang
- Division of Plant SciencesBond Life Sciences CenterUniversity of MissouriColumbiaMOUSA
| | | | | | - Minjeong Kang
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Obiero O. George
- Centre for Biotechnology and BioinformaticsUniversity of NairobiNairobiKenya
| | - Nguu K. Edward
- Department of BiochemistryUniversity of NairobiNairobiKenya
| | - Kan Wang
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Bing Yang
- Division of Plant SciencesBond Life Sciences CenterUniversity of MissouriColumbiaMOUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA)NairobiKenya
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22
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Mbanjo EGN, Rabbi IY, Ferguson ME, Kayondo SI, Eng NH, Tripathi L, Kulakow P, Egesi C. Technological Innovations for Improving Cassava Production in Sub-Saharan Africa. Front Genet 2021; 11:623736. [PMID: 33552138 PMCID: PMC7859516 DOI: 10.3389/fgene.2020.623736] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022] Open
Abstract
Cassava is crucial for food security of millions of people in sub-Saharan Africa. The crop has great potential to contribute to African development and is increasing its income-earning potential for small-scale farmers and related value chains on the continent. Therefore, it is critical to increase cassava production, as well as its quality attributes. Technological innovations offer great potential to drive this envisioned change. This paper highlights genomic tools and resources available in cassava. The paper also provides a glimpse of how these resources have been used to screen and understand the pattern of cassava genetic diversity on the continent. Here, we reviewed the approaches currently used for phenotyping cassava traits, highlighting the methodologies used to link genotypic and phenotypic information, dissect the genetics architecture of key cassava traits, and identify quantitative trait loci/markers significantly associated with those traits. Additionally, we examined how knowledge acquired is utilized to contribute to crop improvement. We explored major approaches applied in the field of molecular breeding for cassava, their promises, and limitations. We also examined the role of national agricultural research systems as key partners for sustainable cassava production.
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Affiliation(s)
| | | | | | | | - Ng Hwa Eng
- CGIAR Excellence in Breeding Platform, El Batan, Mexico
| | - Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Chiedozie Egesi
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- National Root Crops Research Institute, Umudike, Nigeria
- Department of Global Development, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
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23
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Zheng X, Kuijer HNJ, Al-Babili S. Carotenoid Biofortification of Crops in the CRISPR Era. Trends Biotechnol 2020; 39:857-860. [PMID: 33384170 DOI: 10.1016/j.tibtech.2020.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 01/15/2023]
Abstract
Carotenoids are micronutrients important for human health. The continuous improvements in clustered regularly interspaced short palindromic repeats (CRISPR)-based genome-editing techniques make rapid, DNA/transgene-free and targeted multiplex genetic modification a reality, thus promising to accelerate the breeding and generation of 'golden' staple crops. We discuss here the progress and future prospects of CRISPR/Cas9 applications for carotenoid biofortification.
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Affiliation(s)
- Xiongjie Zheng
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Science and Engineering, Center for Desert Agriculture, the BioActives Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Hendrik N J Kuijer
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Science and Engineering, Center for Desert Agriculture, the BioActives Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Salim Al-Babili
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Science and Engineering, Center for Desert Agriculture, the BioActives Laboratory, Thuwal 23955-6900, Saudi Arabia.
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24
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Kotowski M, Sharma S. CRISPR-Based Editing Techniques for Genetic Manipulation of Primary T Cells. Methods Protoc 2020; 3:mps3040079. [PMID: 33217926 PMCID: PMC7720142 DOI: 10.3390/mps3040079] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/15/2022] Open
Abstract
While clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing techniques have been widely adapted for use in immortalised immune cells, efficient manipulation of primary T cells has proved to be more challenging. Nonetheless, the rapid expansion of the CRISPR toolbox accompanied by the development of techniques for delivery of CRISPR components into primary T cells now affords the possibility to genetically manipulate primary T cells both with precision and at scale. Here, we review the key features of the techniques for primary T cell editing and discuss how the new generation of CRISPR-based tools may advance genetic engineering of these immune cells. This improved ability to genetically manipulate primary T cells will further enhance our fundamental understanding of cellular signalling and transcriptional networks in T cells and more importantly has the potential to revolutionise T cell-based therapies.
