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Mäkinen K, Aspelin W, Pollari M, Wang L. How do they do it? The infection biology of potyviruses. Adv Virus Res 2023; 117:1-79. [PMID: 37832990 DOI: 10.1016/bs.aivir.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Affiliation(s)
- Kristiina Mäkinen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
| | - William Aspelin
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Maija Pollari
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Linping Wang
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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2
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Tatineni S, Hein GL. Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies. PHYTOPATHOLOGY 2023; 113:117-141. [PMID: 36095333 DOI: 10.1094/phyto-05-22-0167-rvw] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.
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Affiliation(s)
- Satyanarayana Tatineni
- U.S. Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Gary L Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583
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3
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Rodríguez-Verástegui LL, Ramírez-Zavaleta CY, Capilla-Hernández MF, Gregorio-Jorge J. Viruses Infecting Trees and Herbs That Produce Edible Fleshy Fruits with a Prominent Value in the Global Market: An Evolutionary Perspective. PLANTS (BASEL, SWITZERLAND) 2022; 11:203. [PMID: 35050091 PMCID: PMC8778216 DOI: 10.3390/plants11020203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 05/12/2023]
Abstract
Trees and herbs that produce fruits represent the most valuable agricultural food commodities in the world. However, the yield of these crops is not fully achieved due to biotic factors such as bacteria, fungi, and viruses. Viruses are capable of causing alterations in plant growth and development, thereby impacting the yield of their hosts significantly. In this work, we first compiled the world's most comprehensive list of known edible fruits that fits our definition. Then, plant viruses infecting those trees and herbs that produce fruits with commercial importance in the global market were identified. The identified plant viruses belong to 30 families, most of them containing single-stranded RNA genomes. Importantly, we show the overall picture of the host range for some virus families following an evolutionary approach. Further, the current knowledge about plant-virus interactions, focusing on the main disorders they cause, as well as yield losses, is summarized. Additionally, since accurate diagnosis methods are of pivotal importance for viral diseases control, the current and emerging technologies for the detection of these plant pathogens are described. Finally, the most promising strategies employed to control viral diseases in the field are presented, focusing on solutions that are long-lasting.
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Affiliation(s)
| | - Candy Yuriria Ramírez-Zavaleta
- Cuerpo Académico Procesos Biotecnológicos, Universidad Politécnica de Tlaxcala, Av. Universidad Politécnica 1, San Pedro Xalcaltzinco 90180, Mexico; (C.Y.R.-Z.); (M.F.C.-H.)
| | - María Fernanda Capilla-Hernández
- Cuerpo Académico Procesos Biotecnológicos, Universidad Politécnica de Tlaxcala, Av. Universidad Politécnica 1, San Pedro Xalcaltzinco 90180, Mexico; (C.Y.R.-Z.); (M.F.C.-H.)
| | - Josefat Gregorio-Jorge
- Consejo Nacional de Ciencia y Tecnología, Universidad Politécnica de Tlaxcala, Av. Insurgentes Sur 1582, Col. Crédito Constructor, Ciudad de Mexico 03940, Mexico
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4
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Sharma SK, Gupta OP, Pathaw N, Sharma D, Maibam A, Sharma P, Sanasam J, Karkute SG, Kumar S, Bhattacharjee B. CRISPR-Cas-Led Revolution in Diagnosis and Management of Emerging Plant Viruses: New Avenues Toward Food and Nutritional Security. Front Nutr 2022; 8:751512. [PMID: 34977113 PMCID: PMC8716883 DOI: 10.3389/fnut.2021.751512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/31/2021] [Indexed: 12/14/2022] Open
Abstract
Plant viruses pose a serious threat to agricultural production systems worldwide. The world's population is expected to reach the 10-billion mark by 2057. Under the scenario of declining cultivable land and challenges posed by rapidly emerging and re-emerging plant pathogens, conventional strategies could not accomplish the target of keeping pace with increasing global food demand. Gene-editing techniques have recently come up as promising options to enable precise changes in genomes with greater efficiency to achieve the target of higher crop productivity. Of genome engineering tools, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) proteins have gained much popularity, owing to their simplicity, reproducibility, and applicability in a wide range of species. Also, the application of different Cas proteins, such as Cas12a, Cas13a, and Cas9 nucleases, has enabled the development of more robust strategies for the engineering of antiviral mechanisms in many plant species. Recent studies have revealed the use of various CRISPR-Cas systems to either directly target a viral gene or modify a host genome to develop viral resistance in plants. This review provides a comprehensive record of the use of the CRISPR-Cas system in the development of antiviral resistance in plants and discusses its applications in the overall enhancement of productivity and nutritional landscape of cultivated plant species. Furthermore, the utility of this technique for the detection of various plant viruses could enable affordable and precise in-field or on-site detection. The futuristic potential of CRISPR-Cas technologies and possible challenges with their use and application are highlighted. Finally, the future of CRISPR-Cas in sustainable management of viral diseases, and its practical utility and regulatory guidelines in different parts of the globe are discussed systematically.
