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Yao Q, Shen R, Shao Y, Tian Y, Han P, Zhang X, Zhu JK, Lu Y. Efficient and multiplex gene upregulation in plants through CRISPR-Cas-mediated knockin of enhancers. MOLECULAR PLANT 2024; 17:1472-1483. [PMID: 39049493 DOI: 10.1016/j.molp.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/01/2024] [Accepted: 07/20/2024] [Indexed: 07/27/2024]
Abstract
Gene upregulation through genome editing is important for plant research and breeding. Targeted insertion of short transcriptional enhancers (STEs) into gene promoters may offer a universal solution akin to transgene-mediated overexpression while avoiding the drawbacks associated with transgenesis. Here, we introduce an "in locus activation" technique in rice that leverages well-characterized STEs for refined, heritable, and multiplexed gene upregulation. To address the scarcity of potent enhancers, we developed a large-scale mining approach and discovered a suite of STEs that are capable of enhancing gene expression in rice protoplasts. The in locus integration of these STEs into eight rice genes resulted in substantial transcriptional upregulation in the edited plants, with up to 869.1-fold increases in their transcript levels. Employing a variety of STEs, we achieved delicate control of gene expression, enabling the fine-tuning of key phenotypic traits such as plant height. Our approach also enabled efficient multiplexed gene upregulation, with up to four genes activated simultaneously, significantly enhancing the nicotinamide mononucleotide metabolic pathway. Importantly, heritability studies from the T0 to T3 generations confirmed the stable and heritable nature of STE-driven gene activation. Collectively, our work demonstrates that coupled with STE mining, leveraging genome editing for in locus activation and gene upregulation holds great promise to be widely adopted in fundamental plant research and crop breeding.
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Affiliation(s)
- Qi Yao
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single-Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Rundong Shen
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Yang Shao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yifu Tian
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Peijin Han
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Xuening Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Yuming Lu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single-Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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2
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Chen J, Wang Y. Understanding the salinity resilience and productivity of halophytes in saline environments. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112171. [PMID: 38969140 DOI: 10.1016/j.plantsci.2024.112171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 06/15/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024]
Abstract
The escalating salinity levels in cultivable soil pose a significant threat to agricultural productivity and, consequently, human sustenance. This problem is being exacerbated by natural processes and human activities, coinciding with a period of rapid population growth. Developing halophytic crops is needed to ensure food security is not impaired and land resources can be used sustainably. Evolution has created many close halophyte relatives of our major glycophytic crops, such as Puccinellia tenuiflora (relative of barley and wheat), Oryza coarctata (relative of rice) and Glycine soja (relative of soybean). There are also some halophytes have been subjected to semi-domestication and are considered as minor crops, such as Chenopodium quinoa. In this paper, we examine the prevailing comprehension of robust salinity resilience in halophytes. We summarize the existing strategies and technologies that equip researchers with the means to enhance the salt tolerance capabilities of primary crops and investigate the genetic makeup of halophytes.
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Affiliation(s)
- Jiahong Chen
- State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Wang
- State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China; Dalian Practical Biotechnology Co. LTD., Dalian, Liaoning 116200, China.
