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Zhang R, Chai N, Liu T, Zheng Z, Lin Q, Xie X, Wen J, Yang Z, Liu YG, Zhu Q. The type V effectors for CRISPR/Cas-mediated genome engineering in plants. Biotechnol Adv 2024; 74:108382. [PMID: 38801866 DOI: 10.1016/j.biotechadv.2024.108382] [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: 01/15/2024] [Revised: 05/07/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
A plethora of CRISPR effectors, such as Cas3, Cas9, and Cas12a, are commonly employed as gene editing tools. Among these, Cas12 effectors developed based on Class II type V proteins exhibit distinct characteristics compared to Class II type VI and type II effectors, such as their ability to generate non-allelic DNA double-strand breaks, their compact structures, and the presence of a single RuvC-like nuclease domain. Capitalizing on these advantages, Cas12 family proteins have been increasingly explored and utilized in recent years. However, the characteristics and applications of different subfamilies within the type V protein family have not been systematically summarized. In this review, we focus on the characteristics of type V effector (CRISPR/Cas12) proteins and the current methods used to discover new effector proteins. We also summarize recent modifications based on engineering of type V effectors. In addition, we introduce the applications of type V effectors for gene editing in animals and plants, including the development of base editors, tools for regulating gene expression, methods for gene targeting, and biosensors. We emphasize the prospects for development and application of CRISPR/Cas12 effectors with the goal of better utilizing toolkits based on this protein family for crop improvement and enhanced agricultural production.
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Affiliation(s)
- Ruixiang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Nan Chai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Taoli Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhiye Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qiupeng Lin
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jun Wen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zi Yang
- College of Natural & Agricultural Sciences, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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Mamrutha HM, Zeenat W, Kapil D, Budhagatapalli N, Tikaniya D, Rakesh K, Krishnappa G, Singh G, Singh GP. Evidence and opportunities for developing non-transgenic genome edited crops using site-directed nuclease 1 approach. Crit Rev Biotechnol 2023:1-11. [PMID: 37915126 DOI: 10.1080/07388551.2023.2270581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/18/2023] [Indexed: 11/03/2023]
Abstract
The innovations and progress in genome editing/new breeding technologies have revolutionized research in the field of functional genomics and crop improvement. This revolution has expanded the horizons of agricultural research, presenting fresh possibilities for creating novel plant varieties equipped with desired traits that can effectively combat the challenges posed by climate change. However, the regulation and social acceptance of genome-edited crops still remain as major barriers. Only a few countries considered the site-directed nuclease 1 (SDN1) approach-based genome-edited plants under less or no regulation. Hence, the present review aims to comprise information on the research work conducted using SDN1 in crops by various genome editing tools. It also elucidates the promising candidate genes that can be used for editing and has listed the studies on non-transgenic crops developed through SDN1 either by Agrobacterium-mediated transformation or by ribo nucleoprotein (RNP) complex. The review also hoards the existing regulatory landscape of genome editing and provides an overview of globally commercialized genome-edited crops. These compilations will enable confidence in researchers and policymakers, across the globe, to recognize the full potential of this technology and reconsider the regulatory aspects associated with genome-edited crops. Furthermore, this compilation serves as a valuable resource for researchers embarking on the development of customized non-transgenic crops through the utilization of SDN1.
