1
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Liu C, Kogel K, Ladera‐Carmona M. Harnessing RNA interference for the control of Fusarium species: A critical review. MOLECULAR PLANT PATHOLOGY 2024; 25:e70011. [PMID: 39363756 PMCID: PMC11450251 DOI: 10.1111/mpp.70011] [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: 05/14/2024] [Revised: 08/13/2024] [Accepted: 09/10/2024] [Indexed: 10/05/2024]
Abstract
Fusarium fungi are a pervasive threat to global agricultural productivity. They cause a spectrum of plant diseases that result in significant yield losses and threaten food safety by producing mycotoxins that are harmful to human and animal health. In recent years, the exploitation of the RNA interference (RNAi) mechanism has emerged as a promising avenue for the control of Fusarium-induced diseases, providing both a mechanistic understanding of Fusarium gene function and a potential strategy for environmentally sustainable disease management. However, despite significant progress in elucidating the presence and function of the RNAi pathway in different Fusarium species, a comprehensive understanding of its individual protein components and underlying silencing mechanisms remains elusive. Accordingly, while a considerable number of RNAi-based approaches to Fusarium control have been developed and many reports of RNAi applications in Fusarium control under laboratory conditions have been published, the applicability of this knowledge in agronomic settings remains an open question, and few convincing data on RNAi-based disease control under field conditions have been published. This review aims to consolidate the current knowledge on the role of RNAi in Fusarium disease control by evaluating current research and highlighting important avenues for future investigation.
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Affiliation(s)
- Caihong Liu
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Karl‐Heinz Kogel
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig University GiessenGiessenGermany
- Institut de Biologie Moléculaire des Plantes, CNRSUniversité de StrasbourgStrasbourgFrance
| | - Maria Ladera‐Carmona
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig University GiessenGiessenGermany
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2
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Pant P, Kaur J. Control of Sclerotinia sclerotiorum via an RNA interference (RNAi)-mediated targeting of SsPac1 and SsSmk1. PLANTA 2024; 259:153. [PMID: 38744752 DOI: 10.1007/s00425-024-04430-1] [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: 04/03/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
MAIN CONCLUSION The study evaluates the potential of Spray-Induced Gene Silencing and Host-Induced Gene Silencing for sustainable crop protection against the broad-spectrum necrotrophic fungus Sclerotinia sclerotiorum. Sclerotinia sclerotiorum (Lib.) de Bary, an aggressive ascomycete fungus causes white rot or cottony rot on a broad range of crops including Brassica juncea. The lack of sustainable control measures has necessitated biotechnological interventions such as RNA interference (RNAi) for effective pathogen control. Here we adopted two RNAi-based strategies-Spray-Induced Gene Silencing (SIGS) and Host-Induced Gene Silencing (HIGS) to control S. sclerotiorum. SIGS was successful in controlling white rot on Nicotiana benthamiana and B. juncea by targeting SsPac1, a pH-responsive transcription factor and SsSmk1, a MAP kinase involved in fungal development and pathogenesis. Topical application of dsRNA targeting SsPac1 and SsSmk1 delayed infection initiation and progression on B. juncea. Further, altered hyphal morphology and reduced radial growth were also observed following dsRNA application. We also explored the impact of stable dsRNA expression in A. thaliana against S. sclerotiorum. In this report, we highlight the utility of RNAi as a biofungicide and a tool for preliminary functional genomics.
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Affiliation(s)
- Pratibha Pant
- Department of Genetics, University of Delhi, South Campus, Benito Juarez Marg, New Delhi, 110021, India
| | - Jagreet Kaur
- Department of Genetics, University of Delhi, South Campus, Benito Juarez Marg, New Delhi, 110021, India.
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3
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Lteif M, Pallardy M, Turbica I. Antibodies internalization mechanisms by dendritic cells and their role in therapeutic antibody immunogenicity. Eur J Immunol 2024; 54:e2250340. [PMID: 37985174 DOI: 10.1002/eji.202250340] [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: 05/18/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023]
Abstract
Internalization and processing by antigen-presenting cells such as dendritic cells (DCs) are critical steps for initiating a T-cell response to therapeutic antibodies. Consequences are the production of neutralizing antidrug antibodies altering the clinical response, the presence of immune complexes, and, in some rare cases, hypersensitivity reactions. In recent years, significant progress has been made in the knowledge of cellular uptake mechanisms of antibodies in DCs. The uptake of antibodies could be directly related to their immunogenicity by regulating the quantity of materials entering the DCs in relation to antibody structure. Here, we summarize the latest insights into cellular uptake mechanisms and pathways in DCs. We highlight the approaches to study endocytosis, the impact of endocytosis routes on T-cell response, and discuss the link between how DCs internalize therapeutic antibodies and the potential mechanisms that could give rise to immunogenicity. Understanding these processes could help in developing assays to evaluate the immunogenicity potential of biotherapeutics.
