1
|
Liu S, Ding SW. Antiviral RNA interference inhibits virus vertical transmission in plants. Cell Host Microbe 2024:S1931-3128(24)00316-0. [PMID: 39243759 DOI: 10.1016/j.chom.2024.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/14/2024] [Accepted: 08/12/2024] [Indexed: 09/09/2024]
Abstract
Known for over a century, seed transmission of plant viruses promotes trans-continental virus dissemination and provides the source of infection to trigger devastating disease epidemics in crops. However, it remains unknown whether there is a genetically defined immune pathway to suppress virus vertical transmission in plants. Here, we demonstrate potent immunosuppression of cucumber mosaic virus (CMV) seed transmission in its natural host Arabidopsis thaliana by antiviral RNA interference (RNAi) pathway. Immunofluorescence microscopy reveals predominant embryo infection at four stages of embryo development. We show that antiviral RNAi confers resistance to seed infection with different genetic requirements and drastically enhanced potency compared with the inhibition of systemic infection of whole plants. Moreover, we detect efficient seed transmission of a mutant CMV lacking its RNAi suppressor gene in mutant plants defective in antiviral RNAi, providing further support for the immunosuppression of seed transmission by antiviral RNAi.
Collapse
Affiliation(s)
- Si Liu
- Department of Microbiology & Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Shou-Wei Ding
- Department of Microbiology & Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA.
| |
Collapse
|
2
|
Wen Z, Hu R, Pi Q, Zhang D, Duan J, Li Z, Li Q, Zhao X, Yang M, Zhao X, Liu D, Su Z, Li D, Zhang Y. DEAD-box RNA helicase RH20 positively regulates RNAi-based antiviral immunity in plants by associating with SGS3/RDR6 bodies. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39166471 DOI: 10.1111/pbi.14448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/15/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024]
Abstract
RNA silencing plays a crucial role in defending against viral infections in diverse eukaryotic hosts. Despite extensive studies on core components of the antiviral RNAi pathway such as DCLs, AGOs and RDRs proteins, host factors involved in antiviral RNAi remain incompletely understood. In this study, we employed the proximity labelling approach to identify the host factors required for antiviral RNAi in Nicotiana benthamiana. Using the barley stripe mosaic virus (BSMV)-encoded γb, a viral suppressor of RNA silencing (VSR), as the bait protein, we identified the DEAD-box RNA helicase RH20, a broadly conserved protein in plants and animals with a homologous human protein known as DDX5. We demonstrated the interaction between RH20 and BSMV γb. Knockdown or knockout of RH20 attenuates the accumulation of viral small interfering RNAs, leading to increased susceptibility to BSMV, while overexpression of RH20 enhances resistance to BSMV, a process requiring the cytoplasmic localization and RNA-binding activity of RH20. In addition to BSMV, RH20 also negatively regulates the infection of several other positive-sense RNA viruses, suggesting the broad-spectrum antiviral activity of RH20. Mechanistic analysis revealed the colocalization and interaction of RH20 with SGS3/RDR6, and disruption of either SGS3 or RDR6 undermines the antiviral function of RH20, suggesting RH20 as a new component of the SGS3/RDR6 bodies. As a counter-defence, BSMV γb VSR subverts the RH20-mediated antiviral defence by interfering with the RH20-SGS3 interaction. Our results uncover RH20 as a new positive regulator of antiviral RNAi and provide new potential targets for controlling plant viral diseases.
Collapse
Affiliation(s)
- Zhiyan Wen
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Rujian Hu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qinglin Pi
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dingliang Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiangning Duan
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhen Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qian Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiaoyun Zhao
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Meng Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiaofei Zhao
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Deshui Liu
- Beijing Life Science Academy, Beijing, China
| | - Zhen Su
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dawei Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| |
Collapse
|
3
|
Spada M, Pugliesi C, Fambrini M, Pecchia S. Challenges and Opportunities Arising from Host- Botrytis cinerea Interactions to Outline Novel and Sustainable Control Strategies: The Key Role of RNA Interference. Int J Mol Sci 2024; 25:6798. [PMID: 38928507 PMCID: PMC11203536 DOI: 10.3390/ijms25126798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The necrotrophic plant pathogenic fungus Botrytis cinerea (Pers., 1794), the causative agent of gray mold disease, causes significant losses in agricultural production. Control of this fungal pathogen is quite difficult due to its wide host range and environmental persistence. Currently, the management of the disease is still mainly based on chemicals, which can have harmful effects not only on the environment and on human health but also because they favor the development of strains resistant to fungicides. The flexibility and plasticity of B. cinerea in challenging plant defense mechanisms and its ability to evolve strategies to escape chemicals require the development of new control strategies for successful disease management. In this review, some aspects of the host-pathogen interactions from which novel and sustainable control strategies could be developed (e.g., signaling pathways, molecules involved in plant immune mechanisms, hormones, post-transcriptional gene silencing) were analyzed. New biotechnological tools based on the use of RNA interference (RNAi) are emerging in the crop protection scenario as versatile, sustainable, effective, and environmentally friendly alternatives to the use of chemicals. RNAi-based fungicides are expected to be approved soon, although they will face several challenges before reaching the market.
Collapse
Affiliation(s)
- Maria Spada
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Susanna Pecchia
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| |
Collapse
|
4
|
Sato Y, Kondo H, Suzuki N. Argonaute-independent, Dicer-dependent antiviral defense against RNA viruses. Proc Natl Acad Sci U S A 2024; 121:e2322765121. [PMID: 38865263 PMCID: PMC11194562 DOI: 10.1073/pnas.2322765121] [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: 12/24/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024] Open
Abstract
Antiviral RNA interference (RNAi) is conserved from yeasts to mammals. Dicer recognizes and cleaves virus-derived double-stranded RNA (dsRNA) and/or structured single-stranded RNA (ssRNA) into small-interfering RNAs, which guide effector Argonaute to homologous viral RNAs for digestion and inhibit virus replication. Thus, Argonaute is believed to be essential for antiviral RNAi. Here, we show Argonaute-independent, Dicer-dependent antiviral defense against dsRNA viruses using Cryphonectria parasitica (chestnut blight fungus), which is a model filamentous ascomycetous fungus and hosts a variety of viruses. The fungus has two dicer-like genes (dcl1 and dcl2) and four argonaute-like genes (agl1 to agl4). We prepared a suite of single to quadruple agl knockout mutants with or without dcl disruption. We tested these mutants for antiviral activities against diverse dsRNA viruses and ssRNA viruses. Although both DCL2 and AGL2 worked as antiviral players against some RNA viruses, DCL2 without argonaute was sufficient to block the replication of other RNA viruses. Overall, these results indicate the existence of a Dicer-alone defense and different degrees of susceptibility to it among RNA viruses. We discuss what determines the great difference in susceptibility to the Dicer-only defense.
Collapse
Affiliation(s)
- Yukiyo Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
| |
Collapse
|
5
|
Chen Y, Ma S, Ku H, Huangfu B, Wang K, Du C, Zhang M. Contiguous identity between entire coding regions of transgenic and native genes rather than special regions is essential for a strong co-suppression. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:112016. [PMID: 38311253 DOI: 10.1016/j.plantsci.2024.112016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
The discovery of co-suppression in plants has greatly boosted the study of gene silencing mechanisms, but its triggering mechanism has remained a mystery. In this study, we explored its possible trigger mechanism by using Fatty acid desaturase 2 (FAD2) and Fatty acid elongase 1 (FAE1) strong co-suppression systems. Analysis of small RNAs in FAD2 co-suppression lines showed that siRNAs distributed throughout the coding region of FAD2 with an accumulated peak. However, mutations of the peak siRNA-matched site and siRNA derived site had not alleviated the co-suppression of its transgenic lines. Synthetic FAD2 (AtFAD2sm), which has synonymous mutations in the entire coding region, failed to trigger any co-suppression. Furthermore, 5' and 3' portions of AtFAD2 and AtFAD2sm were swapped to form two hybrid genes, AtFAD2-3sm and AtFAD2-5sm. 80 % and 92 % of their transgenic lines exhibited co-suppression, respectively. Finally, FAE1s with different degrees of the continuous sequence identity compared with AtFAE1 were tested in their Arabidopsis transgenic lines, and the results showed the co-suppression frequency was reduced as their continuous sequence identity stepped down. This work suggests that contiguous identity between the entire coding regions of transgenic and native genes rather than a special region is essential for a strong co-suppression.
Collapse
Affiliation(s)
- Yangyang Chen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Shijie Ma
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, Anhui Province, China.
| | - Hangkai Ku
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Bingyuan Huangfu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Kai Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Chang Du
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China; College of Life Sciences, South China Normal University, Guangzhou, Guangdong 610631, China.
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
6
|
Blagojevic A, Baldrich P, Schiaffini M, Lechner E, Baumberger N, Hammann P, Elmayan T, Garcia D, Vaucheret H, Meyers BC, Genschik P. Heat stress promotes Arabidopsis AGO1 phase separation and association with stress granule components. iScience 2024; 27:109151. [PMID: 38384836 PMCID: PMC10879784 DOI: 10.1016/j.isci.2024.109151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/17/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
In Arabidopsis thaliana, ARGONAUTE1 (AGO1) plays a central role in microRNA (miRNA) and small interfering RNA (siRNA)-mediated silencing. AGO1 associates to the rough endoplasmic reticulum to conduct miRNA-mediated translational repression, mRNA cleavage, and biogenesis of phased siRNAs. Here, we show that a 37°C heat stress (HS) promotes AGO1 protein accumulation in cytosolic condensates where it colocalizes with components of siRNA bodies and of stress granules. AGO1 contains a prion-like domain in its poorly characterized N-terminal Poly-Q domain, which is sufficient to undergo phase separation independently of the presence of SGS3. HS only moderately affects the small RNA repertoire, the loading of AGO1 by miRNAs, and the signatures of target cleavage, suggesting that its localization in condensates protects AGO1 rather than promoting or impairing its activity in reprogramming gene expression during stress. Collectively, our work sheds new light on the impact of high temperature on a main effector of RNA silencing in plants.
Collapse
Affiliation(s)
- Aleksandar Blagojevic
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | | | - Marlene Schiaffini
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Esther Lechner
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Nicolas Baumberger
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, 67084 Strasbourg, France
| | - Taline Elmayan
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Damien Garcia
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Hervé Vaucheret
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Pascal Genschik
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| |
Collapse
|
7
|
Ren Y, Zhang L, Yang X, Lin H, Sang Y, Feng L, Liu J, Kang M. Cryptic divergences and repeated hybridizations within the endangered "living fossil" dove tree ( Davidia involucrata) revealed by whole genome resequencing. PLANT DIVERSITY 2024; 46:169-180. [PMID: 38807904 PMCID: PMC11128880 DOI: 10.1016/j.pld.2024.02.004] [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: 11/02/2023] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 05/30/2024]
Abstract
The identification and understanding of cryptic intraspecific evolutionary units (lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species. However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a "living fossil" dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range. Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.
Collapse
Affiliation(s)
- Yumeng Ren
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Lushui Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xuchen Yang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Hao Lin
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yupeng Sang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Landi Feng
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jianquan Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Minghui Kang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| |
Collapse
|
8
|
Shang B, Li C, Zhang X. How intrinsically disordered proteins order plant gene silencing. Trends Genet 2024; 40:260-275. [PMID: 38296708 PMCID: PMC10932933 DOI: 10.1016/j.tig.2023.12.009] [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: 10/02/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 02/02/2024]
Abstract
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) possess low sequence complexity of amino acids and display non-globular tertiary structures. They can act as scaffolds, form regulatory hubs, or trigger biomolecular condensation to control diverse aspects of biology. Emerging evidence has recently implicated critical roles of IDPs and IDR-contained proteins in nuclear transcription and cytoplasmic post-transcriptional processes, among other molecular functions. We here summarize the concepts and organizing principles of IDPs. We then illustrate recent progress in understanding the roles of key IDPs in machineries that regulate transcriptional and post-transcriptional gene silencing (PTGS) in plants, aiming at highlighting new modes of action of IDPs in controlling biological processes.