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25
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Prabhukarthikeyan SR, Parameswaran C, Keerthana U, Teli B, Jag PTK, Cayalvizhi B, Panneerselvam P, Senapati A, Nagendran K, Kumari S, Yadav MK, Aravindan S, Sanghamitra S. Understanding the Plant-microbe Interactions in CRISPR/CAS9 Era: Indeed a Sprinting Start in Marathon. Curr Genomics 2020; 21:429-443. [PMID: 33093805 PMCID: PMC7536795 DOI: 10.2174/1389202921999200716110853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/21/2020] [Accepted: 06/03/2020] [Indexed: 12/15/2022] Open
Abstract
Plant-microbe interactions can be either beneficial or harmful depending on the nature of the interaction. Multifaceted benefits of plant-associated microbes in crops are well documented. Specifically, the management of plant diseases using beneficial microbes is considered to be eco-friendly and the best alternative for sustainable agriculture. Diseases caused by various phytopathogens are responsible for a significant reduction in crop yield and cause substantial economic losses globally. In an ecosystem, there is always an equally daunting challenge for the establishment of disease and development of resistance by pathogens and plants, respectively. In particular, comprehending the complete view of the complex biological systems of plant-pathogen interactions, co-evolution and plant growth promotions (PGP) at both genetic and molecular levels requires novel approaches to decipher the function of genes involved in their interaction. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein 9) is a fast, emerging, precise, eco-friendly and efficient tool to address the challenges in agriculture and decipher plant-microbe interaction in crops. Nowadays, the CRISPR/CAS9 approach is receiving major attention in the field of functional genomics and crop improvement. Consequently, the present review updates the prevailing knowledge in the deployment of CRISPR/CAS9 techniques to understand plant-microbe interactions, genes edited for the development of fungal, bacterial and viral disease resistance, to elucidate the nodulation processes, plant growth promotion, and future implications in agriculture. Further, CRISPR/CAS9 would be a new tool for the management of plant diseases and increasing productivity for climate resilience farming.
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Affiliation(s)
| | | | - Umapathy Keerthana
- Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), Cuttack, 753006 Odisha, India
| | - Basavaraj Teli
- Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | | | | | - Periyasamy Panneerselvam
- Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), Cuttack, 753006 Odisha, India
| | - Ansuman Senapati
- Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), Cuttack, 753006 Odisha, India
| | - Krishnan Nagendran
- Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, Uttar Pradesh, India
| | - Shweta Kumari
- Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, Uttar Pradesh, India
| | - Manoj Kumar Yadav
- Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), Cuttack, 753006 Odisha, India
| | - Sundaram Aravindan
- Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), Cuttack, 753006 Odisha, India
| | - Samantaray Sanghamitra
- Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), Cuttack, 753006 Odisha, India
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26
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Barter MJ, Cheung K, Falk J, Panagiotopoulos AC, Cosimini C, O'Brien S, Teja-Putri K, Neill G, Deehan DJ, Young DA. Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation. Epigenetics 2020; 16:106-119. [PMID: 32741307 PMCID: PMC7889151 DOI: 10.1080/15592294.2020.1789266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Dynamic modifications of chromatin allow rapid access of the gene regulatory machinery to condensed genomic regions facilitating subsequent gene expression. Inflammatory cytokine stimulation of cells can cause rapid gene expression changes through direct signalling pathway-mediated transcription factor activation and regulatory element binding. Here we used the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to assess regions of the genome that are differentially accessible following treatment of cells with interleukin-1 (IL-1). We identified 126,483 open chromatin regions, with 241 regions significantly differentially accessible following stimulation, with 64 and 177 more or less accessible, respectively. These differentially accessible regions predominantly correspond to regions of the genome marked as enhancers. Motif searching identified an overrepresentation of a number of transcription factors, most notably RelA, in the regions becoming more accessible, with analysis of ChIP-seq data confirmed RelA binding to these regions. A significant correlation in differential chromatin accessibility and gene expression was also observed. Functionality in regulating gene expression was confirmed using CRISPR/Cas9 genome-editing to delete regions that became more accessible following stimulation in the genes MMP13, IKBKE and C1QTNF1. These same regions were also accessible for activation using a dCas9-transcriptional activator and showed enhancer activity in a cellular model. Together, these data describe and functionally validate a number of dynamically accessible chromatin regions involved in inflammatory signalling.
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Affiliation(s)
- Matt J Barter
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Kathleen Cheung
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK.,Faculty of Medical Sciences, Bioinformatics Support Unit, Newcastle University , Newcastle upon Tyne, UK
| | - Julia Falk
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Andreas C Panagiotopoulos
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Caitlin Cosimini
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Siobhan O'Brien
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Karina Teja-Putri
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Graham Neill
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - David J Deehan
- Department of Orthopaedics, Freeman Hospital, Orthopaedics , UK
| | - David A Young
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
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Fraser PD, Aharoni A, Hall RD, Huang S, Giovannoni JJ, Sonnewald U, Fernie AR. Metabolomics should be deployed in the identification and characterization of gene-edited crops. Plant J 2020; 102:897-902. [PMID: 31923321 DOI: 10.1111/tpj.14679] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/17/2019] [Accepted: 01/07/2020] [Indexed: 05/23/2023]
Abstract
Gene-editing techniques are currently revolutionizing biology, allowing far greater precision than previous mutagenic and transgenic approaches. They are becoming applicable to a wide range of plant species and biological processes. Gene editing can rapidly improve a range of crop traits, including disease resistance, abiotic stress tolerance, yield, nutritional quality and additional consumer traits. Unlike transgenic approaches, however, it is not facile to forensically detect gene-editing events at the molecular level, as no foreign DNA exists in the elite line. These limitations in molecular detection approaches are likely to focus more attention on the products generated from the technology than on the process in itself. Rapid advances in sequencing and genome assembly increasingly facilitate genome sequencing as a means of characterizing new varieties generated by gene-editing techniques. Nevertheless, subtle edits such as single base changes or small deletions may be difficult to distinguish from normal variation within a genotype. Given these emerging scenarios, downstream 'omics' technologies reflective of edited affects, such as metabolomics, need to be used in a more prominent manner to fully assess compositional changes in novel foodstuffs. To achieve this goal, metabolomics or 'non-targeted metabolite analysis' needs to make significant advances to deliver greater representation across the metabolome. With the emergence of new edited crop varieties, we advocate: (i) concerted efforts in the advancement of 'omics' technologies, such as metabolomics, and (ii) an effort to redress the use of the technology in the regulatory assessment for metabolically engineered biotech crops.