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3
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Freitas-Alves NS, Moreira-Pinto CE, Távora FTPK, Paes-de-Melo B, Arraes FBM, Lourenço-Tessutti IT, Moura SM, Oliveira AC, Morgante CV, Qi Y, Fatima Grossi-de-Sa M. CRISPR/Cas genome editing in soybean: challenges and new insights to overcome existing bottlenecks. J Adv Res 2024:S2090-1232(24)00367-9. [PMID: 39163906 DOI: 10.1016/j.jare.2024.08.024] [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: 04/13/2024] [Revised: 07/23/2024] [Accepted: 08/16/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND Soybean is a worldwide-cultivated crop due to its applications in the food, feed, and biodiesel industries. Genome editing in soybean began with ZFN and TALEN technologies; however, CRISPR/Cas has emerged and shortly became the preferable approach for soybean genome manipulation since it is more precise, easy to handle, and cost-effective. Recent reports have focused on the conventional Cas9 nuclease, Cas9 nickase (nCas9) derived base editors, and Cas12a (formally Cpf1) as the most commonly used genome editors in soybean. Nonetheless, several challenges in the complex plant genetic engineering pipeline need to be overcome to effectively edit the genome of an elite soybean cultivar. These challenges include (1) optimizing CRISPR cassette design (i.e., gRNA and Cas promoters, gRNA design and testing, number of gRNAs, and binary vector), (2) improving transformation frequency, (3) increasing the editing efficiency ratio of targeted plant cells, and (4) improving soybean crop production. AIM OF REVIEW This review provides an overview of soybean genome editing using CRISPR/Cas technology, discusses current challenges, and highlights theoretical (insights) and practical suggestions to overcome the existing bottlenecks. KEY SCIENTIFIC CONCEPTS OF REVIEW The CRISPR/Cas system was discovered as part of the bacterial innate immune system. It has been used as a biotechnological tool for genome editing and efficiently applied in soybean to unveil gene function, improve agronomic traits such as yield and nutritional grain quality, and enhance biotic and abiotic stress tolerance. To date, the efficiency of gRNAs has been validated using protoplasts and hairy root assays, while stable plant transformation relies on Agrobacterium-mediated and particle bombardment methods. Nevertheless, most steps of the CRISPR/Cas workflow require optimizations to achieve a more effective genome editing in soybean plants.
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Affiliation(s)
- Nayara Sabrina Freitas-Alves
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Clidia E Moreira-Pinto
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Fabiano T P K Távora
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Bruno Paes-de-Melo
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Fabricio B M Arraes
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Isabela T Lourenço-Tessutti
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Stéfanie M Moura
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Antonio C Oliveira
- National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil; Federal University of Pelotas (UFPEL), Pelotas, RS, Brazil
| | - Carolina V Morgante
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil; Embrapa Semi-Arid, Petrolina, PE, Brazil
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná (UFPR), Curitiba, PR, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil; Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil; Catholic University Dom Bosco, Graduate Program in Biotechnology, Campo Grande, MS, Brazil.
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4
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Clark T, Waller MA, Loo L, Moreno CL, Denes CE, Neely GG. CRISPR activation screens: navigating technologies and applications. Trends Biotechnol 2024; 42:1017-1034. [PMID: 38493051 DOI: 10.1016/j.tibtech.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/18/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) activation (CRISPRa) has become an integral part of the molecular biology toolkit. CRISPRa genetic screens are an exciting high-throughput means of identifying genes the upregulation of which is sufficient to elicit a given phenotype. Activation machinery is continually under development to achieve greater, more robust, and more consistent activation. In this review, we offer a succinct technological overview of available CRISPRa architectures and a comprehensive summary of pooled CRISPRa screens. Furthermore, we discuss contemporary applications of CRISPRa across broad fields of research, with the aim of presenting a view of exciting emerging applications for CRISPRa screening.
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Affiliation(s)
- Teleri Clark
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Matthew A Waller
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Lipin Loo
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Cesar L Moreno
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Christopher E Denes
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - G Gregory Neely
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia.
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5
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Zhang C, Tang Y, Tang S, Chen L, Li T, Yuan H, Xu Y, Zhou Y, Zhang S, Wang J, Wen H, Jiang W, Pang Y, Deng X, Cao X, Zhou J, Song X, Liu Q. An inducible CRISPR activation tool for accelerating plant regeneration. PLANT COMMUNICATIONS 2024; 5:100823. [PMID: 38243597 PMCID: PMC11121170 DOI: 10.1016/j.xplc.2024.100823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/21/2024]
Abstract
The inducible CRISPR activation (CRISPR-a) system offers unparalleled precision and versatility for regulating endogenous genes, making it highly sought after in plant research. In this study, we developed a chemically inducible CRISPR-a tool for plants called ER-Tag by combining the LexA-VP16-ER inducible system with the SunTag CRISPR-a system. We systematically compared different induction strategies and achieved high efficiency in target gene activation. We demonstrated that guide RNAs can be multiplexed and pooled for large-scale screening of effective morphogenic genes and gene pairs involved in plant regeneration. Further experiments showed that induced activation of these morphogenic genes can accelerate regeneration and improve regeneration efficiency in both eudicot and monocot plants, including alfalfa, woodland strawberry, and sheepgrass. Our study expands the CRISPR toolset in plants and provides a powerful new strategy for studying gene function when constitutive expression is not feasible or ideal.
