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Cai Y, Liu Z, Wang H, Meng H, Cao Y. Mesoporous Silica Nanoparticles Mediate SiRNA Delivery for Long-Term Multi-Gene Silencing in Intact Plants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2301358. [PMID: 38145358 PMCID: PMC10916655 DOI: 10.1002/advs.202301358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 11/03/2023] [Indexed: 12/26/2023]
Abstract
RNA interference (RNAi) is a powerful tool for understanding and manipulating signaling pathways in plant science, potentially facilitating the accelerated development of novel plant traits and crop yield improvement. The common strategy for delivering siRNA into intact plants using agrobacterium or viruses is complicated and time-consuming, limiting the application of RNAi in plant research. Here, a novel delivery method based on mesoporous silica nanoparticles (MSNs) is reported, which allows for the efficient delivery of siRNA into mature plant leaves via topical application without the aid of mechanical forces, achieving transient gene knockdown with up to 98% silencing efficiency at the molecular level. In addition, this method is nontoxic to plant leaves, enabling the repeated delivery of siRNA for long-term silencing. White spots and yellowing phenotypes are observed after spraying the MSN-siRNA complex targeted at phytoene desaturase and magnesium chelatase genes. After high light treatment, photobleaching phenotypes are also observed by spraying MSNs-siRNA targeted at genes into the Photosystem II repair cycle. Furthermore, the study demonstrated that MSNs can simultaneously silence multiple genes. The results suggest that MSN-mediated siRNA delivery is an effective tool for long-term multi-gene silencing, with great potential for application in plant functional genomic analyses and crop improvement.
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Affiliation(s)
- Yao Cai
- Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and TechnologyChinese Academy of SciencesBeijing100190China
| | - Zhujiang Liu
- Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and TechnologyChinese Academy of SciencesBeijing100190China
| | - Hang Wang
- Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and TechnologyChinese Academy of SciencesBeijing100190China
| | - Huan Meng
- Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and TechnologyChinese Academy of SciencesBeijing100190China
| | - Yuhong Cao
- Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and TechnologyChinese Academy of SciencesBeijing100190China
- School of Nano Science and TechnologyUniversity of Chinese Academy of SciencesBeijing100049China
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2
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Hashemi M, Esbati N, Rashidi M, Gholami S, Raesi R, Bidoki SS, Goharrizi MASB, Motlagh YSM, Khorrami R, Tavakolpournegari A, Nabavi N, Zou R, Mohammadnahal L, Entezari M, Taheriazam A, Hushmandi K. Biological landscape and nanostructural view in development and reversal of oxaliplatin resistance in colorectal cancer. Transl Oncol 2024; 40:101846. [PMID: 38042134 PMCID: PMC10716031 DOI: 10.1016/j.tranon.2023.101846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 12/04/2023] Open
Abstract
The treatment of cancer patients has been mainly followed using chemotherapy and it is a gold standard in improving prognosis and survival rate of patients. Oxaliplatin (OXA) is a third-platinum anti-cancer agent that reduces DNA synthesis in cancer cells to interfere with their growth and cell cycle progression. In spite of promising results of using OXA in cancer chemotherapy, the process of drug resistance has made some challenges. OXA is commonly applied in treatment of colorectal cancer (CRC) as a malignancy of gastrointestinal tract and when CRC cells increase their proliferation and metastasis, they can obtain resistance to OXA chemotherapy. A number of molecular factors such as CHK2, SIRT1, c-Myc, LATS2 and FOXC1 have been considered as regulators of OXA response in CRC cells. The non-coding RNAs are able to function as master regulator of other molecular pathways in modulating OXA resistance. There is a close association between molecular mechanisms such as apoptosis, autophagy, glycolysis and EMT with OXA resistance, so that apoptosis inhibition, pro-survival autophagy induction and stimulation of EMT and glycolysis can induce OXA resistance in CRC cells. A number of anti-tumor compounds including astragaloside IV, resveratrol and nobiletin are able to enhance OXA sensitivity in CRC cells. Nanoparticles for increasing potential of OXA in CRC suppression and reversing OXA resistance have been employed in cancer chemotherapy. These subjects are covered in this review article to shed light on molecular factors resulting in OXA resistance.
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Affiliation(s)
- Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran
| | - Nastaran Esbati
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sadaf Gholami
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran
| | - Rasoul Raesi
- Department of Health Services Management, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Shahabadin Bidoki
- Faculty of medicine, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | | | - Ramin Khorrami
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Alireza Tavakolpournegari
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Noushin Nabavi
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, V6H3Z6, Vancouver, BC, Canada
| | - Rongjun Zou
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, Guangdong, China
| | - Leila Mohammadnahal
- Department of Health Services Management, School of Health, Tehran University of Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
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Song L, Zhang D, Liu T, Jiang C, Li B, Li C, Shen L, Li Y, Wang F, Jiao Y, Yang J. Non-transgenic, PAMAM co-delivery DNA of interactive proteins NbCRVP and NbCalB endows Nicotiana benthamiana with a stronger antiviral effect to RNA viruses. J Nanobiotechnology 2024; 22:23. [PMID: 38191434 PMCID: PMC10773047 DOI: 10.1186/s12951-023-02252-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Viral diseases continue to pose a major threat to the world's commercial crops. The in-depth exploration and efficient utilization of resistance proteins have become crucial strategies for their control. However, current delivery methods for introducing foreign DNA suffer from host range limitations, low transformation efficiencies, tissue damage, or unavoidable DNA integration into the host genome. The nanocarriers provides a convenient channel for the DNA delivery and functional utilization of disease-resistant proteins. RESULTS In this research, we identified a cysteine-rich venom protein (NbCRVP) in Nicotiana benthamiana for the first time. Virus-induced gene silencing and transient overexpression clarified that NbCRVP could inhibit the infection of tobacco mosaic virus, potato virus Y, and cucumber mosaic virus, making it a broad-spectrum antiviral protein. Yeast two-hybrid assay, co-immunoprecipitation, and bimolecular fluorescence complementation revealed that calcium-dependent lipid-binding (CaLB domain) family protein (NbCalB) interacted with NbCRVP to assist NbCRVP playing a stronger antiviral effect. Here, we demonstrated for the first time the efficient co-delivery of DNA expressing NbCRVP and NbCalB into plants using poly(amidoamine) (PAMAM) nanocarriers, achieving stronger broad-spectrum antiviral effects. CONCLUSIONS Our work presents a tool for species-independent transfer of two interacting protein DNA into plant cells in a specific ratio for enhanced antiviral effect without transgenic integration, which further demonstrated new strategies for nanocarrier-mediated DNA delivery of disease-resistant proteins.
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Affiliation(s)
- Liyun Song
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- College of Agriculture and Forestry Science and Technology, Weifang Vocational College, Weifang, 262737, China
| | - Daoshun Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tianbo Liu
- Tobacco Research Institute of Hunan Province, Hunan, 410004, China
| | - Changqing Jiang
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou, 434025, China
| | - Bin Li
- Sichuan Tobacco Company, Chengdu, 610000, China
| | - Changquan Li
- Liupanshui City Company of Guizhou Tobacco Company, Liupanshui, 553000, Guizhou, China
| | - Lili Shen
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Ying Li
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Fenglong Wang
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| | - Yubing Jiao
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| | - Jinguang Yang
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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Anuar MSK, Hashim AM, Ho CL, Wong MY, Sundram S, Saidi NB, Yusof MT. Synergism: biocontrol agents and biostimulants in reducing abiotic and biotic stresses in crop. World J Microbiol Biotechnol 2023; 39:123. [PMID: 36934342 DOI: 10.1007/s11274-023-03579-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/12/2023] [Indexed: 03/20/2023]
Abstract
In today's fast-shifting climate change scenario, crops are exposed to environmental pressures, abiotic and biotic stress. Hence, these will affect the production of agricultural products and give rise to a worldwide economic crisis. The increase in world population has exacerbated the situation with increasing food demand. The use of chemical agents is no longer recommended due to adverse effects towards the environment and health. Biocontrol agents (BCAs) and biostimulants, are feasible options for dealing with yield losses induced by plant stresses, which are becoming more intense due to climate change. BCAs and biostimulants have been recommended due to their dual action in reducing both stresses simultaneously. Although protection against biotic stresses falls outside the generally accepted definition of biostimulant, some microbial and non-microbial biostimulants possess the biocontrol function, which helps reduce biotic pressure on crops. The application of synergisms using BCAs and biostimulants to control crop stresses is rarely explored. Currently, a combined application using both agents offer a great alternative to increase the yield and growth of crops while managing stresses. This article provides an overview of crop stresses and plant stress responses, a general knowledge on synergism, mathematical modelling used for synergy evaluation and type of in vitro and in vivo synergy testing, as well as the application of synergism using BCAs and biostimulants in reducing crop stresses. This review will facilitate an understanding of the combined effect of both agents on improving crop yield and growth and reducing stress while also providing an eco-friendly alternative to agroecosystems.
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Affiliation(s)
- Muhammad Salahudin Kheirel Anuar
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, UPM, Selangor, 43400, Malaysia
| | - Amalia Mohd Hashim
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, UPM, Selangor, 43400, Malaysia
| | - Chai Ling Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, UPM, Selangor, 43400, Malaysia
| | - Mui-Yun Wong
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, UPM, Selangor, 43400, Malaysia
| | - Shamala Sundram
- Biology Research Division, Malaysian Palm Oil Board, Kajang, Selangor, 43000, Malaysia
| | - Noor Baity Saidi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, UPM, Selangor, 43400, Malaysia
| | - Mohd Termizi Yusof
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, UPM, Selangor, 43400, Malaysia.
