1
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Singh R, Caseys C, Kliebenstein DJ. Genetic and molecular landscapes of the generalist phytopathogen Botrytis cinerea. MOLECULAR PLANT PATHOLOGY 2024; 25:e13404. [PMID: 38037862 PMCID: PMC10788480 DOI: 10.1111/mpp.13404] [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: 08/16/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023]
Abstract
Botrytis cinerea Pers. Fr. (teleomorph: Botryotinia fuckeliana) is a necrotrophic fungal pathogen that attacks a wide range of plants. This updated pathogen profile explores the extensive genetic diversity of B. cinerea, highlights the progress in genome sequencing, and provides current knowledge of genetic and molecular mechanisms employed by the fungus to attack its hosts. In addition, we also discuss recent innovative strategies to combat B. cinerea. TAXONOMY Kingdom: Fungi, phylum: Ascomycota, subphylum: Pezizomycotina, class: Leotiomycetes, order: Helotiales, family: Sclerotiniaceae, genus: Botrytis, species: cinerea. HOST RANGE B. cinerea infects almost all of the plant groups (angiosperms, gymnosperms, pteridophytes, and bryophytes). To date, 1606 plant species have been identified as hosts of B. cinerea. GENETIC DIVERSITY This polyphagous necrotroph has extensive genetic diversity at all population levels shaped by climate, geography, and plant host variation. PATHOGENICITY Genetic architecture of virulence and host specificity is polygenic using multiple weapons to target hosts, including secretory proteins, complex signal transduction pathways, metabolites, and mobile small RNA. DISEASE CONTROL STRATEGIES Efforts to control B. cinerea, being a high-diversity generalist pathogen, are complicated. However, integrated disease management strategies that combine cultural practices, chemical and biological controls, and the use of appropriate crop varieties will lessen yield losses. Recently, studies conducted worldwide have explored the potential of small RNA as an efficient and environmentally friendly approach for combating grey mould. However, additional research is necessary, especially on risk assessment and regulatory frameworks, to fully harness the potential of this technology.
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Affiliation(s)
- Ritu Singh
- Department of Plant ScienceUniversity of CaliforniaDavisCaliforniaUSA
| | - Celine Caseys
- Department of Plant ScienceUniversity of CaliforniaDavisCaliforniaUSA
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2
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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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3
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [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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4
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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: 7] [Impact Index Per Article: 7.0] [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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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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6
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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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7
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Singewar K, Fladung M. Double-stranded RNA (dsRNA) technology to control forest insect pests and fungal pathogens: challenges and opportunities. Funct Integr Genomics 2023; 23:185. [PMID: 37243792 DOI: 10.1007/s10142-023-01107-y] [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: 07/04/2022] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/29/2023]
Abstract
Climate change alters the seasonal synchronization between plants and respective pests plus pathogens. The geographical infiltration helps to shift their hosts, resulting in novel outbreaks that damage forests and ecology. Traditional management schemes are unable to control such outbreaks, therefore unconventional and competitive governance is needed to manage forest pests and pathogens. RNA interference (RNAi) mediated double-stranded RNA (dsRNA) treatment method can be implemented to protect forest trees. Exogenous dsRNA triggers the RNAi-mediated gene silencing of a vital gene, and suspends protein production, resulting in the death of targeted pathogens and pests. The dsRNA treatment method is successful for many crop insects and fungi, however, studies of dsRNA against forest pests and pathogens are depleting. Pesticides and fungicides based on dsRNA could be used to combat pathogens that caused outbreaks in different parts of the world. Although the dsRNA has proved its potential, the crucial dilemma and risks including species-specific gene selection, and dsRNA delivery methods cannot be overlooked. Here, we summarized the major fungi pathogens and insect pests that have caused outbreaks, their genomic information, and studies on dsRNA fungi-and pesticides. Current challenges and opportunities in dsRNA target decision, delivery using nanoparticles, direct applications, and a new method using mycorrhiza for forest tree protection are discussed. The importance of affordable next-generation sequencing to minimize the impact on non-target species is discussed. We suggest that collaborative research among forest genomics and pathology institutes could develop necessary dsRNA strategies to protect forest tree species.
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Affiliation(s)
- Kiran Singewar
- Thünen Institute of Forest Genetics, 22927, Großhansdorf, Germany.
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, 22927, Großhansdorf, Germany.