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Affiliation(s)
- Cuimei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yajun Tang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong 261000, China
| | - Shanjie Tang
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Chen
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tong Li
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haidi Yuan
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong 261000, China
| | - Yujun Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yangyan Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Shuaibin Zhang
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianli Wang
- Grass and Science Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang 150086, China
| | - Hongyu Wen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wenbo Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xian Deng
- Key Laboratory of Seed Innovation and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junhui Zhou
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong 261000, China.
| | - Xianwei Song
- Key Laboratory of Seed Innovation and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Qikun Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China.
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6
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Lan H, Shu W, Jiang D, Yu L, Xu G. Cas-based bacterial detection: recent advances and perspectives. Analyst 2024; 149:1398-1415. [PMID: 38357966 DOI: 10.1039/d3an02120c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Persistent bacterial infections pose a formidable threat to global health, contributing to widespread challenges in areas such as food safety, medical hygiene, and animal husbandry. Addressing this peril demands the urgent implementation of swift and highly sensitive detection methodologies suitable for point-of-care testing and large-scale screening. These methodologies play a pivotal role in the identification of pathogenic bacteria, discerning drug-resistant strains, and managing and treating diseases. Fortunately, new technology, the CRISPR/Cas system, has emerged. The clustered regularly interspaced short joint repeats (CRISPR) system, which is part of bacterial adaptive immunity, has already played a huge role in the field of gene editing. It has been employed as a diagnostic tool for virus detection, featuring high sensitivity, specificity, and single-nucleotide resolution. When applied to bacterial detection, it also surpasses expectations. In this review, we summarise recent advances in the detection of bacteria such as Mycobacterium tuberculosis (MTB), methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli (E. coli), Salmonella and Acinetobacter baumannii (A. baumannii) using the CRISPR/Cas system. We emphasize the significance and benefits of this methodology, showcasing the capability of diverse effector proteins to swiftly and precisely recognize bacterial pathogens. Furthermore, the CRISPR/Cas system exhibits promise in the identification of antibiotic-resistant strains. Nevertheless, this technology is not without challenges that need to be resolved. For example, CRISPR/Cas systems must overcome natural off-target effects and require high-quality nucleic acid samples to improve sensitivity and specificity. In addition, limited applicability due to the protospacer adjacent motif (PAM) needs to be addressed to increase its versatility. Despite the challenges, we are optimistic about the future of bacterial detection using CRISPR/Cas. We have already highlighted its potential in medical microbiology. As research progresses, this technology will revolutionize the detection of bacterial infections.
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Affiliation(s)
- Huatao Lan
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Weitong Shu
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Dan Jiang
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Luxin Yu
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Guangxian Xu
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
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7
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AHMAD M. Plant breeding advancements with "CRISPR-Cas" genome editing technologies will assist future food security. FRONTIERS IN PLANT SCIENCE 2023; 14:1133036. [PMID: 36993865 PMCID: PMC10040607 DOI: 10.3389/fpls.2023.1133036] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Genome editing techniques are being used to modify plant breeding, which might increase food production sustainably by 2050. A product made feasible by genome editing is becoming better known, because of looser regulation and widespread acceptance. The world's population and food supply would never have increased proportionally under current farming practices. The development of plants and food production has been greatly impacted by global warming and climate change. Therefore, minimizing these effects is crucial for agricultural production that is sustainable. Crops are becoming more resilient to abiotic stress because of sophisticated agricultural practices and a better understanding of the abiotic stress response mechanism. Both conventional and molecular breeding techniques have been used to create viable crop types both processes are time-consuming. Recently, plant breeders have shown an interest in genome editing approaches for genetic manipulation that use clustered regularly interspaced short palindromic repeats (CRISPR/Cas9). To ensure the security of the food supply in the future, plant kinds with desired traits must be developed. A completely new era in plant breeding has begun because of the revolution in genome editing techniques based on the CRISPR/CRISPR-associated nuclease (Cas9) systems. All plants may effectively target a particular gene or group of loci using Cas9 and single-guide RNA (sgRNA). CRISPR/Cas9 can thereby save time and labor compared to conventional breeding methods. An easy, quick, and efficient method for directly altering the genetic sequences in cells is with the CRISPR and Cas9 systems. The CRISPR-Cas9 system, which was developed from components of the earliest known bacterial immune system, allows for targeted gene breakage and gene editing in a variety of cells/RNA sequences to guide endonuclease cleavage specificity in the CRISPR-Cas9 system. Editing can be directed to practically any genomic site by altering the guide RNA (gRNA) sequence and delivering it to a target cell along with the Cas9 endonuclease. We summarize recent CRISPR/Cas9 plant research findings, investigate potential applications in plant breeding, and make predictions about likely future breakthroughs and approaches to food security through 2050.