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5
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Liu X, Zhang P, Zhao Q, Huang AC. Making small molecules in plants: A chassis for synthetic biology-based production of plant natural products. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:417-443. [PMID: 35852486 DOI: 10.1111/jipb.13330] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Plant natural products have been extensively exploited in food, medicine, flavor, cosmetic, renewable fuel, and other industrial sectors. Synthetic biology has recently emerged as a promising means for the cost-effective and sustainable production of natural products. Compared with engineering microbes for the production of plant natural products, the potential of plants as chassis for producing these compounds is underestimated, largely due to challenges encountered in engineering plants. Knowledge in plant engineering is instrumental for enabling the effective and efficient production of valuable phytochemicals in plants, and also paves the way for a more sustainable future agriculture. In this manuscript, we briefly recap the biosynthesis of plant natural products, focusing primarily on industrially important terpenoids, alkaloids, and phenylpropanoids. We further summarize the plant hosts and strategies that have been used to engineer the production of natural products. The challenges and opportunities of using plant synthetic biology to achieve rapid and scalable production of high-value plant natural products are also discussed.
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Affiliation(s)
- Xinyu Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Peijun Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qiao Zhao
- Shenzhen Institutes of Advanced Technology (SIAT), the Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ancheng C Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
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6
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Morgan JM, Jelenska J, Hensley D, Retterer ST, Morrell-Falvey JL, Standaert RF, Greenberg JT. An efficient and broadly applicable method for transient transformation of plants using vertically aligned carbon nanofiber arrays. FRONTIERS IN PLANT SCIENCE 2022; 13:1051340. [PMID: 36507425 PMCID: PMC9728956 DOI: 10.3389/fpls.2022.1051340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Transient transformation in plants is a useful process for evaluating gene function. However, there is a scarcity of minimally perturbing methods for gene delivery that can be used on multiple organs, plant species, and non-excised tissues. We pioneered and demonstrated the use of vertically aligned carbon nanofiber (VACNF) arrays to efficiently perform transient transformation of different tissues with DNA constructs in multiple plant species. The VACNFs permeabilize plant tissue transiently to allow molecules into cells without causing a detectable stress response. We successfully delivered DNA into leaves, roots and fruit of five plant species (Arabidopsis, poplar, lettuce, Nicotiana benthamiana, and tomato) and confirmed accumulation of the encoded fluorescent proteins by confocal microscopy. Using this system, it is possible to transiently transform plant cells with both small and large plasmids. The method is successful for species recalcitrant to Agrobacterium-mediated transformation. VACNFs provide simple, reliable means of DNA delivery into a variety of plant organs and species.
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Affiliation(s)
- Jessica M Morgan
- Biophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Joanna Jelenska
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, United States
| | - Dale Hensley
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Scott T Retterer
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | - Robert F Standaert
- Department of Chemistry, East Tennessee State University, Johnson City, TN, United States
| | - Jean T Greenberg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, United States
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Ghose AK, Abdullah SNA, Md Hatta MA, Megat Wahab PE. DNA Free CRISPR/DCAS9 Based Transcriptional Activation System for UGT76G1 Gene in Stevia rebaudiana Bertoni Protoplasts. PLANTS (BASEL, SWITZERLAND) 2022; 11:2393. [PMID: 36145794 PMCID: PMC9501275 DOI: 10.3390/plants11182393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
The UDP-glycosyltransferase 76G1 (UGT76G1) is responsible for the conversion of stevioside to rebaudioside A. Four single guide RNAs (sgRNAs) were designed from the UGT76G1 proximal promoter region of stevia by using the online-based tool, benchling. The dCas9 fused with VP64 as a transcriptional activation domain (TAD) was produced and purified for the formation of ribonucleoproteins (RNPs) by mixing with the in vitro transcribed sgRNAs. Protoplast yield was the highest from leaf mesophyll of in vitro grown stevia plantlets (3.16 × 106/g of FW) using ES5 (1.25% cellulase R-10 and 0.75% macerozyme R-10). The RNPs were delivered into the isolated protoplasts through the Polyethylene glycol (PEG)-mediated transfection method. The highest endogenous activation of the UGT76G1 gene was detected at 27.51-fold after 24 h of transfection with RNP30 consisting of CRISPR/dCas9-TAD with sgRNA30 and a similar activation level was obtained using RNP18, RNP33, and RNP34, produced using sgRNA18, sgRNA33, and sgRNA34, respectively. Activation of UGT76G1 by RNP18 led to a significant increase in the expression of the rate-limiting enzyme UGT85C2 by 2.37-fold and there was an increasing trend in the expression of UGT85C2 using RNP30, RNP33, and RNP34. Successful application of CRISPR/dCas9-TAD RNP in activating specific genes can avoid the negative integration effects of introduced DNA in the host genome.
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Affiliation(s)
- Asish Kumar Ghose
- Laboratory of Agronomy and Sustainable Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Biotechnology Division, Bangladesh Sugarcrop Research Institute, Ishurdi, Pabna 6620, Bangladesh
| | - Siti Nor Akmar Abdullah
- Laboratory of Agronomy and Sustainable Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Muhammad Asyraf Md Hatta
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Puteri Edaroyati Megat Wahab
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
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8
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Zhi H, Zhou S, Pan W, Shang Y, Zeng Z, Zhang H. The Promising Nanovectors for Gene Delivery in Plant Genome Engineering. Int J Mol Sci 2022; 23:ijms23158501. [PMID: 35955636 PMCID: PMC9368765 DOI: 10.3390/ijms23158501] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/24/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Highly efficient gene delivery systems are essential for genetic engineering in plants. Traditional delivery methods have been widely used, such as Agrobacterium-mediated transformation, polyethylene glycol (PEG)-mediated delivery, biolistic particle bombardment, and viral transfection. However, genotype dependence and other drawbacks of these techniques limit the application of genetic engineering, particularly genome editing in many crop plants. There is a great need to develop newer gene delivery vectors or methods. Recently, nanomaterials such as mesoporous silica particles (MSNs), AuNPs, carbon nanotubes (CNTs), and layer double hydroxides (LDHs), have emerged as promising vectors for the delivery of genome engineering tools (DNA, RNA, proteins, and RNPs) to plants in a species-independent manner with high efficiency. Some exciting results have been reported, such as the successful delivery of cargo genes into plants and the generation of genome stable transgenic cotton and maize plants, which have provided some new routines for genome engineering in plants. Thus, in this review, we summarized recent progress in the utilization of nanomaterials for plant genetic transformation and discussed the advantages and limitations of different methods. Furthermore, we emphasized the advantages and potential broad applications of nanomaterials in plant genome editing, which provides guidance for future applications of nanomaterials in plant genetic engineering and crop breeding.
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Affiliation(s)
- Heng Zhi
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China; (H.Z.); (S.Z.); (W.P.)
- Institute of Advanced Agricultural Science, Peking University, Weifang 261000, China;
| | - Shengen Zhou
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China; (H.Z.); (S.Z.); (W.P.)
- Institute of Advanced Agricultural Science, Peking University, Weifang 261000, China;
| | - Wenbo Pan
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China; (H.Z.); (S.Z.); (W.P.)
- Institute of Advanced Agricultural Science, Peking University, Weifang 261000, China;
| | - Yun Shang
- Institute of Advanced Agricultural Science, Peking University, Weifang 261000, China;
| | - Zhanghua Zeng
- Institute of Environment and Sustainable Development in Agriculture, CAAS Chinese Academy of Agricultural Science, Beijing 100081, China;
| | - Huawei Zhang
- Institute of Advanced Agricultural Science, Peking University, Weifang 261000, China;
- Correspondence:
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9
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An Z, Cao B, Zhang J, Zhang B, Zhou C, Hu X, Chen W. Efficient Transient Expression of Plasmid DNA Using Poly (2-(N,N-Dimethylamino) Ethyl Methacrylate) in Plant Cells. Front Bioeng Biotechnol 2022; 10:805996. [PMID: 35273955 PMCID: PMC8902165 DOI: 10.3389/fbioe.2022.805996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/19/2022] [Indexed: 11/30/2022] Open
Abstract
Nanomaterials have been widely studied for their potential to become the new generation of nanocarriers in gene transfection, yet it remains still difficult to apply them efficiently and succinctly to plant cells. Poly (2-(N,N-dimethylamino) ethyl methacrylate) (PDMAEMA), which possesses temperature and pH dual-sensitivity, has largely been applied in animal cells, but it is rarely involved in plant cells. As a proof of concept, PDMAEMA as a gene carrier is incubated with plasmid GFP (pGFP) to explore its transfection ability in plants, and cationic polymer polyethylenimine (PEI) is used as a control. pGFP was efficiently condensed into the nanostructure by electrostatic interactions at an N/P (amino group from cationic polymers/phosphate group from plasmid DNA (pDNA)) ratio of 15; after complexation into nanocarriers, pGFP was protected from endonuclease degradation according to the DNase I digestion assay. After incubation with protoplasts and leaves, GFP was observed with confocal microscopy in plant cells. Western blot experiments confirmed GFP expression at the protein level. Toxicity assay showed PDMAEMA had a lower toxicity than PEI. These results showed that transient expression of pGFP was readily achieved in Arabidopsis thaliana and Nicotiana benthamiana. Notably, PDMAEMA showed lower cytotoxicity than PEI upon incubation with Nicotiana benthamiana leaves. PDMAEMA exhibited great potency for DNA delivery in plant cells. This work provides us with new ideas of more concise and more effective methods for plant transformation.