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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: 7] [Impact Index Per Article: 7.0] [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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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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Wu F, Huang Y, Jiang W, Jin W. Genome-wide identification and validation of tomato-encoded sRNA as the cross-species antifungal factors targeting the virulence genes of Botrytis cinerea. FRONTIERS IN PLANT SCIENCE 2023; 14:1072181. [PMID: 36818832 PMCID: PMC9933504 DOI: 10.3389/fpls.2023.1072181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Recent evidence shows that small RNAs are transferred from a species to another through cross-species transmission and exhibit biological activities in the receptor. In this study, we focused on tomato-derived sRNAs play a role of defense against Botrytis cinerea. Bioinformatics method was firstly employed to identify tomato-encoded sRNAs as the cross-species antifungal factors targeting B. cinerea genes. Then the expression levels of some identifed sRNAs were checked in B. cinerea-infected plant using qRT-PCR method. Exogenic RNA-induced gene silences analysis were performed to investigate the antifungal roles of the sRNAs, and the target genes in B. cinerea of antifungal sRNAs would be confirmed by using co-expression analysis. Results showed that a total of 21 B.cinerea-induced sRNAs with high abundance were identified as the cross-kingdom regulator candidates. Among them, three sRNAs containing a miRNA (miR396a-5p) and two siRNA (siR3 and siR14) were selected for experimental validation and bioassay analysis. qRT-PCR confirmed that all of these 3 sRNAs were induced in tomato leaves by B. cinerea infection. Correspondingly, 4 virulence genes of B. cinerea respectively targeted by these 3 sRNAs were down-regulated. Bioassay revealed that all of these 3 cross-species sRNAs could inhibit the virulence and spore gemination of B. cinerea. Correspondingly, the coding genes of B. cinerea targeted by these sRNAs were also down-regulated. Moreover, the virulence inhibition by double strand sRNA was more effective than that by single strand sRNA. The inhibition efficiency of sRNA against B. cinerea increased with the increase of its concentration. Our findings provide new evidence into the coevolution of pathogens and host plants, as well as new directions for the use of plant-derived sRNAs to control pathogens.
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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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Jurick Ii WM. Biotechnology approaches to reduce antimicrobial resistant postharvest pathogens, mycotoxin contamination, and resulting product losses. Curr Opin Biotechnol 2022; 78:102791. [PMID: 36099860 DOI: 10.1016/j.copbio.2022.102791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/27/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022]
Abstract
Postharvest fungal pathogens of stored fruits, nuts, and vegetables cause food spoilage and some produce mycotoxins that harm human health. These fungi can develop resistance to the chemicals used for their control despite judicious use, rotating different chemistries, and routine resistance monitoring. Once antimicrobial resistance develops, these fungi are difficult to control and persist in the field, packing, and storage environments. Therefore, new tools and approaches for control with reduced emphasis on chemicals and movement toward durable, innovative approaches (e.g. double-stranded RNA, translational metagenomics, and host-induced gene silencing) are warranted. The focus of this review is on formative breakthroughs to combat postharvest pathogens and the mycotoxins they produce via translation of fundamental science using biotechnology tools.
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Rodriguez Coy L, Plummer KM, Khalifa ME, MacDiarmid RM. Mycovirus-encoded suppressors of RNA silencing: Possible allies or enemies in the use of RNAi to control fungal disease in crops. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:965781. [PMID: 37746227 PMCID: PMC10512228 DOI: 10.3389/ffunb.2022.965781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/21/2022] [Indexed: 09/26/2023]
Abstract
Plants, fungi, and many other eukaryotes have evolved an RNA interference (RNAi) mechanism that is key for regulating gene expression and the control of pathogens. RNAi inhibits gene expression, in a sequence-specific manner, by recognizing and deploying cognate double-stranded RNA (dsRNA) either from endogenous sources (e.g. pre-micro RNAs) or exogenous origin (e.g. viruses, dsRNA, or small interfering RNAs, siRNAs). Recent studies have demonstrated that fungal pathogens can transfer siRNAs into plant cells to suppress host immunity and aid infection, in a mechanism termed cross-kingdom RNAi. New technologies, based on RNAi are being developed for crop protection against insect pests, viruses, and more recently against fungal pathogens. One example, is host-induced gene silencing (HIGS), which is a mechanism whereby transgenic plants are modified to produce siRNAs or dsRNAs targeting key transcripts of plants, or their pathogens or pests. An alternative gene regulation strategy that also co-opts the silencing machinery is spray-induced gene silencing (SIGS), in which dsRNAs or single-stranded RNAs (ssRNAs) are applied to target genes within a pathogen or pest. Fungi also use their RNA silencing machinery against mycoviruses (fungal viruses) and mycoviruses can deploy virus-encoded suppressors of RNAi (myco-VSRs) as a counter-defence. We propose that myco-VSRs may impact new dsRNA-based management methods, resulting in unintended outcomes, including suppression of management by HIGS or SIGS. Despite a large diversity of mycoviruses being discovered using high throughput sequencing, their biology is poorly understood. In particular, the prevalence of mycoviruses and the cellular effect of their encoded VSRs are under-appreciated when considering the deployment of HIGS and SIGS strategies. This review focuses on mycoviruses, their VSR activities in fungi, and the implications for control of pathogenic fungi using RNAi.