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Affiliation(s)
- Paul D Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Robert D Hall
- Wageningen Research, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, the Netherlands
- Laboratory of Plant Physiology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, the Netherlands
- Netherlands Metabolomics Centre, Einsteinweg 55, Leiden, the Netherlands
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100084, China
| | - James J Giovannoni
- USDA-ARS, Robert W. Holley Center and Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Uwe Sonnewald
- Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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Chohan MO. Deconstructing Neurogenesis, Transplantation and Genome-Editing as Neural Repair Strategies in Brain Disease. Front Cell Dev Biol 2020; 8:116. [PMID: 32232041 PMCID: PMC7082747 DOI: 10.3389/fcell.2020.00116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/11/2020] [Indexed: 01/14/2023] Open
Abstract
Neural repair in injury and disease presents a pressing unmet need in regenerative medicine. Due to the intrinsically reduced ability of the brain to replace lost and damaged neurons, reversing long-term cognitive and functional impairments poses a unique problem. Over the years, advancements in cellular and molecular understanding of neurogenesis mechanisms coupled with sophistication of biotechnology tools have transformed neural repair into a cross-disciplinary field that integrates discoveries from developmental neurobiology, transplantation and tissue engineering to design disease- and patient-specific remedies aimed at boosting either native rehabilitation or delivering exogenous hypoimmunogenic interventions. Advances in deciphering the blueprint of neural ontogenesis and annotation of the human genome has led to the development of targeted therapeutic opportunities that have the potential of treating the most vulnerable patient populations and whose findings from benchside suggest looming clinical translation. This review discusses how findings from studies of adult neurogenesis have informed development of interventions that target endogenous neural regenerative machineries and how advances in biotechnology, including the use of new gene-editing tools, have made possible the development of promising, complex neural transplant-based strategies. Adopting a multi-pronged strategy that is tailored to underlying neural pathology and that encompasses facilitation of endogenous regeneration, correction of patient’s genomic mutations and delivery of transformed neural precursors and mature disease-relevant neuronal populations to replace injured or lost neural tissue remains no longer a fantasy.
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Affiliation(s)
- Muhammad O Chohan
- Department of Psychiatry, Division of Integrative Neuroscience, New York State Psychiatric Institute, New York, NY, United States.,Department of Psychiatry, Division of Child and Adolescent Psychiatry, Columbia University, New York, NY, United States
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Sato M, Miyagasako R, Takabayashi S, Ohtsuka M, Hatada I, Horii T. Sequential i-GONAD: An Improved In Vivo Technique for CRISPR/Cas9-Based Genetic Manipulations in Mice. Cells 2020; 9:E546. [PMID: 32110989 DOI: 10.3390/cells9030546] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 12/25/2022] Open
Abstract
Improved genome-editing via oviductal nucleic acid delivery (i-GONAD) is a technique capable of inducing genomic changes in preimplantation embryos (zygotes) present within the oviduct of a pregnant female. i-GONAD involves intraoviductal injection of a solution containing genome-editing components via a glass micropipette under a dissecting microscope, followed by in vivo electroporation using tweezer-type electrodes. i-GONAD does not involve ex vivo handling of embryos (isolation of zygotes, microinjection or electroporation of zygotes, and egg transfer of the treated embryos to the oviducts of a recipient female), which is required for in vitro genome-editing of zygotes. i-GONAD enables the generation of indels, knock-in (KI) of ~ 1 kb sequence of interest, and large deletion at a target locus. i-GONAD is usually performed on Day 0.7 of pregnancy, which corresponds to the late zygote stage. During the initial development of this technique, we performed i-GONAD on Days 1.4–1.5 (corresponding to the 2-cell stage). Theoretically, this means that at least two GONAD steps (on Day 0.7 and Day 1.4–1.5) must be performed. If this is practically demonstrated, it provides additional options for various clustered regularly interspaced palindrome repeats (CRISPR)/Caspase 9 (Cas9)-based genetic manipulations. For example, it is usually difficult to induce two independent indels at the target sites, which are located very close to each other, by simultaneous transfection of two guide RNAs and Cas9 protein. However, the sequential induction of indels at a target site may be possible when repeated i-GONAD is performed on different days. Furthermore, simultaneous introduction of two mutated lox sites (to which Cre recombinase bind) for making a floxed allele is reported to be difficult, as it often causes deletion of a sequence between the two gRNA target sites. However, differential KI of lox sites may be possible when repeated i-GONAD is performed on different days. In this study, we performed proof-of-principle experiments to demonstrate the feasibility of the proposed approach called “sequential i-GONAD (si-GONAD).”