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Affiliation(s)
- Zishuai An
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Bing Cao
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Junzhe Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Baihong Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Chengqian Zhou
- Neuroscience Laboratory, Hugo Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
| | - Xianglong Hu
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
- *Correspondence: Wenli Chen, ; Xianglong Hu,
| | - Wenli Chen
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
- *Correspondence: Wenli Chen, ; Xianglong Hu,
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Nahirñak V, Almasia NI, González MN, Massa GA, Décima Oneto CA, Feingold SE, Hopp HE, Vazquez Rovere C. State of the Art of Genetic Engineering in Potato: From the First Report to Its Future Potential. FRONTIERS IN PLANT SCIENCE 2022; 12:768233. [PMID: 35082806 PMCID: PMC8784693 DOI: 10.3389/fpls.2021.768233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Potato (Solanum tuberosum L.) is a crop of world importance that produces tubers of high nutritional quality. It is considered one of the promising crops to overcome the challenges of poverty and hunger worldwide. However, it is exposed to different biotic and abiotic stresses that can cause significant losses in production. Thus, potato is a candidate of special relevance for improvements through conventional breeding and biotechnology. Since conventional breeding is time-consuming and challenging, genetic engineering provides the opportunity to introduce/switch-off genes of interest without altering the allelic combination that characterize successful commercial cultivars or to induce targeted sequence modifications by New Breeding Techniques. There is a variety of methods for potato improvement via genetic transformation. Most of them incorporate genes of interest into the nuclear genome; nevertheless, the development of plastid transformation protocols broadened the available approaches for potato breeding. Although all methods have their advantages and disadvantages, Agrobacterium-mediated transformation is the most used approach. Alternative methods such as particle bombardment, protoplast transfection with polyethylene glycol and microinjection are also effective. Independently of the DNA delivery approach, critical steps for a successful transformation are a rapid and efficient regeneration protocol and a selection system. Several critical factors affect the transformation efficiency: vector type, insert size, Agrobacterium strain, explant type, composition of the subculture media, selective agent, among others. Moreover, transient or stable transformation, constitutive or inducible promoters, antibiotic/herbicide resistance or marker-free strategies can be considered. Although great efforts have been made to optimize all the parameters, potato transformation protocols are highly genotype-dependent. Genome editing technologies provide promising tools in genetic engineering allowing precise modification of targeted sequences. Interestingly, transient expression of genome editing components in potato protoplasts was reported to generate edited plants without the integration of any foreign DNA, which is a valuable aspect from both a scientific and a regulatory perspective. In this review, current challenges and opportunities concerning potato genetic engineering strategies developed to date are discussed. We describe their critical parameters and constrains, and the potential application of the available tools for functional analyses or biotechnological purposes. Public concerns and safety issues are also addressed.
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Affiliation(s)
- Vanesa Nahirñak
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Natalia I. Almasia
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Matías N. González
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
| | - Gabriela A. Massa
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Cecilia A. Décima Oneto
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Sergio E. Feingold
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
| | - Horacio E. Hopp
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cecilia Vazquez Rovere
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
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11
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Gong Z, Cheng M, Botella JR. Non-GM Genome Editing Approaches in Crops. Front Genome Ed 2022; 3:817279. [PMID: 34977860 PMCID: PMC8715957 DOI: 10.3389/fgeed.2021.817279] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas-based genome editing technologies have the potential to fast-track large-scale crop breeding programs. However, the rigid cell wall limits the delivery of CRISPR/Cas components into plant cells, decreasing genome editing efficiency. Established methods, such as Agrobacterium tumefaciens-mediated or biolistic transformation have been used to integrate genetic cassettes containing CRISPR components into the plant genome. Although efficient, these methods pose several problems, including 1) The transformation process requires laborious and time-consuming tissue culture and regeneration steps; 2) many crop species and elite varieties are recalcitrant to transformation; 3) The segregation of transgenes in vegetatively propagated or highly heterozygous crops, such as pineapple, is either difficult or impossible; and 4) The production of a genetically modified first generation can lead to public controversy and onerous government regulations. The development of transgene-free genome editing technologies can address many problems associated with transgenic-based approaches. Transgene-free genome editing have been achieved through the delivery of preassembled CRISPR/Cas ribonucleoproteins, although its application is limited. The use of viral vectors for delivery of CRISPR/Cas components has recently emerged as a powerful alternative but it requires further exploration. In this review, we discuss the different strategies, principles, applications, and future directions of transgene-free genome editing methods.
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Affiliation(s)
- Zheng Gong
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Ming Cheng
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Jose R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
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12
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Ahmar S, Mahmood T, Fiaz S, Mora-Poblete F, Shafique MS, Chattha MS, Jung KH. Advantage of Nanotechnology-Based Genome Editing System and Its Application in Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:663849. [PMID: 34122485 PMCID: PMC8194497 DOI: 10.3389/fpls.2021.663849] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/26/2021] [Indexed: 05/05/2023]
Abstract
Agriculture is an important source of human food. However, current agricultural practices need modernizing and strengthening to fulfill the increasing food requirements of the growing worldwide population. Genome editing (GE) technology has been used to produce plants with improved yields and nutritional value as well as with higher resilience to herbicides, insects, and diseases. Several GE tools have been developed recently, including clustered regularly interspaced short palindromic repeats (CRISPR) with nucleases, a customizable and successful method. The main steps of the GE process involve introducing transgenes or CRISPR into plants via specific gene delivery systems. However, GE tools have certain limitations, including time-consuming and complicated protocols, potential tissue damage, DNA incorporation in the host genome, and low transformation efficiency. To overcome these issues, nanotechnology has emerged as a groundbreaking and modern technique. Nanoparticle-mediated gene delivery is superior to conventional biomolecular approaches because it enhances the transformation efficiency for both temporal (transient) and permanent (stable) genetic modifications in various plant species. However, with the discoveries of various advanced technologies, certain challenges in developing a short-term breeding strategy in plants remain. Thus, in this review, nanobased delivery systems and plant genetic engineering challenges are discussed in detail. Moreover, we have suggested an effective method to hasten crop improvement programs by combining current technologies, such as speed breeding and CRISPR/Cas, with nanotechnology. The overall aim of this review is to provide a detailed overview of nanotechnology-based CRISPR techniques for plant transformation and suggest applications for possible crop enhancement.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biological Sciences, Universidad de Talca, Talca, Chile
| | - Tahir Mahmood
- Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | | | | | - Ki-Hung Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
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13
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Genome editing reagent delivery in plants. Transgenic Res 2021; 30:321-335. [PMID: 33728594 DOI: 10.1007/s11248-021-00239-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/20/2021] [Indexed: 10/21/2022]
Abstract
Genome editing holds the potential for rapid crop improvement to meet the challenge of feeding the planet in a changing climate. The delivery of gene editing reagents into the plant cells has been dominated by plasmid vectors delivered using agrobacterium or particle bombardment. This approach involves the production of genetically engineered plants, which need to undergo regulatory approvals. There are various reagent delivery approaches available that have enabled the delivery of DNA-free editing reagents. They invariably involve the use of ribonucleoproteins (RNPs), especially in the case of CRISPR/Cas9-mediated gene editing. The explant of choice for most of the non-DNA approaches utilizes protoplasts as the recipient explant. While the editing efficiency is high in protoplasts, the ability to regenerate individual plants from edited protoplasts remains a challenge. There are various innovative delivery approaches being utilized to perform in planta edits that can be incorporated in the germline cells or inherited via seed. With the modification and adoption of various novel approaches currently being used in animal systems, it seems likely that non-transgenic genome editing will become routine in higher plants.
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14
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Demirer GS, Landry MP. Efficient Transient Gene Knock-down in Tobacco Plants Using Carbon Nanocarriers. Bio Protoc 2021; 11:e3897. [PMID: 33732771 DOI: 10.21769/bioprotoc.3897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/27/2022] Open
Abstract
Gene knock-down in plants is a useful approach to study genotype-phenotype relationships, render disease resistance to crops, and enable efficient biosynthesis of molecules in plants. Small interfering RNA (siRNA)-mediated gene silencing is one of the most common ways to achieve gene knock-down in plants. Traditionally, siRNA is delivered into intact plant cells by coding the siRNA sequences into DNA vectors, which are then delivered through viral and/or bacterial methods. In this protocol, we provide an alternative direct delivery method of siRNA molecules into intact plant cells for efficient transient gene knock-down in model tobacco plant, Nicotiana benthamiana, leaves. Our approach uses one dimensional carbon-based nanomaterials, single-walled carbon nanotubes (SWNTs), to deliver siRNA, and does not rely on viral/bacterial delivery. The distinct advantages of our method are i) there is no need for DNA coding of siRNA sequences, ii) this abiotic method could work in a broader range of plant species than biotic methods, and iii) there are fewer regulatory complications when using abiotic delivery methods, whereby gene silencing is transient without permanent modification of the plant genome. Graphic abstract.
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Affiliation(s)
- Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA 94720, USA.,Innovative Genomics Institute, Berkeley, CA 94702, USA.,Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
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15
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Abstract
Visualization of meiotic chromatin from pollen mother cells has become an essential technique to study meiosis in the model plant Arabidopsis thaliana. Here we present an advanced cytogenetic method that combines improved immunocytology with chromosome painting, thereby generating a tool to quantitatively analyze localization of proteins to any given genomic region. Proteins involved in different processes such as DNA double-strand break formation and recombinational repair can be visualized on meiotic chromatin with the additional feature of assessing their abundance at specific chromosomal locations.