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Affiliation(s)
- M. AHMAD
- Department of Plant Sciences, University of Nebraska, Lincoln, NE, United States
- Department of Genetics and Plant Breeding, Sheri-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Srinagar, India
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8
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Casas-Mollano JA, Zinselmeier M, Sychla A, Smanski MJ. Efficient gene activation in plants by the MoonTag programmable transcriptional activator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528671. [PMID: 36824723 PMCID: PMC9948947 DOI: 10.1101/2023.02.15.528671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
CRISPR/Cas-based transcriptional activators have been developed to induce gene expression in eukaryotic and prokaryotic organisms. The main advantages of CRISPR-Cas based systems is that they can achieve high levels of transcriptional activation and are very easy to program via pairing between the guide RNA and the DNA target strand. SunTag is a second-generation system that activates transcription by recruiting multiple copies of an activation domain (AD) to its target promoters. SunTag is a strong activator; however, in some species it is difficult to stably express. To overcome this problem, we designed MoonTag, a new activator that worked on the same basic principle as SunTag, but whose components are better tolerated when stably expressed in transgenic plants. We demonstrate that MoonTag is capable of inducing high levels of transcription in all plants tested. In Setaria, MoonTag is capable of inducing high levels of transcription of reporter genes as well as of endogenous genes. More important, MoonTag components are expressed in transgenic plants to high levels without any deleterious effects. MoonTag is also able to efficiently activate genes in eudicotyledonous species such as Arabidopsis and tomato. Finally, we show that MoonTag activation is functional across a range of temperatures, which is promising for potential field applications.
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Affiliation(s)
- J Armando Casas-Mollano
- Department of Biochemistry, Molecular Biology, and Biophysics and Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN 55108
| | - Matthew Zinselmeier
- Department of Biochemistry, Molecular Biology, and Biophysics and Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN 55108
- Department of Genetics, Cellular, and Developmental Biology, University of Minnesota, Saint Paul, MN 55108
| | - Adam Sychla
- Department of Biochemistry, Molecular Biology, and Biophysics and Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN 55108
| | - Michael J Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics and Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN 55108
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9
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Clustered regularly interspaced short palindromic repeats tools for plant metabolic engineering: achievements and perspectives. Curr Opin Biotechnol 2023; 79:102856. [PMID: 36473330 DOI: 10.1016/j.copbio.2022.102856] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 12/09/2022]
Abstract
The plant kingdom represents the biggest source of feedstock, food, and added-value compounds. Engineering plant metabolic pathways to increase the phytochemical production or improve the nutraceutical value of crops is challenging because of the intricate interaction networks that link multiple genes, enzymatic steps, and metabolites, even when pathways are fully elucidated. The development of clustered regularly interspaced short palindromic repeats - CRISPR-associated (CRISPR-Cas) technologies has helped to overcome limitations in metabolic engineering, providing efficient and versatile tools for multigene editing. CRISPR approaches in plants were shown to have a remarkable efficiency in genome editing of different species to improve agronomic and metabolic traits. Here, we give an overview of the different achievements and perspectives of CRISPR technology in plant metabolic engineering.