Collapse
Affiliation(s)
- Baoshuan Shang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA.
| |
Collapse
|
9
|
Palukaitis P, Yoon JY. Defense signaling pathways in resistance to plant viruses: Crosstalk and finger pointing. Adv Virus Res 2024; 118:77-212. [PMID: 38461031 DOI: 10.1016/bs.aivir.2024.01.002] [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] [Indexed: 03/11/2024]
Abstract
Resistance to infection by plant viruses involves proteins encoded by plant resistance (R) genes, viz., nucleotide-binding leucine-rich repeats (NLRs), immune receptors. These sensor NLRs are activated either directly or indirectly by viral protein effectors, in effector-triggered immunity, leading to induction of defense signaling pathways, resulting in the synthesis of numerous downstream plant effector molecules that inhibit different stages of the infection cycle, as well as the induction of cell death responses mediated by helper NLRs. Early events in this process involve recognition of the activation of the R gene response by various chaperones and the transport of these complexes to the sites of subsequent events. These events include activation of several kinase cascade pathways, and the syntheses of two master transcriptional regulators, EDS1 and NPR1, as well as the phytohormones salicylic acid, jasmonic acid, and ethylene. The phytohormones, which transit from a primed, resting states to active states, regulate the remainder of the defense signaling pathways, both directly and by crosstalk with each other. This regulation results in the turnover of various suppressors of downstream events and the synthesis of various transcription factors that cooperate and/or compete to induce or suppress transcription of either other regulatory proteins, or plant effector molecules. This network of interactions results in the production of defense effectors acting alone or together with cell death in the infected region, with or without the further activation of non-specific, long-distance resistance. Here, we review the current state of knowledge regarding these processes and the components of the local responses, their interactions, regulation, and crosstalk.
Collapse
Affiliation(s)
- Peter Palukaitis
- Graduate School of Plant Protection and Quarantine, Jeonbuk National University, Jeonju, Jeollabuk-do, Republic of Korea.
| | - Ju-Yeon Yoon
- Graduate School of Plant Protection and Quarantine, Jeonbuk National University, Jeonju, Jeollabuk-do, Republic of Korea.
| |
Collapse
|
10
|
Vaucheret H, Voinnet O. The plant siRNA landscape. THE PLANT CELL 2024; 36:246-275. [PMID: 37772967 PMCID: PMC10827316 DOI: 10.1093/plcell/koad253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Whereas micro (mi)RNAs are considered the clean, noble side of the small RNA world, small interfering (si)RNAs are often seen as a noisy set of molecules whose barbarian acronyms reflect a large diversity of often elusive origins and functions. Twenty-five years after their discovery in plants, however, new classes of siRNAs are still being identified, sometimes in discrete tissues or at particular developmental stages, making the plant siRNA world substantially more complex and subtle than originally anticipated. Focusing primarily on the model Arabidopsis, we review here the plant siRNA landscape, including transposable elements (TE)-derived siRNAs, a vast array of non-TE-derived endogenous siRNAs, as well as exogenous siRNAs produced in response to invading nucleic acids such as viruses or transgenes. We primarily emphasize the extraordinary sophistication and diversity of their biogenesis and, secondarily, the variety of their known or presumed functions, including via non-cell autonomous activities, in the sporophyte, gametophyte, and shortly after fertilization.
Collapse
Affiliation(s)
- Hervé Vaucheret
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH-Zurich), 8092 Zürich, Switzerland
| |
Collapse
|
11
|
Yan D, Han K, Lu Y, Peng J, Rao S, Wu G, Liu Y, Chen J, Zheng H, Yan F. The nanovirus U2 protein suppresses RNA silencing via three conserved cysteine residues. MOLECULAR PLANT PATHOLOGY 2024; 25:e13394. [PMID: 37823358 PMCID: PMC10782648 DOI: 10.1111/mpp.13394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
Nanoviruses have multipartite, circular, single-stranded DNA genomes and cause huge production losses in legumes and other crops. No viral suppressor of RNA silencing (VSR) has yet been reported from a member of the genus Nanovirus. Here, we demonstrate that the nanovirus U2 protein is a VSR. The U2 protein of milk vetch dwarf virus (MDV) suppressed the silencing of the green fluorescent protein (GFP) gene induced by single-stranded and double-stranded RNA, and the systemic spread of the GFP silencing signal. An electrophoretic mobility shift assay showed that the U2 protein was able to bind double-stranded 21-nucleotide small interfering RNA (siRNA). The cysteine residues at positions 43, 79 and 82 in the MDV U2 protein are critical to its nuclear localization, self-interaction and siRNA-binding ability, and were essential for its VSR activity. In addition, expression of the U2 protein via a potato virus X vector induced more severe necrosis symptoms in Nicotiana benthamiana leaves. The U2 proteins of other nanoviruses also acted as VSRs, and the three conserved cysteine residues were indispensable for their VSR activity.
Collapse
Affiliation(s)
- Dankan Yan
- College of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
- Institute of Plant Protection and Agro‐Products SafetyAnhui Academy of Agricultural SciencesHefeiChina
| | - Kelei Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
- Institute of Plant Protection and Agro‐Products SafetyAnhui Academy of Agricultural SciencesHefeiChina
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Shaofei Rao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Guanwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yong Liu
- Institute of Plant ProtectionHunan Academy of Agricultural SciencesChangshaChina
| | - Jianping Chen
- College of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
| |
Collapse
|
12
|
Chen Y, Ku H, Zhao Y, Du C, Zhang M. Quantitative Investigation of FAD2 Cosuppression Reveals RDR6-Dependent and RDR6-Independent Gene Silencing Pathways. Int J Mol Sci 2023; 24:17165. [PMID: 38138994 PMCID: PMC10742939 DOI: 10.3390/ijms242417165] [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: 11/02/2023] [Revised: 11/28/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
The frequency and extent of transgene-mediated cosuppression varies substantially among plant genes. However, the underlying mechanisms leading to strong cosuppression have received little attention. In previous studies, we showed that the expression of FAD2 in the seeds of Arabidopsis results in strong RDR6-mediated cosuppression, where both endogenous and transgenic FAD2 were silenced. Here, the FAD2 strong cosuppression system was quantitatively investigated to identify the genetic factors by the expression of FAD2 in their mutants. The involvement of DCL2, DCL4, AGO1, and EIN5 was first confirmed in FAD2 cosuppression. SKI2, a remover of 3' end aberrant RNAs, was newly identified as being involved in the cosuppression, while DCL3 was identified as antagonistic to DCL2 and DCL3. FAD2 cosuppression was markedly reduced in dcl2, dcl4, and ago1. The existence of an RDR6-independent cosuppression was revealed for the first time, which was demonstrated by weak gene silencing in rdr6 ein5 ski2. Further investigation of FAD2 cosuppression may unveil unknown genetic factor(s).
Collapse
Affiliation(s)
| | | | | | - Chang Du
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.C.); (H.K.); (Y.Z.)
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.C.); (H.K.); (Y.Z.)
| |
Collapse
|
13
|
Fujimoto Y, Iwakawa HO. Mechanisms that regulate the production of secondary siRNAs in plants. J Biochem 2023; 174:491-499. [PMID: 37757447 DOI: 10.1093/jb/mvad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/28/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
Many organisms produce secondary small interfering RNAs (siRNAs) that are triggered by primary small RNAs to regulate various biological processes. Plants have evolved several types of secondary siRNA biogenesis pathways that play important roles in development, stress responses and defense against viruses and transposons. The critical step of these pathways is the production of double-stranded RNAs by RNA-dependent RNA polymerases. This step is normally tightly regulated, but when its control is released, secondary siRNA production is initiated. In this article, we will review the recent advances in secondary siRNA production triggered by microRNAs encoded in the genome and siRNAs derived from invasive nucleic acids. In particular, we will focus on the factors, events, and RNA/DNA elements that promote or inhibit the early steps of secondary siRNA biogenesis.
Collapse
Affiliation(s)
- Yuji Fujimoto
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Hiro-Oki Iwakawa
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| |
Collapse
|
14
|
Flores-Téllez D, Tankmar MD, von Bülow S, Chen J, Lindorff-Larsen K, Brodersen P, Arribas-Hernández L. Insights into the conservation and diversification of the molecular functions of YTHDF proteins. PLoS Genet 2023; 19:e1010980. [PMID: 37816028 PMCID: PMC10617740 DOI: 10.1371/journal.pgen.1010980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/31/2023] [Accepted: 09/17/2023] [Indexed: 10/12/2023] Open
Abstract
YT521-B homology (YTH) domain proteins act as readers of N6-methyladenosine (m6A) in mRNA. Members of the YTHDF clade determine properties of m6A-containing mRNAs in the cytoplasm. Vertebrates encode three YTHDF proteins whose possible functional specialization is debated. In land plants, the YTHDF clade has expanded from one member in basal lineages to eleven so-called EVOLUTIONARILY CONSERVED C-TERMINAL REGION1-11 (ECT1-11) proteins in Arabidopsis thaliana, named after the conserved YTH domain placed behind a long N-terminal intrinsically disordered region (IDR). ECT2, ECT3 and ECT4 show genetic redundancy in stimulation of primed stem cell division, but the origin and implications of YTHDF expansion in higher plants are unknown, as it is unclear whether it involves acquisition of fundamentally different molecular properties, in particular of their divergent IDRs. Here, we use functional complementation of ect2/ect3/ect4 mutants to test whether different YTHDF proteins can perform the same function when similarly expressed in leaf primordia. We show that stimulation of primordial cell division relies on an ancestral molecular function of the m6A-YTHDF axis in land plants that is present in bryophytes and is conserved over YTHDF diversification, as it appears in all major clades of YTHDF proteins in flowering plants. Importantly, although our results indicate that the YTH domains of all arabidopsis ECT proteins have m6A-binding capacity, lineage-specific neo-functionalization of ECT1, ECT9 and ECT11 happened after late duplication events, and involves altered properties of both the YTH domains, and, especially, of the IDRs. We also identify two biophysical properties recurrent in IDRs of YTHDF proteins able to complement ect2 ect3 ect4 mutants, a clear phase separation propensity and a charge distribution that creates electric dipoles. Human and fly YTHDFs do not have IDRs with this combination of properties and cannot replace ECT2/3/4 function in arabidopsis, perhaps suggesting different molecular activities of YTHDF proteins between major taxa.