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Affiliation(s)
- Maria Lteif
- Université Paris-Saclay, Inserm, Inflammation, Microbiome and Immunosurveillance, Orsay, France
| | - Marc Pallardy
- Université Paris-Saclay, Inserm, Inflammation, Microbiome and Immunosurveillance, Orsay, France
| | - Isabelle Turbica
- Université Paris-Saclay, Inserm, Inflammation, Microbiome and Immunosurveillance, Orsay, France
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4
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Degnan RM, Shuey LS, Radford-Smith J, Gardiner DM, Carroll BJ, Mitter N, McTaggart AR, Sawyer A. Double-stranded RNA prevents and cures infection by rust fungi. Commun Biol 2023; 6:1234. [PMID: 38057635 PMCID: PMC10700371 DOI: 10.1038/s42003-023-05618-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
Fungal pathogens that impact perennial plants or natural ecosystems require management strategies beyond fungicides and breeding for resistance. Rust fungi, some of the most economically and environmentally important plant pathogens, have shown amenability to double-stranded RNA (dsRNA) mediated control. To date, dsRNA treatments have been applied prior to infection or together with the inoculum. Here we show that a dsRNA spray can effectively prevent and cure infection by Austropuccinia psidii (cause of myrtle rust) at different stages of the disease cycle. Significant reductions in disease coverage were observed in plants treated with dsRNA targeting essential fungal genes 48 h pre-infection through to 14 days post-infection. For curative treatments, improvements in plant health and photosynthetic capacity were seen 2-6 weeks post-infection. Two-photon microscopy suggests inhibitory activity of dsRNA on intercellular hyphae or haustoria. Our results show that dsRNA acts both preventively and curatively against myrtle rust disease, with treated plants recovering from severe infection. These findings have immediate potential in the management of the more than 10-year epidemic of myrtle rust in Australia.
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Affiliation(s)
- Rebecca M Degnan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
| | - Louise S Shuey
- Department of Agriculture and Fisheries, Queensland Government, Ecosciences Precinct, Dutton Park, Queensland, Australia
| | - Julian Radford-Smith
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | - Donald M Gardiner
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, The University of Queensland, St Lucia, Queensland, Australia
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, The University of Queensland, St Lucia, Queensland, Australia
| | - Alistair R McTaggart
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, The University of Queensland, St Lucia, Queensland, Australia
| | - Anne Sawyer
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, The University of Queensland, St Lucia, Queensland, Australia.
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5
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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: 7] [Impact Index Per Article: 7.0] [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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6
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Carreón-Anguiano KG, Gómez-Tah R, Pech-Balan E, Ek-Hernández GE, De los Santos-Briones C, Islas-Flores I, Canto-Canché B. Pseudocercospora fijiensis Conidial Germination Is Dominated by Pathogenicity Factors and Effectors. J Fungi (Basel) 2023; 9:970. [PMID: 37888226 PMCID: PMC10607838 DOI: 10.3390/jof9100970] [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: 08/11/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
Conidia play a vital role in the survival and rapid spread of fungi. Many biological processes of conidia, such as adhesion, signal transduction, the regulation of oxidative stress, and autophagy, have been well studied. In contrast, the contribution of pathogenicity factors during the development of conidia in fungal phytopathogens has been poorly investigated. To date, few reports have centered on the pathogenicity functions of fungal phytopathogen conidia. Pseudocercospora fijiensis is a hemibiotrophic fungus and the causal agent of the black Sigatoka disease in bananas and plantains. Here, a conidial transcriptome of P. fijiensis was characterized computationally. Carbohydrates, amino acids, and lipid metabolisms presented the highest number of annotations in Gene Ontology. Common conidial functions were found, but interestingly, pathogenicity factors and effectors were also identified. Upon analysis of the resulting proteins against the Pathogen-Host Interaction (PHI) database, 754 hits were identified. WideEffHunter and EffHunter effector predictors identified 618 effectors, 265 of them were shared with the PHI database. A total of 1107 conidial functions devoted to pathogenesis were found after our analysis. Regarding the conidial effectorome, it was found to comprise 40 canonical and 578 non-canonical effectors. Effectorome characterization revealed that RXLR, LysM, and Y/F/WxC are the largest effector families in the P. fijiensis conidial effectorome. Gene Ontology classification suggests that they are involved in many biological processes and metabolisms, expanding our current knowledge of fungal effectors.