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Affiliation(s)
| | - Om Prakash Gupta
- Division of Quality & Basic Science, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Neeta Pathaw
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Devender Sharma
- Crop Improvement Division, ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, India
| | - Albert Maibam
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Parul Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Jyotsana Sanasam
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Suhas Gorakh Karkute
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, India
| | - Sandeep Kumar
- Department of Plant Pathology, Odisha University of Agriculture & Technology, Bhubaneswar, India
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5
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Kappagantu M, Collum TD, Dardick C, Culver JN. Viral Hacks of the Plant Vasculature: The Role of Phloem Alterations in Systemic Virus Infection. Annu Rev Virol 2020; 7:351-370. [PMID: 32453971 DOI: 10.1146/annurev-virology-010320-072410] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For plant viruses, the ability to load into the vascular phloem and spread systemically within a host is an essential step in establishing a successful infection. However, access to the vascular phloem is highly regulated, representing a significant obstacle to virus loading, movement, and subsequent unloading into distal uninfected tissues. Recent studies indicate that during virus infection, phloem tissues are a source of significant transcriptional and translational alterations, with the number of virus-induced differentially expressed genes being four- to sixfold greater in phloem tissues than in surrounding nonphloem tissues. In addition, viruses target phloem-specific components as a means to promote their own systemic movement and disrupt host defense processes. Combined, these studies provide evidence that the vascular phloem plays a significant role in the mediation and control of host responses during infection and as such is a site of considerable modulation by the infecting virus. This review outlines the phloem responses and directed reprograming mechanisms that viruses employ to promote their movement through the vasculature.
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Affiliation(s)
- Madhu Kappagantu
- Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA;
| | - Tamara D Collum
- Foreign Disease-Weed Science Research Unit, US Department of Agriculture Agricultural Research Service, Frederick, Maryland 21702, USA
| | - Christopher Dardick
- Appalachian Fruit Research Station, US Department of Agriculture Agricultural Research Service, Kearneysville, West Virginia 25430, USA
| | - James N Culver
- Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, USA; .,Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742, USA
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6
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Kloth KJ, Kormelink R. Defenses against Virus and Vector: A Phloem-Biological Perspective on RTM- and SLI1-Mediated Resistance to Potyviruses and Aphids. Viruses 2020; 12:E129. [PMID: 31979012 PMCID: PMC7077274 DOI: 10.3390/v12020129] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/17/2020] [Accepted: 01/19/2020] [Indexed: 12/12/2022] Open
Abstract
Combining plant resistance against virus and vector presents an attractive approach to reduce virus transmission and virus proliferation in crops. RestrictedTobacco-etch virus Movement (RTM) genes confer resistance to potyviruses by limiting their long-distance transport. Recently, a close homologue of one of the RTM genes, SLI1, has been discovered but this gene instead confers resistance to Myzus persicae aphids, a vector of potyviruses. The functional connection between resistance to potyviruses and aphids, raises the question whether plants have a basic defense system in the phloem against biotic intruders. This paper provides an overview on restricted potyvirus phloem transport and restricted aphid phloem feeding and their possible interplay, followed by a discussion on various ways in which viruses and aphids gain access to the phloem sap. From a phloem-biological perspective, hypotheses are proposed on the underlying mechanisms of RTM- and SLI1-mediated resistance, and their possible efficacy to defend against systemic viruses and phloem-feeding vectors.