Collapse
Affiliation(s)
- Daniel Flores-Téllez
- University of Copenhagen, Biology Department. Copenhagen, Denmark
- Universidad Francisco de Vitoria, Facultad de Ciencias Experimentales. Pozuelo de Alarcón (Madrid), Spain
| | | | - Sören von Bülow
- University of Copenhagen, Biology Department. Copenhagen, Denmark
| | - Junyu Chen
- University of Copenhagen, Biology Department. Copenhagen, Denmark
| | | | - Peter Brodersen
- University of Copenhagen, Biology Department. Copenhagen, Denmark
| | | |
Collapse
|
15
|
Ebrahimi S, Eini O, Baßler A, Hanke A, Yildirim Z, Wassenegger M, Krczal G, Uslu VV. Beet Curly Top Iran Virus Rep and V2 Suppress Post-Transcriptional Gene Silencing via Distinct Modes of Action. Viruses 2023; 15:1996. [PMID: 37896771 PMCID: PMC10611197 DOI: 10.3390/v15101996] [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: 08/21/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Beet curly top Iran virus (BCTIV) is a yield-limiting geminivirus belonging to the becurtovirus genus. The genome organization of BCTIV is unique such that the complementary strand of BCTIV resembles Mastrevirus, whereas the virion strand organization is similar to the Curtovirus genus. Geminiviruses are known to avoid the plant defense system by suppressing the RNA interference mechanisms both at the transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS) levels. Multiple geminivirus genes have been identified as viral suppressors of RNA silencing (VSR) but VSR activity remains mostly elusive in becurtoviruses. We found that BCTIV-V2 and -Rep could suppress specific Sense-PTGS mechanisms with distinct efficiencies depending on the nature of the silencing inducer and the target gene. Local silencing induced by GFP inverted repeat (IR) could not be suppressed by V2 but was partially reduced by Rep. Accordingly, we documented that Rep but not V2 could suppress systemic silencing induced by GFP-IR. In addition, we showed that the VSR activity of Rep was partly regulated by RNA-dependent RNA Polymerase 6 (RDR6), whereas the VSR activity of V2 was independent of RDR6. Domain mapping for Rep showed that an intact Rep protein was required for the suppression of PTGS. In summary, we showed that BCTIV-Rep and -V2 function as silencing suppressors with distinct modes of action.
Collapse
Affiliation(s)
- Saeideh Ebrahimi
- RLP AgroScience GmbH, Breitenweg 71, 67435 Neustadt an der Weinstraße, Germany
- Department of Plant Protection, University of Zanjan, Zanjan 313, Iran
| | - Omid Eini
- Department of Plant Protection, University of Zanjan, Zanjan 313, Iran
- Department of Phytopathology, Institute for Sugar Beet Research, 37079 Göttingen, Germany
| | - Alexandra Baßler
- RLP AgroScience GmbH, Breitenweg 71, 67435 Neustadt an der Weinstraße, Germany
| | - Arvid Hanke
- RLP AgroScience GmbH, Breitenweg 71, 67435 Neustadt an der Weinstraße, Germany
- MAPS, COS, Heidelberg University, 69120 Heidelberg, Germany
| | - Zeynep Yildirim
- RLP AgroScience GmbH, Breitenweg 71, 67435 Neustadt an der Weinstraße, Germany
| | - Michael Wassenegger
- RLP AgroScience GmbH, Breitenweg 71, 67435 Neustadt an der Weinstraße, Germany
| | - Gabi Krczal
- RLP AgroScience GmbH, Breitenweg 71, 67435 Neustadt an der Weinstraße, Germany
| | - Veli Vural Uslu
- RLP AgroScience GmbH, Breitenweg 71, 67435 Neustadt an der Weinstraße, Germany
- MAPS, COS, Heidelberg University, 69120 Heidelberg, Germany
| |
Collapse
|
16
|
Martínez‐Pérez M, Aparicio F, Arribas‐Hernández L, Tankmar MD, Rennie S, von Bülow S, Lindorff‐Larsen K, Brodersen P, Pallas V. Plant YTHDF proteins are direct effectors of antiviral immunity against an N6-methyladenosine-containing RNA virus. EMBO J 2023; 42:e113378. [PMID: 37431920 PMCID: PMC10505913 DOI: 10.15252/embj.2022113378] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 07/12/2023] Open
Abstract
In virus-host interactions, nucleic acid-directed first lines of defense that allow viral clearance without compromising growth are of paramount importance. Plants use the RNA interference pathway as a basal antiviral immune system, but additional RNA-based mechanisms of defense also exist. The infectivity of a plant positive-strand RNA virus, alfalfa mosaic virus (AMV), relies on the demethylation of viral RNA by the recruitment of the cellular N6-methyladenosine (m6 A) demethylase ALKBH9B, but how demethylation of viral RNA promotes AMV infection remains unknown. Here, we show that inactivation of the Arabidopsis cytoplasmic YT521-B homology domain (YTH)-containing m6 A-binding proteins ECT2, ECT3, and ECT5 is sufficient to restore AMV infectivity in partially resistant alkbh9b mutants. We further show that the antiviral function of ECT2 is distinct from its previously demonstrated function in the promotion of primordial cell proliferation: an ect2 mutant carrying a small deletion in its intrinsically disordered region is partially compromised for antiviral defense but not for developmental functions. These results indicate that the m6 A-YTHDF axis constitutes a novel branch of basal antiviral immunity in plants.
Collapse
Affiliation(s)
- Mireya Martínez‐Pérez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValènciaValenciaSpain
| | - Frederic Aparicio
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValènciaValenciaSpain
| | | | | | - Sarah Rennie
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Sören von Bülow
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | | | - Peter Brodersen
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValènciaValenciaSpain
| |
Collapse
|
17
|
Han Y, Zhang X, Du R, Shan X, Xie D. The phase separation of SGS3 regulates antiviral immunity and fertility in Arabidopsis. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1938-1941. [PMID: 36811803 DOI: 10.1007/s11427-022-2287-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/29/2023] [Indexed: 02/24/2023]
Affiliation(s)
- Yujie Han
- MOE Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaolin Zhang
- MOE Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Shenzhen Branch of Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Ran Du
- Shenzhen Branch of Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xiaoyi Shan
- MOE Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Daoxin Xie
- MOE Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
18
|
Tong X, Zhao JJ, Feng YL, Zou JZ, Ye J, Liu J, Han C, Li D, Wang XB. A selective autophagy receptor VISP1 induces symptom recovery by targeting viral silencing suppressors. Nat Commun 2023; 14:3852. [PMID: 37385991 PMCID: PMC10310818 DOI: 10.1038/s41467-023-39426-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 06/09/2023] [Indexed: 07/01/2023] Open
Abstract
Selective autophagy is a double-edged sword in antiviral immunity and regulated by various autophagy receptors. However, it remains unclear how to balance the opposite roles by one autophagy receptor. We previously identified a virus-induced small peptide called VISP1 as a selective autophagy receptor that facilitates virus infections by targeting components of antiviral RNA silencing. However, we show here that VISP1 can also inhibit virus infections by mediating autophagic degradation of viral suppressors of RNA silencing (VSRs). VISP1 targets the cucumber mosaic virus (CMV) 2b protein for degradation and attenuates its suppression activity on RNA silencing. Knockout and overexpression of VISP1 exhibit compromised and enhanced resistance against late infection of CMV, respectively. Consequently, VISP1 induces symptom recovery from CMV infection by triggering 2b turnover. VISP1 also targets the C2/AC2 VSRs of two geminiviruses and enhances antiviral immunity. Together, VISP1 induces symptom recovery from severe infections of plant viruses through controlling VSR accumulation.
Collapse
Affiliation(s)
- Xin Tong
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
- College of Plant Protection, China Agricultural University, 100193, Beijing, China
| | - Jia-Jia Zhao
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Ya-Lan Feng
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Jing-Ze Zou
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Jian Ye
- State Key laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Junfeng Liu
- College of Plant Protection, China Agricultural University, 100193, Beijing, China
| | - Chenggui Han
- College of Plant Protection, China Agricultural University, 100193, Beijing, China
| | - Dawei Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Xian-Bing Wang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, 100193, Beijing, China.
| |
Collapse
|
19
|
Liu S, Han Y, Li WX, Ding SW. Infection Defects of RNA and DNA Viruses Induced by Antiviral RNA Interference. Microbiol Mol Biol Rev 2023; 87:e0003522. [PMID: 37052496 PMCID: PMC10304667 DOI: 10.1128/mmbr.00035-22] [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] [Indexed: 04/14/2023] Open
Abstract
Immune recognition of viral genome-derived double-stranded RNA (dsRNA) molecules and their subsequent processing into small interfering RNAs (siRNAs) in plants, invertebrates, and mammals trigger specific antiviral immunity known as antiviral RNA interference (RNAi). Immune sensing of viral dsRNA is sequence-independent, and most regions of viral RNAs are targeted by virus-derived siRNAs which extensively overlap in sequence. Thus, the high mutation rates of viruses do not drive immune escape from antiviral RNAi, in contrast to other mechanisms involving specific virus recognition by host immune proteins such as antibodies and resistance (R) proteins in mammals and plants, respectively. Instead, viruses actively suppress antiviral RNAi at various key steps with a group of proteins known as viral suppressors of RNAi (VSRs). Some VSRs are so effective in virus counter-defense that potent inhibition of virus infection by antiviral RNAi is undetectable unless the cognate VSR is rendered nonexpressing or nonfunctional. Since viral proteins are often multifunctional, resistance phenotypes of antiviral RNAi are accurately defined by those infection defects of VSR-deletion mutant viruses that are efficiently rescued by host deficiency in antiviral RNAi. Here, we review and discuss in vivo infection defects of VSR-deficient RNA and DNA viruses resulting from the actions of host antiviral RNAi in model systems.
Collapse
Affiliation(s)
- Si Liu
- Department of Microbiology & Plant Pathology, University of California, Riverside, California, USA
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Yanhong Han
- Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wan-Xiang Li
- Department of Microbiology & Plant Pathology, University of California, Riverside, California, USA
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Shou-Wei Ding
- Department of Microbiology & Plant Pathology, University of California, Riverside, California, USA
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| |
Collapse
|
20
|
Hu W, Dai Z, Liu P, Deng C, Shen W, Li Z, Cui H. The Single Distinct Leader Protease Encoded by Alpinia oxyphylla Mosaic Virus (Genus Macluravirus) Suppresses RNA Silencing Through Interfering with Double-Stranded RNA Synthesis. PHYTOPATHOLOGY 2023; 113:1103-1114. [PMID: 36576401 DOI: 10.1094/phyto-10-22-0371-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The genomic 5'-terminal regions of viruses in the family Potyviridae (potyvirids) encode two types of leader proteases: serine-protease (P1) and cysteine-protease (HCPro), which differ greatly in the arrangement and sequence composition among inter-genus viruses. Most potyvirids have the same tandemly arranged P1 and HCPro, whereas viruses in the genus Macluravirus encode a single distinct leader protease, a truncated version of HCPro with yet-unknown functions. We investigated the RNA silencing suppression (RSS) activity and its underpinning mechanism of the distinct HCPro from alpinia oxyphylla mosaic macluravirus (aHCPro). Sequence analysis revealed that macluraviral HCPros have obvious truncations in the N-terminal and middle regions when aligned to their counterparts in potyviruses (well-characterized viral suppressors of RNA silencing). Nearly all defined elements essential for the RSS activity of potyviral counterparts are not distinguished in macluraviral HCPros. Here, we demonstrated that aHCPro exhibits a similar anti-silencing activity with the potyviral counterpart. However, aHCPro fails to block both the local and systemic spreading of RNA silencing. In line, aHCPro interferes with the dsRNA synthesis, an upstream step in the RNA silencing pathway. Affinity-purification and NanoLC-MS/MS analysis revealed that aHCPro has no association with core components or their potential interactors involving in dsRNA synthesis from the protein layer. Instead, the ectopic expression of aHCPro significantly reduces the transcript abundance of RDR2, RDR6, SGS3, and SDE5. This study represents the first report on the anti-silencing function of Macluravirus-encoded HCPro and the underlying molecular mechanism.
