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Zarrabian M, Sherif SM. Silence is not always golden: A closer look at potential environmental and ecotoxicological impacts of large-scale dsRNA application. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175311. [PMID: 39122031 DOI: 10.1016/j.scitotenv.2024.175311] [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: 06/05/2024] [Revised: 08/02/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
RNA interference (RNAi) technology has emerged as a pivotal strategy in sustainable pest management, offering a targeted approach that significantly mitigates the environmental and health risks associated with traditional insecticides. Originally implemented through genetically modified organisms (GMOs) to produce specific RNAi constructs, the technology has evolved in response to public and regulatory concerns over GMOs. This evolution has spurred the development of non-transgenic RNAi applications such as spray-induced gene silencing (SIGS), which employs double-stranded RNA (dsRNA) to silence pest genes directly without altering the plant's genetic makeup. Despite its advantages in specificity and reduced ecological footprint, SIGS faces significant obstacles, particularly the instability of dsRNA in field conditions, which limits its practical efficacy. To overcome these limitations, innovative delivery mechanisms have been developed. These include nanotechnology-based systems, minicells, and nanovesicles, which are designed to protect dsRNA from degradation and enhance its delivery to target organisms. While these advancements have improved the stability and application efficiency of dsRNA, comprehensive assessments of their environmental safety and the potential for increased exposure risks to non-target organisms remain incomplete. This comprehensive review aims to elucidate the environmental fate of dsRNA and evaluate the potential risks associated with its widespread application on non-target organisms, encompassing soil microorganisms, beneficial insects, host plants, and mammals. The objective is to establish a more refined framework for RNAi risk assessment within environmental and ecotoxicological contexts, thereby fostering the development of safer, non-transgenic RNAi-based pest control strategies.
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Affiliation(s)
- Mohammad Zarrabian
- Virginia Tech, School of Plant and Environmental Sciences, Alson H. Smith Jr. Agricultural Research, and Extension Center, Winchester, VA 22602, United States
| | - Sherif M Sherif
- Virginia Tech, School of Plant and Environmental Sciences, Alson H. Smith Jr. Agricultural Research, and Extension Center, Winchester, VA 22602, United States.
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2
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Capriotti L, Molesini B, Pandolfini T, Jin H, Baraldi E, Cecchin M, Mezzetti B, Sabbadini S. RNA interference-based strategies to control Botrytis cinerea infection in cultivated strawberry. PLANT CELL REPORTS 2024; 43:201. [PMID: 39048858 PMCID: PMC11269516 DOI: 10.1007/s00299-024-03288-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
KEY MESSAGE Gene silencing of BcDCL genes improves gray mold disease control in the cultivated strawberry. Gene silencing technology offers new opportunities to develop new formulations or new pathogen-resistant plants for reducing impacts of agricultural systems. Recent studies offered the proof of concept that the symptoms of gray mold can be reduced by downregulating Dicer-like 1 (DCL1) and 2 (DCL2) genes of Botrytis cinerea. In this study, we demonstrate that both solutions based on dsRNA topical treatment and in planta expression targeting BcDCL1 and BcDCL2 genes can be used to control the strawberry gray mold, the most harmful disease for different fruit crops. 50, 70 and 100 ng μL-1 of naked BcDCL1/2 dsRNA, sprayed on plants of Fragaria x ananassa cultivar Romina in the greenhouse, displayed significant reduction of susceptibility, compared to the negative controls, but to a lesser extent than the chemical fungicide. Three independent lines of Romina cultivar were confirmed for their stable expression of the hairpin gene construct that targets the Bc-DCL1 and 2 sequences (hp-Bc-DCL1/2), and for the production of hp construct-derived siRNAs, by qRT-PCR and Northern blot analyses. In vitro and in vivo detached leaves, and fruits from the hp-Bc-DCL1/2 lines showed significantly enhanced tolerance to this fungal pathogen compared to the control. This decreased susceptibility was correlated to the reduced fungal biomass and the downregulation of the Bc-DCL1 and 2 genes in B. cinerea. These results confirm the potential of both RNAi-based products and plants for protecting the cultivated strawberry from B. cinerea infection, reducing the impact of chemical pesticides on the environment and the health of consumers.
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Affiliation(s)
- Luca Capriotti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Barbara Molesini
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Tiziana Pandolfini
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Elena Baraldi
- Department of Agricultural and Food Science, DISTAL, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Michela Cecchin
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.
| | - Silvia Sabbadini
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.
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3
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Shuwen H, Yifei S, Xinyue W, Zhanbo Q, Xiang Y, Xi Y. Advances in bacteria-based drug delivery systems for anti-tumor therapy. Clin Transl Immunology 2024; 13:e1518. [PMID: 38939727 PMCID: PMC11208082 DOI: 10.1002/cti2.1518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/07/2024] [Accepted: 06/01/2024] [Indexed: 06/29/2024] Open
Abstract
In recent years, bacteria have gained considerable attention as a promising drug carrier that is critical in improving the effectiveness and reducing the side effects of anti-tumor drugs. Drug carriers can be utilised in various forms, including magnetotactic bacteria, bacterial biohybrids, minicells, bacterial ghosts and bacterial spores. Additionally, functionalised and engineered bacteria obtained through gene engineering and surface modification could provide enhanced capabilities for drug delivery. This review summarises the current studies on bacteria-based drug delivery systems for anti-tumor therapy and discusses the prospects and challenges of bacteria as drug carriers. Furthermore, our findings aim to provide new directions and guidance for the research on bacteria-based drug systems.