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Affiliation(s)
- Karen J. Kloth
- Laboratory of Entomology, Wageningen University and Research, 6700 AA Wageningen, The Netherlands
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University and Research, 6700 AA Wageningen, The Netherlands;
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7
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Martínez-Turiño S, García JA. Potyviral coat protein and genomic RNA: A striking partnership leading virion assembly and more. Adv Virus Res 2020; 108:165-211. [PMID: 33837716 DOI: 10.1016/bs.aivir.2020.09.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Potyvirus genus clusters a significant and expanding number of widely distributed plant viruses, responsible for large losses impacting most crops of economic interest. The potyviral genome is a single-stranded, linear, positive-sense RNA of around 10kb that is encapsidated in flexuous rod-shaped filaments, mostly made up of a helically arranged coat protein (CP). Beyond its structural role of protecting the viral genome, the potyviral CP is a multitasking protein intervening in practically all steps of the virus life cycle. In particular, interactions between the CP and the viral RNA must be tightly controlled to allow the correct assignment of the RNA to each of its functions through the infection process. This review attempts to bring together the most relevant available information regarding the architecture and modus operandi of potyviral CP and virus particles, highlighting significant discoveries, but also substantial gaps in the existing knowledge on mechanisms orchestrating virion assembly and disassembly. Biotechnological applications based on potyvirus nanoparticles is another important topic addressed here.
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8
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Rodamilans B, Valli A, García JA. Molecular Plant-Plum Pox Virus Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:6-17. [PMID: 31454296 DOI: 10.1094/mpmi-07-19-0189-fi] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Plum pox virus, the agent that causes sharka disease, is among the most important plant viral pathogens, affecting Prunus trees across the globe. The fabric of interactions that the virus is able to establish with the plant regulates its life cycle, including RNA uncoating, translation, replication, virion assembly, and movement. In addition, plant-virus interactions are strongly conditioned by host specificities, which determine infection outcomes, including resistance. This review attempts to summarize the latest knowledge regarding Plum pox virus-host interactions, giving a comprehensive overview of their relevance for viral infection and plant survival, including the latest advances in genetic engineering of resistant species.
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Affiliation(s)
- Bernardo Rodamilans
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Adrián Valli
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan Antonio García
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
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9
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De Mori G, Falchi R, Testolin R, Bassi D, Savazzini F, Dondini L, Tartarini S, Palmisano F, Minafra A, Spadotto A, Scalabrin S, Geuna F. Resistance to Sharka in Apricot: Comparison of Phase-Reconstructed Resistant and Susceptible Haplotypes of 'Lito' Chromosome 1 and Analysis of Candidate Genes. FRONTIERS IN PLANT SCIENCE 2019; 10:1576. [PMID: 31867032 PMCID: PMC6905379 DOI: 10.3389/fpls.2019.01576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
Sharka, a common disease among most stone fruit crops, is caused by the Plum Pox Virus (PPV). Resistant genotypes have been found in apricot (Prunus armeniaca L.), one of which-the cultivar 'Lito' heterozygous for the resistance-has been used to map a major quantitative trait locus (QTL) on linkage group 1, following a pseudo-test-cross mating design with 231 individuals. In addition, 19 SNP markers were selected from among the hundreds previously developed, which allowed the region to be limited to 236 kb on chromosome 1. A 'Lito' bacterial artificial chromosome (BAC) library was produced, screened with markers of the region, and positive BAC clones were sequenced. Resistant (R) and susceptible (S) haplotypes were assembled independently. To refine the assembly, the whole genome of 'Lito' was sequenced to high coverage (98×) using PacBio technology, enabling the development of a detailed assembly of the region that was able to predict and annotate the genes in the QTL region. The selected cultivar 'Lito' allowed not only to discriminate structural variants between the two haplotypic regions but also to distinguish specific allele expression, contributing towards mining the PPVres locus. In light of these findings, genes previously indicated (i.e., MATHd genes) to have a possible role in PPV resistance were further analyzed, and new candidates were discussed. Although the results are not conclusive, the accurate and independent assembly of R and S haplotypes of 'Lito' is a valuable resource to predict and test alternative transcription and regulation mechanisms underpinning PPV resistance.