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Affiliation(s)
- Karla Gisel Carreón-Anguiano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - Rufino Gómez-Tah
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - Efren Pech-Balan
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - Gemaly Elisama Ek-Hernández
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - César De los Santos-Briones
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico;
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
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7
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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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8
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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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9
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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 PMCID: PMC10220346 DOI: 10.1007/s10142-023-01107-y] [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: 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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10
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Borniego ML, Innes RW. Extracellular RNA: mechanisms of secretion and potential functions. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2389-2404. [PMID: 36609873 PMCID: PMC10082932 DOI: 10.1093/jxb/erac512] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/21/2022] [Indexed: 06/06/2023]
Abstract
Extracellular RNA (exRNA) has long been considered as cellular waste that plants can degrade and utilize to recycle nutrients. However, recent findings highlight the need to reconsider the biological significance of RNAs found outside of plant cells. A handful of studies suggest that the exRNA repertoire, which turns out to be an extremely heterogenous group of non-coding RNAs, comprises species as small as a dozen nucleotides to hundreds of nucleotides long. They are found mostly in free form or associated with RNA-binding proteins, while very few are found inside extracellular vesicles (EVs). Despite their low abundance, small RNAs associated with EVs have been a focus of exRNA research due to their putative role in mediating trans-kingdom RNAi. Therefore, non-vesicular exRNAs have remained completely under the radar until very recently. Here we summarize our current knowledge of the RNA species that constitute the extracellular RNAome and discuss mechanisms that could explain the diversity of exRNAs, focusing not only on the potential mechanisms involved in RNA secretion but also on post-release processing of exRNAs. We will also share our thoughts on the putative roles of vesicular and extravesicular exRNAs in plant-pathogen interactions, intercellular communication, and other physiological processes in plants.
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Affiliation(s)
- M Lucía Borniego
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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11
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Hatit MZC, Dobrowolski CN, Lokugamage MP, Loughrey D, Ni H, Zurla C, Da Silva Sanchez AJ, Radmand A, Huayamares SG, Zenhausern R, Paunovska K, Peck HE, Kim J, Sato M, Feldman JI, Rivera MA, Cristian A, Kim Y, Santangelo PJ, Dahlman JE. Nanoparticle stereochemistry-dependent endocytic processing improves in vivo mRNA delivery. Nat Chem 2023; 15:508-515. [PMID: 36864143 DOI: 10.1038/s41557-023-01138-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/13/2023] [Indexed: 03/04/2023]
Abstract
Stereochemistry can alter small-molecule pharmacokinetics, safety and efficacy. However, it is unclear whether the stereochemistry of a single compound within a multicomponent colloid such as a lipid nanoparticle (LNP) can influence its activity in vivo. Here we report that LNPs containing stereopure 20α-hydroxycholesterol (20α) delivered mRNA to liver cells up to 3-fold more potently than LNPs containing a mixture of both 20α- and 20β-hydroxycholesterols (20mix). This effect was not driven by LNP physiochemical traits. Instead, in vivo single-cell RNA sequencing and imaging revealed that 20mix LNPs were sorted into phagocytic pathways more than 20α LNPs, resulting in key differences between LNP biodistribution and subsequent LNP functional delivery. These data are consistent with the fact that nanoparticle biodistribution is necessary, but not sufficient, for mRNA delivery, and that stereochemistry-dependent interactions between LNPs and target cells can improve mRNA delivery.
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Affiliation(s)
- Marine Z C Hatit
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Curtis N Dobrowolski
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Melissa P Lokugamage
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - David Loughrey
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Huanzhen Ni
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Chiara Zurla
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alejandro J Da Silva Sanchez
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Afsane Radmand
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Sebastian G Huayamares
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Ryan Zenhausern
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Kalina Paunovska
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Hannah E Peck
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jinwhan Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
- School of Electrical & Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Manaka Sato
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Jacob I Feldman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Michael-Alexander Rivera
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Ana Cristian
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - YongTae Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Philip J Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - James E Dahlman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA.