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Affiliation(s)
- Han Shuwen
- Huzhou Central HospitalAffiliated Central Hospital Huzhou UniversityyHuzhouZhejiang ProvinceChina
- Huzhou Central HospitalFifth Affiliated Clinical Medical College of Zhejiang Chinese Medical UniversityHuzhouZhejiang ProvinceChina
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of HuzhouHuzhouZhejiang ProvinceChina
| | - Song Yifei
- Huzhou Central HospitalAffiliated Central Hospital Huzhou UniversityyHuzhouZhejiang ProvinceChina
| | - Wu Xinyue
- Huzhou Central HospitalAffiliated Central Hospital Huzhou UniversityyHuzhouZhejiang ProvinceChina
| | - Qu Zhanbo
- Huzhou Central HospitalAffiliated Central Hospital Huzhou UniversityyHuzhouZhejiang ProvinceChina
- Huzhou Central HospitalFifth Affiliated Clinical Medical College of Zhejiang Chinese Medical UniversityHuzhouZhejiang ProvinceChina
| | - Yu Xiang
- Huzhou Central HospitalAffiliated Central Hospital Huzhou UniversityyHuzhouZhejiang ProvinceChina
| | - Yang Xi
- Huzhou Central HospitalAffiliated Central Hospital Huzhou UniversityyHuzhouZhejiang ProvinceChina
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Spada M, Pugliesi C, Fambrini M, Pecchia S. Challenges and Opportunities Arising from Host- Botrytis cinerea Interactions to Outline Novel and Sustainable Control Strategies: The Key Role of RNA Interference. Int J Mol Sci 2024; 25:6798. [PMID: 38928507 PMCID: PMC11203536 DOI: 10.3390/ijms25126798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The necrotrophic plant pathogenic fungus Botrytis cinerea (Pers., 1794), the causative agent of gray mold disease, causes significant losses in agricultural production. Control of this fungal pathogen is quite difficult due to its wide host range and environmental persistence. Currently, the management of the disease is still mainly based on chemicals, which can have harmful effects not only on the environment and on human health but also because they favor the development of strains resistant to fungicides. The flexibility and plasticity of B. cinerea in challenging plant defense mechanisms and its ability to evolve strategies to escape chemicals require the development of new control strategies for successful disease management. In this review, some aspects of the host-pathogen interactions from which novel and sustainable control strategies could be developed (e.g., signaling pathways, molecules involved in plant immune mechanisms, hormones, post-transcriptional gene silencing) were analyzed. New biotechnological tools based on the use of RNA interference (RNAi) are emerging in the crop protection scenario as versatile, sustainable, effective, and environmentally friendly alternatives to the use of chemicals. RNAi-based fungicides are expected to be approved soon, although they will face several challenges before reaching the market.
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Affiliation(s)
- Maria Spada
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Susanna Pecchia
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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Vatanparast M, Merkel L, Amari K. Exogenous Application of dsRNA in Plant Protection: Efficiency, Safety Concerns and Risk Assessment. Int J Mol Sci 2024; 25:6530. [PMID: 38928236 PMCID: PMC11204322 DOI: 10.3390/ijms25126530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The use of double-stranded RNA (dsRNA) for plant protection shows great potential as a sustainable alternative to traditional pesticides. This review summarizes the current state of knowledge on using exogenous dsRNA in plant protection and includes the latest findings on the safety and efficiency of this strategy. The review also emphasizes the need for a cautious and comprehensive approach, considering safety considerations such as off-target effects and formulation challenges. The regulatory landscape in different regions is also discussed, underscoring the need for specific guidelines tailored to dsRNA-based pesticides. The review provides a crucial resource for researchers, regulators, and industry stakeholders, promoting a balanced approach incorporating innovation with thorough safety assessments. The continuous dialog emphasized in this review is essential for shaping the future of dsRNA-based plant protection. As the field advances, collaboration among scientists, regulators, and industry partners will play a vital role in establishing guidelines and ensuring the responsible, effective, and sustainable use of dsRNA in agriculture.
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Affiliation(s)
| | | | - Khalid Amari
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plant, Institute for Biosafety in Plant Biotechnology, D-06484 Quedlinburg, Germany
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Ortolá B, Daròs JA. RNA Interference in Insects: From a Natural Mechanism of Gene Expression Regulation to a Biotechnological Crop Protection Promise. BIOLOGY 2024; 13:137. [PMID: 38534407 DOI: 10.3390/biology13030137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]
Abstract
Insect pests rank among the major limiting factors in agricultural production worldwide. In addition to direct effect on crops, some phytophagous insects are efficient vectors for plant disease transmission. Large amounts of conventional insecticides are required to secure food production worldwide, with a high impact on the economy and environment, particularly when beneficial insects are also affected by chemicals that frequently lack the desired specificity. RNA interference (RNAi) is a natural mechanism gene expression regulation and protection against exogenous and endogenous genetic elements present in most eukaryotes, including insects. Molecules of double-stranded RNA (dsRNA) or highly structured RNA are the substrates of cellular enzymes to produce several types of small RNAs (sRNAs), which play a crucial role in targeting sequences for transcriptional or post-transcriptional gene silencing. The relatively simple rules that underlie RNAi regulation, mainly based in Watson-Crick complementarity, have facilitated biotechnological applications based on these cellular mechanisms. This includes the promise of using engineered dsRNA molecules, either endogenously produced in crop plants or exogenously synthesized and applied onto crops, as a new generation of highly specific, sustainable, and environmentally friendly insecticides. Fueled on this expectation, this article reviews current knowledge about the RNAi pathways in insects, and some other applied questions such as production and delivery of recombinant RNA, which are critical to establish RNAi as a reliable technology for insect control in crop plants.
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Affiliation(s)
- Beltrán Ortolá
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain
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Chen A, Halilovic L, Shay JH, Koch A, Mitter N, Jin H. Improving RNA-based crop protection through nanotechnology and insights from cross-kingdom RNA trafficking. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102441. [PMID: 37696727 PMCID: PMC10777890 DOI: 10.1016/j.pbi.2023.102441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/21/2023] [Accepted: 08/06/2023] [Indexed: 09/13/2023]
Abstract
Spray-induced gene silencing (SIGS) is a powerful and eco-friendly method for crop protection. Based off the discovery of RNA uptake ability in many fungal pathogens, the application of exogenous RNAs targeting pathogen/pest genes results in gene silencing and infection inhibition. However, SIGS remains hindered by the rapid degradation of RNA in the environment. As extracellular vesicles are used by plants, animals, and microbes in nature to transport RNAs for cross-kingdom/species RNA interference between hosts and microbes/pests, nanovesicles and other nanoparticles have been used to prevent RNA degradation. Efforts examining the effect of nanoparticles on RNA stability and internalization have identified key attributes that can inform better nanocarrier designs for SIGS. Understanding sRNA biogenesis, cross-kingdom/species RNAi, and how plants and pathogens/pests naturally interact are paramount for the design of SIGS strategies. Here, we focus on nanotechnology advancements for the engineering of innovative RNA-based disease control strategies against eukaryotic pathogens and pests.