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Affiliation(s)
- Gloria De Mori
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Rachele Falchi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Raffaele Testolin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy
| | - Federica Savazzini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Francesco Palmisano
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Locorotondo, Italy
| | - Angelantonio Minafra
- National Research Council, Institute for Sustainable Plant Protection, Bari, Italy
| | | | - Simone Scalabrin
- IGA Technology Services, Science and Technology Park, ZIU, Udine, Italy
| | - Filippo Geuna
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy
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10
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Rubio B, Cosson P, Caballero M, Revers F, Bergelson J, Roux F, Schurdi-Levraud V. Genome-wide association study reveals new loci involved in Arabidopsis thaliana and Turnip mosaic virus (TuMV) interactions in the field. THE NEW PHYTOLOGIST 2019; 221:2026-2038. [PMID: 30282123 DOI: 10.1111/nph.15507] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/18/2018] [Indexed: 05/12/2023]
Abstract
The genetic architecture of plant response to viruses has often been studied in model nonnatural pathosystems under controlled conditions. There is an urgent need to elucidate the genetic architecture of the response to viruses in a natural setting. A field experiment was performed in each of two years. In total, 317 Arabidopsis thaliana accessions were inoculated with its natural Turnip mosaic virus (TuMV). The accessions were phenotyped for viral accumulation, frequency of infected plants, stem length and symptoms. Genome-wide association mapping was performed. Arabidopsis thaliana exhibits extensive natural variation in its response to TuMV in the field. The underlying genetic architecture reveals a more quantitative picture than in controlled conditions. Ten genomic regions were consistently identified across the two years. RTM3 (Restricted TEV Movement 3) is a major candidate for the response to TuMV in the field. New candidate genes include Dead box helicase 1, a Tim Barrel domain protein and the eukaryotic translation initiation factor eIF3b. To our knowledge, this study is the first to report the genetic architecture of quantitative response of A. thaliana to a naturally occurring virus in a field environment, thereby highlighting relevant candidate genes involved in plant virus interactions in nature.