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Affiliation(s)
- H M Mamrutha
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
| | - Wadhwa Zeenat
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
| | - Deswal Kapil
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Nagaveni Budhagatapalli
- Institute of Plant Biochemistry, Center for Plant Genome Engineering, Heinrich-Heine-University, Düsseldorf, Germany
| | - Divya Tikaniya
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Kumar Rakesh
- Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | - Gyanendra Singh
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
| | - G P Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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3
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Sharma N, Raman H, Wheeler D, Kalenahalli Y, Sharma R. Data-driven approaches to improve water-use efficiency and drought resistance in crop plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111852. [PMID: 37659733 DOI: 10.1016/j.plantsci.2023.111852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023]
Abstract
With the increasing population, there lies a pressing demand for food, feed and fibre, while the changing climatic conditions pose severe challenges for agricultural production worldwide. Water is the lifeline for crop production; thus, enhancing crop water-use efficiency (WUE) and improving drought resistance in crop varieties are crucial for overcoming these challenges. Genetically-driven improvements in yield, WUE and drought tolerance traits can buffer the worst effects of climate change on crop production in dry areas. While traditional crop breeding approaches have delivered impressive results in increasing yield, the methods remain time-consuming and are often limited by the existing allelic variation present in the germplasm. Significant advances in breeding and high-throughput omics technologies in parallel with smart agriculture practices have created avenues to dramatically speed up the process of trait improvement by leveraging the vast volumes of genomic and phenotypic data. For example, individual genome and pan-genome assemblies, along with transcriptomic, metabolomic and proteomic data from germplasm collections, characterised at phenotypic levels, could be utilised to identify marker-trait associations and superior haplotypes for crop genetic improvement. In addition, these omics approaches enable the identification of genes involved in pathways leading to the expression of a trait, thereby providing an understanding of the genetic, physiological and biochemical basis of trait variation. These data-driven gene discoveries and validation approaches are essential for crop improvement pipelines, including genomic breeding, speed breeding and gene editing. Herein, we provide an overview of prospects presented using big data-driven approaches (including artificial intelligence and machine learning) to harness new genetic gains for breeding programs and develop drought-tolerant crop varieties with favourable WUE and high-yield potential traits.
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Affiliation(s)
- Niharika Sharma
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW 2800, Australia.
| | - Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW 2800, Australia
| | - Yogendra Kalenahalli
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana 502324, India
| | - Rita Sharma
- Department of Biological Sciences, BITS Pilani, Pilani Campus, Rajasthan 333031, India
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4
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Maharajan T, Krishna TPA, Rakkammal K, Ceasar SA, Ramesh M. Application of CRISPR/Cas system in cereal improvement for biotic and abiotic stress tolerance. PLANTA 2022; 256:106. [PMID: 36326904 DOI: 10.1007/s00425-022-04023-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Application of the recently developed CRISPR/Cas tools might help enhance cereals' growth and yield under biotic and abiotic stresses. Cereals are the most important food crops for human life and an essential source of nutrients for people in developed and developing countries. The growth and yield of all major cereals are affected by both biotic and abiotic stresses. To date, molecular breeding and functional genomic studies have contributed to the understanding and improving cereals' growth and yield under biotic and abiotic stresses. Clustered, regularly inter-spaced, short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been predicted to play a major role in precision plant breeding and developing non-transgenic cereals that can tolerate adverse effects of climate change. Variants of next-generation CRISPR/Cas tools, such as prime editor, base editor, CRISPR activator and repressor, chromatin imager, Cas12a, and Cas12b, are currently used in various fields, including plant science. However, few studies have been reported on applying the CRISPR/Cas system to understand the mechanism of biotic and abiotic stress tolerance in cereals. Rice is the only plant used frequently for such studies. Genes responsible for biotic and abiotic stress tolerance have not yet been studied by CRISPR/Cas system in other major cereals (sorghum, barley, maize and small millets). Examining the role of genes that respond to biotic and abiotic stresses using the CRISPR/Cas system may help enhance cereals' growth and yield under biotic and abiotic stresses. It will help to develop new and improved cultivars with biotic- and abiotic-tolerant traits for better yields to strengthen food security. This review provides information for cereal researchers on the current status of the CRISPR/Cas system for improving biotic and abiotic stress tolerance in cereals.