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Affiliation(s)
- Angela Chen
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Lida Halilovic
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Jia-Hong Shay
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Aline Koch
- Institute of Plant Sciences Cell Biology and Plant Biochemistry, Plant RNA Transport, University of Regensburg, Regensburg, Germany
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
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McLaughlin MS, Roy M, Abbasi PA, Carisse O, Yurgel SN, Ali S. Why Do We Need Alternative Methods for Fungal Disease Management in Plants? PLANTS (BASEL, SWITZERLAND) 2023; 12:3822. [PMID: 38005718 PMCID: PMC10675458 DOI: 10.3390/plants12223822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023]
Abstract
Fungal pathogens pose a major threat to food production worldwide. Traditionally, chemical fungicides have been the primary means of controlling these pathogens, but many of these fungicides have recently come under increased scrutiny due to their negative effects on the health of humans, animals, and the environment. Furthermore, the use of chemical fungicides can result in the development of resistance in populations of phytopathogenic fungi. Therefore, new environmentally friendly alternatives that provide adequate levels of disease control are needed to replace chemical fungicides-if not completely, then at least partially. A number of alternatives to conventional chemical fungicides have been developed, including plant defence elicitors (PDEs); biological control agents (fungi, bacteria, and mycoviruses), either alone or as consortia; biochemical fungicides; natural products; RNA interference (RNAi) methods; and resistance breeding. This article reviews the conventional and alternative methods available to manage fungal pathogens, discusses their strengths and weaknesses, and identifies potential areas for future research.
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Affiliation(s)
- Michael S. McLaughlin
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 4H5, Canada
| | - Maria Roy
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
| | - Pervaiz A. Abbasi
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
| | - Odile Carisse
- Saint-Jean-sur-Richelieu Research Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 7B5, Canada;
| | - Svetlana N. Yurgel
- United States Department of Agriculture (USDA), Agricultural Research Service, Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350, USA;
| | - Shawkat Ali
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
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Osborne CJ, Cohnstaedt LW, Silver KS. Outlook on RNAi-Based Strategies for Controlling Culicoides Biting Midges. Pathogens 2023; 12:1251. [PMID: 37887767 PMCID: PMC10610143 DOI: 10.3390/pathogens12101251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
Culicoides are small biting midges with the capacity to transmit important livestock pathogens around much of the world, and their impacts on animal welfare are likely to expand. Hemorrhagic diseases resulting from Culicoides-vectored viruses, for example, can lead to millions of dollars in economic damages for producers. Chemical insecticides can reduce Culicoides abundance but may not suppress population numbers enough to prevent pathogen transmission. These insecticides can also cause negative effects on non-target organisms and ecosystems. RNA interference (RNAi) is a cellular regulatory mechanism that degrades mRNA and suppresses gene expression. Studies have examined the utility of this mechanism for insect pest control, and with it, have described the hurdles towards producing, optimizing, and applying these RNAi-based products. These methods hold promise for being highly specific and environmentally benign when compared to chemical insecticides and are more transient than engineering transgenic insects. Given the lack of available control options for Culicoides, RNAi-based products could be an option to treat large areas with minimal environmental impact. In this study, we describe the state of current Culicoides control methods, successes and hurdles towards using RNAi for pest control, and the necessary research required to bring an RNAi-based control method to fruition for Culicoides midges.
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Affiliation(s)
- Cameron J. Osborne
- Department of Entomology, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA;
| | - Lee W. Cohnstaedt
- Foreign Arthropod-Borne Animal Diseases Research Unit, National Bio- and Agro-Defense Facility, Agricultural Research Service, United Stated Department of Agriculture, Manhattan, KS 66502, USA
| | - Kristopher S. Silver
- Department of Entomology, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA;
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Bhagta S, Bhardwaj V, Kant A. Exogenous dsRNA trigger RNAi in Venturia inaequalis resulting in down regulation of target genes and growth reduction. Mol Biol Rep 2023; 50:8421-8429. [PMID: 37620739 DOI: 10.1007/s11033-023-08736-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/02/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Venturia inaequalis is an apple scab causing fungal pathogen. It is a highly contagious and destructive pathogen which rapidly spreads infection in the surrounding orchards if not managed. The management and control of disease require multiple fungicides to be sprayed at different development stages of the apple. Persistent applications of fungicides also raises environmental concerns. Here, we demonstrate the potential of using spray induced gene silencing (SIGS) by developing target specific gene constructs for the synthesis of corresponding double-stranded RNA (dsRNA). METHODS AND RESULTS The exogenous application of dsRNAs was found to reduce mycelial growth and spore formation of V. inaequalis on culture plates. Four genes of V. inaequalis viz. CIN1, CE5, VICE12 and VICE16 which get upregulated during infection, were selected as targets for the development of gene construct expressing the corresponding dsRNA. The effect of exogenously supplied in vitro synthesized dsRNA on V. inaequalis was assessed in culture bioassay experiments with respect to growth, and spore formation. The expression level of the target genes in treated and control fungus was evaluated using quantitative PCR. Fungus treated with VICE12 targeted dsRNA showed maximum reduction in colony size (~ 55%), conidia formation (~ 93%) and expression level of the corresponding gene (2.2 fold), which was followed by CIN1-dsRNA. VICE16-dsRNA treatment was least effective with 32% reduction in growth, the non-significant effect of conidial spore formation and 1.13 fold down regulation of corresponding target gene expression level. CONCLUSION The result of this investigation validates the hypothesis that RNAi is evoked in V. inaequalis by exogenously supplied dsRNA and spray induced gene silencing (SIGS) based solutions may reduce burden of fungicide usage on apple crop against apple scab disease in future.
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Affiliation(s)
- Suhani Bhagta
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Anil Kant
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India.