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Affiliation(s)
- Bernadette Rubio
- Univ. Bordeaux INRA, UMR Biologie du Fruit et Pathologie, 1332, 71 avenue Edouard Bourlaux, 33883, Villenave d'Ornon cedex, France
| | - Patrick Cosson
- Univ. Bordeaux INRA, UMR Biologie du Fruit et Pathologie, 1332, 71 avenue Edouard Bourlaux, 33883, Villenave d'Ornon cedex, France
| | - Mélodie Caballero
- Univ. Bordeaux INRA, UMR Biologie du Fruit et Pathologie, 1332, 71 avenue Edouard Bourlaux, 33883, Villenave d'Ornon cedex, France
| | - Frédéric Revers
- INRA, UMR 1202 BIOGECO, Université de Bordeaux, 69 Route d'Arcachon, 33612, Cestas Cedex, France
| | - Joy Bergelson
- Ecology & Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Fabrice Roux
- LIPM, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Valérie Schurdi-Levraud
- Univ. Bordeaux INRA, UMR Biologie du Fruit et Pathologie, 1332, 71 avenue Edouard Bourlaux, 33883, Villenave d'Ornon cedex, France
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11
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Zhang Z, Tong X, Liu SY, Chai LX, Zhu FF, Zhang XP, Zou JZ, Wang XB. Genetic analysis of a Piezo-like protein suppressing systemic movement of plant viruses in Arabidopsis thaliana. Sci Rep 2019; 9:3187. [PMID: 30816193 PMCID: PMC6395819 DOI: 10.1038/s41598-019-39436-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/24/2019] [Indexed: 01/01/2023] Open
Abstract
As obligate intracellular phytopathogens, plant viruses must take advantage of hosts plasmodesmata and phloem vasculature for their local and long-distance transports to establish systemic infection in plants. In contrast to well-studied virus local transports, molecular mechanisms and related host genes governing virus systemic trafficking are far from being understood. Here, we performed a forward genetic screening to identify Arabidopsis thaliana mutants with enhanced susceptibility to a 2b-deleted mutant of cucumber mosaic virus (CMV-2aT∆2b). We found that an uncharacterized Piezo protein (AtPiezo), an ortholog of animal Piezo proteins with mechanosensitive (MS) cation channel activities, was required for inhibiting systemic infection of CMV-2aT∆2b and turnip mosaic virus tagged a green fluorescent protein (GFP) (TuMV-GFP). AtPiezo is induced by virus infection, especially in the petioles of rosette leaves. Thus, we for the first time demonstrate the biological function of Piezo proteins in plants, which might represent a common antiviral strategy because many monocot and dicot plant species have a single Piezo ortholog.
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Affiliation(s)
- Zhen Zhang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xin Tong
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Song-Yu Liu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Long-Xiang Chai
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fei-Fan Zhu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiao-Peng Zhang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jing-Ze Zou
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xian-Bing Wang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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12
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The Tug-of-War between Plants and Viruses: Great Progress and Many Remaining Questions. Viruses 2019; 11:v11030203. [PMID: 30823402 PMCID: PMC6466000 DOI: 10.3390/v11030203] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/18/2019] [Accepted: 02/23/2019] [Indexed: 12/19/2022] Open
Abstract
Plants are persistently challenged by various phytopathogens. To protect themselves, plants have evolved multilayered surveillance against all pathogens. For intracellular parasitic viruses, plants have developed innate immunity, RNA silencing, translation repression, ubiquitination-mediated and autophagy-mediated protein degradation, and other dominant resistance gene-mediated defenses. Plant viruses have also acquired diverse strategies to suppress and even exploit host defense machinery to ensure their survival. A better understanding of the defense and counter-defense between plants and viruses will obviously benefit from the development of efficient and broad-spectrum virus resistance for sustainable agriculture. In this review, we summarize the cutting edge of knowledge concerning the defense and counter-defense between plants and viruses, and highlight the unexploited areas that are especially worth investigating in the near future.