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12
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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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13
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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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14
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Wytinck N, Ziegler DJ, Walker PL, Sullivan DS, Biggar KT, Khan D, Sakariyahu SK, Wilkins O, Whyard S, Belmonte MF. Host induced gene silencing of the Sclerotinia sclerotiorum ABHYDROLASE-3 gene reduces disease severity in Brassica napus. PLoS One 2022; 17:e0261102. [PMID: 36018839 PMCID: PMC9417021 DOI: 10.1371/journal.pone.0261102] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/29/2022] [Indexed: 11/19/2022] Open
Abstract
Sclerotinia sclerotiorum is a pathogenic fungus that infects hundreds of crop species, causing extensive yield loss every year. Chemical fungicides are used to control this phytopathogen, but with concerns about increasing resistance and impacts on non-target species, there is a need to develop alternative control measures. In the present study, we engineered Brassica napus to constitutively express a hairpin (hp)RNA molecule to silence ABHYRDOLASE-3 in S. sclerotiorum. We demonstrate the potential for Host Induced Gene Silencing (HIGS) to protect B. napus from S. sclerotiorum using leaf, stem and whole plant infection assays. The interaction between the transgenic host plant and invading pathogen was further characterized at the molecular level using dual-RNA sequencing and at the anatomical level through microscopy to understand the processes and possible mechanisms leading to increased tolerance to this damaging necrotroph. We observed significant shifts in the expression of genes relating to plant defense as well as cellular differences in the form of structural barriers around the site of infection in the HIGS-protected plants. Our results provide proof-of-concept that HIGS is an effective means of limiting damage caused by S. sclerotiorum to the plant and demonstrates the utility of this biotechnology in the development of resistance against fungal pathogens.
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Affiliation(s)
- Nick Wytinck
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Dylan J. Ziegler
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Philip L. Walker
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Daniel S. Sullivan
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kirsten T. Biggar
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Deirdre Khan
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Solihu K. Sakariyahu
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Olivia Wilkins
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Steve Whyard
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Mark F. Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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15
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Bilir Ö, Göl D, Hong Y, McDowell JM, Tör M. Small RNA-based plant protection against diseases. FRONTIERS IN PLANT SCIENCE 2022; 13:951097. [PMID: 36061762 PMCID: PMC9434005 DOI: 10.3389/fpls.2022.951097] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Plant diseases cause significant decreases in yield and quality of crops and consequently pose a very substantial threat to food security. In the continuous search for environmentally friendly crop protection, exploitation of RNA interferance machinery is showing promising results. It is well established that small RNAs (sRNAs) including microRNA (miRNA) and small interfering RNA (siRNA) are involved in the regulation of gene expression via both transcriptional and post-transcriptional RNA silencing. sRNAs from host plants can enter into pathogen cells during invasion and silence pathogen genes. This process has been exploited through Host-Induced Gene Silencing (HIGS), in which plant transgenes that produce sRNAs are engineered to silence pest and pathogen genes. Similarly, exogenously applied sRNAs can enter pest and pathogen cells, either directly or via the hosts, and silence target genes. This process has been exploited in Spray-Induced Gene Silencing (SIGS). Here, we focus on the role of sRNAs and review how they have recently been used against various plant pathogens through HIGS or SIGS-based methods and discuss advantages and drawbacks of these approaches.