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Mann CWG, Sawyer A, Gardiner DM, Mitter N, Carroll BJ, Eamens AL. RNA-Based Control of Fungal Pathogens in Plants. Int J Mol Sci 2023; 24:12391. [PMID: 37569766 PMCID: PMC10418863 DOI: 10.3390/ijms241512391] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Our duty to conserve global natural ecosystems is increasingly in conflict with our need to feed an expanding population. The use of conventional pesticides not only damages the environment and vulnerable biodiversity but can also still fail to prevent crop losses of 20-40% due to pests and pathogens. There is a growing call for more ecologically sustainable pathogen control measures. RNA-based biopesticides offer an eco-friendly alternative to the use of conventional fungicides for crop protection. The genetic modification (GM) of crops remains controversial in many countries, though expression of transgenes inducing pathogen-specific RNA interference (RNAi) has been proven effective against many agronomically important fungal pathogens. The topical application of pathogen-specific RNAi-inducing sprays is a more responsive, GM-free approach to conventional RNAi transgene-based crop protection. The specific targeting of essential pathogen genes, the development of RNAi-nanoparticle carrier spray formulations, and the possible structural modifications to the RNA molecules themselves are crucial to the success of this novel technology. Here, we outline the current understanding of gene silencing pathways in plants and fungi and summarize the pioneering and recent work exploring RNA-based biopesticides for crop protection against fungal pathogens, with a focus on spray-induced gene silencing (SIGS). Further, we discuss factors that could affect the success of RNA-based control strategies, including RNA uptake, stability, amplification, and movement within and between the plant host and pathogen, as well as the cost and design of RNA pesticides.
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Affiliation(s)
- Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
| | - Anne Sawyer
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Donald M. Gardiner
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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12
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He B, Wang H, Liu G, Chen A, Calvo A, Cai Q, Jin H. Fungal small RNAs ride in extracellular vesicles to enter plant cells through clathrin-mediated endocytosis. Nat Commun 2023; 14:4383. [PMID: 37474601 PMCID: PMC10359353 DOI: 10.1038/s41467-023-40093-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 07/12/2023] [Indexed: 07/22/2023] Open
Abstract
Small RNAs (sRNAs) of the fungal pathogen Botrytis cinerea can enter plant cells and hijack host Argonaute protein 1 (AGO1) to silence host immunity genes. However, the mechanism by which these fungal sRNAs are secreted and enter host cells remains unclear. Here, we demonstrate that B. cinerea utilizes extracellular vesicles (EVs) to secrete Bc-sRNAs, which are then internalized by plant cells through clathrin-mediated endocytosis (CME). The B. cinerea tetraspanin protein, Punchless 1 (BcPLS1), serves as an EV biomarker and plays an essential role in fungal pathogenicity. We observe numerous Arabidopsis clathrin-coated vesicles (CCVs) around B. cinerea infection sites and the colocalization of B. cinerea EV marker BcPLS1 and Arabidopsis CLATHRIN LIGHT CHAIN 1, one of the core components of CCV. Meanwhile, BcPLS1 and the B. cinerea-secreted sRNAs are detected in purified CCVs after infection. Arabidopsis knockout mutants and inducible dominant-negative mutants of key components of the CME pathway exhibit increased resistance to B. cinerea infection. Furthermore, Bc-sRNA loading into Arabidopsis AGO1 and host target gene suppression are attenuated in those CME mutants. Together, our results demonstrate that fungi secrete sRNAs via EVs, which then enter host plant cells mainly through CME.
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Affiliation(s)
- Baoye He
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Huan Wang
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Guosheng Liu
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Angela Chen
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Alejandra Calvo
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
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13
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He B, Wang H, Liu G, Chen A, Calvo A, Cai Q, Jin H. Fungal small RNAs ride in extracellular vesicles to enter plant cells through clathrin-mediated endocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.545159. [PMID: 37398405 PMCID: PMC10312686 DOI: 10.1101/2023.06.15.545159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Small RNAs (sRNAs) of the fungal pathogen Botrytis cinerea can enter plant cells and hijack host Argonaute protein 1 (AGO1) to silence host immunity genes. However, the mechanism by which these fungal sRNAs are secreted and enter host cells remains unclear. Here, we demonstrate that B. cinerea utilizes extracellular vesicles (EVs) to secrete Bc-sRNAs, which are then internalized by plant cells through clathrin-mediated endocytosis (CME). The B. cinerea tetraspanin protein, Punchless 1 (BcPLS1), serves as an EV biomarker and plays an essential role in fungal pathogenicity. We observe numerous Arabidopsis clathrin-coated vesicles (CCVs) around B. cinerea infection sites and the colocalization of B. cinerea EV marker BcPLS1 and Arabidopsis CLATHRIN LIGHT CHAIN 1, one of the core components of CCV. Meanwhile, BcPLS1 and the B. cinerea-secreted sRNAs are detected in purified CCVs after infection. Arabidopsis knockout mutants and inducible dominant-negative mutants of key components of CME pathway exhibit increased resistance to B. cinerea infection. Furthermore, Bc-sRNA loading into Arabidopsis AGO1 and host target gene suppression are attenuated in those CME mutants. Together, our results demonstrate that fungi secrete sRNAs via EVs, which then enter host plant cells mainly through CME.
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Affiliation(s)
- Baoye He
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Huan Wang
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Guosheng Liu
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Angela Chen
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Alejandra Calvo
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
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14
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Koeppe S, Kawchuk L, Kalischuk M. RNA Interference Past and Future Applications in Plants. Int J Mol Sci 2023; 24:ijms24119755. [PMID: 37298705 DOI: 10.3390/ijms24119755] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Antisense RNA was observed to elicit plant disease resistance and post-translational gene silencing (PTGS). The universal mechanism of RNA interference (RNAi) was shown to be induced by double-stranded RNA (dsRNA), an intermediate produced during virus replication. Plant viruses with a single-stranded positive-sense RNA genome have been instrumental in the discovery and characterization of systemic RNA silencing and suppression. An increasing number of applications for RNA silencing have emerged involving the exogenous application of dsRNA through spray-induced gene silencing (SIGS) that provides specificity and environmentally friendly options for crop protection and improvement.