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13
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Yoshida T, Shiraishi T, Hagiwara-Komoda Y, Komatsu K, Maejima K, Okano Y, Fujimoto Y, Yusa A, Yamaji Y, Namba S. The Plant Noncanonical Antiviral Resistance Protein JAX1 Inhibits Potexviral Replication by Targeting the Viral RNA-Dependent RNA Polymerase. J Virol 2019; 93:e01506-18. [PMID: 30429349 PMCID: PMC6340027 DOI: 10.1128/jvi.01506-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/08/2018] [Indexed: 11/20/2022] Open
Abstract
Understanding the innate immune mechanisms of plants is necessary for the breeding of disease-resistant lines. Previously, we identified the antiviral resistance gene JAX1 from Arabidopsis thaliana, which inhibits infection by potexviruses. JAX1 encodes a unique jacalin-type lectin protein. In this study, we analyzed the molecular mechanisms of JAX1-mediated resistance. JAX1 restricted the multiplication of a potexviral replicon lacking movement-associated proteins, suggesting inhibition of viral replication. Therefore, we developed an in vitro potato virus X (PVX) translation/replication system using vacuole- and nucleus-free lysates from tobacco protoplasts, and we revealed that JAX1 inhibits viral RNA synthesis but not the translation of the viral RNA-dependent RNA polymerase (RdRp). JAX1 did not affect the replication of a resistance-breaking mutant of PVX. Blue native polyacrylamide gel electrophoresis of fractions separated by sucrose gradient sedimentation showed that PVX RdRp constituted the high-molecular-weight complex that seems to be crucial for viral replication. JAX1 was detected in this complex of the wild-type PVX replicon but not in that of the resistance-breaking mutant. In addition, JAX1 interacted with the RdRp of the wild-type virus but not with that of a virus with a point mutation at the resistance-breaking residue. These results suggest that JAX1 targets RdRp to inhibit potexviral replication.IMPORTANCE Resistance genes play a crucial role in plant antiviral innate immunity. The roles of conventional nucleotide-binding leucine-rich repeat (NLR) proteins and the associated defense pathways have long been studied. In contrast, recently discovered resistance genes that do not encode NLR proteins (non-NLR resistance genes) have not been investigated extensively. Here we report that the non-NLR resistance factor JAX1, a unique jacalin-type lectin protein, inhibits de novo potexviral RNA synthesis by targeting the huge complex of viral replicase. This is unlike other known antiviral resistance mechanisms. Molecular elucidation of the target in lectin-type protein-mediated antiviral immunity will enhance our understanding of the non-NLR-mediated plant resistance system.
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Affiliation(s)
- Tetsuya Yoshida
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takuya Shiraishi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuka Hagiwara-Komoda
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ken Komatsu
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukari Okano
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuji Fujimoto
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Akira Yusa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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14
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Bortolamiol-Bécet D, Monsion B, Chapuis S, Hleibieh K, Scheidecker D, Alioua A, Bogaert F, Revers F, Brault V, Ziegler-Graff V. Phloem-Triggered Virus-Induced Gene Silencing Using a Recombinant Polerovirus. Front Microbiol 2018; 9:2449. [PMID: 30405546 PMCID: PMC6206295 DOI: 10.3389/fmicb.2018.02449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/25/2018] [Indexed: 01/22/2023] Open
Abstract
The phloem-limited poleroviruses infect Arabidopsis thaliana without causing noticeable disease symptoms. In order to facilitate visual infection identification, we developed virus-induced gene silencing (VIGS) vectors derived from Turnip yellows virus (TuYV). Short sequences from the host gene AtCHLI1 required for chlorophyll biosynthesis [42 nucleotides in sense or antisense orientation or as an inverted-repeat (IR), or an 81 nucleotide sense fragment] were inserted into the 3' non-coding region of the TuYV genome to screen for the most efficient and robust silencing vector. All recombinant viruses produced a clear vein chlorosis phenotype on infected Arabidopsis plants due to the expression inhibition of the AtCHLI1 gene. The introduction of a sense-oriented sequence into TuYV genome resulted in a virus exhibiting a more sustainable chlorosis than the virus containing an IR of the same length. This observation was correlated with a higher stability of the sense sequence insertion in the viral genome. In order to evaluate the impact of the TuYV silencing suppressor P0 in the VIGS mechanism a P0 knock-out mutation was introduced into the recombinant TuYV viruses. They induced a similar but milder vein clearing phenotype due to lower viral accumulation. This indicates that P0 does not hinder the performances of the TuYV silencing effect and confirms that in the viral infection context, P0 has no major impact on the production, propagation and action of the short distance silencing signal in phloem cells. Finally, we showed that TuYV can be used to strongly silence the phloem specific AtRTM1 gene. The TuYV-derived VIGS vectors therefore represent powerful tools to easily detect and monitor TuYV in infected plants and conduct functional analysis of phloem-restricted genes. Moreover this example indicates the potential of poleroviruses for use in functional genomic studies of agronomic plants.