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Affiliation(s)
- Özlem Bilir
- Department of Biotechnology, Trakya Agricultural Research Institute, Edirne, Turkey
| | - Deniz Göl
- Department of Biology, School of Science and the Environment, University of Worcester, Worcester, United Kingdom
| | - Yiguo Hong
- Department of Biology, School of Science and the Environment, University of Worcester, Worcester, United Kingdom
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - John M. McDowell
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Mahmut Tör
- Department of Biology, School of Science and the Environment, University of Worcester, Worcester, United Kingdom
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16
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Touzdjian Pinheiro Kohlrausch Távora F, de Assis dos Santos Diniz F, de Moraes Rêgo-Machado C, Chagas Freitas N, Barbosa Monteiro Arraes F, Chumbinho de Andrade E, Furtado LL, Osiro KO, Lima de Sousa N, Cardoso TB, Márcia Mertz Henning L, Abrão de Oliveira Molinari P, Feingold SE, Hunter WB, Fátima Grossi de Sá M, Kobayashi AK, Lima Nepomuceno A, Santiago TR, Correa Molinari HB. CRISPR/Cas- and Topical RNAi-Based Technologies for Crop Management and Improvement: Reviewing the Risk Assessment and Challenges Towards a More Sustainable Agriculture. Front Bioeng Biotechnol 2022; 10:913728. [PMID: 35837551 PMCID: PMC9274005 DOI: 10.3389/fbioe.2022.913728] [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: 04/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated gene (Cas) system and RNA interference (RNAi)-based non-transgenic approaches are powerful technologies capable of revolutionizing plant research and breeding. In recent years, the use of these modern technologies has been explored in various sectors of agriculture, introducing or improving important agronomic traits in plant crops, such as increased yield, nutritional quality, abiotic- and, mostly, biotic-stress resistance. However, the limitations of each technique, public perception, and regulatory aspects are hindering its wide adoption for the development of new crop varieties or products. In an attempt to reverse these mishaps, scientists have been researching alternatives to increase the specificity, uptake, and stability of the CRISPR and RNAi system components in the target organism, as well as to reduce the chance of toxicity in nontarget organisms to minimize environmental risk, health problems, and regulatory issues. In this review, we discuss several aspects related to risk assessment, toxicity, and advances in the use of CRISPR/Cas and topical RNAi-based technologies in crop management and breeding. The present study also highlights the advantages and possible drawbacks of each technology, provides a brief overview of how to circumvent the off-target occurrence, the strategies to increase on-target specificity, the harm/benefits of association with nanotechnology, the public perception of the available techniques, worldwide regulatory frameworks regarding topical RNAi and CRISPR technologies, and, lastly, presents successful case studies of biotechnological solutions derived from both technologies, raising potential challenges to reach the market and being social and environmentally safe.
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Affiliation(s)
| | | | | | | | | | | | | | - Karen Ofuji Osiro
- Department of Phytopathology, University of Brasília, Brasília, Brazil
- Embrapa Agroenergy, Brasília, Brazil
| | | | | | | | | | | | - Wayne B. Hunter
- USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL, United States
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17
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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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18
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Duanis‐Assaf D, Galsurker O, Davydov O, Maurer D, Feygenberg O, Sagi M, Poverenov E, Fluhr R, Alkan N. Double-stranded RNA targeting fungal ergosterol biosynthesis pathway controls Botrytis cinerea and postharvest grey mould. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:226-237. [PMID: 34520611 PMCID: PMC8710829 DOI: 10.1111/pbi.13708] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/12/2021] [Accepted: 09/02/2021] [Indexed: 06/01/2023]
Abstract
Pathogenic fungi cause major postharvest losses. During storage and ripening, fruit becomes highly susceptible to fungi that cause postharvest disease. Fungicides are effective treatments to limit disease. However, due to increased public concern for their possible side effects, there is a need to develop new strategies to control postharvest fungal pathogens. Botrytis cinerea, a common postharvest pathogen, was shown to uptake small double-stranded RNA (dsRNA) molecules from the host plant. Such dsRNA can regulate gene expression through the RNA interference system. This work aimed to develop a synthetic dsRNA simultaneously targeting three essential transcripts active in the fungal ergosterol biosynthesis pathway (dsRNA-ERG). Our results show initial uptake of dsRNA in the emergence zone of the germination tube that spreads throughout the fungus and results in down-regulation of all three targeted transcripts. Application of dsRNA-ERG decreased B. cinerea germination and growth in in vitro conditions and various fruits, leading to reduce grey-mould decay. The inhibition of growth or decay was reversed by the addition of ergosterol. While dual treatment with dsRNA-ERG and ergosterol-inhibitor fungicide reduced by 100-fold the required amount of fungicide to achieve the same protection rate. The application of dsRNA-ERG induced systemic protection as shown by decreased decay development at inoculation points distant from the treatment point in tomato and pepper fruits. Overall, this study suggests that dsRNA-ERG can effectively control B. cinerea growth and grey-mould development suggesting its efficacy as a future method for postharvest control of fungal pathogens.