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10
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Ding X, Yu L, Chen L, Li Y, Zhang J, Sheng H, Ren Z, Li Y, Yu X, Jin S, Cao J. Recent Progress and Future Prospect of CRISPR/Cas-Derived Transcription Activation (CRISPRa) System in Plants. Cells 2022; 11:3045. [PMID: 36231007 PMCID: PMC9564188 DOI: 10.3390/cells11193045] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/17/2022] [Accepted: 09/23/2022] [Indexed: 11/23/2022] Open
Abstract
Genome editing technology has become one of the hottest research areas in recent years. Among diverse genome editing tools, the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated proteins system (CRISPR/Cas system) has exhibited the obvious advantages of specificity, simplicity, and flexibility over any previous genome editing system. In addition, the emergence of Cas9 mutants, such as dCas9 (dead Cas9), which lost its endonuclease activity but maintains DNA recognition activity with the guide RNA, provides powerful genetic manipulation tools. In particular, combining the dCas9 protein and transcriptional activator to achieve specific regulation of gene expression has made important contributions to biotechnology in medical research as well as agriculture. CRISPR/dCas9 activation (CRISPRa) can increase the transcription of endogenous genes. Overexpression of foreign genes by traditional transgenic technology in plant cells is the routine method to verify gene function by elevating genes transcription. One of the main limitations of the overexpression is the vector capacity constraint that makes it difficult to express multiple genes using the typical Ti plasmid vectors from Agrobacterium. The CRISPRa system can overcome these limitations of the traditional gene overexpression method and achieve multiple gene activation by simply designating several guide RNAs in one vector. This review summarizes the latest progress based on the development of CRISPRa systems, including SunTag, dCas9-VPR, dCas9-TV, scRNA, SAM, and CRISPR-Act and their applications in plants. Furthermore, limitations, challenges of current CRISPRa systems and future prospective applications are also discussed.
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Affiliation(s)
- Xiao Ding
- Institute of Cotton, Shanxi Agricultural University, Yuncheng 044000, China
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Yu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Luo Chen
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yujie Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinlun Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanyan Sheng
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhengwei Ren
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunlong Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohan Yu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinglin Cao
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China
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11
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Moreno-Giménez E, Selma S, Calvache C, Orzáez D. GB_SynP: A Modular dCas9-Regulated Synthetic Promoter Collection for Fine-Tuned Recombinant Gene Expression in Plants. ACS Synth Biol 2022; 11:3037-3048. [PMID: 36044643 PMCID: PMC9486966 DOI: 10.1021/acssynbio.2c00238] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Indexed: 01/24/2023]
Abstract
Programmable transcriptional factors based on the CRISPR architecture are becoming commonly used in plants for endogenous gene regulation. In plants, a potent CRISPR tool for gene induction is the so-called dCasEV2.1 activation system, which has shown remarkable genome-wide specificity combined with a strong activation capacity. To explore the ability of dCasEV2.1 to act as a transactivator for orthogonal synthetic promoters, a collection of DNA parts was created (GB_SynP) for combinatorial synthetic promoter building. The collection includes (i) minimal promoter parts with the TATA box and 5'UTR regions, (ii) proximal parts containing single or multiple copies of the target sequence for the gRNA, thus functioning as regulatory cis boxes, and (iii) sequence-randomized distal parts that ensure the adequate length of the resulting promoter. A total of 35 promoters were assembled using the GB_SynP collection, showing in all cases minimal background and predictable activation levels depending on the proximal parts used. GB_SynP was also employed in a combinatorial expression analysis of an autoluminescence pathway in Nicotiana benthamiana, showing the value of this tool in extracting important biological information such as the determination of the limiting steps in an enzymatic pathway.