Collapse
Affiliation(s)
- Weiyao Hu
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Zhaoji Dai
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Peilan Liu
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Changhui Deng
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Wentao Shen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Zengping Li
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Hongguang Cui
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| |
Collapse
|
21
|
Kim YJ. Crosstalk between RNA silencing and RNA quality control in plants. BMB Rep 2023; 56:321-325. [PMID: 37156633 PMCID: PMC10315563 DOI: 10.5483/bmbrep.2023-0049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/20/2023] [Accepted: 05/04/2023] [Indexed: 06/06/2024] Open
Abstract
RNAs are pivotal molecules acting as messengers of genetic information and regulatory molecules for cellular development and survival. From birth to death, RNAs face constant cellular decision for the precise control of cellular function and activity. Most eukaryotic cells employ conserved machineries for RNA decay including RNA silencing and RNA quality control (RQC). In plants, RQC monitors endogenous RNAs and degrades aberrant and dysfunctional species, whereas RNA silencing promotes RNA degradation to repress the expression of selected endogenous RNAs or exogenous RNA derived from transgenes and virus. Interestingly, emerging evidences have indicated that RQC and RNA silencing interact with each by sharing target RNAs and regulatory components. Such interaction should be tightly organized for proper cellular survival. However, it is still elusive that how each machinery specifically recognizes target RNAs. In this review, we summarize recent advances on RNA silencing and RQC pathway and discuss potential mechanisms underlying the interaction between the two machineries. [BMB Reports 2023; 56(6): 321-325].
Collapse
Affiliation(s)
- Yun Ju Kim
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
| |
Collapse
|
22
|
Bazin J, Elvira-Matelot E, Blein T, Jauvion V, Bouteiller N, Cao J, Crespi MD, Vaucheret H. Synergistic action of the Arabidopsis spliceosome components PRP39a and SmD1b in promoting posttranscriptional transgene silencing. THE PLANT CELL 2023; 35:1917-1935. [PMID: 36970782 PMCID: PMC10226559 DOI: 10.1093/plcell/koad091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 05/30/2023]
Abstract
Besides regulating splicing, the conserved spliceosome component SmD1 (Small nuclear ribonucleoprotein D1)b promotes posttranscriptional silencing of sense transgenes (S-PTGS [post-transcriptional genesilencing]). Here, we show that the conserved spliceosome component PRP39 (Pre-mRNA-processing factor 39)a also plays a role in S-PTGS in Arabidopsis thaliana. However, PRP39a and SmD1b actions appear distinct in both splicing and S-PTGS. Indeed, RNAseq-based analysis of expression level and alternative splicing in prp39a and smd1b mutants identified different sets of deregulated transcripts and noncoding RNAs. Moreover, double mutant analyses involving prp39a or smd1b and RNA quality control (RQC) mutants revealed distinct genetic interactions for SmD1b and PRP39a with nuclear RQC machineries, suggesting nonredundant roles in the RQC/PTGS interplay. Supporting this hypothesis, a prp39a smd1b double mutant exhibited enhanced suppression of S-PTGS compared to the single mutants. Because the prp39a and smd1b mutants (i) showed no major changes in the expression of PTGS or RQC components or in small RNA production and (ii) do not alter PTGS triggered by inverted-repeat transgenes directly producing dsRNA (IR-PTGS), PRP39a, and SmD1b appear to synergistically promote a step specific to S-PTGS. We propose that, independently from their specific roles in splicing, PRP39a and SmD1b limit 3'-to-5' and/or 5'-to-3' degradation of transgene-derived aberrant RNAs in the nucleus, thus favoring the export of aberrant RNAs to the cytoplasm where their conversion into double-stranded RNA (dsRNA) initiates S-PTGS.
Collapse
Affiliation(s)
- Jérémie Bazin
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Universités Paris-Sud, Evry, Paris-Diderot, Sorbonne Paris-Cité, Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Emilie Elvira-Matelot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Thomas Blein
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Universités Paris-Sud, Evry, Paris-Diderot, Sorbonne Paris-Cité, Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Vincent Jauvion
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Nathalie Bouteiller
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Jun Cao
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Martin D Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Universités Paris-Sud, Evry, Paris-Diderot, Sorbonne Paris-Cité, Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Hervé Vaucheret
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| |
Collapse
|
23
|
Hang R, Xu Y, Wang X, Hu H, Flynn N, You C, Chen X. Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation. Proc Natl Acad Sci U S A 2023; 120:e2301081120. [PMID: 37011204 PMCID: PMC10104536 DOI: 10.1073/pnas.2301081120] [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: 01/24/2023] [Accepted: 03/07/2023] [Indexed: 04/05/2023] Open
Abstract
Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S ribosomal RNA (rRNA) 3' end maturation during late-stage 40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the genome-wide effects of eIF5B have not been studied at the single-nucleotide resolution in any organism, and 18S rRNA 3' end maturation is poorly understood in plants. Arabidopsis HOT3/eIF5B1 was found to promote development and heat stress acclimation by translational regulation, but its molecular function remained unknown. Here, we show that HOT3 is a late-stage ribosome biogenesis factor that facilitates 18S rRNA 3' end processing and is a translation initiation factor that globally impacts the transition from initiation to elongation. By developing and implementing 18S-ENDseq, we revealed previously unknown events in 18S rRNA 3' end maturation or metabolism. We quantitatively defined processing hotspots and identified adenylation as the prevalent nontemplated RNA addition at the 3' ends of pre-18S rRNAs. Aberrant 18S rRNA maturation in hot3 further activated RNA interference to generate RDR1- and DCL2/4-dependent risiRNAs mainly from a 3' portion of 18S rRNA. We further showed that risiRNAs in hot3 were predominantly localized in ribosome-free fractions and were not responsible for the 18S rRNA maturation or translation initiation defects in hot3. Our study uncovered the molecular function of HOT3/eIF5B1 in 18S rRNA maturation at the late 40S assembly stage and revealed the regulatory crosstalk among ribosome biogenesis, messenger RNA (mRNA) translation initiation, and siRNA biogenesis in plants.
Collapse
Affiliation(s)
- Runlai Hang
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Ye Xu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Xufeng Wang
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Hao Hu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Nora Flynn
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Chenjiang You
- College of Life Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong510642, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA92521
- School of Life Sciences, Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing100871, China
| |
Collapse
|
24
|
Noris E, Pegoraro M, Palzhoff S, Urrejola C, Wochner N, Kober S, Ruoff K, Matić S, Schnepf V, Weisshaar N, Wege C. Differential Effects of RNA-Dependent RNA Polymerase 6 (RDR6) Silencing on New and Old World Begomoviruses in Nicotiana benthamiana. Viruses 2023; 15:v15040919. [PMID: 37112899 PMCID: PMC10143181 DOI: 10.3390/v15040919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
RNA-dependent RNA polymerases (RDRs) are key players in the antiviral defence mediated by RNA silencing in plants. RDR6 is one of the major components of the process, regulating the infection of certain RNA viruses. To better clarify its function against DNA viruses, we analyzed the effect of RDR6 inactivation (RDR6i) in N. benthamiana plants on two phloem-limited begomoviruses, the bipartite Abutilon mosaic virus (AbMV) and the monopartite tomato yellow leaf curl Sardinia virus (TYLCSV). We observed exacerbated symptoms and DNA accumulation for the New World virus AbMV in RDR6i plants, varying with the plant growth temperature (ranging from 16 °C to 33 °C). However, for the TYLCSV of Old World origin, RDR6 depletion only affected symptom expression at elevated temperatures and to a minor extent; it did not affect the viral titre. The accumulation of viral siRNA differed between the two begomoviruses, being increased in RDR6i plants infected by AbMV but decreased in those infected by TYLCSV compared to wild-type plants. In situ hybridization revealed a 6.5-fold increase in the number of AbMV-infected nuclei in RDR6i plants but without egress from the phloem tissues. These results support the concept that begomoviruses adopt different strategies to counteract plant defences and that TYLCSV evades the functions exerted by RDR6 in this host.
Collapse
Affiliation(s)
- Emanuela Noris
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy
| | - Mattia Pegoraro
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy
| | - Sandra Palzhoff
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Catalina Urrejola
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Nicolai Wochner
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Sigi Kober
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Kerstin Ruoff
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Slavica Matić
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy
| | - Vera Schnepf
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Nina Weisshaar
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Christina Wege
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| |
Collapse
|
25
|
Ding SW. Transgene Silencing, RNA Interference, and the Antiviral Defense Mechanism Directed by Small Interfering RNAs. PHYTOPATHOLOGY 2023; 113:616-625. [PMID: 36441873 DOI: 10.1094/phyto-10-22-0358-ia] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
One important discovery in plant pathology over recent decades is the natural antiviral defense mechanism mediated by RNA interference (RNAi). In antiviral RNAi, virus infection triggers Dicer processing of virus-specific double-stranded RNA into small interfering RNAs (siRNAs). Frequently, further amplified by host enzyme and cofactors, these virus-derived siRNAs direct specific virus clearance in an Argonaute protein-containing effector complex. The siRNAs derived from viruses and viroids accumulate to very high levels during infection. Because they overlap extensively in nucleotide sequence, this allows for deep sequencing and bioinformatics assembly of total small RNAs for rapid discovery and identification of viruses and viroids. Antiviral RNAi acts as the primary defense mechanism against both RNA and DNA viruses in plants, yet viruses still successfully infect plants. They do so because all currently recognized plant viruses combat the RNAi response by encoding at least one protein as a viral suppressor of RNAi (VSR) required for infection, even though plant viruses have small genome sizes with a limited coding capacity. This review article will recapitulate the key findings that have revealed the genetic pathway for the biogenesis and antiviral activity of viral siRNAs and the specific role of VSRs in infection by antiviral RNAi suppression. Moreover, early pioneering studies on transgene silencing, RNAi, and virus-plant/virus-virus interactions paved the road to the discovery of antiviral RNAi.
Collapse
Affiliation(s)
- Shou-Wei Ding
- Department of Microbiology & Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA
| |
Collapse
|
26
|
Silencing suppressor protein PRT of rice tungro bacilliform virus interacts with the plant RNA silencing-related protein SGS3. Virology 2023; 581:71-80. [PMID: 36921478 DOI: 10.1016/j.virol.2023.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023]
Abstract
BACKGROUND Rice tungro bacilliform virus (RTBV) is a double stranded DNA containing virus which causes the devastating tungro disease of rice in association with an RNA virus, rice tungro spherical virus. RNA silencing is an evolutionarily conserved antiviral defence pathway in plants as well as in several classes of higher organisms. Many viruses, in turn, encode proteins which are termed Viral Suppressor of RNA Silencing (VSR) because they downregulate or suppress RNA silencing. RESULTS Using an RNA silencing suppressor assay we show that RTBV protease (PRT) acts as a mild VSR. A truncated version of PRT gene abolished the silencing suppression activity. We also show in planta interaction of PRT with the SGS3 protein of Solanum tuberosum and Arabidopsis thaliana using bimolecular fluorescence complementation assay (BIFC). Transient expression of PRT in Nicotiana benthamiana caused an increased accumulation of the begomovirus Sri Lankan cassava mosaic virus (SLCMV) DNA-A, which indicated a virulence function imparted on an unrelated virus. CONCLUSION The finding supports the idea that PRT acts as suppressor of RNA silencing and this action may be mediated by its interaction with SGS3.
Collapse
|
27
|
Vaucheret H. Epigenetic management of self and non-self: lessons from 40 years of transgenic plants. C R Biol 2023; 345:149-174. [PMID: 36847123 DOI: 10.5802/crbiol.96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 12/02/2022]
Abstract
Plant varieties exhibiting unstable or variegated phenotypes, or showing virus recovery have long remained a mystery. It is only with the development of transgenic plants 40 years ago that the epigenetic features underlying these phenomena were elucidated. Indeed, the study of transgenic plants that did not express the introduced sequences revealed that transgene loci sometimes undergo transcriptional gene silencing (TGS) or post-transcriptional gene silencing (PTGS) by activating epigenetic defenses that naturally control transposable elements, duplicated genes or viruses. Even when they do not trigger TGS or PTGS spontaneously, stably expressed transgenes driven by viral promoters set apart from endogenous genes in their epigenetic regulation. As a result, transgenes driven by viral promoters are capable of undergoing systemic PTGS throughout the plant, whereas endogenous genes can only undergo local PTGS in cells where RNA quality control is impaired. Together, these results indicate that the host genome distinguishes self from non-self at the epigenetic level, allowing PTGS to eliminate non-self, and preventing PTGS to become systemic and kill the plant when it is locally activated against deregulated self.
