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Li J, Zhang BS, Wu HW, Liu CL, Guo HS, Zhao JH. The RNA-binding domain of DCL3 is required for long-distance RNAi signaling. ABIOTECH 2024; 5:17-28. [PMID: 38576436 PMCID: PMC10987413 DOI: 10.1007/s42994-023-00124-6] [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: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 04/06/2024]
Abstract
Small RNA (sRNA)-mediated RNA silencing (also known as RNA interference, or RNAi) is a conserved mechanism in eukaryotes that includes RNA degradation, DNA methylation, heterochromatin formation and protein translation repression. In plants, sRNAs can move either cell-to-cell or systemically, thereby acting as mobile silencing signals to trigger noncell autonomous silencing. However, whether and what proteins are also involved in noncell autonomous silencing have not been elucidated. In this study, we utilized a previously reported inducible RNAi plant, PDSi, which can induce systemic silencing of the endogenous PDS gene, and we demonstrated that DCL3 is involved in systemic PDS silencing through its RNA binding activity. We confirmed that the C-terminus of DCL3, including the predicted RNA-binding domain, is capable of binding short RNAs. Mutations affecting RNA binding, but not processing activity, reduced systemic PDS silencing, indicating that DCL3 binding to RNAs is required for the induction of systemic silencing. Cucumber mosaic virus infection assays showed that the RNA-binding activity of DCL3 is required for antiviral RNAi in systemically noninoculated leaves. Our findings demonstrate that DCL3 acts as a signaling agent involved in noncell autonomous silencing and an antiviral effect in addition to its previously known function in the generation of 24-nucleotide sRNAs. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00124-6.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Bo-Sen Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Hua-Wei Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Cheng-Lan Liu
- Qilu Zhongke Academy of Modern Microbiology Technology, Jinan, 250022 China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
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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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Bhagta S, Bhardwaj V, Kant A. Exogenous dsRNA trigger RNAi in Venturia inaequalis resulting in down regulation of target genes and growth reduction. Mol Biol Rep 2023; 50:8421-8429. [PMID: 37620739 DOI: 10.1007/s11033-023-08736-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/02/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Venturia inaequalis is an apple scab causing fungal pathogen. It is a highly contagious and destructive pathogen which rapidly spreads infection in the surrounding orchards if not managed. The management and control of disease require multiple fungicides to be sprayed at different development stages of the apple. Persistent applications of fungicides also raises environmental concerns. Here, we demonstrate the potential of using spray induced gene silencing (SIGS) by developing target specific gene constructs for the synthesis of corresponding double-stranded RNA (dsRNA). METHODS AND RESULTS The exogenous application of dsRNAs was found to reduce mycelial growth and spore formation of V. inaequalis on culture plates. Four genes of V. inaequalis viz. CIN1, CE5, VICE12 and VICE16 which get upregulated during infection, were selected as targets for the development of gene construct expressing the corresponding dsRNA. The effect of exogenously supplied in vitro synthesized dsRNA on V. inaequalis was assessed in culture bioassay experiments with respect to growth, and spore formation. The expression level of the target genes in treated and control fungus was evaluated using quantitative PCR. Fungus treated with VICE12 targeted dsRNA showed maximum reduction in colony size (~ 55%), conidia formation (~ 93%) and expression level of the corresponding gene (2.2 fold), which was followed by CIN1-dsRNA. VICE16-dsRNA treatment was least effective with 32% reduction in growth, the non-significant effect of conidial spore formation and 1.13 fold down regulation of corresponding target gene expression level. CONCLUSION The result of this investigation validates the hypothesis that RNAi is evoked in V. inaequalis by exogenously supplied dsRNA and spray induced gene silencing (SIGS) based solutions may reduce burden of fungicide usage on apple crop against apple scab disease in future.
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Affiliation(s)
- Suhani Bhagta
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Anil Kant
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India.
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Wen HG, Zhao JH, Zhang BS, Gao F, Wu XM, Yan YS, Zhang J, Guo HS. Microbe-induced gene silencing boosts crop protection against soil-borne fungal pathogens. NATURE PLANTS 2023; 9:1409-1418. [PMID: 37653339 DOI: 10.1038/s41477-023-01507-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/02/2023] [Indexed: 09/02/2023]
Abstract
Small RNA (sRNA)-mediated trans-kingdom RNA interference (RNAi) between host and pathogen has been demonstrated and utilized. However, interspecies RNAi in rhizospheric microorganisms remains elusive. In this study, we developed a microbe-induced gene silencing (MIGS) technology by using a rhizospheric beneficial fungus, Trichoderma harzianum, to exploit an RNAi engineering microbe and two soil-borne pathogenic fungi, Verticillium dahliae and Fusarium oxysporum, as RNAi recipients. We first detected the feasibility of MIGS in inducing GFP silencing in V. dahliae. Then by targeting a fungal essential gene, we further demonstrated the effectiveness of MIGS in inhibiting fungal growth and protecting dicotyledon cotton and monocotyledon rice plants against V. dahliae and F. oxysporum. We also showed steerable MIGS specificity based on a selected target sequence. Our data verify interspecies RNAi in rhizospheric fungi and the potential application of MIGS in crop protection. In addition, the in situ propagation of a rhizospheric beneficial microbe would be optimal in ensuring the stability and sustainability of sRNAs, avoiding the use of nanomaterials to carry chemically synthetic sRNAs. Our finding reveals that exploiting MIGS-based biofungicides would offer straightforward design and implementation, without the need of host genetic modification, in crop protection against phytopathogens.
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Affiliation(s)
- Han-Guang Wen
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China
| | - Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China.
| | - Bo-Sen Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China
| | - Feng Gao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China
| | - Xue-Ming Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China
| | - Yong-Sheng Yan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China.
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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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Maksimov IV, Shein MY, Burkhanova GF. RNA Interference in Plant Protection from Fungal and Oomycete Infection. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822100106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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Ai G, Yang DL, Dou D. The warfare for plant highway: vascular plant-microbe interaction pinpoints lignin. STRESS BIOLOGY 2022; 2:24. [PMID: 37676368 PMCID: PMC10441898 DOI: 10.1007/s44154-022-00047-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/19/2022] [Indexed: 09/08/2023]
Abstract
Plant vascular pathogens are one kind of destructive pathogens in agricultural production. However, mechanisms behind the vascular pathogen-recognition and the subsequent defense responses of plants are not well known. A recent pioneering study on plant vascular immunity discovered a conserved MKP1-MPK-MYB signaling cascade that activates lignin biosynthesis in vascular tissues to confer vascular resistance in both monocot rice and the dicot Arabidopsis. The breakthrough provides a novel view on plant immunity to vascular pathogens and offers a potential strategy for the future breeding of disease-resistant crops.
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Affiliation(s)
- Gan Ai
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dong-Lei Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Daolong Dou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
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