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Affiliation(s)
- Danielle Duanis‐Assaf
- Department of Postharvest Science of Fresh ProduceAgricultural Research Organization (ARO)Volcani InstituteRishon LeZionIsrael
- Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Ortal Galsurker
- Department of Postharvest Science of Fresh ProduceAgricultural Research Organization (ARO)Volcani InstituteRishon LeZionIsrael
| | - Olga Davydov
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Dalia Maurer
- Department of Postharvest Science of Fresh ProduceAgricultural Research Organization (ARO)Volcani InstituteRishon LeZionIsrael
| | - Oleg Feygenberg
- Department of Postharvest Science of Fresh ProduceAgricultural Research Organization (ARO)Volcani InstituteRishon LeZionIsrael
| | - Moshe Sagi
- French Associates Institute for Agricultural and Biotechnology of DrylandsBlaustein Institutes for Desert ResearchBen‐Gurion University of the NegevBeer ShevaIsrael
| | - Elena Poverenov
- Department of Food Science of Fresh ProduceAgricultural Research Organization (ARO)Volcani InstituteRishon LeZionIsrael
| | - Robert Fluhr
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Noam Alkan
- Department of Postharvest Science of Fresh ProduceAgricultural Research Organization (ARO)Volcani InstituteRishon LeZionIsrael
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19
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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: 34] [Impact Index Per Article: 11.3] [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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20
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Shetty A, Bhosale SD, Tripathi SK, Buchacher T, Biradar R, Rasool O, Moulder R, Galande S, Lahesmaa R. Interactome Networks of FOSL1 and FOSL2 in Human Th17 Cells. ACS OMEGA 2021; 6:24834-24847. [PMID: 34604665 PMCID: PMC8482465 DOI: 10.1021/acsomega.1c03681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 05/10/2023]
Abstract
Dysregulated function of Th17 cells has implications in immunodeficiencies and autoimmune disorders. Th17 cell differentiation is orchestrated by a complex network of transcription factors, including several members of the activator protein (AP-1) family. Among the latter, FOSL1 and FOSL2 modulate the effector functions of Th17 cells. However, the molecular mechanisms underlying these effects are unclear, owing to the poorly characterized protein interaction networks of FOSL factors. Here, we establish the first interactomes of FOSL1 and FOSL2 in human Th17 cells, using affinity purification-mass spectrometry analysis. In addition to the known JUN proteins, we identified several novel binding partners of FOSL1 and FOSL2. Gene ontology analysis found a significant fraction of these interactors to be associated with RNA-binding activity, which suggests new mechanistic links. Intriguingly, 29 proteins were found to share interactions with FOSL1 and FOSL2, and these included key regulators of Th17 fate. We further validated the binding partners identified in this study by using parallel reaction monitoring targeted mass spectrometry and other methods. Our study provides key insights into the interaction-based signaling mechanisms of FOSL proteins that potentially govern Th17 cell differentiation and associated pathologies.
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Affiliation(s)
- Ankitha Shetty
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
- Centre
of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Santosh D. Bhosale
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- Protein
Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark
| | - Subhash Kumar Tripathi
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
| | - Tanja Buchacher
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Rahul Biradar
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Omid Rasool
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Robert Moulder
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Sanjeev Galande
- Centre
of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Riitta Lahesmaa
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
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21
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Giudice G, Moffa L, Varotto S, Cardone MF, Bergamini C, De Lorenzis G, Velasco R, Nerva L, Chitarra W. Novel and emerging biotechnological crop protection approaches. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1495-1510. [PMID: 33945200 PMCID: PMC8384607 DOI: 10.1111/pbi.13605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/01/2021] [Accepted: 04/13/2021] [Indexed: 05/05/2023]
Abstract
Traditional breeding or genetically modified organisms (GMOs) have for a long time been the sole approaches to effectively cope with biotic and abiotic stresses and implement the quality traits of crops. However, emerging diseases as well as unpredictable climate changes affecting agriculture over the entire globe force scientists to find alternative solutions required to quickly overcome seasonal crises. In this review, we first focus on cisgenesis and genome editing as challenging biotechnological approaches for breeding crops more tolerant to biotic and abiotic stresses. In addition, we take into consideration a toolbox of new techniques based on applications of RNA interference and epigenome modifications, which can be adopted for improving plant resilience. Recent advances in these biotechnological applications are mainly reported for non-model plants and woody crops in particular. Indeed, the characterization of RNAi machinery in plants is fundamental to transform available information into biologically or biotechnologically applicable knowledge. Finally, here we discuss how these innovative and environmentally friendly techniques combined with traditional breeding can sustain a modern agriculture and be of potential contribution to climate change mitigation.