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Giraldo PA, Shinozuka H, Spangenberg GC, Cogan NO, Smith KF. Safety Assessment of Genetically Modified Feed: Is There Any Difference From Food? Front Plant Sci 2019; 10:1592. [PMID: 31921242 PMCID: PMC6918800 DOI: 10.3389/fpls.2019.01592] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Food security is one of major concerns for the growing global population. Modern agricultural biotechnologies, such as genetic modification, are a possible solution through enabling an increase of production, more efficient use of natural resources, and reduced environmental impacts. However, new crop varieties with altered genetic materials may be subjected to safety assessments to fulfil the regulatory requirements, prior to marketing. The aim of the assessment is to evaluate the impact of products from the new crop variety on human, animal, and the environmental health. Although, many studies on the risk assessment of genetically modified (GM) food have been published, little consideration to GM feedstuff has been given, despite that between 70 to 90% of all GM crops and their biomass are used as animal feed. In addition, in some GM plants such as forages that are only used for animal feeds, the assessment of the genetic modification may be of relevance only to livestock feeding. In this article, the regulatory framework of GM crops intended for animal feed is reviewed using the available information on GM food as the baseline. Although, the majority of techniques used for the safety assessment of GM food can be used in GM feed, many plant parts used for livestock feeding are inedible to humans. Therefore, the concentration of novel proteins in different plant tissues and level of exposure to GM feedstuff in the diet of target animals should be considered. A further development of specific methodologies for the assessment of GM crops intended for animal consumption is required, in order to provide a more accurate and standardized assessment to the GM feed safety.
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Affiliation(s)
- Paula A. Giraldo
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Melbourne, VIC, Australia
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - Hiroshi Shinozuka
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - German C. Spangenberg
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
- School of Applied Systems Biology, La Trobe University, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - Noel O.I. Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
- School of Applied Systems Biology, La Trobe University, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - Kevin F. Smith
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Melbourne, VIC, Australia
- Agriculture Victoria Research, Hamilton, VIC, Australia
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Byambaa S, Uosaki H, Hara H, Nagao Y, Abe T, Shibata H, Nureki O, Ohmori T, Hanazono Y. Generation of novel Il2rg-knockout mice with clustered regularly interspaced short palindromic repeats (CRISPR) and Cas9. Exp Anim 2019; 69:189-198. [PMID: 31801915 PMCID: PMC7220705 DOI: 10.1538/expanim.19-0120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
X-linked severe combined immunodeficiency (X-SCID) is an inherited genetic disorder. A majority of X-SCID subjects carries point mutations in the Interleukin-2 receptor gamma chain (IL2RG) gene. In contrast, Il2rg-knockout mice recapitulating X-SCID phenotype lack a large part of Il2rg instead of point mutations. In this study, we generated novel X-SCID mouse strains with small insertion and deletion (InDel) mutations in Il2rg by using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9. To this end, we injected Streptococcus pyogenes Cas9 (SpCas9) mRNA and single guide RNA targeting the exon 2, 3 or 4 of Il2rg into mouse zygotes. In the F0 generation, we obtained 35 pups and 25 out of them were positive for Surveyor assay, and most of mutants displayed dramatic reductions of T and B lymphocytes in the peripheral blood. By amplicon sequencing, 15 out of 31 founder mice were determined as monoallelic mutants with possible minor mosaicisms while 10 mice were mosaic. Finally, we established new strains with 7-nucleotide deletion and 1-nucleotide insertions in the exon 2 and the exons 3 and 4, respectively. Although no IL2RG protein was detected on T cells of exons 3 and 4 mutants, IL2RG protein was unexpectedly detected in the exon 2 mutants. These data indicated that CRISPR/Cas9 targeting Il2rg causes InDel mutations effectively and generates genetically X-SCID mice. Genetic mutations, however, did not necessarily grant phenotypical alteration, which requires an intensive analysis after establishing a strain to confirm their phenotypes.
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Affiliation(s)
- Suvd Byambaa
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
| | - Hideki Uosaki
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan.,Center for Development of Advanced Medical Technology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
| | - Hiromasa Hara
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan.,Center for Development of Advanced Medical Technology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
| | - Yasumitsu Nagao
- Center for Development of Advanced Medical Technology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan.,Center for Experimental Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
| | - Tomoyuki Abe
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan.,Center for Development of Advanced Medical Technology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
| | - Hiroaki Shibata
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan.,Center for Development of Advanced Medical Technology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tsukasa Ohmori
- Department of Biochemistry, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
| | - Yutaka Hanazono
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan.,Center for Development of Advanced Medical Technology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
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Mohring F, Hart MN, Rawlinson TA, Henrici R, Charleston JA, Diez Benavente E, Patel A, Hall J, Almond N, Campino S, Clark TG, Sutherland CJ, Baker DA, Draper SJ, Moon RW. Rapid and iterative genome editing in the malaria parasite Plasmodium knowlesi provides new tools for P. vivax research. eLife 2019; 8:45829. [PMID: 31205002 PMCID: PMC6579517 DOI: 10.7554/elife.45829] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/28/2019] [Indexed: 12/14/2022] Open
Abstract
Tackling relapsing Plasmodium vivax and zoonotic Plasmodium knowlesi infections is critical to reducing malaria incidence and mortality worldwide. Understanding the biology of these important and related parasites was previously constrained by the lack of robust molecular and genetic approaches. Here, we establish CRISPR-Cas9 genome editing in a culture-adapted P. knowlesi strain and define parameters for optimal homology-driven repair. We establish a scalable protocol for the production of repair templates by PCR and demonstrate the flexibility of the system by tagging proteins with distinct cellular localisations. Using iterative rounds of genome-editing we generate a transgenic line expressing P. vivax Duffy binding protein (PvDBP), a lead vaccine candidate. We demonstrate that PvDBP plays no role in reticulocyte restriction but can alter the macaque/human host cell tropism of P. knowlesi. Critically, antibodies raised against the P. vivax antigen potently inhibit proliferation of this strain, providing an invaluable tool to support vaccine development.