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Affiliation(s)
- Diane Bortolamiol-Bécet
- Institut de biologie moléculaire des plantes, CNRS-UPR 2357, Université de Strasbourg, Strasbourg, France.,Architecture et Réactivité de l'ARN, Institut de biologie moléculaire et cellulaire CNRS-UPR 9002, Université de Strasbourg, Strasbourg, France
| | - Baptiste Monsion
- Institut de biologie moléculaire des plantes, CNRS-UPR 2357, Université de Strasbourg, Strasbourg, France.,UMR1161 Virologie, INRA, ANSES, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | - Sophie Chapuis
- Institut de biologie moléculaire des plantes, CNRS-UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Kamal Hleibieh
- Institut de biologie moléculaire des plantes, CNRS-UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Danièle Scheidecker
- Institut de biologie moléculaire des plantes, CNRS-UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Abdelmalek Alioua
- Institut de biologie moléculaire des plantes, CNRS-UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Florent Bogaert
- SVQV, INRA UMR 1131, Université de Strasbourg, Colmar, France
| | - Frédéric Revers
- BFP, INRA UMR 1332, Univ. Bordeaux, Villenave d'Ornon, France.,BIOGECO, INRA UMR 1202, Univ. Bordeaux, Pessac, France
| | | | - Véronique Ziegler-Graff
- Institut de biologie moléculaire des plantes, CNRS-UPR 2357, Université de Strasbourg, Strasbourg, France
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15
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Cabanillas DG, Jiang J, Movahed N, Germain H, Yamaji Y, Zheng H, Laliberté JF. Turnip Mosaic Virus Uses the SNARE Protein VTI11 in an Unconventional Route for Replication Vesicle Trafficking. THE PLANT CELL 2018; 30:2594-2615. [PMID: 30150314 PMCID: PMC6241277 DOI: 10.1105/tpc.18.00281] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/17/2018] [Accepted: 08/25/2018] [Indexed: 05/11/2023]
Abstract
Infection of plant cells by RNA viruses leads to the generation of organelle-like subcellular structures that contain the viral replication complex. During Turnip mosaic virus (TuMV) infection of Nicotiana benthamiana, the viral membrane protein 6K2 plays a key role in the release of motile replication vesicles from the host endoplasmic reticulum (ER). Here, we demonstrate that 6K2 contains a GxxxG motif within its predicted transmembrane domain that is vital for TuMV infection. Replacement of the Gly with Val within this motif inhibited virus production, and this was due to a relocation of the viral protein to the Golgi apparatus and the plasma membrane. This indicated that passage of 6K2 through the Golgi apparatus is a dead-end avenue for virus infection. Impairing the fusion of transport vesicles between the ER and the Golgi apparatus by overexpression of the SNARE Sec22 protein resulted in enhanced intercellular virus movement. Likewise, expression of nonfunctional, Golgi-located synaptotagmin during infection enhanced TuMV intercellular movement. 6K2 copurified with VTI11, a prevacuolar compartment SNARE protein. An Arabidopsis thaliana vti11 mutant was completely resistant to TuMV infection. We conclude that TuMV replication vesicles bypass the Golgi apparatus and take an unconventional pathway that may involve prevacuolar compartments/multivesicular bodies for virus infection.