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Affiliation(s)
- Jason Sims
- Max Perutz Labs, Department of Chromosome Biology, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota St. Paul, St. Paul, MN, USA
| | - Peter Schlögelhofer
- Max Perutz Labs, Department of Chromosome Biology, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
| | - Marie-Therese Kurzbauer
- Max Perutz Labs, Department of Chromosome Biology, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria.
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16
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Bhatta BP, Malla S. Improving Horticultural Crops via CRISPR/Cas9: Current Successes and Prospects. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1360. [PMID: 33066510 PMCID: PMC7602190 DOI: 10.3390/plants9101360] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/03/2020] [Accepted: 10/12/2020] [Indexed: 12/23/2022]
Abstract
Horticultural crops include a diverse array of crops comprising fruits, vegetables, nuts, flowers, aromatic and medicinal plants. They provide nutritional, medicinal, and aesthetic benefits to mankind. However, these crops undergo many biotic (e.g., diseases, pests) and abiotic stresses (e.g., drought, salinity). Conventional breeding strategies to improve traits in crops involve the use of a series of backcrossing and selection for introgression of a beneficial trait into elite germplasm, which is time and resource consuming. Recent new plant breeding tools such as clustered regularly interspaced short palindromic repeats (CRISPR) /CRISPR-associated protein-9 (Cas9) technique have the potential to be rapid, cost-effective, and precise tools for crop improvement. In this review article, we explore the CRISPR/Cas9 technology, its history, classification, general applications, specific uses in horticultural crops, challenges, existing resources, associated regulatory aspects, and the way forward.
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Affiliation(s)
- Bed Prakash Bhatta
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA;
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USA
| | - Subas Malla
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USA
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17
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Gentzel IN, Park CH, Bellizzi M, Xiao G, Gadhave KR, Murphree C, Yang Q, LaMantia J, Redinbaugh MG, Balint-Kurti P, Sit TL, Wang GL. A CRISPR/dCas9 toolkit for functional analysis of maize genes. PLANT METHODS 2020; 16:133. [PMID: 33024447 PMCID: PMC7532566 DOI: 10.1186/s13007-020-00675-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 09/24/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has become a powerful tool for functional genomics in plants. The RNA-guided nuclease can be used to not only generate precise genomic mutations, but also to manipulate gene expression when present as a deactivated protein (dCas9). RESULTS In this study, we describe a vector toolkit for analyzing dCas9-mediated activation (CRISPRa) or inactivation (CRISPRi) of gene expression in maize protoplasts. An improved maize protoplast isolation and transfection method is presented, as well as a description of dCas9 vectors to enhance or repress maize gene expression. CONCLUSIONS We anticipate that this maize protoplast toolkit will streamline the analysis of gRNA candidates and facilitate genetic studies of important trait genes in this transformation-recalcitrant plant.
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Affiliation(s)
- Irene N. Gentzel
- Department of Plant Pathology, The Ohio State University, 483B Kottman Hall, 2021 Coffey Road, Columbus, OH 43210 USA
| | - Chan Ho Park
- Department of Plant Pathology, The Ohio State University, 483B Kottman Hall, 2021 Coffey Road, Columbus, OH 43210 USA
| | - Maria Bellizzi
- Department of Plant Pathology, The Ohio State University, 483B Kottman Hall, 2021 Coffey Road, Columbus, OH 43210 USA
| | - Guiqing Xiao
- Department of Plant Pathology, The Ohio State University, 483B Kottman Hall, 2021 Coffey Road, Columbus, OH 43210 USA
| | - Kiran R. Gadhave
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695 USA
| | - Colin Murphree
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695 USA
| | - Qin Yang
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695 USA
| | - Jonathan LaMantia
- Corn, Soybean and Wheat Quality Research Unit, USDA-ARS, Wooster, OH 44691 USA
| | - Margaret G. Redinbaugh
- Department of Plant Pathology, The Ohio State University, 483B Kottman Hall, 2021 Coffey Road, Columbus, OH 43210 USA
- Corn, Soybean and Wheat Quality Research Unit, USDA-ARS, Wooster, OH 44691 USA
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695 USA
| | - Tim L. Sit
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695 USA
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, 483B Kottman Hall, 2021 Coffey Road, Columbus, OH 43210 USA
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18
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Sandhya D, Jogam P, Allini VR, Abbagani S, Alok A. The present and potential future methods for delivering CRISPR/Cas9 components in plants. J Genet Eng Biotechnol 2020; 18:25. [PMID: 32638190 PMCID: PMC7340682 DOI: 10.1186/s43141-020-00036-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/04/2020] [Indexed: 01/07/2023]
Abstract
Background CRISPR/Cas9 genome editing technology is a DNA manipulation tool for trait improvement. This technology has been demonstrated and successfully applied to edit the genome in various species of plants. The delivery of CRISPR/Cas9 components within rigid plant cells is very crucial for high editing efficiency. Here, we insight the strengths and weaknesses of each method of delivery. Main text The mutation efficiency of genome editing may vary and affected by different factors. Out of various factors, the delivery of CRISPR/Cas9 components into cells and genome is vital. The way of delivery defines whether the edited plant is transgenic or transgene-free. In many countries, the transgenic approach of improvement is a significant limitation in the regulatory approval of genetically modified crops. Gene editing provides an opportunity for generating transgene-free edited genome of the plant. Nevertheless, the mode of delivery of the CRISPR/Cas9 component is of crucial importance for genome modification in plants. Different delivery methods such as Agrobacterium-mediated, bombardment or biolistic method, floral-dip, and PEG-mediated protoplast are frequently applied to crops for efficient genome editing. Conclusion We have reviewed different delivery methods with prons and cons for genome editing in plants. A novel nanoparticle and pollen magnetofection-mediated delivery systems which would be very useful in the near future. Further, the factors affecting editing efficiency, such as the promoter, transformation method, and selection pressure, are discussed in the present review.
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Affiliation(s)
- Dulam Sandhya
- Department of Biotechnology, Kakatiya University, Warangal, Telangana, India
| | - Phanikanth Jogam
- Department of Biotechnology, Kakatiya University, Warangal, Telangana, India
| | | | - Sadanandam Abbagani
- Department of Biotechnology, Kakatiya University, Warangal, Telangana, India.
| | - Anshu Alok
- Department of Biotechnology, UIET, Panjab University, Chandigarh, India.
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19
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Facing Climate Change: Application of Microbial Biostimulants to Mitigate Stress in Horticultural Crops. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10060794] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In the current scenario of rapidly evolving climate change, crop plants are more frequently subjected to stresses of both abiotic and biotic origin, including exposure to unpredictable and extreme climatic events, changes in plant physiology, growing season and phytosanitary hazard, and increased losses up to 30% and 50% in global agricultural productions. Plants coevolved with microbial symbionts, which are involved in major functions both at the ecosystem and plant level. The use of microbial biostimulants, by exploiting this symbiotic interaction, represents a sustainable strategy to increase plant performances and productivity, even under stresses due to climate changes. Microbial biostimulants include beneficial fungi, yeasts and eubacteria sharing the ability to improve plant nutrition, growth, productivity and stress tolerance. This work reports the current knowledge on microbial biostimulants and provides a critical review on their possible use to mitigate the biotic and abiotic stresses caused by climate changes. Currently, available products often provide a general amelioration of cultural conditions, but their action mechanisms are largely undetermined and their effects often unreliable. Future research may lead to more specifically targeted products, based on the characterization of plant-microbe and microbial community interactions.
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20
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Tiedge K, Muchlinski A, Zerbe P. Genomics-enabled analysis of specialized metabolism in bioenergy crops: current progress and challenges. Synth Biol (Oxf) 2020; 5:ysaa005. [PMID: 32995549 PMCID: PMC7445794 DOI: 10.1093/synbio/ysaa005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/03/2020] [Accepted: 05/25/2020] [Indexed: 11/25/2022] Open
Abstract
Plants produce a staggering diversity of specialized small molecule metabolites that play vital roles in mediating environmental interactions and stress adaptation. This chemical diversity derives from dynamic biosynthetic pathway networks that are often species-specific and operate under tight spatiotemporal and environmental control. A growing divide between demand and environmental challenges in food and bioenergy crop production has intensified research on these complex metabolite networks and their contribution to crop fitness. High-throughput omics technologies provide access to ever-increasing data resources for investigating plant metabolism. However, the efficiency of using such system-wide data to decode the gene and enzyme functions controlling specialized metabolism has remained limited; due largely to the recalcitrance of many plants to genetic approaches and the lack of 'user-friendly' biochemical tools for studying the diverse enzyme classes involved in specialized metabolism. With emphasis on terpenoid metabolism in the bioenergy crop switchgrass as an example, this review aims to illustrate current advances and challenges in the application of DNA synthesis and synthetic biology tools for accelerating the functional discovery of genes, enzymes and pathways in plant specialized metabolism. These technologies have accelerated knowledge development on the biosynthesis and physiological roles of diverse metabolite networks across many ecologically and economically important plant species and can provide resources for application to precision breeding and natural product metabolic engineering.