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Affiliation(s)
- Theivanayagam Maharajan
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683104, India
| | - T P Ajeesh Krishna
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683104, India
| | - Kasinathan Rakkammal
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, 630003, India
| | - Stanislaus Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683104, India.
| | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, 630003, India
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5
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Ali Q, Yu C, Hussain A, Ali M, Ahmar S, Sohail MA, Riaz M, Ashraf MF, Abdalmegeed D, Wang X, Imran M, Manghwar H, Zhou L. Genome Engineering Technology for Durable Disease Resistance: Recent Progress and Future Outlooks for Sustainable Agriculture. FRONTIERS IN PLANT SCIENCE 2022; 13:860281. [PMID: 35371164 PMCID: PMC8968944 DOI: 10.3389/fpls.2022.860281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/22/2022] [Indexed: 05/15/2023]
Abstract
Crop production worldwide is under pressure from multiple factors, including reductions in available arable land and sources of water, along with the emergence of new pathogens and development of resistance in pre-existing pathogens. In addition, the ever-growing world population has increased the demand for food, which is predicted to increase by more than 100% by 2050. To meet these needs, different techniques have been deployed to produce new cultivars with novel heritable mutations. Although traditional breeding continues to play a vital role in crop improvement, it typically involves long and laborious artificial planting over multiple generations. Recently, the application of innovative genome engineering techniques, particularly CRISPR-Cas9-based systems, has opened up new avenues that offer the prospects of sustainable farming in the modern agricultural industry. In addition, the emergence of novel editing systems has enabled the development of transgene-free non-genetically modified plants, which represent a suitable option for improving desired traits in a range of crop plants. To date, a number of disease-resistant crops have been produced using gene-editing tools, which can make a significant contribution to overcoming disease-related problems. Not only does this directly minimize yield losses but also reduces the reliance on pesticide application, thereby enhancing crop productivity that can meet the globally increasing demand for food. In this review, we describe recent progress in genome engineering techniques, particularly CRISPR-Cas9 systems, in development of disease-resistant crop plants. In addition, we describe the role of CRISPR-Cas9-mediated genome editing in sustainable agriculture.
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Affiliation(s)
- Qurban Ali
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Chenjie Yu
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Amjad Hussain
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mohsin Ali
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology, and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Muhammad Aamir Sohail
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Riaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Muhammad Furqan Ashraf
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Dyaaaldin Abdalmegeed
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
- Department of Botany and Microbiology, Faculty of Science, Tanta University, Tanta, Egypt
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Muhammad Imran
- Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agriculture University, Guangzhou, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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6
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Matres JM, Hilscher J, Datta A, Armario-Nájera V, Baysal C, He W, Huang X, Zhu C, Valizadeh-Kamran R, Trijatmiko KR, Capell T, Christou P, Stoger E, Slamet-Loedin IH. Genome editing in cereal crops: an overview. Transgenic Res 2021; 30:461-498. [PMID: 34263445 PMCID: PMC8316241 DOI: 10.1007/s11248-021-00259-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/15/2021] [Indexed: 02/06/2023]
Abstract
Genome-editing technologies offer unprecedented opportunities for crop improvement with superior precision and speed. This review presents an analysis of the current state of genome editing in the major cereal crops- rice, maize, wheat and barley. Genome editing has been used to achieve important agronomic and quality traits in cereals. These include adaptive traits to mitigate the effects of climate change, tolerance to biotic stresses, higher yields, more optimal plant architecture, improved grain quality and nutritional content, and safer products. Not all traits can be achieved through genome editing, and several technical and regulatory challenges need to be overcome for the technology to realize its full potential. Genome editing, however, has already revolutionized cereal crop improvement and is poised to shape future agricultural practices in conjunction with other breeding innovations.
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Affiliation(s)
- Jerlie Mhay Matres
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Akash Datta
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Victoria Armario-Nájera
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Can Baysal
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Wenshu He
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Xin Huang
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Rana Valizadeh-Kamran
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Kurniawan R Trijatmiko
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Teresa Capell
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Inez H Slamet-Loedin
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines.