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Affiliation(s)
- Franziska Mohring
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Melissa Natalie Hart
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Ryan Henrici
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - James A Charleston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Ernest Diez Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Avnish Patel
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Joanna Hall
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control, Health Protection Agency, Hertfordshire, United Kingdom
| | - Neil Almond
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control, Health Protection Agency, Hertfordshire, United Kingdom
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Colin J Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - David A Baker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Simon J Draper
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Robert William Moon
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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33
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Diakatou M, Manes G, Bocquet B, Meunier I, Kalatzis V. Genome Editing as a Treatment for the Most Prevalent Causative Genes of Autosomal Dominant Retinitis Pigmentosa. Int J Mol Sci 2019; 20:E2542. [PMID: 31126147 DOI: 10.3390/ijms20102542] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 02/07/2023] Open
Abstract
: Inherited retinal dystrophies (IRDs) are a clinically and genetically heterogeneous group of diseases with more than 250 causative genes. The most common form is retinitis pigmentosa. IRDs lead to vision impairment for which there is no universal cure. Encouragingly, a first gene supplementation therapy has been approved for an autosomal recessive IRD. However, for autosomal dominant IRDs, gene supplementation therapy is not always pertinent because haploinsufficiency is not the only cause. Disease-causing mechanisms are often gain-of-function or dominant-negative, which usually require alternative therapeutic approaches. In such cases, genome-editing technology has raised hopes for treatment. Genome editing could be used to i) invalidate both alleles, followed by supplementation of the wild type gene, ii) specifically invalidate the mutant allele, with or without gene supplementation, or iii) to correct the mutant allele. We review here the most prevalent genes causing autosomal dominant retinitis pigmentosa and the most appropriate genome-editing strategy that could be used to target their different causative mutations.
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Chaudhary J, Alisha A, Bhatt V, Chandanshive S, Kumar N, Mir Z, Kumar A, Yadav SK, Shivaraj SM, Sonah H, Deshmukh R. Mutation Breeding in Tomato: Advances, Applicability and Challenges. Plants (Basel) 2019; 8:E128. [PMID: 31091747 PMCID: PMC6572636 DOI: 10.3390/plants8050128] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/09/2019] [Accepted: 05/11/2019] [Indexed: 02/04/2023]
Abstract
Induced mutagenesis is one of the most effective strategies for trait improvement without altering the well-optimized genetic background of the cultivars. In this review, several currently accessible methods such as physical, chemical and insertional mutagenesis have been discussed concerning their efficient exploration for the tomato crop improvement. Similarly, challenges for the adaptation of genome-editing, a newly developed technique providing an opportunity to induce precise mutation, have been addressed. Several efforts of genome-editing have been demonstrated in tomato and other crops, exploring its effectiveness and convenience for crop improvement. Descriptive data compiled here from such efforts will be helpful for the efficient exploration of technological advances. However, uncertainty about the regulation of genome-edited crops is still a significant concern, particularly when timely trait improvement in tomato cultivars is needed. In this regard, random approaches of induced mutagenesis are still promising if efficiently explored in breeding applications. Precise identification of casual mutation is a prerequisite for the molecular understanding of the trait development as well as its utilization for the breeding program. Recent advances in sequencing techniques provide an opportunity for the precise detection of mutagenesis-induced sequence variations at a large scale in the genome. Here, we reviewed several novel next-generation sequencing based mutation mapping approaches including Mutmap, MutChromeSeq, and whole-genome sequencing-based mapping which has enormous potential to accelerate the mutation breeding in tomato. The proper utilization of the existing well-characterized tomato mutant resources combined with novel mapping approaches would inevitably lead to rapid enhancement of tomato quality and yield. This article provides an overview of the principles and applications of mutagenesis approaches in tomato and discusses the current progress and challenges involved in tomato mutagenesis research.
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Affiliation(s)
- Juhi Chaudhary
- Department of Biology, Oberlin College, Oberlin, OH 44074, USA.
| | - Alisha Alisha
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Vacha Bhatt
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Sonali Chandanshive
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Nirbhay Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Zahoor Mir
- National Research Center on Plant Biotechnology, New Delhi, Delhi 110012, India.
| | - Ashwini Kumar
- Division of Plant Pathology, ICAR-IARI, New Delhi, Delhi 110001, Inida.
| | - Satish K Yadav
- National Bureau of Plant Genetic Resources, New Delhi, Delhi 110012, India.
| | - S M Shivaraj
- Faculté des sciences de l'agriculture et de l'alimentation (FSAA), Université Laval, Quebec, QC G1V 0A6, Canada.