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Affiliation(s)
- Kira Tiedge
- Department of Plant Biology, University of California-Davis, Davis, CA 95616, USA
| | - Andrew Muchlinski
- Department of Plant Biology, University of California-Davis, Davis, CA 95616, USA
| | - Philipp Zerbe
- Department of Plant Biology, University of California-Davis, Davis, CA 95616, USA
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21
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Demirer GS, Zhang H, Goh NS, Pinals RL, Chang R, Landry MP. Carbon nanocarriers deliver siRNA to intact plant cells for efficient gene knockdown. SCIENCE ADVANCES 2020; 6:eaaz0495. [PMID: 32637592 PMCID: PMC7314522 DOI: 10.1126/sciadv.aaz0495] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 05/08/2020] [Indexed: 05/19/2023]
Abstract
Posttranscriptional gene silencing (PTGS) is a powerful tool to understand and control plant metabolic pathways, which is central to plant biotechnology. PTGS is commonly accomplished through delivery of small interfering RNA (siRNA) into cells. Standard plant siRNA delivery methods (Agrobacterium and viruses) involve coding siRNA into DNA vectors and are only tractable for certain plant species. Here, we develop a nanotube-based platform for direct delivery of siRNA and show high silencing efficiency in intact plant cells. We demonstrate that nanotubes successfully deliver siRNA and silence endogenous genes, owing to effective intracellular delivery and nanotube-induced protection of siRNA from nuclease degradation. This study establishes that nanotubes could enable a myriad of plant biotechnology applications that rely on RNA delivery to intact cells.
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Affiliation(s)
- Gozde S. Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Natalie S. Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rebecca L. Pinals
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Roger Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Markita P. Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute, Berkeley, CA 94702, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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22
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Lai M, Liu G, Li R, Bai H, Zhao J, Xiao P, Mei J. Hsa_circ_0079662 induces the resistance mechanism of the chemotherapy drug oxaliplatin through the TNF-α pathway in human colon cancer. J Cell Mol Med 2020; 24:5021-5027. [PMID: 32243061 PMCID: PMC7205783 DOI: 10.1111/jcmm.15122] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/24/2019] [Accepted: 12/05/2019] [Indexed: 12/21/2022] Open
Abstract
The aim of the study was to research the biological functions of circRNA (hsa_circ_0079662) and its underlying mechanism in colorectal cancer. Drug-resistant cell lines (HT29-LOHP, HCT116-LOHP, HCT8-LOHP) were separately dealt with oxaliplatin concentration gradient (0.1-10 μmol/L). Real-time PCR, Western blotting, dual-luciferase assay, miRNA pull-down assay, coimmunoprecipitation and ELASA were performed to explore the mechanism of chemotherapy drug oxaliplatin resistance in CRC. The results showed that the expression of hsa_circ_0079662 was increased in drug-resistant cell lines by RT-PCR. The expression of HOXA9, TRIP6, Vcam-1, VEGFC, MMP3, MMP9 and MMP14 was higher by Western blotting. Interaction between HOXA9 and TRIP6 in CO-IP detection. Additionally, the cytokines TNF-α, IL-1 and IL-6 were also found. In conclusion, hsa_circ_0079662, as a ceRNA binding with hsa-mir-324-5p, can regulate target gene HOXA9 and induced the mechanism of chemotherapy drug oxaliplatin resistance in CRC through the TNF-α pathway in human colon cancer.
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Affiliation(s)
- Mingfen Lai
- Department of OncologyThe Second Clinical Medical School of Southern Medical UniversityGuangzhouChina
| | - Guiju Liu
- Department of OncologyZhengzhou People's Hospital Affiliated to Southern Medical UniversityZhengzhouChina
| | - Ruijun Li
- Department of OncologyZhengzhou People's Hospital Affiliated to Southern Medical UniversityZhengzhouChina
| | - Hua Bai
- Department of OncologyZhengzhou People's Hospital Affiliated to Southern Medical UniversityZhengzhouChina
| | - Jizhi Zhao
- Department of OncologyZhengzhou People's Hospital Affiliated to Southern Medical UniversityZhengzhouChina
| | - Peng Xiao
- Department of OncologyZhengzhou People's Hospital Affiliated to Southern Medical UniversityZhengzhouChina
| | - Jiazhuan Mei
- Department of OncologyZhengzhou People's Hospital Affiliated to Southern Medical UniversityZhengzhouChina
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Rustgi S, Kashyap S, Ankrah N, von Wettstein D. Use of Microspore-Derived Calli as Explants for Biolistic Transformation of Common Wheat. Methods Mol Biol 2020; 2124:263-279. [PMID: 32277459 DOI: 10.1007/978-1-0716-0356-7_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
There are specific advantages of using microspores as explants: (1) A small number of explant donors are required to obtain the desired number of pollen embryoids for genetic transformation and (2) microspores constitute a synchronous mass of haploid cells, which are transformable by various means and convertible to doubled haploids therefore allow production of homozygous genotypes in a single generation. Additionally, it has been demonstrated in wheat and other crops that microspores can be easily induced to produce embryoids and biolistic approach to produce a large number of transformants. In view of these listed advantages, we optimized the use of microspore-derived calli for biolistic transformation of wheat. The procedure takes about 6 months to obtain the viable transformants in the spring wheat background. In the present communication, we demonstrated the use of this method to produce the reduced immunogenicity wheat genotypes.
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Affiliation(s)
- Sachin Rustgi
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Centre, Florence, SC, USA. .,Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
| | - Samneet Kashyap
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Centre, Florence, SC, USA
| | - Nii Ankrah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Diter von Wettstein
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
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Wolter F, Puchta H. In planta gene targeting can be enhanced by the use of CRISPR/Cas12a. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1083-1094. [PMID: 31381206 DOI: 10.1111/tpj.14488] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 07/08/2019] [Accepted: 07/29/2019] [Indexed: 05/20/2023]
Abstract
The controlled change of plant genomes by homologous recombination (HR) is still difficult to achieve. We previously developed the in planta gene targeting (ipGT) technology which depends on the simultaneous activation of the target locus by a double-strand break and the excision of the target vector. Whereas the use of SpCas9 resulted in low ipGT frequencies in Arabidopsis, we were recently able to improve the efficiency by using egg cell-specific expression of the potent but less broadly applicable SaCas9 nuclease. In this study, we now tested whether we could improve ipGT further, by either performing it in cells with enhanced intrachromosomal HR efficiencies or by the use of Cas12a, a different kind of CRISPR/Cas nuclease with an alternative cutting mechanism. We could show before that plants possess three kinds of DNA ATPase complexes, which all lead to instabilities of homologous genomic repeats if lost by mutation. As these proteins act in independent pathways, we tested ipGT in double mutants in which intrachromosomal HR is enhanced 20-80-fold. However, we were not able to obtain higher ipGT frequencies, indicating that mechanisms for gene targeting (GT) and chromosomal repeat-induced HR differ. However, using LbCas12a, the GT frequencies were higher than with SaCas9, despite a lower non-homologous end-joining (NHEJ) induction efficiency, demonstrating the particular suitability of Cas12a to induce HR. As SaCas9 has substantial restrictions due to its longer GC rich PAM sequence, the use of LbCas12a with its AT-rich PAM broadens the range of ipGT drastically, particularly when targeting in CG-deserts like promoters and introns.
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Affiliation(s)
- Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
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Farooq N, Nawaz MA, Mukhtar Z, Ali I, Hundleby P, Ahmad N. Investigating the In Vitro Regeneration Potential of Commercial Cultivars of Brassica. PLANTS (BASEL, SWITZERLAND) 2019; 8:E558. [PMID: 31795525 PMCID: PMC6963692 DOI: 10.3390/plants8120558] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 11/24/2019] [Accepted: 11/26/2019] [Indexed: 01/11/2023]
Abstract
In vitro regeneration is a pre-requisite for developing transgenic plants through tissue culture-based genetic engineering approaches. Huge variations among different genotypes of the genus Brassica necessitate the identification of a set of regeneration conditions for a genotype, which can be reliably used in transformation experiments. In this study, we evaluated the morphogenesis potential of four commercial cultivars (Faisal canola, Punjab canola, Aari canola, Nifa Gold) and one model, Westar, from four different explants namely cotyledons, hypocotyls, petioles and roots on three different Brassica regeneration protocols, BRP-I, -II and -III. The regeneration efficiency was observed in the range of 6-73%, 4-79.3%, 0-50.6%, and 0-42.6% from cotyledons, petioles, hypocotyls and roots, respectively, whereas, the regeneration response in terms of average shoots per explant was found to be 0.76-10.9, 0.2-3.2, 0-3.4 and 0-2.7 from these explants. Of the commercial varieties tested, almost all varieties showed poorer regeneration than Westar except Aari canola. In comparison to Westar, its regeneration frequency from cotyledons was up to 7.5-fold higher on BRP-I, while it produced up to 21.9-fold more shoots per explant. Our data show that the explant has strong influence on the regeneration response, ranging from 24% to 92%. While the growth of commercial cultivars was least affected by the regeneration conditions provided, the effect on Westar was twice that of the commercial cultivars. After determining the optimal explant type and regeneration conditions, we also determined the minimum kanamycin concentration levels required to selectively inhibit the growth of untransformed cells for these cultivars. Regenerated shoots of Aari canola could be successfully grown to maturity within 16-18 weeks, with no altered phenotype noted and normal seed yields obtained. Therefore, the commercial variety, Aari canola, could be a good candidate for future genetic transformation studies.