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7
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Maheshwari C, Coe RA, Karki S, Covshoff S, Tapia R, Tyagi A, Hibberd JM, Furbank RT, Quick WP, Lin HC. Targeted knockdown of ribulose-1, 5-bisphosphate carboxylase-oxygenase in rice mesophyll cells. JOURNAL OF PLANT PHYSIOLOGY 2021; 260:153395. [PMID: 33684805 PMCID: PMC8090977 DOI: 10.1016/j.jplph.2021.153395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/06/2021] [Accepted: 02/21/2021] [Indexed: 05/22/2023]
Abstract
We generated antisense constructs targeting two of the five Rubisco small subunit genes (OsRBCS2 and 4) which account for between 30-40 % of the RBCS transcript abundance in leaf blades. The constructs were driven by a maize phosphoenolpyruvate carboxylase (PEPC) promoter known to have enriched expression in mesophyll cells (MCs). In the resulting lines leaf, Rubisco protein content was reduced by between 30-50 % and CO2 assimilation rate was limited under photorespiratory and non-photorespiratory conditions. A relationship between Rubisco protein content and CO2 assimilation rate was found. This was associated with a significant reduction in dry biomass accumulation and grain yield of between 37-70%. In addition to serving as a resource for reducing Rubisco accumulation in a cell-preferential manner, these lines allow us to characterize gene function and isoform specific suppression on photosynthesis and growth. Our results suggest that the knockdown of multiple genes is required to completely reduce Rubisco accumulation in MCs.
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Affiliation(s)
- Chirag Maheshwari
- C4Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Robert A Coe
- C4Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Shanta Karki
- C4Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Ronald Tapia
- C4Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Aruna Tyagi
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Acton, 2601, Australia
| | - William Paul Quick
- C4Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines; Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Hsiang-Chun Lin
- C4Rice Centre, International Rice Research Institute (IRRI), Los Baños, Philippines.
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8
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Tong B, Dong H, Cui Y, Jiang P, Jin Z, Zhang D. The Versatile Type V CRISPR Effectors and Their Application Prospects. Front Cell Dev Biol 2021; 8:622103. [PMID: 33614630 PMCID: PMC7889808 DOI: 10.3389/fcell.2020.622103] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
The class II clustered regularly interspaced short palindromic repeats (CRISPR)–Cas systems, characterized by a single effector protein, can be further subdivided into types II, V, and VI. The application of the type II CRISPR effector protein Cas9 as a sequence-specific nuclease in gene editing has revolutionized this field. Similarly, Cas13 as the effector protein of type VI provides a convenient tool for RNA manipulation. Additionally, the type V CRISPR–Cas system is another valuable resource with many subtypes and diverse functions. In this review, we summarize all the subtypes of the type V family that have been identified so far. According to the functions currently displayed by the type V family, we attempt to introduce the functional principle, current application status, and development prospects in biotechnology for all major members.
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Affiliation(s)
- Baisong Tong
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yali Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Pingtao Jiang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhaoxia Jin
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
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9
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Zamani-Nour S, Lin HC, Walker BJ, Mettler-Altmann T, Khoshravesh R, Karki S, Bagunu E, Sage TL, Quick WP, Weber APM. Overexpression of the chloroplastic 2-oxoglutarate/malate transporter disturbs carbon and nitrogen homeostasis in rice. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:137-152. [PMID: 32710115 PMCID: PMC7816853 DOI: 10.1093/jxb/eraa343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/07/2020] [Accepted: 07/21/2020] [Indexed: 05/07/2023]
Abstract
The chloroplastic 2-oxaloacetate (OAA)/malate transporter (OMT1 or DiT1) takes part in the malate valve that protects chloroplasts from excessive redox poise through export of malate and import of OAA. Together with the glutamate/malate transporter (DCT1 or DiT2), it connects carbon with nitrogen assimilation, by providing 2-oxoglutarate for the GS/GOGAT (glutamine synthetase/glutamate synthase) reaction and exporting glutamate to the cytoplasm. OMT1 further plays a prominent role in C4 photosynthesis: OAA resulting from phosphoenolpyruvate carboxylation is imported into the chloroplast, reduced to malate by plastidic NADP-malate dehydrogenase, and then exported for transport to bundle sheath cells. Both transport steps are catalyzed by OMT1, at the rate of net carbon assimilation. To engineer C4 photosynthesis into C3 crops, OMT1 must be expressed in high amounts on top of core C4 metabolic enzymes. We report here high-level expression of ZmOMT1 from maize in rice (Oryza sativa ssp. indica IR64). Increased activity of the transporter in transgenic rice was confirmed by reconstitution of transporter activity into proteoliposomes. Unexpectedly, overexpression of ZmOMT1 in rice negatively affected growth, CO2 assimilation rate, total free amino acid content, tricarboxylic acid cycle metabolites, as well as sucrose and starch contents. Accumulation of high amounts of aspartate and the impaired growth phenotype of OMT1 rice lines could be suppressed by simultaneous overexpression of ZmDiT2. Implications for engineering C4 rice are discussed.