Collapse
|
28
|
Halder K, Chaudhuri A, Abdin MZ, Datta A. Tweaking the Small Non-Coding RNAs to Improve Desirable Traits in Plant. Int J Mol Sci 2023; 24:ijms24043143. [PMID: 36834556 PMCID: PMC9966754 DOI: 10.3390/ijms24043143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/09/2023] Open
Abstract
Plant transcriptome contains an enormous amount of non-coding RNAs (ncRNAs) that do not code for proteins but take part in regulating gene expression. Since their discovery in the early 1990s, much research has been conducted to elucidate their function in the gene regulatory network and their involvement in plants' response to biotic/abiotic stresses. Typically, 20-30 nucleotide-long small ncRNAs are a potential target for plant molecular breeders because of their agricultural importance. This review summarizes the current understanding of three major classes of small ncRNAs: short-interfering RNAs (siRNAs), microRNA (miRNA), and transacting siRNAs (tasiRNAs). Furthermore, their biogenesis, mode of action, and how they have been utilized to improve crop productivity and disease resistance are discussed here.
Collapse
Affiliation(s)
- Koushik Halder
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Abira Chaudhuri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Correspondence: (A.C.); (A.D.); Tel.: +91-1126742750 or +91-1126735119 (A.D.)
| | - Malik Z. Abdin
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Asis Datta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Correspondence: (A.C.); (A.D.); Tel.: +91-1126742750 or +91-1126735119 (A.D.)
| |
Collapse
|
29
|
Liu L, Wang H, Fu Y, Tang W, Zhao P, Ren Y, Liu Z, Wu K, Zhang X. Turnip crinkle virus-encoded suppressor of RNA silencing interacts with Arabidopsis SGS3 to enhance virus infection. MOLECULAR PLANT PATHOLOGY 2023; 24:154-166. [PMID: 36433724 PMCID: PMC9831285 DOI: 10.1111/mpp.13282] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 10/21/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Most plant viruses encode suppressors of RNA silencing (VSRs) to protect themselves from antiviral RNA silencing in host plants. The capsid protein (CP) of Turnip crinkle virus (TCV) is a well-characterized VSR, whereas SUPPRESSOR OF GENE SILENCING 3 (SGS3) is an important plant-encoded component of the RNA silencing pathways. Whether the VSR activity of TCV CP requires it to engage SGS3 in plant cells has yet to be investigated. Here, we report that TCV CP interacts with SGS3 of Arabidopsis in both yeast and plant cells. The interaction was identified with the yeast two-hybrid system, and corroborated with bimolecular fluorescence complementation and intracellular co-localization assays in Nicotiana benthamiana cells. While multiple partial TCV CP fragments could independently interact with SGS3, its hinge domain connecting the surface and protruding domains appears to be essential for this interaction. Conversely, SGS3 enlists its N-terminal domain and the XS rice gene X and SGS3 (XS) domain as the primary CP-interacting sites. Interestingly, SGS3 appears to stimulate TCV accumulation because viral RNA levels of a TCV mutant with low VSR activities decreased in the sgs3 knockout mutants, but increased in the SGS3-overexpressing transgenic plants. Transgenic Arabidopsis plants overexpressing TCV CP exhibited developmental abnormalities that resembled sgs3 knockout mutants and caused similar defects in the biogenesis of trans-acting small interfering RNAs. Our data suggest that TCV CP interacts with multiple RNA silencing pathway components that include SGS3, as well as previously reported DRB4 (dsRNA-binding protein 4) and AGO2 (ARGONAUTE protein 2), to achieve efficient suppression of RNA silencing-mediated antiviral defence.
Collapse
Affiliation(s)
- Linyu Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan ProvinceHainan Institute for Tropical Agriculture ResourcesHaikouChina
- School of Biological and Geographical SciencesYili Normal UniversityYiliChina
| | - Haiyan Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan ProvinceHainan Institute for Tropical Agriculture ResourcesHaikouChina
| | - Yan Fu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan ProvinceHainan Institute for Tropical Agriculture ResourcesHaikouChina
| | - Wen Tang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan ProvinceHainan Institute for Tropical Agriculture ResourcesHaikouChina
| | - Pingjuan Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan ProvinceHainan Institute for Tropical Agriculture ResourcesHaikouChina
| | - Yanli Ren
- School of Biological and Geographical SciencesYili Normal UniversityYiliChina
| | - Zhixin Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan ProvinceHainan Institute for Tropical Agriculture ResourcesHaikouChina
| | - Kunxin Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan ProvinceHainan Institute for Tropical Agriculture ResourcesHaikouChina
| | - Xiuchun Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan ProvinceHainan Institute for Tropical Agriculture ResourcesHaikouChina
| |
Collapse
|
30
|
Phase separation of SGS3 drives siRNA body formation and promotes endogenous gene silencing. Cell Rep 2023; 42:111985. [PMID: 36640363 DOI: 10.1016/j.celrep.2022.111985] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/26/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
The generation of small interfering RNA (siRNA) involves many RNA processing components, including SUPPRESSOR OF GENE SILENCING 3 (SGS3), RNA-DEPENDENT RNA POLYMERASE 6 (RDR6), and DICER-LIKE proteins (DCLs). Nonetheless, how these components are coordinated to produce siRNAs is unclear. Here, we show that SGS3 forms condensates via phase separation in vivo and in vitro. SGS3 interacts with RDR6 and drives it to form siRNA bodies in cytoplasm, which is promoted by SGS3-targeted RNAs. Disrupting SGS3 phase separation abrogates siRNA body assembly and siRNA biogenesis, whereas coexpression of SGS3 and RDR6 induces siRNA body formation in tobacco and yeast cells. Dysfunction in translation and mRNA decay increases the number of siRNA bodies, whereas DCL2/4 mutations enhance their size. Purification of SGS3 condensates identifies numerous RNA-binding proteins and siRNA processing components. Together, our findings reveal that SGS3 phase separation-mediated formation of siRNA bodies is essential for siRNA production and gene silencing.
Collapse
|
31
|
Sehki H, Yu A, Elmayan T, Vaucheret H. TYMV and TRV infect Arabidopsis thaliana by expressing weak suppressors of RNA silencing and inducing host RNASE THREE LIKE1. PLoS Pathog 2023; 19:e1010482. [PMID: 36696453 PMCID: PMC9901757 DOI: 10.1371/journal.ppat.1010482] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 02/06/2023] [Accepted: 01/10/2023] [Indexed: 01/26/2023] Open
Abstract
Post-Transcriptional Gene Silencing (PTGS) is a defense mechanism that targets invading nucleic acids of endogenous (transposons) or exogenous (pathogens, transgenes) origins. During plant infection by viruses, virus-derived primary siRNAs target viral RNAs, resulting in both destruction of single-stranded viral RNAs (execution step) and production of secondary siRNAs (amplification step), which maximizes the plant defense. As a counter-defense, viruses express proteins referred to as Viral Suppressor of RNA silencing (VSR). Some viruses express VSRs that totally inhibit PTGS, whereas other viruses express VSRs that have limited effect. Here we show that infection with the Turnip yellow mosaic virus (TYMV) is enhanced in Arabidopsis ago1, ago2 and dcl4 mutants, which are impaired in the execution of PTGS, but not in dcl2, rdr1 and rdr6 mutants, which are impaired in the amplification of PTGS. Consistently, we show that the TYMV VSR P69 localizes in siRNA-bodies, which are the site of production of secondary siRNAs, and limits PTGS amplification. Moreover, TYMV induces the production of the host enzyme RNASE THREE-LIKE 1 (RTL1) to further reduce siRNA accumulation. Infection with the Tobacco rattle virus (TRV), which also encodes a VSR limiting PTGS amplification, induces RTL1 as well to reduce siRNA accumulation and promote infection. Together, these results suggest that RTL1 could be considered as a host susceptibility gene that is induced by viruses as a strategy to further limit the plant PTGS defense when VSRs are insufficient.
Collapse
Affiliation(s)
- Hayat Sehki
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Agnès Yu
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Taline Elmayan
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- * E-mail:
| |
Collapse
|
32
|
Feng C, Torimaru K, Lim MYT, Chak LL, Shiimori M, Tsuji K, Tanaka T, Iida J, Okamura K. A novel eukaryotic RdRP-dependent small RNA pathway represses antiviral immunity by controlling an ERK pathway component in the black-legged tick. PLoS One 2023; 18:e0281195. [PMID: 36996253 PMCID: PMC10062562 DOI: 10.1371/journal.pone.0281195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 01/17/2023] [Indexed: 04/01/2023] Open
Abstract
Small regulatory RNAs (sRNAs) are involved in antiviral defense and gene regulation. Although roles of RNA-dependent RNA Polymerases (RdRPs) in sRNA biology are extensively studied in nematodes, plants and fungi, understanding of RdRP homologs in other animals is still lacking. Here, we study sRNAs in the ISE6 cell line, which is derived from the black-legged tick, an important vector of human and animal pathogens. We find abundant classes of ~22nt sRNAs that require specific combinations of RdRPs and sRNA effector proteins (Argonautes or AGOs). RdRP1-dependent sRNAs possess 5'-monophosphates and are mainly derived from RNA polymerase III-transcribed genes and repetitive elements. Knockdown of some RdRP homologs misregulates genes including RNAi-related genes and the regulator of immune response Dsor1. Sensor assays demonstrate that Dsor1 is downregulated by RdRP1 through the 3'UTR that contains a target site of RdRP1-dependent repeat-derived sRNAs. Consistent with viral gene repression by the RNAi mechanism using virus-derived small interfering RNAs, viral transcripts are upregulated by AGO knockdown. On the other hand, RdRP1 knockdown unexpectedly results in downregulation of viral transcripts. This effect is dependent on Dsor1, suggesting that antiviral immunity is enhanced by RdRP1 knockdown through Dsor1 upregulation. We propose that tick sRNA pathways control multiple aspects of immune response via RNAi and regulation of signaling pathways.
Collapse
Affiliation(s)
- Canran Feng
- Nara Institute of Science and Technology, Nara, Japan
| | | | - Mandy Yu Theng Lim
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Li-Ling Chak
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Singapore
| | | | - Kosuke Tsuji
- Nara Institute of Science and Technology, Nara, Japan
| | - Tetsuya Tanaka
- Joint Faculty of Veterinary Medicine, Laboratory of Infectious Diseases, Kagoshima University, Kagoshima, Japan
| | - Junko Iida
- Nara Institute of Science and Technology, Nara, Japan
| | - Katsutomo Okamura
- Nara Institute of Science and Technology, Nara, Japan
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
33
|
Jay F, Brioudes F, Voinnet O. A contemporary reassessment of the enhanced transient expression system based on the tombusviral silencing suppressor protein P19. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:186-204. [PMID: 36403224 PMCID: PMC10107623 DOI: 10.1111/tpj.16032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/27/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Transient transgenic expression accelerates pharming and facilitates protein studies in plants. One embodiment of the approach involves leaf infiltration of Agrobacterium strains whose T-DNA is engineered with the gene(s) of interest. However, gene expression during 'agro-infiltration' is intrinsically and universally impeded by the onset of post-transcriptional gene silencing (PTGS). Nearly 20 years ago, a simple method was developed, whereby co-expression of the tombusvirus-encoded P19 protein suppresses PTGS and thus enhances transient gene expression. Yet, how PTGS is activated and suppressed by P19 during the process has remained unclear to date. Here, we address these intertwined questions in a manner also rationalizing how vastly increased protein yields are achieved using a minimal viral replicon as a transient gene expression vector. We also explore, in side-by-side analyses, why some proteins do not accumulate to the expected high levels in the assay, despite vastly increased mRNA levels. We validate that enhanced co-expression of multiple constructs is achieved within the same transformed cells, and illustrate how the P19 system allows rapid protein purification for optimized downstream in vitro applications. Finally, we assess the suitability of the P19 system for subcellular localization studies - an originally unanticipated, yet increasingly popular application - and uncover shortcomings of this specific implement. In revisiting the P19 system using contemporary knowledge, this study sheds light onto its hitherto poorly understood mechanisms while further illustrating its versatility but also some of its limits.