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Affiliation(s)
- Nisma Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan
| | - Muhammad Asif Nawaz
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan
| | - Iftikhar Ali
- Nuclear Institute for Agriculture and Biology, Faisalabad 38000, Pakistan
| | - Penny Hundleby
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Niaz Ahmad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan
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Akhtar K, Wang W, Ren G, Khan A, Feng Y, Yang G, Wang H. Integrated use of straw mulch with nitrogen fertilizer improves soil functionality and soybean production. ENVIRONMENT INTERNATIONAL 2019; 132:105092. [PMID: 31442740 DOI: 10.1016/j.envint.2019.105092] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/08/2019] [Accepted: 08/10/2019] [Indexed: 06/10/2023]
Abstract
Mulching can effectively maintain and improve soil health and functionality. The mechanisms, however, have not been fully elucidated. Therefore, the effects of temperature on the biogeochemical properties of soil were investigated in the present study in relation to nitrogen management and soil functionality. The results of the 3-year field experiments showed that integrated straw mulch (S) and nitrogen fertilizer (N) treatments enhanced the activities of soil urease, invertase, alkaline phosphatase, and catalase by >1.8, 2.1, 2.0 and 1.4 fold, respectively, compared with the control treatment. Furthermore, these treatments increased soil available N by 28%, phosphorus by 45%, and potassium by 55%. In general, the soil organic carbon, dissolved carbon and labile organic carbon content in the treated plot were approximately 1.2-2.9 folds greater than in the control plot. These improvements in soil fertility and carbon indices increased the biomass and grain yield of soybean (67 and 75%, respectively) during the three-year study period. During 2015-2017, the straw mulch and nitrogen fertilizer treatment increased the soil moisture (23%) and decreased the soil temperature (8%) in comparison to the control in the 0-0.2 m soil depth and, therefore, improved soil enzyme activities, nutrient availability, and carbon stocks, and ultimately, soil functionality and sustainability, in the semiarid region.
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Affiliation(s)
- Kashif Akhtar
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Northwest A & F University, Yangling 712100, China; The Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Yangling 712100, China
| | - Weiyu Wang
- College of Agronomy, Northwest A & F University, Yangling 712100, China; The Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Yangling 712100, China
| | - Guangxin Ren
- College of Agronomy, Northwest A & F University, Yangling 712100, China; The Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Yangling 712100, China
| | - Ahmad Khan
- Department of Agronomy, Faculty of Crop Production, The University of Agriculture Peshawar, Khyber Pakhtunkhwa 25000, Pakistan
| | - Yongzhong Feng
- College of Agronomy, Northwest A & F University, Yangling 712100, China; The Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Yangling 712100, China
| | - Gaihe Yang
- College of Agronomy, Northwest A & F University, Yangling 712100, China; The Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Yangling 712100, China.
| | - Haiyan Wang
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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Arndell T, Sharma N, Langridge P, Baumann U, Watson-Haigh NS, Whitford R. gRNA validation for wheat genome editing with the CRISPR-Cas9 system. BMC Biotechnol 2019; 19:71. [PMID: 31684940 PMCID: PMC6829922 DOI: 10.1186/s12896-019-0565-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/30/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The CRISPR-Cas9 system is a powerful and versatile tool for crop genome editing. However, achieving highly efficient and specific editing in polyploid species can be a challenge. The efficiency and specificity of the CRISPR-Cas9 system depends critically on the gRNA used. Here, we assessed the activities and specificities of seven gRNAs targeting 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in hexaploid wheat protoplasts. EPSPS is the biological target of the widely used herbicide glyphosate. RESULTS The seven gRNAs differed substantially in their on-target activities, with mean indel frequencies ranging from 0% to approximately 20%. There was no obvious correlation between experimentally determined and in silico predicted on-target gRNA activity. The presence of a single mismatch within the seed region of the guide sequence greatly reduced but did not abolish gRNA activity, whereas the presence of an additional mismatch, or the absence of a PAM, all but abolished gRNA activity. Large insertions (≥20 bp) of DNA vector-derived sequence were detected at frequencies up to 8.5% of total indels. One of the gRNAs exhibited several properties that make it potentially suitable for the development of non-transgenic glyphosate resistant wheat. CONCLUSIONS We have established a rapid and reliable method for gRNA validation in hexaploid wheat protoplasts. The method can be used to identify gRNAs that have favourable properties. Our approach is particularly suited to polyploid species, but should be applicable to any plant species amenable to protoplast transformation.
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Affiliation(s)
- Taj Arndell
- Present address: CSIRO, Agriculture and Food, Canberra, ACT Australia
| | - Niharika Sharma
- Present address: New South Wales Department of Primary Industries, Research Excellence, Orange, NSW Australia
| | - Peter Langridge
- School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
| | - Ute Baumann
- School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
| | - Nathan S. Watson-Haigh
- Present address: Bioinformatics Hub, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Ryan Whitford
- School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
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Demirer GS, Zhang H, Goh NS, González-Grandío E, Landry MP. Carbon nanotube-mediated DNA delivery without transgene integration in intact plants. Nat Protoc 2019; 14:2954-2971. [PMID: 31534231 PMCID: PMC10496593 DOI: 10.1038/s41596-019-0208-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/06/2019] [Indexed: 11/09/2022]
Abstract
Exogenous biomolecule delivery into plants is difficult because the plant cell wall poses a dominant transport barrier, thereby limiting the efficiency of plant genetic engineering. Traditional DNA delivery methods for plants suffer from host-species limitations, low transformation efficiencies, tissue damage, or unavoidable and uncontrolled DNA integration into the host genome. We have demonstrated efficient plasmid DNA delivery into intact plants of several species with functionalized high-aspect-ratio carbon nanotube (CNT) nanoparticles (NPs), enabling efficient DNA delivery into a variety of non-model plant species (arugula, wheat, and cotton) and resulting in high protein expression levels without transgene integration. Herein, we provide a protocol that can be implemented by plant biologists and adapted to produce functionalized single-walled CNTs (SWNTs) with surface chemistries optimized for delivery of plasmid DNA in a plant species-independent manner. This protocol describes how to prepare, construct, and optimize polyethylenimine (PEI)-functionalized SWNTs and perform plasmid DNA loading. The authors also provide guidance on material characterization, gene expression evaluation, and storage conditions. The entire protocol, from the covalent functionalization of SWNTs to expression quantification, can be completed in 5 d.
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Affiliation(s)
- Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Eduardo González-Grandío
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute (IGI), Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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29
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Jansing J, Schiermeyer A, Schillberg S, Fischer R, Bortesi L. Genome Editing in Agriculture: Technical and Practical Considerations. Int J Mol Sci 2019; 20:E2888. [PMID: 31200517 PMCID: PMC6627516 DOI: 10.3390/ijms20122888] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/29/2019] [Accepted: 06/06/2019] [Indexed: 01/31/2023] Open
Abstract
The advent of precise genome-editing tools has revolutionized the way we create new plant varieties. Three groups of tools are now available, classified according to their mechanism of action: Programmable sequence-specific nucleases, base-editing enzymes, and oligonucleotides. The corresponding techniques not only lead to different outcomes, but also have implications for the public acceptance and regulatory approval of genome-edited plants. Despite the high efficiency and precision of the tools, there are still major bottlenecks in the generation of new and improved varieties, including the efficient delivery of the genome-editing reagents, the selection of desired events, and the regeneration of intact plants. In this review, we evaluate current delivery and regeneration methods, discuss their suitability for important crop species, and consider the practical aspects of applying the different genome-editing techniques in agriculture.
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Affiliation(s)
- Julia Jansing
- Aachen-Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Brightlands Chemelot Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands.
| | - Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany.
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany.
| | - Rainer Fischer
- Indiana Biosciences Research Institute (IBRI), 1345 W. 16th St. Suite 300, Indianapolis, IN 46202, USA.
| | - Luisa Bortesi
- Aachen-Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Brightlands Chemelot Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands.
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30
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Demirer GS, Zhang H, Matos JL, Goh NS, Cunningham FJ, Sung Y, Chang R, Aditham AJ, Chio L, Cho MJ, Staskawicz B, Landry MP. High aspect ratio nanomaterials enable delivery of functional genetic material without DNA integration in mature plants. NATURE NANOTECHNOLOGY 2019; 14:456-464. [PMID: 30804481 PMCID: PMC10461892 DOI: 10.1038/s41565-019-0382-5] [Citation(s) in RCA: 240] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/18/2019] [Indexed: 05/19/2023]
Abstract
Genetic engineering of plants is at the core of sustainability efforts, natural product synthesis and crop engineering. The plant cell wall is a barrier that limits the ease and throughput of exogenous biomolecule delivery to plants. Current delivery methods either suffer from host-range limitations, low transformation efficiencies, tissue damage or unavoidable DNA integration into the host genome. Here, we demonstrate efficient diffusion-based biomolecule delivery into intact plants of several species with pristine and chemically functionalized high aspect ratio nanomaterials. Efficient DNA delivery and strong protein expression without transgene integration is accomplished in Nicotiana benthamiana (Nb), Eruca sativa (arugula), Triticum aestivum (wheat) and Gossypium hirsutum (cotton) leaves and arugula protoplasts. We find that nanomaterials not only facilitate biomolecule transport into plant cells but also protect polynucleotides from nuclease degradation. Our work provides a tool for species-independent and passive delivery of genetic material, without transgene integration, into plant cells for diverse biotechnology applications.