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Affiliation(s)
- Sarah Koeppe
- Department of Plant Agriculture, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada
| | - Lawrence Kawchuk
- Research Centre, Agriculture and Agri-Food Canada, 5403 1 Ave S., Lethbridge, AB T1J 4B1, Canada
| | - Melanie Kalischuk
- Department of Plant Agriculture, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada
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15
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Cai Q, Halilovic L, Shi T, Chen A, He B, Wu H, Jin H. Extracellular vesicles: cross-organismal RNA trafficking in plants, microbes, and mammalian cells. EXTRACELLULAR VESICLES AND CIRCULATING NUCLEIC ACIDS 2023; 4:262-282. [PMID: 37575974 PMCID: PMC10419970 DOI: 10.20517/evcna.2023.10] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Extracellular vesicles (EVs) are membrane-enclosed nanometer-scale particles that transport biological materials such as RNAs, proteins, and metabolites. EVs have been discovered in nearly all kingdoms of life as a form of cellular communication across different cells and between interacting organisms. EV research has primarily focused on EV-mediated intra-organismal transport in mammals, which has led to the characterization of a plethora of EV contents from diverse cell types with distinct and impactful physiological effects. In contrast, research into EV-mediated transport in plants has focused on inter-organismal interactions between plants and interacting microbes. However, the overall molecular content and functions of plant and microbial EVs remain largely unknown. Recent studies into the plant-pathogen interface have demonstrated that plants produce and secrete EVs that transport small RNAs into pathogen cells to silence virulence-related genes. Plant-interacting microbes such as bacteria and fungi also secrete EVs which transport proteins, metabolites, and potentially RNAs into plant cells to enhance their virulence. This review will focus on recent advances in EV-mediated communications in plant-pathogen interactions compared to the current state of knowledge of mammalian EV capabilities and highlight the role of EVs in cross-kingdom RNA interference.
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Affiliation(s)
- Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430072, Hubei, China
| | - Lida Halilovic
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92507, United States
| | - Ting Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430072, Hubei, China
| | - Angela Chen
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92507, United States
| | - Baoye He
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92507, United States
| | - Huaitong Wu
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92507, United States
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92507, United States
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16
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Qiao L, Niño‐Sánchez J, Hamby R, Capriotti L, Chen A, Mezzetti B, Jin H. Artificial nanovesicles for dsRNA delivery in spray-induced gene silencing for crop protection. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:854-865. [PMID: 36601704 PMCID: PMC10037145 DOI: 10.1111/pbi.14001] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Spray-induced gene silencing (SIGS) is an innovative and eco-friendly technology where topical application of pathogen gene-targeting RNAs to plant material can enable disease control. SIGS applications remain limited because of the instability of RNA, which can be rapidly degraded when exposed to various environmental conditions. Inspired by the natural mechanism of cross-kingdom RNAi through extracellular vesicle trafficking, we describe herein the use of artificial nanovesicles (AVs) for RNA encapsulation and control against the fungal pathogen, Botrytis cinerea. AVs were synthesized using three different cationic lipid formulations, DOTAP + PEG, DOTAP and DODMA, and examined for their ability to protect and deliver double stranded RNA (dsRNA). All three formulations enabled dsRNA delivery and uptake by B. cinerea. Further, encapsulating dsRNA in AVs provided strong protection from nuclease degradation and from removal by leaf washing. This improved stability led to prolonged RNAi-mediated protection against B. cinerea both on pre- and post-harvest plant material using AVs. Specifically, the AVs extended the protection duration conferred by dsRNA to 10 days on tomato and grape fruits and to 21 days on grape leaves. The results of this work demonstrate how AVs can be used as a new nanocarrier to overcome RNA instability in SIGS for crop protection.
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Affiliation(s)
- Lulu Qiao
- Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome BiologyUniversity of CaliforniaLos AngelesCAUSA
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life SciencesZhejiang UniversityHangzhouChina
| | - Jonatan Niño‐Sánchez
- Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome BiologyUniversity of CaliforniaLos AngelesCAUSA
- Department of Plant Production and Forest ResourcesUniversity of ValladolidPalenciaSpain
- Sustainable Forest Management Research Institute (iuFOR)University of ValladolidPalenciaSpain
| | - Rachael Hamby
- Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome BiologyUniversity of CaliforniaLos AngelesCAUSA
| | - Luca Capriotti
- Department of Agricultural, Food and Environmental SciencesMarche Polytechnic UniversityAnconaItaly
| | - Angela Chen
- Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome BiologyUniversity of CaliforniaLos AngelesCAUSA
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental SciencesMarche Polytechnic UniversityAnconaItaly
| | - Hailing Jin
- Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome BiologyUniversity of CaliforniaLos AngelesCAUSA
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17
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Mat Jalaluddin NS, Asem M, Harikrishna JA, Ahmad Fuaad AAH. Recent Progress on Nanocarriers for Topical-Mediated RNAi Strategies for Crop Protection-A Review. Molecules 2023; 28:2700. [PMID: 36985671 PMCID: PMC10054734 DOI: 10.3390/molecules28062700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/19/2023] Open
Abstract
To fulfil the growing needs of the global population, sustainability in food production must be ensured. Insect pests and pathogens are primarily responsible for one-third of food losses and harmful synthetic pesticides have been applied to protect crops from these pests and other pathogens such as viruses and fungi. An alternative pathogen control mechanism that is more "friendly" to the environment can be developed by externally applying double-stranded RNAs (dsRNAs) to suppress gene expression. However, the use of dsRNA sprays in open fields is complicated with respect to variable efficiencies in the dsRNA delivery, and the stability of the dsRNA on and in the plants, and because the mechanisms of gene silencing may differ between plants and between different pathogen targets. Thus, nanocarrier delivery systems have been especially used with the goal of improving the efficacy of dsRNAs. Here, we highlight recent developments in nanoparticle-mediated nanocarriers to deliver dsRNA, including layered double hydroxide, carbon dots, carbon nanotubes, gold nanoparticles, chitosan nanoparticles, silica nanoparticles, liposomes, and cell-penetrating peptides, by review of the literature and patent landscape. The effects of nanoparticle size and surface modification on the dsRNA uptake efficiency in plants are also discussed. Finally, we emphasize the overall limitation of dsRNA sprays, the risks associated, and the potential safety concerns for spraying dsRNAs on crops.