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Affiliation(s)
- Elena Moreno-Giménez
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Sara Selma
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Camilo Calvache
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Diego Orzáez
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
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12
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Danila F, Schreiber T, Ermakova M, Hua L, Vlad D, Lo S, Chen Y, Lambret‐Frotte J, Hermanns AS, Athmer B, von Caemmerer S, Yu S, Hibberd JM, Tissier A, Furbank RT, Kelly S, Langdale JA. A single promoter-TALE system for tissue-specific and tuneable expression of multiple genes in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1786-1806. [PMID: 35639605 PMCID: PMC9398400 DOI: 10.1111/pbi.13864] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/06/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
In biological discovery and engineering research, there is a need to spatially and/or temporally regulate transgene expression. However, the limited availability of promoter sequences that are uniquely active in specific tissue-types and/or at specific times often precludes co-expression of multiple transgenes in precisely controlled developmental contexts. Here, we developed a system for use in rice that comprises synthetic designer transcription activator-like effectors (dTALEs) and cognate synthetic TALE-activated promoters (STAPs). The system allows multiple transgenes to be expressed from different STAPs, with the spatial and temporal context determined by a single promoter that drives expression of the dTALE. We show that two different systems-dTALE1-STAP1 and dTALE2-STAP2-can activate STAP-driven reporter gene expression in stable transgenic rice lines, with transgene transcript levels dependent on both dTALE and STAP sequence identities. The relative strength of individual STAP sequences is consistent between dTALE1 and dTALE2 systems but differs between cell-types, requiring empirical evaluation in each case. dTALE expression leads to off-target activation of endogenous genes but the number of genes affected is substantially less than the number impacted by the somaclonal variation that occurs during the regeneration of transformed plants. With the potential to design fully orthogonal dTALEs for any genome of interest, the dTALE-STAP system thus provides a powerful approach to fine-tune the expression of multiple transgenes, and to simultaneously introduce different synthetic circuits into distinct developmental contexts.
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Affiliation(s)
- Florence Danila
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Plant Sciences Division, Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Tom Schreiber
- Department of Cell and Metabolic BiologyLeibniz Institute of Plant BiochemistryHalleGermany
| | - Maria Ermakova
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Plant Sciences Division, Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Lei Hua
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Daniela Vlad
- Department of Plant SciencesUniversity of OxfordOxfordUK
| | - Shuen‐Fang Lo
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan
| | - Yi‐Shih Chen
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | | | - Anna S. Hermanns
- Department of Plant SciencesUniversity of OxfordOxfordUK
- Present address:
Plant Breeding and Genetics Section, School of Integrative Plant ScienceCornell UniversityIthacaNew YorkUSA
| | - Benedikt Athmer
- Department of Cell and Metabolic BiologyLeibniz Institute of Plant BiochemistryHalleGermany
| | - Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Plant Sciences Division, Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Su‐May Yu
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | | | - Alain Tissier
- Department of Cell and Metabolic BiologyLeibniz Institute of Plant BiochemistryHalleGermany
| | - Robert T. Furbank
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Plant Sciences Division, Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Steven Kelly
- Department of Plant SciencesUniversity of OxfordOxfordUK
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13
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Van Vu T, Das S, Hensel G, Kim JY. Genome editing and beyond: what does it mean for the future of plant breeding? PLANTA 2022; 255:130. [PMID: 35587292 PMCID: PMC9120101 DOI: 10.1007/s00425-022-03906-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 04/26/2022] [Indexed: 05/04/2023]
Abstract
MAIN CONCLUSION Genome editing offers revolutionized solutions for plant breeding to sustain food production to feed the world by 2050. Therefore, genome-edited products are increasingly recognized via more relaxed legislation and community adoption. The world population and food production are disproportionally growing in a manner that would have never matched each other under the current agricultural practices. The emerging crisis is more evident with the subtle changes in climate and the running-off of natural genetic resources that could be easily used in breeding in conventional ways. Under these circumstances, affordable CRISPR-Cas-based gene-editing technologies have brought hope and charged the old plant breeding machine with the most energetic and powerful fuel to address the challenges involved in feeding the world. What makes CRISPR-Cas the most powerful gene-editing technology? What are the differences between it and the other genetic engineering/breeding techniques? Would its products be labeled as "conventional" or "GMO"? There are so many questions to be answered, or that cannot be answered within the limitations of our current understanding. Therefore, we would like to discuss and answer some of the mentioned questions regarding recent progress in technology development. We hope this review will offer another view on the role of CRISPR-Cas technology in future of plant breeding for food production and beyond.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, km 02, Pham Van Dong Road, Co Nhue 1, Bac Tu Liem, Hanoi, 11917, Vietnam
| | - Swati Das
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225, Düsseldorf, Germany.
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371, Olomouc, Czech Republic.