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Affiliation(s)
- Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Juliana L Matos
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute (IGI), Berkeley, CA, USA
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Francis J Cunningham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Younghun Sung
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Roger Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Abhishek J Aditham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Linda Chio
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Myeong-Je Cho
- Innovative Genomics Institute (IGI), Berkeley, CA, USA
| | - Brian Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute (IGI), Berkeley, CA, USA
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute (IGI), Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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31
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Bartkowski B, Baum CM. Dealing With Rejection: An Application of the Exit-Voice Framework to Genome-Edited Food. Front Bioeng Biotechnol 2019; 7:57. [PMID: 30968021 PMCID: PMC6439340 DOI: 10.3389/fbioe.2019.00057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/04/2019] [Indexed: 01/31/2023] Open
Abstract
Genome editing has been hailed as both a revolutionary technology and potential solution to many agriculture-related and sustainability problems. However, owing to the past challenges and controversy generated by widespread rejection of genetic engineering, especially once applied to agriculture and food production, such innovations have also prompted their fair share of concern. Generally speaking, much of the discussion centers on the inadequacy or uncertainty of current regulatory regimes, partly owing to the vastly different approaches in the European Union and United States. Insofar as this focus on regulatory regimes is stimulated by the desire to bridge the divide between proponents and critics of genome editing, it risks losing sight of an essential aim of regulatory action: effectively responding to and fostering trust in consumers and the public. In this article, we thus assign priority to understanding the contours of individual dissatisfaction and its related responses. Toward this end, we apply and extend Hirschman's exit-voice framework to bring together, synthesize, and give much-needed substance to the diverse expressions of dissatisfaction and discontent with novel genome-editing technologies. Through the resulting synthetic framework, we then identify and evaluate which governance approaches can prevent actions seen to be problematic and, moreover, open up the space for a more active public. In this context, we devote specific attention to (i) use of labeling as a means to enable "exit" of consumers from markets and (ii) public deliberation as a possible expression of "voice." Indeed, both options are proposed and utilized in the context of genome editing, e.g., as a way for skeptical consumers to express their viewpoints, seek change in prevailing food systems, and navigate the conflicts and tensions from applying unique sets of values to assess the balance of risks and benefits. So far missing, though, is an evaluation of how well such efforts offer effective means for public expression, which is why we also link this framework to the wider issue of consumer sovereignty. Having done so, we conclude with a brief commentary on the potential and limitations of both options in the existing institutional framework of the EU.
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Affiliation(s)
- Bartosz Bartkowski
- Department of Economics, UFZ–Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Chad M. Baum
- Institute for Food and Resource Economics and Bioeconomy Science Center, University of BonnBonn, Germany
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32
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González MN, Massa GA, Andersson M, Turesson H, Olsson N, Fält AS, Storani L, Décima Oneto CA, Hofvander P, Feingold SE. Reduced Enzymatic Browning in Potato Tubers by Specific Editing of a Polyphenol Oxidase Gene via Ribonucleoprotein Complexes Delivery of the CRISPR/Cas9 System. FRONTIERS IN PLANT SCIENCE 2019; 10:1649. [PMID: 31998338 PMCID: PMC6962139 DOI: 10.3389/fpls.2019.01649] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/22/2019] [Indexed: 05/05/2023]
Abstract
Polyphenol Oxidases (PPOs) catalyze the conversion of phenolic substrates to quinones, leading to the formation of dark-colored precipitates in fruits and vegetables. This process, known as enzymatic browning, is the cause of undesirable changes in organoleptic properties and the loss of nutritional quality in plant-derived products. In potato (Solanum tubersoum L.), PPOs are encoded by a multi-gene family with different expression patterns. Here, we have studied the application of the CRISPR/Cas9 system to induce mutations in the StPPO2 gene in the tetraploid cultivar Desiree. We hypothesized that the specific editing of this target gene would result in a lower PPO activity in the tuber with the consequent reduction of the enzymatic browning. Ribonucleoprotein complexes (RNPs), formed by two sgRNAs and Cas9 nuclease, were transfected to potato protoplasts. Up to 68% of regenerated plants contained mutations in at least one allele of the target gene, while 24% of edited lines carried mutations in all four alleles. No off-target mutations were identified in other analyzed StPPO genes. Mutations induced in the four alleles of StPPO2 gene, led to lines with a reduction of up to 69% in tuber PPO activity and a reduction of 73% in enzymatic browning, compared to the control. Our results demonstrate that the CRISPR/Cas9 system can be applied to develop potato varieties with reduced enzymatic browning in tubers, by the specific editing of a single member of the StPPO gene family.
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Affiliation(s)
- Matías Nicolás González
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio de Agrobiotecnología, INTA - EEA Balcarce, Balcarce, Argentina
- *Correspondence: Matías Nicolás González,
| | - Gabriela Alejandra Massa
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio de Agrobiotecnología, INTA - EEA Balcarce, Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Helle Turesson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Niklas Olsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Ann-Sofie Fält
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Leonardo Storani
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio de Agrobiotecnología, INTA - EEA Balcarce, Balcarce, Argentina
| | | | - Per Hofvander
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Brand A, Quimbaya M, Tohme J, Chavarriaga-Aguirre P. Arabidopsis LEC1 and LEC2 Orthologous Genes Are Key Regulators of Somatic Embryogenesis in Cassava. FRONTIERS IN PLANT SCIENCE 2019; 10:673. [PMID: 31191582 PMCID: PMC6541005 DOI: 10.3389/fpls.2019.00673] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 05/03/2019] [Indexed: 05/22/2023]
Abstract
High genotype-dependent variation in friable embryogenic callus (FEC) induction and subsequent somaclonal variation constitute bottlenecks for the application and scaling of genetic transformation (GT) technology to more farmer- and industry-preferred cassava varieties. The understanding and identification of molecular factors underlying embryogenic development in cassava may help to overcome these constraints. Here, we described the Arabidopsis thaliana LEAFY COTYLEDON (LEC) LEC1 and LEC2 orthologous genes in cassava, designated as MeLEC1 and MeLEC2, respectively. Expression analyses showed that both, MeLEC1 and MeLEC2, are expressed at higher levels in somatic embryogenic (SE) tissues in contrast with differentiated mature tissues. The rapid expression increase of MeLEC genes at early SE induction times strongly suggests that they are involved in the transition from a somatic to an embryonic state, and probably, in the competence acquisition for SE development in cassava. The independent overexpression of the MeLEC genes resulted in different regenerated events with embryogenic characteristics such as MeLEC1OE plants with cotyledon-like leaves and MeLEC2OE plants with somatic-like embryos that emerged over the surface of mature leaves. Transcript increases of other embryo-specific regulating factors were also detected in MeLECOE plants, supporting their mutual interaction in the embryo development coordination. The single overexpression of MeLEC2 was enough to reprogram the vegetative cells and induce direct somatic embryogenesis, which converts this gene into a tool that could improve the recovery of transformed plants of recalcitrant genotypes. The identification of MeLEC genes contributes not only to improve our understanding of SE process in cassava, but also provides viable alternatives to optimize GT and advance in gene editing in this crop, through the development of genotype-independent protocols.
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Affiliation(s)
- Alejandro Brand
- International Center for Tropical Agriculture, Cali, Colombia
| | - Mauricio Quimbaya
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana Cali, Cali, Colombia
| | - Joe Tohme
- International Center for Tropical Agriculture, Cali, Colombia
| | - Paul Chavarriaga-Aguirre
- International Center for Tropical Agriculture, Cali, Colombia
- *Correspondence: Paul Chavarriaga-Aguirre,
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Busov VB. Manipulation of Growth and Architectural Characteristics in Trees for Increased Woody Biomass Production. FRONTIERS IN PLANT SCIENCE 2018; 9:1505. [PMID: 30459780 PMCID: PMC6232754 DOI: 10.3389/fpls.2018.01505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/26/2018] [Indexed: 06/09/2023]
Abstract
Growth and architectural traits in trees are economically and environmentally important and thus of considerable importance to the improvement of forest and fruit trees. These traits are complex and result from the operation of a number of molecular mechanisms. This review will focus on the regulation of crown architecture, secondary woody growth and adventitious rooting. These traits and processes have significant impact on deployment, management, and productivity of tree crops. The majority of the described work comes from experiments in model plants, poplar, apple, peach, and plum because these species allow functional analysis of the involved genes and have significant genomics resources. However, these studies convincingly show conserved mechanisms for elaboration of specific growth and architectural traits. The conservation of these mechanisms suggest that they can be used as a blueprint for the improvement of these traits and processes in phylogenetically diverse tree crops. We will specifically consider the involvement of flowering time, transcription factors and hormone-associated genes. The review will also discuss the impact of recent technological advances as well as the challenges to the dissection of these traits in trees.
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Lee J, Arun Kumar S, Jhan YY, Bishop CJ. Engineering DNA vaccines against infectious diseases. Acta Biomater 2018; 80:31-47. [PMID: 30172933 PMCID: PMC7105045 DOI: 10.1016/j.actbio.2018.08.033] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 08/14/2018] [Accepted: 08/23/2018] [Indexed: 12/30/2022]
Abstract
Engineering vaccine-based therapeutics for infectious diseases is highly challenging, as trial formulations are often found to be nonspecific, ineffective, thermally or hydrolytically unstable, and/or toxic. Vaccines have greatly improved the therapeutic landscape for treating infectious diseases and have significantly reduced the threat by therapeutic and preventative approaches. Furthermore, the advent of recombinant technologies has greatly facilitated growth within the vaccine realm by mitigating risks such as virulence reversion despite making the production processes more cumbersome. In addition, seroconversion can also be enhanced by recombinant technology through kinetic and nonkinetic approaches, which are discussed herein. Recombinant technologies have greatly improved both amino acid-based vaccines and DNA-based vaccines. A plateau of interest has been reached between 2001 and 2010 for the scientific community with regard to DNA vaccine endeavors. The decrease in interest may likely be attributed to difficulties in improving immunogenic properties associated with DNA vaccines, although there has been research demonstrating improvement and optimization to this end. Despite improvement, to the extent of our knowledge, there are currently no regulatory body-approved DNA vaccines for human use (four vaccines approved for animal use). This article discusses engineering DNA vaccines against infectious diseases while discussing advantages and disadvantages of each, with an emphasis on applications of these DNA vaccines. Statement of Significance This review paper summarizes the state of the engineered/recombinant DNA vaccine field, with a scope entailing “Engineering DNA vaccines against infectious diseases”. We endeavor to emphasize recent advances, recapitulating the current state of the field. In addition to discussing DNA therapeutics that have already been clinically translated, this review also examines current research developments, and the challenges thwarting further progression. Our review covers: recombinant DNA-based subunit vaccines; internalization and processing; enhancing immune protection via adjuvants; manufacturing and engineering DNA; the safety, stability and delivery of DNA vaccines or plasmids; controlling gene expression using plasmid engineering and gene circuits; overcoming immunogenic issues; and commercial successes. We hope that this review will inspire further research in DNA vaccine development.