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
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35
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Sim SB, Kauwe AN, Ruano REY, Rendon P, Geib SM. The ABCs of CRISPR in Tephritidae: developing methods for inducing heritable mutations in the genera Anastrepha, Bactrocera and Ceratitis. Insect Mol Biol 2019; 28:277-289. [PMID: 30422347 DOI: 10.1111/imb.12550] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Tephritid fruit flies are destructive agricultural pests that are the targets of expensive population eradication and suppression efforts. Genetic pest management is one of the strategies for reducing or eliminating tephritid populations, relying upon the genetic manipulation of insects to render them sterile or capable of transmitting deleterious traits through gene drive. Currently, radiation, chemical mutagenesis, and transgenic techniques are employed to generate agents for genetic pest management, but new methods must be explored and developed for all tephritid pest species. Targeted mutagenesis induced by nonhomologous end join repair of clustered regularly interspaced short palindromic repeats and the CRISPR associated protein 9 (Cas9) (commonly known as CRISPR/Cas9) has been demonstrated to be an efficient method for creating knock-out mutants and can be utilized to create germline mutations in Tephritidae. In this paper, we describe detailed methods to knockout the white gene in three tephritid species in the genera Anastrepha, Bactrocera and Ceratitis, including the first demonstration of CRISPR/Cas9 induced mutations in the genus Anastrepha. Lastly, we discuss the variables in tephritid systems that directed method development as well as recommendations for performing injections in remote containment facilities with little molecular biology capabilities. These methods and recommendations combined can serve as a guide for others to use in pursuit of developing CRISPR/Cas9 methods in tephritid systems.
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Affiliation(s)
- S B Sim
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, Hilo, HI, USA
| | - A N Kauwe
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, Hilo, HI, USA
| | - R E Y Ruano
- IAEA Technical Cooperation- Latin America and Caribbean Section, Guatemala City, Guatemala
| | - P Rendon
- IAEA Technical Cooperation- Latin America and Caribbean Section, Guatemala City, Guatemala
| | - S M Geib
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, Hilo, HI, USA
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Nadakuduti SS, Starker CG, Ko DK, Jayakody TB, Buell CR, Voytas DF, Douches DS. Evaluation of Methods to Assess in vivo Activity of Engineered Genome-Editing Nucleases in Protoplasts. Front Plant Sci 2019; 10:110. [PMID: 30800139 PMCID: PMC6376315 DOI: 10.3389/fpls.2019.00110] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 01/23/2019] [Indexed: 06/01/2023]
Abstract
Genome-editing is being implemented in increasing number of plant species using engineered sequence specific nucleases (SSNs) such as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated systems (CRISPR/Cas9), Transcription activator like effector nucleases (TALENs), and more recently CRISPR/Cas12a. As the tissue culture and regeneration procedures to generate gene-edited events are time consuming, large-scale screening methodologies that rapidly facilitate validation of genome-editing reagents are critical. Plant protoplast cells provide a rapid platform to validate genome-editing reagents. Protoplast transfection with plasmids expressing genome-editing reagents represents an efficient and cost-effective method to screen for in vivo activity of genome-editing constructs and resulting targeted mutagenesis. In this study, we compared three existing methods for detection of editing activity, the T7 endonuclease I assay (T7EI), PCR/restriction enzyme (PCR/RE) digestion, and amplicon-sequencing, with an alternative method which involves tagging a double-stranded oligodeoxynucleotide (dsODN) into the SSN-induced double stranded break and detection of on-target activity of gene-editing reagents by PCR and agarose gel electrophoresis. To validate these methods, multiple reagents including TALENs, CRISPR/Cas9 and Cas9 variants, eCas9(1.1) (enhanced specificity) and Cas9-HF1 (high-fidelity1) were engineered for targeted mutagenesis of Acetolactate synthase1 (ALS1), 5-Enolpyruvylshikimate- 3-phosphate synthase1 (EPSPS1) and their paralogs in potato. While all methods detected editing activity, the PCR detection of dsODN integration provided the most straightforward and easiest method to assess on-target activity of the SSN as well as a method for initial qualitative evaluation of the functionality of genome-editing constructs. Quantitative data on mutagenesis frequencies obtained by amplicon-sequencing of ALS1 revealed that the mutagenesis frequency of CRISPR/Cas9 reagents is better than TALENs. Context-based choice of method for evaluation of gene-editing reagents in protoplast systems, along with advantages and limitations associated with each method, are discussed.