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Affiliation(s)
- Shirin Zamani-Nour
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany
| | - Hsiang-Chun Lin
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Berkley J Walker
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany
| | - Tabea Mettler-Altmann
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany
| | - Roxana Khoshravesh
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Shanta Karki
- National Center for Fruit Development, Kirtipur, Kathmandu, Nepal
| | - Efren Bagunu
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Tammy L Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - W Paul Quick
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany
- Correspondence:
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Ahmar S, Saeed S, Khan MHU, Ullah Khan S, Mora-Poblete F, Kamran M, Faheem A, Maqsood A, Rauf M, Saleem S, Hong WJ, Jung KH. A Revolution toward Gene-Editing Technology and Its Application to Crop Improvement. Int J Mol Sci 2020; 21:E5665. [PMID: 32784649 PMCID: PMC7461041 DOI: 10.3390/ijms21165665] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022] Open
Abstract
Genome editing is a relevant, versatile, and preferred tool for crop improvement, as well as for functional genomics. In this review, we summarize the advances in gene-editing techniques, such as zinc-finger nucleases (ZFNs), transcription activator-like (TAL) effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) associated with the Cas9 and Cpf1 proteins. These tools support great opportunities for the future development of plant science and rapid remodeling of crops. Furthermore, we discuss the brief history of each tool and provide their comparison and different applications. Among the various genome-editing tools, CRISPR has become the most popular; hence, it is discussed in the greatest detail. CRISPR has helped clarify the genomic structure and its role in plants: For example, the transcriptional control of Cas9 and Cpf1, genetic locus monitoring, the mechanism and control of promoter activity, and the alteration and detection of epigenetic behavior between single-nucleotide polymorphisms (SNPs) investigated based on genetic traits and related genome-wide studies. The present review describes how CRISPR/Cas9 systems can play a valuable role in the characterization of the genomic rearrangement and plant gene functions, as well as the improvement of the important traits of field crops with the greatest precision. In addition, the speed editing strategy of gene-family members was introduced to accelerate the applications of gene-editing systems to crop improvement. For this, the CRISPR technology has a valuable advantage that particularly holds the scientist's mind, as it allows genome editing in multiple biological systems.