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Affiliation(s)
- Gaetano Giudice
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Department of Agricultural and Environmental Sciences ‐ Production, Landscape, Agroenergy (DiSAA)University of MilanoMilanoItaly
| | - Loredana Moffa
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A)University of UdineUdineItaly
| | - Serena Varotto
- Department of Agronomy Animals Food Natural Resources and Environment (DAFNAE)University of PadovaLegnaroPDItaly
| | - Maria Francesca Cardone
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)TuriBAItaly
| | - Carlo Bergamini
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)TuriBAItaly
| | - Gabriella De Lorenzis
- Department of Agricultural and Environmental Sciences ‐ Production, Landscape, Agroenergy (DiSAA)University of MilanoMilanoItaly
| | - Riccardo Velasco
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
| | - Luca Nerva
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)TorinoItaly
| | - Walter Chitarra
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)TorinoItaly
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Cai Q, He B, Wang S, Fletcher S, Niu D, Mitter N, Birch PRJ, Jin H. Message in a Bubble: Shuttling Small RNAs and Proteins Between Cells and Interacting Organisms Using Extracellular Vesicles. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:497-524. [PMID: 34143650 PMCID: PMC8369896 DOI: 10.1146/annurev-arplant-081720-010616] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Communication between plant cells and interacting microorganisms requires the secretion and uptake of functional molecules to and from the extracellular environment and is essential for the survival of both plants and their pathogens. Extracellular vesicles (EVs) are lipid bilayer-enclosed spheres that deliver RNA, protein, and metabolite cargos from donor to recipient cells and participate in many cellular processes. Emerging evidencehas shown that both plant and microbial EVs play important roles in cross-kingdom molecular exchange between hosts and interacting microbes to modulate host immunity and pathogen virulence. Recent studies revealed that plant EVs function as a defense system by encasing and delivering small RNAs (sRNAs) into pathogens, thereby mediating cross-species and cross-kingdom RNA interference to silence virulence-related genes. This review focuses on the latest advances in our understanding of plant and microbial EVs and their roles in transporting regulatory molecules, especially sRNAs, between hosts and pathogens. EV biogenesis and secretion are also discussed, as EV function relies on these important processes.
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Affiliation(s)
- Qiang Cai
- Department of Microbiology and Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92507, USA;
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Baoye He
- Department of Microbiology and Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92507, USA;
| | - Shumei Wang
- Department of Microbiology and Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92507, USA;
| | - Stephen Fletcher
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Dongdong Niu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Paul R J Birch
- Division of Plant Sciences, School of Life Science, University of Dundee at James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Hailing Jin
- Department of Microbiology and Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92507, USA;
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Souibgui E, Bruel C, Choquer M, de Vallée A, Dieryckx C, Dupuy JW, Latorse MP, Rascle C, Poussereau N. Clathrin Is Important for Virulence Factors Delivery in the Necrotrophic Fungus Botrytis cinerea. FRONTIERS IN PLANT SCIENCE 2021; 12:668937. [PMID: 34220891 PMCID: PMC8244658 DOI: 10.3389/fpls.2021.668937] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Abstract
Fungi are the most prevalent plant pathogens, causing annually important damages. To infect and colonize their hosts, they secrete effectors including hydrolytic enzymes able to kill and macerate plant tissues. These secreted proteins are transported from the Endoplasmic Reticulum and the Golgi apparatus to the extracellular space through intracellular vesicles. In pathogenic fungi, intracellular vesicles were described but their biogenesis and their role in virulence remain unclear. In this study, we report the essential role of clathrin heavy chain (CHC) in the pathogenicity of Botrytis cinerea, the agent of gray mold disease. To investigate the importance of this protein involved in coat vesicles formation in eukaryotic cells, a T-DNA insertional mutant reduced in the expression of the CHC-encoding gene, and a mutant expressing a dominant-negative form of CHC were studied. Both mutants were strongly affected in pathogenicity. Characterization of the mutants revealed altered infection cushions and an important defect in protein secretion. This study demonstrates the essential role of clathrin in the infectious process of a plant pathogenic fungus and more particularly its role in virulence factors delivery.