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Affiliation(s)
- Satya Swathi Nadakuduti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Colby G. Starker
- Department of Genetics, Cell Biology and Development and Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, United States
| | - Dae Kwan Ko
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Thilani B. Jayakody
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Plant Resilience Institute, Michigan State University, East Lansing, MI, United States
- Michigan State University AgBioResearch, Michigan State University, East Lansing, MI, United States
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology and Development and Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, United States
| | - David S. Douches
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- Michigan State University AgBioResearch, Michigan State University, East Lansing, MI, United States
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Abstract
The CRISPR-Cas9, a part of the defence mechanism from bacteria, has rapidly become the simplest, fastest and the most precise genome-editing tool available. The therapeutic applications of CRISPR are boundless: correction of mutations in several disorders, inactivation of oncogenes and viral oncoproteins, and activation of tumor suppressor genes. In this review, we expose recent advances concerning animal models of cancer that use CRISPR-Cas9, addressing also the current efforts to develop CRISPR-Cas9-based therapies, focusing on proof-of-concept studies. Finally, the review exposes some of the main challenges that this genome-editing tool faces. The key issue remains: does CRISPR-Cas9 have real potential for therapeutic application or will it just remain a wonderful research tool?
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Affiliation(s)
- Diogo Estêvão
- Molecular Oncology & Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal Porto, Portugal.,Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal Porto, Portugal
| | - Natália Rios Costa
- Molecular Oncology & Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal Porto, Portugal
| | - Rui Gil da Costa
- Laboratory for Process Engineering, Environment, Biotechnology & Energy (LEPABE), Faculty of Engineering of the University of Porto (FEUP), 4200-465 Porto, Portugal.,Center for the Research & Technology of Agro-Environmental & Biological Sciences (CITAB), University of Trás-os-Montes & Alto Douro (UTAD), 5001-911 Vila Real, Portugal
| | - Rui Medeiros
- Molecular Oncology & Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal Porto, Portugal.,Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal Porto, Portugal.,Research Department of the Portuguese League Against Cancer (Liga Portuguesa Contra o Cancro - Núcleo Regional do Norte), 4200-177 Porto, Portugal Porto, Portugal.,Biomedical Research Center (CEBIMED), Faculty of Health Sciences of the Fernando Pessoa University, 4249-004 Porto, Portugal Porto, Portugal
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Nadakuduti SS, Buell CR, Voytas DF, Starker CG, Douches DS. Genome Editing for Crop Improvement - Applications in Clonally Propagated Polyploids With a Focus on Potato ( Solanum tuberosum L.). Front Plant Sci 2018; 9:1607. [PMID: 30483283 PMCID: PMC6243044 DOI: 10.3389/fpls.2018.01607] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/17/2018] [Indexed: 05/05/2023]
Abstract
Genome-editing has revolutionized biology. When coupled with a recently streamlined regulatory process by the U.S. Department of Agriculture and the potential to generate transgene-free varieties, genome-editing provides a new avenue for crop improvement. For heterozygous, polyploid and vegetatively propagated crops such as cultivated potato, Solanum tuberosum Group Tuberosum L., genome-editing presents tremendous opportunities for trait improvement. In potato, traits such as improved resistance to cold-induced sweetening, processing efficiency, herbicide tolerance, modified starch quality and self-incompatibility have been targeted utilizing CRISPR/Cas9 and TALEN reagents in diploid and tetraploid clones. However, limited progress has been made in other such crops including sweetpotato, strawberry, grapes, citrus, banana etc., In this review we summarize the developments in genome-editing platforms, delivery mechanisms applicable to plants and then discuss the recent developments in regulation of genome-edited crops in the United States and The European Union. Next, we provide insight into the challenges of genome-editing in clonally propagated polyploid crops, their current status for trait improvement with future prospects focused on potato, a global food security crop.
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Affiliation(s)
- Satya Swathi Nadakuduti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- *Correspondence: Satya Swathi Nadakuduti, David S. Douches,
| | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Plant Resilience Institute, Michigan State University, East Lansing, MI, United States
- AgBioResearch – Michigan State University, East Lansing, MI, United States
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology, and Development, Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, United States
| | - Colby G. Starker
- Department of Genetics, Cell Biology, and Development, Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, United States
| | - David S. Douches
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- AgBioResearch – Michigan State University, East Lansing, MI, United States
- *Correspondence: Satya Swathi Nadakuduti, David S. Douches,
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Liu L, Chen P, Wang M, Li X, Wang J, Yin M, Wang Y. C2c1-sgRNA Complex Structure Reveals RNA-Guided DNA Cleavage Mechanism. Mol Cell 2017; 65:310-322. [PMID: 27989439 DOI: 10.1016/j.molcel.2016.11.040] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/21/2016] [Accepted: 11/29/2016] [Indexed: 11/28/2022]
Abstract
C2c1 is a type V-B CRISPR-Cas system dual-RNA-guided DNA endonuclease. Here, we report the crystal structure of Alicyclobacillus acidoterrestris C2c1 in complex with a chimeric single-molecule guide RNA (sgRNA). AacC2c1 exhibits a bi-lobed architecture consisting of a REC and NUC lobe. The sgRNA scaffold forms a tetra-helical structure, distinct from previous predictions. The crRNA is located in the central channel of C2c1, and the tracrRNA resides in an external surface groove. Although AacC2c1 lacks a PAM-interacting domain, our analysis revealed that the PAM duplex has a similar binding position found in Cpf1. Importantly, C2c1-sgRNA system is highly sensitive to single-nucleotide mismatches between guide RNA and target DNA. The resulting reduction in off-target cleavage renders C2c1 a valuable addition to the current arsenal of genome-editing tools. Together, our findings indicate that sgRNA assembly is achieved through a mechanism distinct from that reported previously for Cas9 or Cpf1 endonucleases.