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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14
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Rozov SM, Permyakova NV, Sidorchuk YV, Deineko EV. Optimization of Genome Knock-In Method: Search for the Most Efficient Genome Regions for Transgene Expression in Plants. Int J Mol Sci 2022; 23:ijms23084416. [PMID: 35457234 PMCID: PMC9027324 DOI: 10.3390/ijms23084416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/01/2022] [Accepted: 04/14/2022] [Indexed: 02/04/2023] Open
Abstract
Plant expression systems are currently regarded as promising alternative platforms for the production of recombinant proteins, including the proteins for biopharmaceutical purposes. However, the accumulation level of a target protein in plant expression systems is still rather low compared with the other existing systems, namely, mammalian, yeast, and E. coli cells. To solve this problem, numerous methods and approaches have been designed and developed. At the same time, the random nature of the distribution of transgenes over the genome can lead to gene silencing, variability in the accumulation of recombinant protein, and also to various insertional mutations. The current research study considered inserting target genes into pre-selected regions of the plant genome (genomic “safe harbors”) using the CRISPR/Cas system. Regions of genes expressed constitutively and at a high transcriptional level in plant cells (housekeeping genes) that are of interest as attractive targets for the delivery of target genes were characterized. The results of the first attempts to deliver target genes to the regions of housekeeping genes are discussed. The approach of “euchromatization” of the transgene integration region using the modified dCas9 associated with transcription factors is considered. A number of the specific features in the spatial chromatin organization allowing individual genes to efficiently transcribe are discussed.
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15
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Xiong X, Li Z, Liang J, Liu K, Li C, Li JF. A cytosine base editor toolkit with varying activity windows and target scopes for versatile gene manipulation in plants. Nucleic Acids Res 2022; 50:3565-3580. [PMID: 35286371 PMCID: PMC8989527 DOI: 10.1093/nar/gkac166] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/20/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas-derived base editing tools empower efficient alteration of genomic cytosines or adenines associated with essential genetic traits in plants and animals. Diversified target sequences and customized editing products call for base editors with distinct features regarding the editing window and target scope. Here we developed a toolkit of plant base editors containing AID10, an engineered human AID cytosine deaminase. When fused to the N-terminus or C-terminus of the conventional Cas9 nickase (nSpCas9), AID10 exhibited a broad or narrow activity window at the protospacer adjacent motif (PAM)-distal and -proximal protospacer, respectively, while AID10 fused to both termini conferred an additive activity window. We further replaced nSpCas9 with orthogonal or PAM-relaxed Cas9 variants to widen target scopes. Moreover, we devised dual base editors with AID10 located adjacently or distally to the adenine deaminase ABE8e, leading to juxtaposed or spaced cytosine and adenine co-editing at the same target sequence in plant cells. Furthermore, we expanded the application of this toolkit in plants for tunable knockdown of protein-coding genes via creating upstream open reading frame and for loss-of-function analysis of non-coding genes, such as microRNA sponges. Collectively, this toolkit increases the functional diversity and versatility of base editors in basic and applied plant research.
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Affiliation(s)
- Xiangyu Xiong
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhenxiang Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jieping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kehui Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chenlong Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jian-Feng Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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16
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Kar S, Bordiya Y, Rodriguez N, Kim J, Gardner EC, Gollihar JD, Sung S, Ellington AD. Orthogonal control of gene expression in plants using synthetic promoters and CRISPR-based transcription factors. PLANT METHODS 2022; 18:42. [PMID: 35351174 PMCID: PMC8966344 DOI: 10.1186/s13007-022-00867-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/01/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND The construction and application of synthetic genetic circuits is frequently improved if gene expression can be orthogonally controlled, relative to the host. In plants, orthogonality can be achieved via the use of CRISPR-based transcription factors that are programmed to act on natural or synthetic promoters. The construction of complex gene circuits can require multiple, orthogonal regulatory interactions, and this in turn requires that the full programmability of CRISPR elements be adapted to non-natural and non-standard promoters that have few constraints on their design. Therefore, we have developed synthetic promoter elements in which regions upstream of the minimal 35S CaMV promoter are designed from scratch to interact via programmed gRNAs with dCas9 fusions that allow activation of gene expression. RESULTS A panel of three, mutually orthogonal promoters that can be acted on by artificial gRNAs bound by CRISPR regulators were designed. Guide RNA expression targeting these promoters was in turn controlled by either Pol III (U6) or ethylene-inducible Pol II promoters, implementing for the first time a fully artificial Orthogonal Control System (OCS). Following demonstration of the complete orthogonality of the designs, the OCS was tied to cellular metabolism by putting gRNA expression under the control of an endogenous plant signaling molecule, ethylene. The ability to form complex circuitry was demonstrated via the ethylene-driven, ratiometric expression of fluorescent proteins in single plants. CONCLUSIONS The design of synthetic promoters is highly generalizable to large tracts of sequence space, allowing Orthogonal Control Systems of increasing complexity to potentially be generated at will. The ability to tie in several different basal features of plant molecular biology (Pol II and Pol III promoters, ethylene regulation) to the OCS demonstrates multiple opportunities for engineering at the system level. Moreover, given the fungibility of the core 35S CaMV promoter elements, the derived synthetic promoters can potentially be utilized across a variety of plant species.