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Affiliation(s)
| | - Maimunah Asem
- Peptide Laboratory, Drug Design & Development Research Group (DDDRG), Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Abdullah Al Hadi Ahmad Fuaad
- Peptide Laboratory, Drug Design & Development Research Group (DDDRG), Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
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18
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Li M, Sun X, Yin M, Shen J, Yan S. Recent Advances in Nanoparticle-Mediated Co-Delivery System: A Promising Strategy in Medical and Agricultural Field. Int J Mol Sci 2023; 24:5121. [PMID: 36982200 PMCID: PMC10048901 DOI: 10.3390/ijms24065121] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 03/10/2023] Open
Abstract
Drug and gene delivery systems mediated by nanoparticles have been widely studied for life science in the past decade. The application of nano-delivery systems can dramatically improve the stability and delivery efficiency of carried ingredients, overcoming the defects of administration routes in cancer therapy, and possibly maintaining the sustainability of agricultural systems. However, delivery of a drug or gene alone sometimes cannot achieve a satisfactory effect. The nanoparticle-mediated co-delivery system can load multiple drugs and genes simultaneously, and improve the effectiveness of each component, thus amplifying efficacy and exhibiting synergistic effects in cancer therapy and pest management. The co-delivery system has been widely reported in the medical field, and studies on its application in the agricultural field have recently begun to emerge. In this progress report, we summarize recent progress in the preparation and application of drug and gene co-delivery systems and discuss the remaining challenges and future perspectives in the design and fabrication.
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Affiliation(s)
- Mingshan Li
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xiaowei Sun
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Meizhen Yin
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jie Shen
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shuo Yan
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China
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19
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Knockdown of Bmp1 and Pls1 Virulence Genes by Exogenous Application of RNAi-Inducing dsRNA in Botrytis cinerea. Int J Mol Sci 2023; 24:ijms24054869. [PMID: 36902297 PMCID: PMC10003348 DOI: 10.3390/ijms24054869] [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: 11/09/2022] [Revised: 02/09/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
Botrytis cinerea is a pathogen of wide agronomic and scientific importance partly due to its tendency to develop fungicide resistance. Recently, there has been great interest in the use of RNA interference as a control strategy against B. cinerea. In order to reduce the possible effects on non-target species, the sequence-dependent nature of RNAi can be used as an advantage to customize the design of dsRNA molecules. We selected two genes related to virulence: BcBmp1 (a MAP kinase essential for fungal pathogenesis) and BcPls1 (a tetraspanin related to appressorium penetration). After performing a prediction analysis of small interfering RNAs, dsRNAs of 344 (BcBmp1) and 413 (BcPls1) nucleotides were synthesized in vitro. We tested the effect of topical applications of dsRNAs, both in vitro by a fungal growth assay in microtiter plates and in vivo on artificially inoculated detached lettuce leaves. In both cases, topical applications of dsRNA led to gene knockdown with a delay in conidial germination for BcBmp1, an evident growth retardation for BcPls1, and a strong reduction in necrotic lesions on lettuce leaves for both genes. Furthermore, a strongly reduced expression of the BcBmp1 and BcPls1 genes was observed in both in vitro and in vivo experiments, suggesting that these genes could be promising targets for the development of RNAi-based fungicides against B. cinerea.
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20
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Degnan RM, McTaggart AR, Shuey LS, Pame LJS, Smith GR, Gardiner DM, Nock V, Soffe R, Sale S, Garrill A, Carroll BJ, Mitter N, Sawyer A. Exogenous double-stranded RNA inhibits the infection physiology of rust fungi to reduce symptoms in planta. MOLECULAR PLANT PATHOLOGY 2023; 24:191-207. [PMID: 36528383 PMCID: PMC9923395 DOI: 10.1111/mpp.13286] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 06/01/2023]
Abstract
Rust fungi (Pucciniales) are a diverse group of plant pathogens in natural and agricultural systems. They pose ongoing threats to the diversity of native flora and cause annual crop yield losses. Agricultural rusts are predominantly managed with fungicides and breeding for resistance, but new control strategies are needed on non-agricultural plants and in fragile ecosystems. RNA interference (RNAi) induced by exogenous double-stranded RNA (dsRNA) has promise as a sustainable approach for managing plant-pathogenic fungi, including rust fungi. We investigated the mechanisms and impact of exogenous dsRNA on rust fungi through in vitro and whole-plant assays using two species as models, Austropuccinia psidii (the cause of myrtle rust) and Coleosporium plumeriae (the cause of frangipani rust). In vitro, dsRNA either associates externally or is internalized by urediniospores during the early stages of germination. The impact of dsRNA on rust infection architecture was examined on artificial leaf surfaces. dsRNA targeting predicted essential genes significantly reduced germination and inhibited development of infection structures, namely appressoria and penetration pegs. Exogenous dsRNA sprayed onto 1-year-old trees significantly reduced myrtle rust symptoms. Furthermore, we used comparative genomics to assess the wide-scale amenability of dsRNA to control rust fungi. We sequenced genomes of six species of rust fungi, including three new families (Araucariomyceaceae, Phragmidiaceae, and Skierkaceae) and identified key genes of the RNAi pathway across 15 species in eight families of Pucciniales. Together, these findings indicate that dsRNA targeting essential genes has potential for broad-use management of rust fungi across natural and agricultural systems.