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Bull SE, Seung D, Chanez C, Mehta D, Kuon JE, Truernit E, Hochmuth A, Zurkirchen I, Zeeman SC, Gruissem W, Vanderschuren H. Accelerated ex situ breeding of GBSS- and PTST1-edited cassava for modified starch. SCIENCE ADVANCES 2018; 4:eaat6086. [PMID: 30191180 PMCID: PMC6124905 DOI: 10.1126/sciadv.aat6086] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/20/2018] [Indexed: 05/12/2023]
Abstract
Crop diversification required to meet demands for food security and industrial use is often challenged by breeding time and amenability of varieties to genome modification. Cassava is one such crop. Grown for its large starch-rich storage roots, it serves as a staple food and a commodity in the multibillion-dollar starch industry. Starch is composed of the glucose polymers amylopectin and amylose, with the latter strongly influencing the physicochemical properties of starch during cooking and processing. We demonstrate that CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9)-mediated targeted mutagenesis of two genes involved in amylose biosynthesis, PROTEIN TARGETING TO STARCH (PTST1) or GRANULE BOUND STARCH SYNTHASE (GBSS), can reduce or eliminate amylose content in root starch. Integration of the Arabidopsis FLOWERING LOCUS T gene in the genome-editing cassette allowed us to accelerate flowering-an event seldom seen under glasshouse conditions. Germinated seeds yielded S1, a transgene-free progeny that inherited edited genes. This attractive new plant breeding technique for modified cassava could be extended to other crops to provide a suite of novel varieties with useful traits for food and industrial applications.
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Affiliation(s)
- Simon E. Bull
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
- Corresponding author. (S.E.B.); (H.V.)
| | - David Seung
- Plant Biochemistry, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Christelle Chanez
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Devang Mehta
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Joel-Elias Kuon
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Elisabeth Truernit
- Plant Biochemistry, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Anton Hochmuth
- Plant Biochemistry, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Irene Zurkirchen
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Samuel C. Zeeman
- Plant Biochemistry, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Wilhelm Gruissem
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Hervé Vanderschuren
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
- Plant Genetics, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
- Corresponding author. (S.E.B.); (H.V.)
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37
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Wolter F, Klemm J, Puchta H. Efficient in planta gene targeting in Arabidopsis using egg cell-specific expression of the Cas9 nuclease of Staphylococcus aureus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:735-746. [PMID: 29573495 DOI: 10.1111/tpj.13893] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/17/2018] [Accepted: 02/21/2018] [Indexed: 05/22/2023]
Abstract
Gene targeting (GT), the programmed change of genomic sequences by homologous recombination (HR), is still a major challenge in plants. We previously developed an in planta GT strategy by simultaneously releasing from the genome a dsDNA donor molecule and creating a double-stranded break (DSB) at a specific site within the targeted gene. Using Cas9 form Streptococcus pyogenes (SpCas9) under the control of a ubiquitin gene promoter, we obtained seeds harbouring GT events, although at a low frequency. In the present research we tested different developmentally controlled promotors and different kinds of DNA lesions for their ability to enhance GT of the acetolactate synthase (ALS) gene of Arabidopsis. For this purpose, we used Staphylococcus aureus Cas9 (SaCas9) nuclease and the SpCas9 nickase in various combinations. Thus, we analysed the effect of single-stranded break (SSB) activation of a targeted gene and/or the HR donor region. Moreover, we tested whether DSBs with 5' or 3' overhangs can improve in planta GT. Interestingly, the use of the SaCas9 nuclease controlled by an egg cell-specific promoter was the most efficient: depending on the line, in the very best case 6% of all seeds carried GT events. In a third of all lines, the targeting occurred around the 1% range of the tested seeds. Molecular analysis revealed that in about half of the cases perfect HR of both DSB ends occurred. Thus, using the improved technology, it should now be feasible to introduce any directed change into the Arabidopsis genome at will.
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Affiliation(s)
- Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Jeannette Klemm
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
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Roggenkamp E, Giersch RM, Schrock MN, Turnquist E, Halloran M, Finnigan GC. Tuning CRISPR-Cas9 Gene Drives in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2018; 8:999-1018. [PMID: 29348295 PMCID: PMC5844318 DOI: 10.1534/g3.117.300557] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/16/2018] [Indexed: 12/11/2022]
Abstract
Control of biological populations is an ongoing challenge in many fields, including agriculture, biodiversity, ecological preservation, pest control, and the spread of disease. In some cases, such as insects that harbor human pathogens (e.g., malaria), elimination or reduction of a small number of species would have a dramatic impact across the globe. Given the recent discovery and development of the CRISPR-Cas9 gene editing technology, a unique arrangement of this system, a nuclease-based "gene drive," allows for the super-Mendelian spread and forced propagation of a genetic element through a population. Recent studies have demonstrated the ability of a gene drive to rapidly spread within and nearly eliminate insect populations in a laboratory setting. While there are still ongoing technical challenges to design of a more optimal gene drive to be used in wild populations, there are still serious ecological and ethical concerns surrounding the nature of this powerful biological agent. Here, we use budding yeast as a safe and fully contained model system to explore mechanisms that might allow for programmed regulation of gene drive activity. We describe four conserved features of all CRISPR-based drives and demonstrate the ability of each drive component-Cas9 protein level, sgRNA identity, Cas9 nucleocytoplasmic shuttling, and novel Cas9-Cas9 tandem fusions-to modulate drive activity within a population.
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Affiliation(s)
- Emily Roggenkamp
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Rachael M Giersch
- Department of Biology, Kansas State University, Manhattan, Kansas 66506
| | - Madison N Schrock
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
- Department of Biology, Kansas State University, Manhattan, Kansas 66506
| | - Emily Turnquist
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Megan Halloran
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Gregory C Finnigan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
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Basgall EM, Goetting SC, Goeckel ME, Giersch RM, Roggenkamp E, Schrock MN, Halloran M, Finnigan GC. Gene drive inhibition by the anti-CRISPR proteins AcrIIA2 and AcrIIA4 in Saccharomyces cerevisiae. MICROBIOLOGY-SGM 2018; 164:464-474. [PMID: 29488867 PMCID: PMC5982135 DOI: 10.1099/mic.0.000635] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Given the widespread use and application of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas gene editing system across many fields, a major focus has been the development, engineering and discovery of molecular means to precisely control and regulate the enzymatic function of the Cas9 nuclease. To date, a variety of Cas9 variants and fusion assemblies have been proposed to provide temporally inducible and spatially controlled editing functions. The discovery of a new class of ‘anti-CRISPR’ proteins, evolved from bacteriophage in response to the prokaryotic nuclease-based immune system, provides a new platform for control over genomic editing. One Cas9-based application of interest to the field of population control is that of the ‘gene drive’. Here, we demonstrate use of the AcrIIA2 and AcrIIA4 proteins to inhibit active gene drive systems in budding yeast. Furthermore, an unbiased mutational scan reveals that titration of Cas9 inhibition may be possible by modification of the anti-CRISPR primary sequence.
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Affiliation(s)
- Erianna M. Basgall
- Department of Biochemistry and Molecular Biophysics, 141 Chalmers Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Samantha C. Goetting
- Department of Biochemistry and Molecular Biophysics, 141 Chalmers Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Megan E. Goeckel
- Department of Biochemistry and Molecular Biophysics, 141 Chalmers Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Rachael M. Giersch
- Department of Biology, 116 Ackert Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Emily Roggenkamp
- Department of Biochemistry and Molecular Biophysics, 141 Chalmers Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Madison N. Schrock
- Department of Biochemistry and Molecular Biophysics, 141 Chalmers Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Megan Halloran
- Department of Biochemistry and Molecular Biophysics, 141 Chalmers Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Gregory C. Finnigan
- Department of Biochemistry and Molecular Biophysics, 141 Chalmers Hall, Kansas State University, Manhattan, KS 66506, USA
- *Correspondence: Gregory C. Finnigan,
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Abstract
Plant tissue culture (PTC) is a set of techniques for culturing cells, tissues, or organs in an aseptic medium with a defined chemical composition, in a controlled environment. Tissue culture, when combined with molecular biology techniques, becomes a powerful tool for the study of metabolic pathways, elucidation of cellular processes, genetic improvement and, through genetic engineering, the generation of cell lines resistant to biotic and abiotic stress, obtaining improved plants of agronomic interest, or studying the complex cellular genome. In this chapter, we analyze in general the use of plant tissue culture, in particular protoplasts and calli, in the implementation of CRISPR/Cas9 technology.
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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.). FRONTIERS IN PLANT SCIENCE 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] [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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Abstract
The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.
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43
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Hess GT, Tycko J, Yao D, Bassik MC. Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes. Mol Cell 2017; 68:26-43. [PMID: 28985508 PMCID: PMC5997582 DOI: 10.1016/j.molcel.2017.09.029] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 12/26/2022]
Abstract
The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.
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Affiliation(s)
- Gaelen T Hess
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - Josh Tycko
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - David Yao
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA.
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