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Affiliation(s)
- Sunny Ahmar
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Sumbul Saeed
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Muhammad Hafeez Ullah Khan
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Shahid Ullah Khan
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile;
| | - Muhammad Kamran
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China;
| | - Aroosha Faheem
- Sate Key Laboratory of Agricultural Microbiology and State Key Laboratory of Microbial Biosensor, College of Life Sciences Huazhong Agriculture University Wuhan, Wuhan 430070, China;
| | - Ambreen Maqsood
- Department of Plant Pathology, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Muhammad Rauf
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan;
| | - Saba Saleem
- Department of Bioscience, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan;
| | - Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea;
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea;
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Zafar K, Sedeek KEM, Rao GS, Khan MZ, Amin I, Kamel R, Mukhtar Z, Zafar M, Mansoor S, Mahfouz MM. Genome Editing Technologies for Rice Improvement: Progress, Prospects, and Safety Concerns. Front Genome Ed 2020; 2:5. [PMID: 34713214 PMCID: PMC8525367 DOI: 10.3389/fgeed.2020.00005] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022] Open
Abstract
Rice (Oryza sativa) is an important staple food crop worldwide; to meet the growing nutritional requirements of the increasing population in the face of climate change, qualitative and quantitative traits of rice need to be improved. Stress-tolerant crop varieties must be developed with stable or higher yields under stress conditions. Genome editing and speed breeding have improved the accuracy and pace of rice breeding. New breeding technologies including genome editing have been established in rice, expanding the potential for crop improvement. Recently, other genome editing techniques such as CRISPR-directed evolution, CRISPR-Cas12a, and base editors have also been used for efficient genome editing in rice. Since rice is an excellent model system for functional studies due to its small genome and close syntenic relationships with other cereal crops, new genome-editing technologies continue to be developed for use in rice. In this review, we focus on genome-editing tools for rice improvement to address current challenges and provide examples of genome editing in rice. We also shed light on expanding the scope of genome editing and systems for delivering homology-directed repair templates. Finally, we discuss safety concerns and methods for obtaining transgene-free crops.
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Affiliation(s)
- Kashaf Zafar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
- Department of Biotechnology, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Pakistan
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Khalid E. M. Sedeek
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Gundra Sivakrishna Rao
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Muhammad Zuhaib Khan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Radwa Kamel
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Mehak Zafar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Ahmar S, Gill RA, Jung KH, Faheem A, Qasim MU, Mubeen M, Zhou W. Conventional and Molecular Techniques from Simple Breeding to Speed Breeding in Crop Plants: Recent Advances and Future Outlook. Int J Mol Sci 2020; 21:E2590. [PMID: 32276445 PMCID: PMC7177917 DOI: 10.3390/ijms21072590] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 01/28/2023] Open
Abstract
In most crop breeding programs, the rate of yield increment is insufficient to cope with the increased food demand caused by a rapidly expanding global population. In plant breeding, the development of improved crop varieties is limited by the very long crop duration. Given the many phases of crossing, selection, and testing involved in the production of new plant varieties, it can take one or two decades to create a new cultivar. One possible way of alleviating food scarcity problems and increasing food security is to develop improved plant varieties rapidly. Traditional farming methods practiced since quite some time have decreased the genetic variability of crops. To improve agronomic traits associated with yield, quality, and resistance to biotic and abiotic stresses in crop plants, several conventional and molecular approaches have been used, including genetic selection, mutagenic breeding, somaclonal variations, whole-genome sequence-based approaches, physical maps, and functional genomic tools. However, recent advances in genome editing technology using programmable nucleases, clustered regularly interspaced short palindromic repeats (CRISPR), and CRISPR-associated (Cas) proteins have opened the door to a new plant breeding era. Therefore, to increase the efficiency of crop breeding, plant breeders and researchers around the world are using novel strategies such as speed breeding, genome editing tools, and high-throughput phenotyping. In this review, we summarize recent findings on several aspects of crop breeding to describe the evolution of plant breeding practices, from traditional to modern speed breeding combined with genome editing tools, which aim to produce crop generations with desired traits annually.
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Affiliation(s)
- Sunny Ahmar
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; (S.A.); (M.U.Q.)
| | - Rafaqat Ali Gill
- Oil Crops Research Institute, Chinese Academy of Agriculture Sciences, Wuhan 430070, China;
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Aroosha Faheem
- State Key Laboratory of Agricultural Microbiology and State Key Laboratory of Microbial Biosensor, College of Life Sciences Huazhong Agriculture University, Wuhan 430070, China
| | - Muhammad Uzair Qasim
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; (S.A.); (M.U.Q.)
| | - Mustansar Mubeen
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
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