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Affiliation(s)
- Rebecca M. Degnan
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQueenslandAustralia
| | - Alistair R. McTaggart
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | - Louise S. Shuey
- Queensland Department of Agriculture and FisheriesEcosciences PrecinctDutton ParkQueenslandAustralia
| | - Leny Jane S. Pame
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQueenslandAustralia
| | - Grant R. Smith
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
| | - Donald M. Gardiner
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | - Volker Nock
- Department of Electrical and Computer EngineeringUniversity of CanterburyChristchurchNew Zealand
| | - Rebecca Soffe
- Department of Electrical and Computer EngineeringUniversity of CanterburyChristchurchNew Zealand
- Present address:
School of EngineeringRMIT UniversityMelbourneVictoriaAustralia
| | - Sarah Sale
- Department of Electrical and Computer EngineeringUniversity of CanterburyChristchurchNew Zealand
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Ashley Garrill
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Bernard J. Carroll
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQueenslandAustralia
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | - Anne Sawyer
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQueenslandAustralia
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural ScienceThe University of QueenslandSt LuciaQueenslandAustralia
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21
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Qiao L, Niño-Sánchez J, Hamby R, Capriotti L, Chen A, Mezzetti B, Jin H. Artificial nanovesicles for dsRNA delivery in spray induced gene silencing for crop protection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522662. [PMID: 36711993 PMCID: PMC9882009 DOI: 10.1101/2023.01.03.522662] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Spray-Induced Gene Silencing (SIGS) is an innovative and eco-friendly technology where topical application of pathogen gene-targeting RNAs to plant material can enable disease control. SIGS applications remain limited because of the instability of dsRNA, which can be rapidly degraded when exposed to various environmental conditions. Inspired by the natural mechanism of cross-kingdom RNAi through extracellular vesicle trafficking, we describe herein the use of artificial nanovesicles (AVs) for dsRNA encapsulation and control against the fungal pathogen, Botrytis cinerea. AVs were synthesized using three different cationic lipid formulations, DOTAP + PEG, DOTAP, and DODMA, and examined for their ability to protect and deliver dsRNA. All three formulations enabled dsRNA delivery and uptake by B. cinerea. Further, encapsulating dsRNA in AVs provided strong protection from nuclease degradation and from removal by leaf washing. This improved stability led to prolonged RNAi-mediated protection against B. cinerea both on pre- and post-harvest plant material using AVs. Specifically, the AVs extended the protection duration conferred by dsRNA to 10 days on tomato and grape fruits and to 21 days on grape leaves. The results of this work demonstrate how AVs can be used as a new nanocarrier to overcome dsRNA instability in SIGS for crop protection.
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Affiliation(s)
- Lulu Qiao
- Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jonatan Niño-Sánchez
- Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
- Department of Plant Production and Forest Resources, University of Valladolid, Palencia 34004, Spain
- Sustainable Forest Management Research Institute (iuFOR). University of Valladolid, Palencia 34004, Spain
| | - Rachael Hamby
- Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Luca Capriotti
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy
| | - Angela Chen
- Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy
| | - Hailing Jin
- Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
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22
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Hough J, Howard JD, Brown S, Portwood DE, Kilby PM, Dickman MJ. Strategies for the production of dsRNA biocontrols as alternatives to chemical pesticides. Front Bioeng Biotechnol 2022; 10:980592. [PMID: 36299286 PMCID: PMC9588923 DOI: 10.3389/fbioe.2022.980592] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/23/2022] [Indexed: 01/09/2023] Open
Abstract
Current crop pest control strategies rely on insecticidal and fungicidal sprays, plant genetic resistance, transgenes and agricultural practices. However, many insects, plant viruses, and fungi have no current means of control or have developed resistance against traditional pesticides. dsRNA is emerging as a novel sustainable method of plant protection as an alternative to traditional chemical pesticides. The successful commercialisation of dsRNA based biocontrols for effective pest management strategies requires the economical production of large quantities of dsRNA combined with suitable delivery methods to ensure RNAi efficacy against the target pest. A number of methods exist for the production and delivery of dsRNA based biocontrols and here we review alternative methods currently employed and emerging new approaches for their production. Additionally, we highlight potential challenges that will need to be addressed prior to widespread adoption of dsRNA biocontrols as novel sustainable alternatives to traditional chemical pesticides.
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Affiliation(s)
- James Hough
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingtom
| | - John D. Howard
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingtom
| | - Stephen Brown
- Sheffield RNAi Screening Facility, School of Biosciences, University of Sheffield, Sheffield, United Kingtom
| | - David E. Portwood
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Peter M. Kilby
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Mark J. Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingtom
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23
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Ray P, Sahu D, Aminedi R, Chandran D. Concepts and considerations for enhancing RNAi efficiency in phytopathogenic fungi for RNAi-based crop protection using nanocarrier-mediated dsRNA delivery systems. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:977502. [PMID: 37746174 PMCID: PMC10512274 DOI: 10.3389/ffunb.2022.977502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/19/2022] [Indexed: 09/26/2023]
Abstract
Existing, emerging, and reemerging strains of phytopathogenic fungi pose a significant threat to agricultural productivity globally. This risk is further exacerbated by the lack of resistance source(s) in plants or a breakdown of resistance by pathogens through co-evolution. In recent years, attenuation of essential pathogen gene(s) via double-stranded (ds) RNA-mediated RNA interference (RNAi) in host plants, a phenomenon known as host-induced gene silencing, has gained significant attention as a way to combat pathogen attack. Yet, due to biosafety concerns regarding transgenics, country-specific GMO legislation has limited the practical application of desirable attributes in plants. The topical application of dsRNA/siRNA targeting essential fungal gene(s) through spray-induced gene silencing (SIGS) on host plants has opened up a transgene-free avenue for crop protection. However, several factors influence the outcome of RNAi, including but not limited to RNAi mechanism in plant/fungi, dsRNA/siRNA uptake efficiency, dsRNA/siRNA design parameters, dsRNA stability and delivery strategy, off-target effects, etc. This review emphasizes the significance of these factors and suggests appropriate measures to consider while designing in silico and in vitro experiments for successful RNAi in open-field conditions. We also highlight prospective nanoparticles as smart delivery vehicles for deploying RNAi molecules in plant systems for long-term crop protection and ecosystem compatibility. Lastly, we provide specific directions for future investigations that focus on blending nanotechnology and RNAi-based fungal control for practical applications.