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Affiliation(s)
- Shaunak Kar
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
| | - Yogendra Bordiya
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, TX, USA
| | - Nestor Rodriguez
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Junghyun Kim
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Elizabeth C Gardner
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Sibum Sung
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
| | - Andrew D Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
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17
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Park J, Demirer GS, Cheung LS. Toolboxes for plant systems biology research. Curr Opin Biotechnol 2022; 75:102692. [PMID: 35144172 DOI: 10.1016/j.copbio.2022.102692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/22/2021] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
Abstract
The terms 'systems' and 'synthetic biology' are often used together, with most scientists striding between the two fields rather than adhering to a single side. Often too, scientists want to understand a system to inform the design of gene circuits that could endow it with new functions. However, this does not need to be the progression of research, as synthetic constructs can help improve our understanding of a system. Here, we review synthetic biology tool kits with the potential to overcome pleiotropic effects, compensatory mechanisms, and redundancy in plants. Combined with -omics techniques, these tools could reveal novel insights on plant growth and development, an aim that has gained renewed urgency given the impact of climate change on crop productivity.
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Affiliation(s)
- Jihyun Park
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gozde S Demirer
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA; Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lily S Cheung
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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18
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Pan C, Wu X, Markel K, Malzahn AA, Kundagrami N, Sretenovic S, Zhang Y, Cheng Y, Shih PM, Qi Y. CRISPR-Act3.0 for highly efficient multiplexed gene activation in plants. NATURE PLANTS 2021; 7:942-953. [PMID: 34168320 DOI: 10.1038/s41477-021-00953-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 05/27/2021] [Indexed: 05/22/2023]
Abstract
RNA-guided CRISPR activation (CRISPRa) systems have been developed in plants. However, the simultaneous activation of multiple genes remains challenging. Here, we develop a highly robust CRISPRa system working in rice, Arabidopsis and tomato, CRISPR-Act3.0, through systematically exploring different effector recruitment strategies and various transcription activators based on deactivated Streptococcus pyogenes Cas9 (dSpCas9). The CRISPR-Act3.0 system results in fourfold to sixfold higher activation than the state-of-the-art CRISPRa systems. We further develop a tRNA-gR2.0 (single guide RNA 2.0) expression system enabling CRISPR-Act3.0-based robust activation of up to seven genes for metabolic engineering in rice. In addition, CRISPR-Act3.0 allows the simultaneous modification of multiple traits in Arabidopsis, which are stably transmitted to the T3 generations. On the basis of CRISPR-Act3.0, we elucidate guide RNA targeting rules for effective transcriptional activation. To target T-rich protospacer adjacent motifs (PAMs), we transfer this activation strategy to CRISPR-dCas12b and further improve the dAaCas12b-based CRISPRa system. Moreover, we develop a potent near-PAM-less CRISPR-Act3.0 system on the basis of the SpRY dCas9 variant, which outperforms the dCas9-NG system in both activation potency and targeting scope. Altogether, our study has substantially improved the CRISPRa technology in plants and provided plant researchers a powerful toolbox for efficient gene activation in foundational and translational research.
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Affiliation(s)
- Changtian Pan
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Xincheng Wu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Kasey Markel
- Department of Plant Biology, University of California, Davis, CA, USA
| | - Aimee A Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Neil Kundagrami
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yanhao Cheng
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Patrick M Shih
- Department of Plant Biology, University of California, Davis, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
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