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Affiliation(s)
- Lorena Rodriguez Coy
- Australian Research Council Research Hub for Sustainable Crop Protection, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Kim M. Plummer
- Australian Research Council Research Hub for Sustainable Crop Protection, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Mahmoud E. Khalifa
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta, Egypt
| | - Robin M. MacDiarmid
- BioProtection, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Liu X, Bai Y, Zhang Z. Priming defense by transiently suppressing plant susceptibility genes in ornamental crops: A novel strategy for post-harvest diseases management. FRONTIERS IN PLANT SCIENCE 2022; 13:1025165. [PMID: 36186046 PMCID: PMC9520194 DOI: 10.3389/fpls.2022.1025165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Xintong Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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Bocos-Asenjo IT, Niño-Sánchez J, Ginésy M, Diez JJ. New Insights on the Integrated Management of Plant Diseases by RNA Strategies: Mycoviruses and RNA Interference. Int J Mol Sci 2022; 23:9236. [PMID: 36012499 PMCID: PMC9409477 DOI: 10.3390/ijms23169236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
RNA-based strategies for plant disease management offer an attractive alternative to agrochemicals that negatively impact human and ecosystem health and lead to pathogen resistance. There has been recent interest in using mycoviruses for fungal disease control after it was discovered that some cause hypovirulence in fungal pathogens, which refers to a decline in the ability of a pathogen to cause disease. Cryphonectria parasitica, the causal agent of chestnut blight, has set an ideal model of management through the release of hypovirulent strains. However, mycovirus-based management of plant diseases is still restricted by limited approaches to search for viruses causing hypovirulence and the lack of protocols allowing effective and systemic virus infection in pathogens. RNA interference (RNAi), the eukaryotic cell system that recognizes RNA sequences and specifically degrades them, represents a promising. RNA-based disease management method. The natural occurrence of cross-kingdom RNAi provides a basis for host-induced gene silencing, while the ability of most pathogens to uptake exogenous small RNAs enables the use of spray-induced gene silencing techniques. This review describes the mechanisms behind and the potential of two RNA-based strategies, mycoviruses and RNAi, for plant disease management. Successful applications are discussed, as well as the research gaps and limitations that remain to be addressed.
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Affiliation(s)
- Irene Teresa Bocos-Asenjo
- Department of Plant Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
- iuFOR-Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
| | - Jonatan Niño-Sánchez
- Department of Plant Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
- iuFOR-Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
| | - Mireille Ginésy
- Department of Plant Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
- iuFOR-Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
| | - Julio Javier Diez
- Department of Plant Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
- iuFOR-Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
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Jeong JY, Kim M, Park SH, Kim B, Oh SI, Kim E, Jung H. Residual Level, Histology, and Blood Biochemistry of Tebuconazole: A Repeated Dose 28-Day Oral Toxicity Study in Pigs. Food Sci Anim Resour 2022; 42:712-722. [PMID: 35855269 PMCID: PMC9289805 DOI: 10.5851/kosfa.2022.e31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Jin Young Jeong
- Animal Nutrition & Physiology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
- Corresponding author: Jin Young Jeong, Animal Nutrition & Physiology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea, Tel: +82-63-238-7487, Fax: +82-63-238-7497, E-mail:
| | - Minji Kim
- Animal Nutrition & Physiology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
| | - Seol Hwa Park
- Animal Nutrition & Physiology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
| | - Byeonghyeon Kim
- Animal Nutrition & Physiology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
| | - Sang-Ik Oh
- Division of Animal Disease & Health, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
| | - Eunju Kim
- Division of Animal Disease & Health, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
| | - Hyunjung Jung
- Animal Nutrition & Physiology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
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Shomron A, Duanis-Assaf D, Galsurker O, Golberg A, Alkan N. Extract from the Macroalgae Ulva rigida Induces Table Grapes Resistance to Botrytis cinerea. Foods 2022; 11:foods11050723. [PMID: 35267356 PMCID: PMC8909532 DOI: 10.3390/foods11050723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 02/05/2023] Open
Abstract
Fungal pathogens are a central cause of the high wastage rates of harvested fruit and vegetables. Seaweeds from the genus Ulva are fast-growing edible green macroalgae whose species can be found on the shore of every continent, and therefore present a resource that can be utilized on a global scale. In this study, we found that the application of ulvan extract, a sulfated polysaccharide extracted from Ulva rigida (1000 mg/L), elicited table grapes defense and reduced the incidence and decay area of Botrytis cinerea by 43% and 41%, respectively. In addition, compared to the control group at two days post-treatment, ulvan extract elicited a variety of defense-related biomarkers such as a 43% increase in the activity of reactive oxygen species, 4-fold increase in the activity of catalase, 2-fold increase in the activity of superoxide dismutase and 1.4-fold increase in the activity of chitinase. No increase was observed in phenylalanine ammonia-lyase activity, and the treatment did not affect fruit quality parameters such as the pH levels, sugar levels, and titratable acidity of grapes. These results illustrate the potential of ulvan extract to naturally induce the plant defense response and to reduce postharvest decay.
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Affiliation(s)
- Alon Shomron
- Department of Environmental Studies, Porter School of Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel;
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion 7505101, Israel; (D.D.-A.); (O.G.)
| | - Danielle Duanis-Assaf
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion 7505101, Israel; (D.D.-A.); (O.G.)
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Ortal Galsurker
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion 7505101, Israel; (D.D.-A.); (O.G.)
| | - Alexander Golberg
- Department of Environmental Studies, Porter School of Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel;
- Correspondence: (A.G.); (N.A.)
| | - Noam Alkan
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion 7505101, Israel; (D.D.-A.); (O.G.)
- Correspondence: (A.G.); (N.A.)
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