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Affiliation(s)
- Poonam Ray
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Debashish Sahu
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Raghavendra Aminedi
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Divya Chandran
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
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Yang W, Wang B, Lei G, Chen G, Liu D. Advances in nanocarriers to improve the stability of dsRNA in the environment. Front Bioeng Biotechnol 2022; 10:974646. [PMID: 36051593 PMCID: PMC9424858 DOI: 10.3389/fbioe.2022.974646] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/14/2022] [Indexed: 11/20/2022] Open
Abstract
RNAi technology, known as a revolutionary technology in the history of pesticides, has been identified as a very promising novel approach for crop protection, which is of great significance for achieving the sustainable agricultural development of the United Nations Food and Agriculture Organization. Although many studies have shown that RNA biopesticides have strong application prospects, its stability seriously restricts the commercial use. As the core component of RNAi, double-stranded RNA (dsRNA) is unstable in its natural form. Therefore, how to ensure the stability of dsRNA is one of the most significant challenges in realizing the commercial use of RNA biopesticides. Nanomaterials such as cationic polymers and lipofectamine can improve the stability of dsRNA in the environment, which has been proved. This paper reviews the recent research progress of nanomaterials that can be used to improve the environmental stability of dsRNA, and discusses the advantages and limitations of different nanomaterials combined with dsRNA, which provides reference for the selection of dsRNA nanoformulations.
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Affiliation(s)
| | | | | | | | - Dehai Liu
- *Correspondence: Dehai Liu, ; Guocan Chen,
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Exploring the Effectiveness and Durability of Trans-Kingdom Silencing of Fungal Genes in the Vascular Pathogen Verticillium dahliae. Int J Mol Sci 2022; 23:ijms23052742. [PMID: 35269884 PMCID: PMC8910871 DOI: 10.3390/ijms23052742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 02/04/2023] Open
Abstract
Host-induced gene silencing (HIGS) based on trans-kingdom RNA interference (RNAi) has been successfully exploited to engineer host resistance to pests and pathogens, including fungi and oomycetes. However, revealing the mechanisms underlying trans-kingdom RNAi between hosts and pathogens lags behind applications. The effectiveness and durability of trans-kingdom silencing of pathogenic genes are uncharacterized. In this study, using our transgenic 35S-VdH1i cotton plants in which dsVdH1-derived small RNAs (siVdH1) accumulated, small RNA sequencing analysis revealed that siVdH1s exclusively occur within the double-stranded (ds)VdH1 region, and no transitive siRNAs were produced beyond this region in recovered hyphae of Verticillium dahliae (V. dahliae). Accordingly, we found that VdH1 silencing was reduced over time in recovered hyphae cultured in vitro, inferring that once the fungus got rid of the 35S-VdH1i cotton plants would gradually regain their pathogenicity. To explore whether continually exporting dsRNAs/siRNAs from transgenic plants into recipient fungal cells guaranteed the effectiveness and stability of HIGS, we created GFP/RFP double-labeled V. dahliae and transgenic Arabidopsis expressing dsGFP (35S-GFPi plants). Confocal images visually demonstrate the efficient silencing of GFP in V. dahliae that colonized host vascular tissues. Taken together, our results demonstrate that HIGS effectively triggers long-lasting trans-kingdom RNAi during plant vasculature V. dahliae interactions, despite no amplification or transitivity of RNAi being noted in this soil-borne fungal pathogen.
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Pantoja Angles A, Valle-Pérez AU, Hauser C, Mahfouz MM. Microbial Biocontainment Systems for Clinical, Agricultural, and Industrial Applications. Front Bioeng Biotechnol 2022; 10:830200. [PMID: 35186907 PMCID: PMC8847691 DOI: 10.3389/fbioe.2022.830200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/06/2022] [Indexed: 12/19/2022] Open
Abstract
Many applications of synthetic biology require biological systems in engineered microbes to be delivered into diverse environments, such as for in situ bioremediation, biosensing, and applications in medicine and agriculture. To avoid harming the target system (whether that is a farm field or the human gut), such applications require microbial biocontainment systems (MBSs) that inhibit the proliferation of engineered microbes. In the past decade, diverse molecular strategies have been implemented to develop MBSs that tightly control the proliferation of engineered microbes; this has enabled medical, industrial, and agricultural applications in which biological processes can be executed in situ. The customization of MBSs also facilitate the integration of sensing modules for which different compounds can be produced and delivered upon changes in environmental conditions. These achievements have accelerated the generation of novel microbial systems capable of responding to external stimuli with limited interference from the environment. In this review, we provide an overview of the current approaches used for MBSs, with a specific focus on applications that have an immediate impact on multiple fields.
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Affiliation(s)
- Aaron Pantoja Angles
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Alexander U. Valle-Pérez
- Laboratory for Nanomedicine, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Charlotte Hauser
- Laboratory for Nanomedicine, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Magdy M. Mahfouz, ; Charlotte Hauser,
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Magdy M. Mahfouz, ; Charlotte Hauser,
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Rank AP, Koch A. Lab-to-Field Transition of RNA Spray Applications - How Far Are We? FRONTIERS IN PLANT SCIENCE 2021; 12:755203. [PMID: 34721485 PMCID: PMC8554022 DOI: 10.3389/fpls.2021.755203] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 09/15/2021] [Indexed: 05/15/2023]
Abstract
The drastic loss of biodiversity has alarmed the public and raised sociopolitical demand for chemical pesticide-free plant production, which is now treated by governments worldwide as a top priority. Given this global challenge, RNAi-based technologies are rapidly evolving as a promising substitute to conventional chemical pesticides. Primarily, genetically modified (GM) crops expressing double-stranded (ds)RNA-mediating gene silencing of foreign transcripts have been developed. However, since the cultivation of GM RNAi crops is viewed negatively in numerous countries, GM-free exogenous RNA spray applications attract tremendous scientific and political interest. The sudden rise in demand for pesticide alternatives has boosted research on sprayable RNA biopesticides, generating significant technological developments and advancing the potential for field applications in the near future. Here we review the latest advances that could pave the way for a quick lab-to-field transition for RNA sprays, which, as safe, selective, broadly applicable, and cost-effective biopesticides, represent an innovation in sustainable crop production. Given these latest advances, we further discuss technological limitations, knowledge gaps in the research, safety concerns and regulatory requirements that need to be considered and addressed before RNA sprays can become a reliable and realistic agricultural approach.
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Affiliation(s)
| | - Aline Koch
- Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
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