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MESH Headings
- Alicyclobacillus/enzymology
- Alicyclobacillus/genetics
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Associated Proteins/chemistry
- CRISPR-Associated Proteins/genetics
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA Breaks, Double-Stranded
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Endodeoxyribonucleases/chemistry
- Endodeoxyribonucleases/genetics
- Endodeoxyribonucleases/metabolism
- Models, Molecular
- Nucleic Acid Conformation
- Nucleic Acid Heteroduplexes/chemistry
- Nucleic Acid Heteroduplexes/genetics
- Nucleic Acid Heteroduplexes/metabolism
- Protein Binding
- Protein Interaction Domains and Motifs
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Structure-Activity Relationship
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Affiliation(s)
- Liang Liu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng Chen
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xueyan Li
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiuyu Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Maolu Yin
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanli Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China.
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Lee N, Shin J, Park JH, Lee GM, Cho S, Cho BK. Targeted Gene Deletion Using DNA-Free RNA-Guided Cas9 Nuclease Accelerates Adaptation of CHO Cells to Suspension Culture. ACS Synth Biol 2016; 5:1211-1219. [PMID: 26854539 DOI: 10.1021/acssynbio.5b00249] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chinese hamster ovary (CHO) cells are the preferred host for the production of a wide array of biopharmaceuticals. Thus, efficient and rational CHO cell line engineering methods have been in high demand to improve quality and productivity. Here, we provide a novel genome engineering platform for increasing desirable phenotypes of CHO cells based upon the integrative protocol of high-throughput RNA sequencing and DNA-free RNA-guided Cas9 (CRISPR associated protein9) nuclease-based genome editing. For commercial production of therapeutic proteins, CHO cells have been adapted for suspension culture in serum-free media, which is highly beneficial with respect to productivity and economics. To engineer CHO cells for rapid adaptation to a suspension culture, we exploited strand-specific RNA-seq to identify genes differentially expressed according to their adaptation trajectory in serum-free media. More than 180 million sequencing reads were generated and mapped to the currently available 109,152 scaffolds of the CHO-K1 genome. We identified significantly downregulated genes according to the adaptation trajectory and then verified their effects using the genome editing method. Growth-based screening and targeted amplicon sequencing revealed that the functional deletions of Igfbp4 and AqpI gene accelerate suspension adaptation of CHO-K1 cells. The availability of this strand-specific transcriptome sequencing and DNA-free RNA-guided Cas9 nuclease mediated genome editing facilitates the rational design of the CHO cell genome for efficient production of high quality therapeutic proteins.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - JongOh Shin
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - Jin Hyoung Park
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
- Intelligent Synthetic Biology Center, Daejeon 305-701, Republic of Korea
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41
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Liu R, Chen L, Jiang Y, Zhou Z, Zou G. Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system. Cell Discov 2015; 1:15007. [PMID: 27462408 PMCID: PMC4860831 DOI: 10.1038/celldisc.2015.7] [Citation(s) in RCA: 277] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 02/28/2015] [Indexed: 02/03/2023] Open
Abstract
Filamentous fungi have wide applications in biotechnology. The CRISPR/Cas9 system is a powerful genome-editing method that facilitates genetic alterations of genomes in a variety of organisms. However, a genome-editing approach has not been reported in filamentous fungi. Here, we demonstrated the establishment of a CRISPR/Cas9 system in the filamentous fungus Trichoderma reesei by specific codon optimization and in vitro RNA transcription. It was shown that the CRISPR/Cas9 system was controllable and conditional through inducible Cas9 expression. This system generated site-specific mutations in target genes through efficient homologous recombination, even using short homology arms. This system also provided an applicable and promising approach to targeting multiple genes simultaneously. Our results illustrate that the CRISPR/Cas9 system is a powerful genome-manipulating tool for T. reesei and most likely for other filamentous fungal species, which may accelerate studies on functional genomics and strain improvement in these filamentous fungi.
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Affiliation(s)
- Rui Liu
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Ling Chen
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Yanping Jiang
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Gen Zou
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
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Mashimo T. Gene targeting technologies in rats: zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats. Dev Growth Differ 2013; 56:46-52. [PMID: 24372523 DOI: 10.1111/dgd.12110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 11/18/2013] [Accepted: 11/18/2013] [Indexed: 12/21/2022]
Abstract
The laboratory rat has been widely used as an animal model in biomedical science for more than 150 years. Applying zinc-finger nucleases or transcription activator-like effector nucleases to rat embryos via microinjection is an efficient genome editing tool for generating targeted knockout rats. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated endonucleases have been used as an effective tool for precise and multiplex genome editing in mice and rats. In this review, the advantages and disadvantages of these site-specific nuclease technologies for genetic analysis and manipulation in rats are discussed.
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Affiliation(s)
- Tomoji Mashimo
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho Sakyo-ku, Kyoto, 606-8501, Japan
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