Collapse
Affiliation(s)
- Florence Jay
- Department of BiologySwiss Federal Institute of Technology (ETH‐Zürich)Universitätstrasse 28092ZürichSwitzerland
| | - Florian Brioudes
- Department of BiologySwiss Federal Institute of Technology (ETH‐Zürich)Universitätstrasse 28092ZürichSwitzerland
| | - Olivier Voinnet
- Department of BiologySwiss Federal Institute of Technology (ETH‐Zürich)Universitätstrasse 28092ZürichSwitzerland
| |
Collapse
|
34
|
Minow MAA, Coneva V, Lesy V, Misyura M, Colasanti J. Plant gene silencing signals move from the phloem to influence gene expression in shoot apical meristems. BMC PLANT BIOLOGY 2022; 22:606. [PMID: 36550422 PMCID: PMC9783409 DOI: 10.1186/s12870-022-03998-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Small RNAs (sRNA) are potent regulators of gene expression that can diffuse short distances between cells and move long distances through plant vasculature. However, the degree to which sRNA silencing signals can move from the phloem to the shoot apical meristem (SAM) remains unclear. RESULTS Two independent transgenic approaches were used to examine whether phloem sRNA silencing can reach different domains of the SAM and silence SAM-expressed genes. First, the phloem companion-cell specific SUCROSE-PROTON SYMPORTER2 (SUC2) promoter was used to drive expression of an inverted repeat to target the FD gene, an exclusively SAM-localized floral regulator. Second, the SUC2 promoter was used to express an artificial microRNA (aMiR) designed to target a synthetic CLAVATA3 (CLV3) transgene in SAM stem cells. Both phloem silencing signals phenocopied the loss of function of their targets and altered target gene expression suggesting that a phloem-to-SAM silencing communication axis exists, connecting distal regions of the plant to SAM stem cells. CONCLUSIONS Demonstration of phloem-to-SAM silencing reveals a regulatory link between somatic sRNA expressed in distal regions of the plant and the growing shoot. Since the SAM stem cells ultimately produce the gametes, we discuss the intriguing possibility that phloem-to-SAM sRNA trafficking could allow transient somatic sRNA expression to manifest stable, transgenerational epigenetic changes.
Collapse
Affiliation(s)
- Mark A. A. Minow
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
| | - Viktoriya Coneva
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
| | - Victoria Lesy
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
| | - Max Misyura
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
| | - Joseph Colasanti
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
| |
Collapse
|
35
|
H. El-Sappah A, Qi S, A. Soaud S, Huang Q, M. Saleh A, A. S. Abourehab M, Wan L, Cheng GT, Liu J, Ihtisham M, Noor Z, Rouf Mir R, Zhao X, Yan K, Abbas M, Li J. Natural resistance of tomato plants to Tomato yellow leaf curl virus. FRONTIERS IN PLANT SCIENCE 2022; 13:1081549. [PMID: 36600922 PMCID: PMC9807178 DOI: 10.3389/fpls.2022.1081549] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Tomato yellow leaf curl virus (TYLCV) is one of the most harmful afflictions in the world that affects tomato growth and production. Six regular antagonistic genes (Ty-1, Ty-2, Ty-3, Ty-4, ty-5, and Ty-6) have been transferred from wild germplasms to commercial cultivars as TYLCV protections. With Ty-1 serving as an appropriate source of TYLCV resistance, only Ty-1, Ty-2, and Ty-3 displayed substantial levels of opposition in a few strains. It has been possible to clone three TYLCV opposition genes (Ty-1/Ty-3, Ty-2, and ty-5) that target three antiviral safety mechanisms. However, it significantly impacts obtaining permanent resistance to TYLCV, trying to maintain opposition whenever possible, and spreading opposition globally. Utilizing novel methods, such as using resistance genes and identifying new resistance resources, protects against TYLCV in tomato production. To facilitate the breeders make an informed decision and testing methods for TYLCV blockage, this study highlights the portrayal of typical obstruction genes, common opposition sources, and subatomic indicators. The main goal is to provide a fictitious starting point for the identification and application of resistance genes as well as the maturation of tomato varieties that are TYLCV-resistant.
Collapse
Affiliation(s)
- Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Shiming Qi
- College of Agriculture and Ecological Engineering, Hexi University, Zhangye, China
| | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Qiulan Huang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Alaa M. Saleh
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | | | - Lingyun Wan
- Key Laboratory of Guangxi for High-quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Guo-ting Cheng
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Science, Yan’an University, Yan’an, China
| | - Jingyi Liu
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Muhammad Ihtisham
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Zarqa Noor
- School of Chemical Engineering Beijing Institute of Technology, Beijing, China
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST–Kashmir, Sopore, India
| | - Xin Zhao
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Kuan Yan
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Jia Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| |
Collapse
|
36
|
Orchid fleck dichorhavirus movement protein shows RNA silencing suppressor activity. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To counteract RNA interference-mediated antiviral defence, virus genomes evolved to express proteins that inhibit this plant defence mechanism. Using six independent biological approaches, we show that orchid fleck dichorhavirus citrus strain (OFV-citrus) movement protein (MP) may act as a viral suppressor of RNA silencing (VSR). By using the alfalfa mosaic virus (AMV) RNA 3 expression vector, it was observed that the MP triggered necrosis response in transgenic tobacco leaves and increased the viral RNA (vRNA) accumulation. The use of the potato virus X (PVX) expression system revealed that the cis expression of MP increased both the severity of the PVX infection and the accumulation of PVX RNAs, further supporting that MP could act as an RNA silencing suppressor (RSS). From the analysis of the RSS-defective turnip crinkle virus (TCV), we do not find local RSS activity for MP, suggesting a link between MP suppressor activity and the prevention of systemic silencing. In the analysis of local suppressive activity using the GFP-based agroinfiltration assay in Nicotiana benthamiana (16 c line), we do not identify local RSS activity for the five OFV RNA1-encoded proteins. However, when evaluating the small interfering RNA (siRNA) accumulation, we find that the expression of MP significantly reduces the accumulation of GFP-derived siRNA. Finally, we examine whether the MP can prevent systemic silencing in 16c plants. Our findings show that MP inhibits the long-distance spread of RNA silencing, but does not affect the short-distance spread. Together, our findings indicate that MP is part of OFV’s counter-defence mechanism, acting mainly in the prevention of systemic long-distance silencing. This work presents the first report of a VSR for a member of the genus Dichorhavirus.
Collapse
|
37
|
Singh M, Kumar M, Califf KE, Cigan AM. Transcriptional gene silencing in bread wheat (Triticum aestivum L.) and its application to regulate male fertility for hybrid seed production. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2149-2158. [PMID: 35869675 PMCID: PMC9616518 DOI: 10.1111/pbi.13895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/06/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Transcriptional gene silencing (TGS) can offer a straightforward tool for functional analysis of plant genes, particularly in polyploid species such as wheat, where genetic redundancy poses a challenge in applying mutagenesis approaches, including CRISPR gene editing. In this study, we demonstrate efficient TGS in wheat, mediated by constitutive RNA expression of a promoter inverted repeat (pIR). pIR-mediated TGS of two anther-specific genes, TaMs45 and TaMs1, abolished their function resulting in male sterility. Whilst TGS of TaMs45 required transcriptional silencing of all three homoeologs, a B-genome-specific pIR for TaMs1 was sufficient to confer male sterility. We further show that the pIRs effect TGS of TaMs45 gene through DNA methylation of homologous promoter sequence, successfully suppressing transcription of all three homoeologs. Applying pIR-mediated TGS in wheat, we have generated a dominant male fertility system for production of hybrid seed and demonstrated the efficacy of this system under greenhouse and field conditions. This report describes the first successful TGS in wheat, whilst providing a dominant negative approach as alternative to gene knockout strategies for hybrid wheat breeding and seed production.
Collapse
Affiliation(s)
| | | | | | - A. Mark Cigan
- Corteva AgriscienceJohnstonIowaUSA
- Present address:
Genus plcDeForestWisconsinUSA
| |
Collapse
|
38
|
Zhang H, Gao J, Chen J, Peng Y, Han Z. RNA-dependent RNA polymerase could extend the lasting validity period of exogenous dsRNA. PEST MANAGEMENT SCIENCE 2022; 78:4569-4578. [PMID: 35831266 DOI: 10.1002/ps.7076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 07/04/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Previous studies have found that pesticide double-stranded (ds)RNA usually has a long-lasting validity period in plants. However, it is uncertain if any factors in plants could extend dsRNA duration. It has been reported that RNA-dependent RNA polymerases (RdRP) in plants and some other eukaryotes could catalyze RNA amplification and be involved in RNAi (interference). Thus, this study evaluated the effect of RdRP on the tissue content, activity, and duration of exogenous dsRNA. RESULTS We found that RdRP knockdown in Arabidopsis thaliana had no significant effect on tissue contents of reporter dsRNA parent molecules (8.91% reduction), but it caused significant decrease in the tissue contents of derived short fragments of 200, 120 and 59 bp tested (51.22%, 52.83% and 59.35%, respectively). Aphid inoculation tests showed that the same dose of insecticidal dsAgZFP exhibited a significantly lower lethal effect (mortality 58.8%) in the plants with RdRP knockdown than in the control plants with normal RdRP (86.0%). For Caenorhabditis elegans, the worms treated simultaneously with dsRdRP and reporter dsRNA had similar body contents to reporter dsRNA parent molecules and its long-fragment derivative (200 bp) as the control (1.28- and 1.07-fold greater, respectively). However, 120- and 59-bp short-fragment derivatives were significantly reduced by 28.78% and 59.84%, respectively, which also diminished faster in the descendants. CONCLUSIONS We conclude that RdRP could significantly enhance the tissue content of dsRNA derivatives by catalyzing amplification, thus improving dsRNA activity and extending its lasting validity period. Otherwise, RNAi by exogenous dsRNA was proven to be noninheritable in A. thaliana. This work confirmed the merit of dsRNA as a plant protectant. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
- Hainan Zhang
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jing Gao
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jiasheng Chen
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yue Peng
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhaojun Han
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
39
|
Kumar M, Tripathi PK, Ayzenshtat D, Marko A, Forotan Z, Bocobza SE. Increased rates of gene-editing events using a simplified RNAi configuration designed to reduce gene silencing. PLANT CELL REPORTS 2022; 41:1987-2003. [PMID: 35849200 DOI: 10.1007/s00299-022-02903-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
An optimal RNAi configuration that could restrict gene expression most efficiently was determined. This approach was also used to target PTGS and yielded higher rates of gene-editing events. Although it was characterized long ago, transgene silencing still strongly impairs transgene overexpression, and thus is a major barrier to plant crop gene-editing. The development of strategies that could prevent transgene silencing is therefore essential to the success of gene editing assays. Transgene silencing occurs via the RNA silencing process, which regulates the expression of essential genes and protects the plant from viral infections. The RNA silencing machinery thereby controls central biological processes such as growth, development, genome integrity, and stress resistance. RNA silencing is typically induced by aberrant RNA, that may lack 5' or 3' processing, or may consist in double-stranded or hairpin RNA, and involves DICER and ARGONAUTE family proteins. In this study, RNAi inducing constructs were designed in eleven different configurations and were evaluated for their capacity to induce silencing in Nicotiana spp. using transient and stable transformation assays. Using reporter genes, it was found that the overexpression of a hairpin consisting of a forward tandem inverted repeat that started with an ATG and that was not followed downstream by a transcription terminator, could downregulate gene expression most potently. Furthermore, using this method, the downregulation of the NtSGS3 gene caused a significant increase in transgene expression both in transient and stable transformation assays. This SGS3 silencing approach was also employed in gene-editing assays and caused higher rates of gene-editing events. Taken together, these findings suggested the optimal genetic configuration to cause RNA silencing and showed that this strategy may be used to restrict PTGS during gene-editing experiments.