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Affiliation(s)
- Eytham Souibgui
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
| | - Christophe Bruel
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
| | - Mathias Choquer
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
| | - Amélie de Vallée
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
| | - Cindy Dieryckx
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
| | - Jean William Dupuy
- Plateforme Protéome, Centre de Génomique Fonctionnelle, Université de Bordeaux, Bordeaux, France
| | | | - Christine Rascle
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
| | - Nathalie Poussereau
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
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24
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Šečić E, Kogel KH. Requirements for fungal uptake of dsRNA and gene silencing in RNAi-based crop protection strategies. Curr Opin Biotechnol 2021; 70:136-142. [PMID: 34000482 DOI: 10.1016/j.copbio.2021.04.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 02/01/2023]
Abstract
Growing evidence indicates that RNAi is an effective control strategy for agronomically important fungi. To implement RNAi-based crop protection strategies, dsRNA molecules are either sprayed on foliage or generated by genetically engineered plants. Here, we summarize current knowledge of the mechanisms governing dsRNA uptake and RNAi-mediated gene silencing in fungi, as well as the factors that influence these phenomena. Of primary importance is dsRNA design, as identifying an appropriate gene for silencing and determining which region of the gene to target are critical for maximizing efficiency. Strategies for enhancing dsRNA uptake, potentially by using formulations and/or carriers that prevent dsRNA degradation by (a)biotic factors and possibly facilitate translocation, also are a key consideration. Finally, determining whether the fungal pathogen of interest contains a functional RNAi machinery is a major consideration. Integrated experimental confirmation of these important factors is necessary for the successful development of crop protection strategies against fungal pathogens.
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Affiliation(s)
- Ena Šečić
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany.
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Ivashuta S, Iandolino A, Watson G. Exogenous RNA as a Regulatory Signal during a Plant's Interaction with the Biotic Environment: An Evolutionary Perspective and Future Applications in Agriculture. PLANTS (BASEL, SWITZERLAND) 2021; 10:532. [PMID: 33808982 PMCID: PMC8000970 DOI: 10.3390/plants10030532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 11/23/2022]
Abstract
Environmental RNAi (eRNAi) is a sequence-specific regulation of endogenous gene expression in a responsive organism by exogenous RNA. While exogenous RNA transfer between organisms of different kingdoms of life have been unambiguously identified in nature, our understanding of the biological significance of this phenomenon remains obscure, particularly within an evolutionary context. During the last decade multiple reports utilizing various mechanisms of natural eRNAi phenomena have been attempted to develop new agricultural traits and products including weed, disease and insect control. Although these attempts yielded mixed results, this concept remains extremely attractive for many agricultural applications. To better utilize eRNAi for practical applications, we would like to emphasize the necessity of understanding the biological significance of this phenomenon within an evolutionary context and learn from nature by developing advanced tools to identify and study new cases of exogeneous RNA transfer and eRNAi. In this opinion article we would like to look at the exogeneous RNA transfer from an evolutionary perspective, propose that new cases of exogeneous RNA transfer still remain to be identified in nature, and address a knowledge gap in understanding the biological function and significance of RNA transfer. We believe such approach may eventually result in a more successful use of this phenomenon for practical applications in agriculture.
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Wytinck N, Manchur CL, Li VH, Whyard S, Belmonte MF. dsRNA Uptake in Plant Pests and Pathogens: Insights into RNAi-Based Insect and Fungal Control Technology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1780. [PMID: 33339102 PMCID: PMC7765514 DOI: 10.3390/plants9121780] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/07/2020] [Accepted: 12/13/2020] [Indexed: 12/11/2022]
Abstract
Efforts to develop more environmentally friendly alternatives to traditional broad-spectrum pesticides in agriculture have recently turned to RNA interference (RNAi) technology. With the built-in, sequence-specific knockdown of gene targets following delivery of double-stranded RNA (dsRNA), RNAi offers the promise of controlling pests and pathogens without adversely affecting non-target species. Significant advances in the efficacy of this technology have been observed in a wide range of species, including many insect pests and fungal pathogens. Two different dsRNA application methods are being developed. First, host induced gene silencing (HIGS) harnesses dsRNA production through the thoughtful and precise engineering of transgenic plants and second, spray induced gene silencing (SIGS) that uses surface applications of a topically applied dsRNA molecule. Regardless of the dsRNA delivery method, one aspect that is critical to the success of RNAi is the ability of the target organism to internalize the dsRNA and take advantage of the host RNAi cellular machinery. The efficiency of dsRNA uptake mechanisms varies across species, and in some uptake is negligible, rendering them effectively resistant to this new generation of control technologies. If RNAi-based methods of control are to be used widely, it is critically important to understand the mechanisms underpinning dsRNA uptake. Understanding dsRNA uptake mechanisms will also provide insight into the design and formulation of dsRNAs for improved delivery and provide clues into the development of potential host resistance to these technologies.
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Affiliation(s)
| | | | | | | | - Mark F. Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (N.W.); (C.L.M.); (V.H.L.); (S.W.)
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