Collapse
Affiliation(s)
- Manoj Kumar
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Pankaj Kumar Tripathi
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Dana Ayzenshtat
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Adar Marko
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Zohar Forotan
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Samuel E Bocobza
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel.
| |
Collapse
|
40
|
Comprehensive In Silico Analysis of RNA Silencing-Related Genes and Their Regulatory Elements in Wheat (Triticum aestivum L.). BIOMED RESEARCH INTERNATIONAL 2022; 2022:4955209. [PMID: 36177060 PMCID: PMC9513535 DOI: 10.1155/2022/4955209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022]
Abstract
Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are known as the three major gene families that act as the critical components of RNA interference or silencing mechanisms through the noncoding small RNA molecules (miRNA and siRNA) to regulate the expressions of protein-coding genes in eukaryotic organisms. However, most of their characteristics including structures, chromosomal location, subcellular locations, regulatory elements, and gene networking were not rigorously studied. Our analysis identified 7 TaDCL, 39 TaAGO, and 16 TaRDR genes as RNA interference (RNAi) genes from the wheat genome. Phylogenetic analysis of predicted RNAi proteins with the RNAi proteins of Arabidopsis and rice showed that the predicted proteins of TaDCL, TaAGO, and TaRDR groups are clustered into four, eight, and four subgroups, respectively. Domain, 3D protein structure, motif, and exon-intron structure analyses showed that these proteins conserve identical characteristics within groups and maintain differences between groups. The nonsynonymous/synonymous mutation ratio (Ka/Ks) < 1 suggested that these protein sequences conserve some purifying functions. RNAi genes networking with TFs revealed that ERF, MIKC-MADS, C2H2, BBR-BPC, MYB, and Dof are the key transcriptional regulators of the predicted RNAi-related genes. The cis-regulatory element (CREs) analysis detected some important CREs of RNAi genes that are significantly associated with light, stress, and hormone responses. Expression analysis based on an online database exhibited that almost all of the predicted RNAi genes are expressed in different tissues and organs. A case-control study from the gene expression level showed that some RNAi genes significantly responded to the drought and heat stresses. Overall results would therefore provide an excellent basis for in-depth molecular investigation of these genes and their regulatory elements for wheat crop improvement against different stressors.
Collapse
|
41
|
Cui R, Li H, Zhao J, Li X, Gan J, Ma J. Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1. Nucleic Acids Res 2022; 50:10169-10186. [PMID: 36039765 PMCID: PMC9508822 DOI: 10.1093/nar/gkac727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/01/2022] [Accepted: 08/27/2022] [Indexed: 11/19/2022] Open
Abstract
Neurospora crassa protein QDE-1, a member of the two-barrel polymerase superfamily, possesses both DNA- and RNA-dependent RNA polymerase (DdRP and RdRP) activities. The dual activities are essential for the production of double-stranded RNAs (dsRNAs), the precursors of small interfering RNAs (siRNAs) in N. crassa. Here, we report five complex structures of N-terminal truncated QDE-1 (QDE-1ΔN), representing four different reaction states: DNA/RNA-templated elongation, the de novo initiation of RNA synthesis, the first step of nucleotide condensation during de novo initiation and initial NTP loading. The template strand is aligned by a bridge-helix and double-psi beta-barrels 2 (DPBB2), the RNA product is held by DPBB1 and the slab domain. The DNA template unpairs with the RNA product at position –7, but the RNA template remains paired. The NTP analog coordinates with cations and is precisely positioned at the addition site by a rigid trigger loop and a proline-containing loop in the active center. The unique C-terminal tail from the QDE-1 dimer partner inserts into the substrate-binding cleft and plays regulatory roles in RNA synthesis. Collectively, this work elucidates the conserved mechanisms for DNA/RNA-dependent dual activities by QDE-1 and other two-barrel polymerase superfamily members.
Collapse
Affiliation(s)
- Ruixue Cui
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hao Li
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jin Zhao
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xuhang Li
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinbiao Ma
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| |
Collapse
|
42
|
RLL5, an F-box-containing protein, involved in preventing transgene silencing and in maintaining global DNA methylation in Arabidopsis. Biochem Biophys Res Commun 2022; 609:1-8. [DOI: 10.1016/j.bbrc.2022.03.135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 12/30/2022]
|
43
|
Liu S, Chen M, Li R, Li WX, Gal-On A, Jia Z, Ding SW. Identification of positive and negative regulators of antiviral RNA interference in Arabidopsis thaliana. Nat Commun 2022; 13:2994. [PMID: 35637208 PMCID: PMC9151786 DOI: 10.1038/s41467-022-30771-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 05/18/2022] [Indexed: 02/06/2023] Open
Abstract
Virus-host coevolution often drives virus immune escape. However, it remains unknown whether natural variations of plant virus resistance are enriched in genes of RNA interference (RNAi) pathway known to confer essential antiviral defense in plants. Here, we report two genome-wide association study screens to interrogate natural variation among wild-collected Arabidopsis thaliana accessions in quantitative resistance to the endemic cucumber mosaic virus (CMV). We demonstrate that the highest-ranked gene significantly associated with resistance from both screens acts to regulate antiviral RNAi in ecotype Columbia-0. One gene, corresponding to Reduced Dormancy 5 (RDO5), enhances resistance by promoting amplification of the virus-derived small interfering RNAs (vsiRNAs). Interestingly, the second gene, designated Antiviral RNAi Regulator 1 (VIR1), dampens antiviral RNAi so its genetic inactivation by CRISPR/Cas9 editing enhances both vsiRNA production and CMV resistance. Our findings identify positive and negative regulators of the antiviral RNAi defense that may play important roles in virus-host coevolution.
Collapse
Affiliation(s)
- Si Liu
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, USA
| | - Meijuan Chen
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, USA
| | - Ruidong Li
- Department of Botany & Plant Sciences, University of California, Riverside, CA, USA
| | - Wan-Xiang Li
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, USA
| | - Amit Gal-On
- Department of Plant Pathology and Weed Science, Volcani Center, Rishon LeZion, 7528809, Israel
| | - Zhenyu Jia
- Department of Botany & Plant Sciences, University of California, Riverside, CA, USA.
| | - Shou-Wei Ding
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, USA.
| |
Collapse
|
44
|
Hotspot siRNA Confers Plant Resistance against Viral Infection. BIOLOGY 2022; 11:biology11050714. [PMID: 35625441 PMCID: PMC9138956 DOI: 10.3390/biology11050714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary A hallmark of antiviral RNAi is the production of viral siRNA (vsiRNA). Profiling of vsiRNAs indicates that certain hotspot regions of viral genome or transcribed viral RNAs are more prone to RNAi-mediated cleavage. However, the biological relevance of hotspot vsiRNAs to the host innate defence remains to be elucidated. Here, we show that direct targeting a hotspot by synthetic vsiRNA confers plant resistance to virus infection. Hotspot and coldspot vsiRNAs, based on vsiRNA profile of the African cassava mosaic virus (ACMV), were synthesised. However, only the double-stranded hotspot vsiRNA protected plants from ACMV infection with undetectable levels of viral DNA replication and viral mRNA. We further demonstrated that the hotspot vsiRNA-mediated virus resistance had a threshold effect and required an active RDR6. These data show that hotspot vsiRNAs bear a functional significance on antiviral RNAi, suggesting that they may have the potential as exogenous protection agents for controlling destructive plant viral diseases. Abstract A hallmark of antiviral RNA interference (RNAi) is the production of viral small interfering RNA (vsiRNA). Profiling of vsiRNAs indicates that certain regions of viral RNA genome or transcribed viral RNA, dubbed vsiRNA hotspots, are more prone to RNAi-mediated cleavage for vsiRNA biogenesis. However, the biological relevance of hotspot vsiRNAs to the host innate defence against pathogens remains to be elucidated. Here, we show that direct targeting a hotspot by a synthetic vsiRNA confers host resistance to virus infection. Using Northern blotting and RNAseq, we obtained a profile of vsiRNAs of the African cassava mosaic virus (ACMV), a single-stranded DNA virus. Sense and anti-sense strands of small RNAs corresponding to a hotspot and a coldspot vsiRNA were synthesised. Co-inoculation of Nicotiana benthamiana with the double-stranded hotspot siRNA protected plants from ACMV infection, where viral DNA replication and accumulation of viral mRNA were undetectable. The sense or anti-sense strand of this hotspot vsiRNA, and the coldspot vsiRNA in both double-stranded and single-stranded formats possessed no activity in viral protection. We further demonstrated that the hotspot vsiRNA-mediated virus resistance had a threshold effect and required an active RDR6. These data show that hotspot vsiRNAs bear a functional significance on antiviral RNAi, suggesting that they may have the potential as an exogenous protection agent for controlling destructive viral diseases in plants.
Collapse
|
45
|
Chen J, Zheng L, Shi X, Zhang S, Tan X, Zhao X, Lu B, Ye Q, Miao S, Liu Y, Zhang D. The nonstructural protein NSs encoded by tomato zonate spot virus suppresses RNA silencing by interacting with NbSGS3. MOLECULAR PLANT PATHOLOGY 2022; 23:707-719. [PMID: 35184365 PMCID: PMC8995058 DOI: 10.1111/mpp.13192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 05/21/2023]
Abstract
Viral suppressors of RNA silencing (VSRs) are encoded by diverse viruses to counteract the RNA silencing-mediated defence mounted by the virus-infected host cells. In this study, we identified the NSs protein encoded by tomato zonate spot virus (TZSV) as a potent VSR, and used a potato virus X (PVX)-based heterologous expression system to demonstrate TZSV NSs as a viral pathogenicity factor that intensified PVX symptoms in Nicotiana benthamiana. We then used a yeast two-hybrid screen to identify the suppressor of gene silencing 3 protein of N. benthamiana (NbSGS3), a known component of the plant RNA silencing pathway, as an interaction partner of TZSV NSs. We verified this interaction in plant cells with bimolecular fluorescence complementation, subcellular colocalization, and co-immunoprecipitation. We further revealed that the NSs-NbSGS3 interaction correlated with the VSR activity of TZSV NSs. TZSV NSs reduced the concentration of NbSGS3 protein in plant cells, probably through the ubiquitination and autophagy pathways. Interestingly, TZSV infection, but not NSs overexpression, significantly up-regulated the NbSGS3 transcript levels. Our data indicate that TZSV NSs suppresses RNA silencing of the host plant and enhances TZSV pathogenicity through its interaction with NbSGS3. This study reveals a novel molecular mechanism of NSs-mediated suppression of plant host antiviral defence.
Collapse
Affiliation(s)
- Jianbin Chen
- Longping BranchGraduate School of Hunan UniversityChangshaChina
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangshaChina
| | - Limin Zheng
- Longping BranchGraduate School of Hunan UniversityChangshaChina
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangshaChina
| | - Xiaobin Shi
- Longping BranchGraduate School of Hunan UniversityChangshaChina
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangshaChina
| | - Songbai Zhang
- Longping BranchGraduate School of Hunan UniversityChangshaChina
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangshaChina
| | - Xinqiu Tan
- Longping BranchGraduate School of Hunan UniversityChangshaChina
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangshaChina
| | - Xingyue Zhao
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangshaChina
| | - Bingxin Lu
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangshaChina
| | - Qian Ye
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangshaChina
| | - Shuyue Miao
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangshaChina
| | - Yong Liu
- Longping BranchGraduate School of Hunan UniversityChangshaChina
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangshaChina
| | - Deyong Zhang
- Longping BranchGraduate School of Hunan UniversityChangshaChina
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangshaChina
| |
Collapse
|
46
|
Lin CS, Hsu CT, Yuan YH, Zheng PX, Wu FH, Cheng QW, Wu YL, Wu TL, Lin S, Yue JJ, Cheng YH, Lin SI, Shih MC, Sheen J, Lin YC. DNA-free CRISPR-Cas9 gene editing of wild tetraploid tomato Solanum peruvianum using protoplast regeneration. PLANT PHYSIOLOGY 2022; 188:1917-1930. [PMID: 35088855 PMCID: PMC8968427 DOI: 10.1093/plphys/kiac022] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/10/2021] [Indexed: 05/24/2023]
Abstract
Wild tomatoes (Solanum peruvianum) are important genomic resources for tomato research and breeding. Development of a foreign DNA-free clustered regularly interspaced short palindromic repeat (CRISPR)-Cas delivery system has potential to mitigate public concern about genetically modified organisms. Here, we established a DNA-free CRISPR-Cas9 genome editing system based on an optimized protoplast regeneration protocol of S. peruvianum, an important resource for tomato introgression breeding. We generated mutants for genes involved in small interfering RNAs biogenesis, RNA-DEPENDENT RNA POLYMERASE 6 (SpRDR6), and SUPPRESSOR OF GENE SILENCING 3 (SpSGS3); pathogen-related peptide precursors, PATHOGENESIS-RELATED PROTEIN-1 (SpPR-1) and PROSYSTEMIN (SpProSys); and fungal resistance (MILDEW RESISTANT LOCUS O, SpMlo1) using diploid or tetraploid protoplasts derived from in vitro-grown shoots. The ploidy level of these regenerants was not affected by PEG-Ca2+-mediated transfection, CRISPR reagents, or the target genes. By karyotyping and whole genome sequencing analysis, we confirmed that CRISPR-Cas9 editing did not introduce chromosomal changes or unintended genome editing sites. All mutated genes in both diploid and tetraploid regenerants were heritable in the next generation. spsgs3 null T0 regenerants and sprdr6 null T1 progeny had wiry, sterile phenotypes in both diploid and tetraploid lines. The sterility of the spsgs3 null mutant was partially rescued, and fruits were obtained by grafting to wild-type (WT) stock and pollination with WT pollen. The resulting seeds contained the mutated alleles. Tomato yellow leaf curl virus proliferated at higher levels in spsgs3 and sprdr6 mutants than in the WT. Therefore, this protoplast regeneration technique should greatly facilitate tomato polyploidization and enable the use of CRISPR-Cas for S. peruvianum domestication and tomato breeding.
Collapse
Affiliation(s)
| | - Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Hsuan Yuan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Po-Xing Zheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Fu-Hui Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Qiao-Wei Cheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Lin Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Ting-Li Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Steven Lin
- Institute of Biochemistry, Academia Sinica, Taipei 115, Taiwan
| | - Jin-Jun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311, China
| | - Ying-Huey Cheng
- Plant Pathology Division, Taiwan Agricultural Research Institute, Taichung 413, Taiwan
| | - Shu-I Lin
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei 106, Taiwan
| | | | | | | |
Collapse
|
47
|
Jin L, Chen M, Xiang M, Guo Z. RNAi-Based Antiviral Innate Immunity in Plants. Viruses 2022; 14:v14020432. [PMID: 35216025 PMCID: PMC8875485 DOI: 10.3390/v14020432] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/13/2022] Open
Abstract
Multiple antiviral immunities were developed to defend against viral infection in hosts. RNA interference (RNAi)-based antiviral innate immunity is evolutionarily conserved in eukaryotes and plays a vital role against all types of viruses. During the arms race between the host and virus, many viruses evolve viral suppressors of RNA silencing (VSRs) to inhibit antiviral innate immunity. Here, we reviewed the mechanism at different stages in RNAi-based antiviral innate immunity in plants and the counteractions of various VSRs, mainly upon infection of RNA viruses in model plant Arabidopsis. Some critical challenges in the field were also proposed, and we think that further elucidating conserved antiviral innate immunity may convey a broad spectrum of antiviral strategies to prevent viral diseases in the future.
Collapse
|
48
|
FDDM1 and FDDM2, Two SGS3-like Proteins, Function as a Complex to Affect DNA Methylation in Arabidopsis. Genes (Basel) 2022; 13:genes13020339. [PMID: 35205382 PMCID: PMC8872474 DOI: 10.3390/genes13020339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 12/10/2022] Open
Abstract
DNA methylation is an important epigenetic modification required for the specific regulation of gene expression and the maintenance of genome stability in plants and animals. However, the mechanism of DNA demethylation remains largely unknown. Here, we show that two SGS3-like proteins, FACTOR OF DNA DEMETHYLATION 1 (FDDM1) and FDDM2, negatively affect the DNA methylation levels at ROS1-dependend DNA loci in Arabidopsis. FDDM1 binds dsRNAs with 5′ overhangs through its XS (rice gene X and SGS3) domain and forms a heterodimer with FDDM2 through its XH (rice gene X Homology) domain. A lack of FDDM1 or FDDM2 increased DNA methylation levels at several ROS1-dependent DNA loci. However, FDDM1 and FDDM2 may not have an additive effect on DNA methylation levels. Moreover, the XS and XH domains are required for the function of FDDM1. Taken together, these results suggest that FDDM1 and FDDM2 act as a heterodimer to positively modulate DNA demethylation. Our finding extends the function of plant-specific SGS3-like proteins.
Collapse
|
49
|
Zhang X, Rashid MO, Zhao TY, Li YY, He MJ, Wang Y, Li DW, Yu JL, Han CG. The Carboxyl Terminal Regions of P0 Protein Are Required for Systemic Infections of Poleroviruses. Int J Mol Sci 2022; 23:1945. [PMID: 35216065 PMCID: PMC8875975 DOI: 10.3390/ijms23041945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/27/2022] [Accepted: 02/04/2022] [Indexed: 02/04/2023] Open
Abstract
P0 proteins encoded by poleroviruses Brassica yellows virus (BrYV) and Potato leafroll virus (PLRV) are viral suppressors of RNA silencing (VSR) involved in abolishing host RNA silencing to assist viral infection. However, other roles that P0 proteins play in virus infection remain unclear. Here, we found that C-terminal truncation of P0 resulted in compromised systemic infection of BrYV and PLRV. C-terminal truncation affected systemic but not local VSR activities of P0 proteins, but neither transient nor ectopic stably expressed VSR proteins could rescue the systemic infection of BrYV and PLRV mutants. Moreover, BrYV mutant failed to establish systemic infection in DCL2/4 RNAi or RDR6 RNAi plants, indicating that systemic infection might be independent of the VSR activity of P0. Partially rescued infection of BrYV mutant by the co-infected PLRV implied the functional conservation of P0 proteins within genus. However, although C-terminal truncation mutant of BrYV P0 showed weaker interaction with its movement protein (MP) when compared to wild-type P0, wild-type and mutant PLRV P0 showed similar interaction with its MP. In sum, our findings revealed the role of P0 in virus systemic infection and the requirement of P0 carboxyl terminal region for the infection.
Collapse
Affiliation(s)
- Xin Zhang
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (X.Z.); (M.-O.R.); (Y.-Y.L.); (M.-J.H.); (Y.W.); (D.-W.L.); (J.-L.Y.)
| | - Mamun-Or Rashid
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (X.Z.); (M.-O.R.); (Y.-Y.L.); (M.-J.H.); (Y.W.); (D.-W.L.); (J.-L.Y.)
| | - Tian-Yu Zhao
- China National Center for Biotechnology Development, Beijing 100039, China;
| | - Yuan-Yuan Li
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (X.Z.); (M.-O.R.); (Y.-Y.L.); (M.-J.H.); (Y.W.); (D.-W.L.); (J.-L.Y.)
| | - Meng-Jun He
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (X.Z.); (M.-O.R.); (Y.-Y.L.); (M.-J.H.); (Y.W.); (D.-W.L.); (J.-L.Y.)
| | - Ying Wang
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (X.Z.); (M.-O.R.); (Y.-Y.L.); (M.-J.H.); (Y.W.); (D.-W.L.); (J.-L.Y.)
| | - Da-Wei Li
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (X.Z.); (M.-O.R.); (Y.-Y.L.); (M.-J.H.); (Y.W.); (D.-W.L.); (J.-L.Y.)
| | - Jia-Lin Yu
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (X.Z.); (M.-O.R.); (Y.-Y.L.); (M.-J.H.); (Y.W.); (D.-W.L.); (J.-L.Y.)
| | - Cheng-Gui Han
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (X.Z.); (M.-O.R.); (Y.-Y.L.); (M.-J.H.); (Y.W.); (D.-W.L.); (J.-L.Y.)
| |
Collapse
|
50
|
Vigh ML, Bressendorff S, Thieffry A, Arribas-Hernández L, Brodersen P. Nuclear and cytoplasmic RNA exosomes and PELOTA1 prevent miRNA-induced secondary siRNA production in Arabidopsis. Nucleic Acids Res 2022; 50:1396-1415. [PMID: 35037064 PMCID: PMC8860578 DOI: 10.1093/nar/gkab1289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 12/13/2021] [Accepted: 01/03/2022] [Indexed: 11/14/2022] Open
Abstract
Amplification of short interfering RNA (siRNAs) via RNA-dependent RNA polymerases (RdRPs) is of fundamental importance in RNA silencing. Plant microRNA (miRNA) action generally does not involve engagement of RdRPs, in part thanks to a poorly understood activity of the cytoplasmic exosome adaptor SKI2. Here, we show that inactivation of the exosome subunit RRP45B and SKI2 results in similar patterns of miRNA-induced siRNA production. Furthermore, loss of the nuclear exosome adaptor HEN2 leads to secondary siRNA production from miRNA targets largely distinct from those producing siRNAs in ski2. Importantly, mutation of the Release Factor paralogue PELOTA1 required for subunit dissociation of stalled ribosomes causes siRNA production from miRNA targets overlapping with, but distinct from, those affected in ski2 and rrp45b mutants. We also show that in exosome mutants, miRNA targets can be sorted into producers and non-producers of illicit secondary siRNAs based on trigger miRNA levels and miRNA:target affinity rather than on presence of 5′-cleavage fragments. We propose that stalled RNA-Induced Silencing Complex (RISC) and ribosomes, but not mRNA cleavage fragments released from RISC, trigger siRNA production, and that the exosome limits siRNA amplification by reducing RISC dwell time on miRNA target mRNAs while PELOTA1 does so by reducing ribosome stalling.
Collapse
Affiliation(s)
- Maria L Vigh
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Simon Bressendorff
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Axel Thieffry
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Laura Arribas-Hernández
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Peter Brodersen
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| |
Collapse
|