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Affiliation(s)
- Daniel Garcia Cabanillas
- Institut National de la Recherche Scientifique, Institut Armand-Frappier, Laval, Québec H7V 1B7, Canada
| | - Jun Jiang
- Institut National de la Recherche Scientifique, Institut Armand-Frappier, Laval, Québec H7V 1B7, Canada
| | - Nooshin Movahed
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry, and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec G9A 5H7, Canada
| | - Yasuyuki Yamaji
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 1138657, Japan
| | - Huanquan Zheng
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
| | - Jean-François Laliberté
- Institut National de la Recherche Scientifique, Institut Armand-Frappier, Laval, Québec H7V 1B7, Canada
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16
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[Virus resistance genes in plants]. Uirusu 2018; 68:13-20. [PMID: 31105131 DOI: 10.2222/jsv.68.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Plants defend themselves from virus infection by RNA silencing and resistance (R) gene-mediated mechanisms. Many dominant R genes encode nucleotide-binding site and leucine-rich repeat (NB-LRR)-containing proteins. NB-LRR proteins are also encoded by R genes against bacteria or fungi, suggesting a similar mechanism underlies defense systems to diverse pathogens. In contrast, several non-NB-LRR-type R genes have recently been cloned, each of which differs from others in sequences and functions. In this review, we introduce a diversity of R gene-mediated plant defense systems against viruses. Tm-1, JAX1, and Scmv1, resistance genes against tomato mosaic virus, potexviruses, and sugarcane mosaic virus, respectively, inhibit virus multiplication at a single cell level. The RTM1, RTM2, RTM3 genes of Arabidopsis thaliana inhibit systemic transport of potyviruses through the phloem. STV11 of rice against rice stripe virus and Ty-1 and Ty-3 genes of tomato against tomato yellow leaf curl virus allow low level virus multiplication and confer tolerance. The wide diversity of plant defense systems against viruses implies their recent emergence. We suggest that plants evolved new defense systems to counter infection by viruses that had overcome pre-existing defense systems (RNA silencing and NB-LRR-type R gene-mediated systems).
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17
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Amuge T, Berger DK, Katari MS, Myburg AA, Goldman SL, Ferguson ME. A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus. Sci Rep 2017; 7:9747. [PMID: 28852026 PMCID: PMC5575035 DOI: 10.1038/s41598-017-09617-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/21/2017] [Indexed: 12/13/2022] Open
Abstract
A time-course transcriptome analysis of two cassava varieties that are either resistant or susceptible to cassava brown streak disease (CBSD) was conducted using RNASeq, after graft inoculation with Ugandan cassava brown streak virus (UCBSV). From approximately 1.92 billion short reads, the largest number of differentially expressed genes (DEGs) was obtained in the resistant (Namikonga) variety at 2 days after grafting (dag) (3887 DEGs) and 5 dag (4911 DEGs). At the same time points, several defense response genes (encoding LRR-containing, NBARC-containing, pathogenesis-related, late embryogenesis abundant, selected transcription factors, chaperones, and heat shock proteins) were highly expressed in Namikonga. Also, defense-related GO terms of 'translational elongation', 'translation factor activity', 'ribosomal subunit' and 'phosphorelay signal transduction', were overrepresented in Namikonga at these time points. More reads corresponding to UCBSV sequences were recovered from the susceptible variety (Albert) (733 and 1660 read counts per million (cpm)) at 45 dag and 54 dag compared to Namikonga (10 and 117 cpm respectively). These findings suggest that Namikonga's resistance involves restriction of multiplication of UCBSV within the host. These findings can be used with other sources of evidence to identify candidate genes and biomarkers that would contribute substantially to knowledge-based resistance breeding.
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Affiliation(s)
- T Amuge
- National Crops Resources Research Institute (NaCRRI), Namulonge, Uganda
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - D K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - M S Katari
- Center for Genomics and Systems Biology, New York University, New York, USA
| | - A A Myburg
- Genetics Department, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - S L Goldman
- Center for Genomics and Systems Biology, New York University, New York, USA
| | - M E Ferguson
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya.
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18
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Sofer L, Cabanillas DG, Gayral M, Téplier R, Pouzoulet J, Ducousso M, Dufin L, Bréhélin C, Ziegler-Graff V, Brault V, Revers F. Identification of host factors potentially involved in RTM-mediated resistance during potyvirus long distance movement. Arch Virol 2017; 162:1855-1865. [PMID: 28251380 DOI: 10.1007/s00705-017-3292-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/29/2017] [Indexed: 12/28/2022]
Abstract
The long distance movement of potyviruses is a poorly understood step of the viral cycle. Only factors inhibiting this process, referred to as "Restricted TEV Movement" (RTM), have been identified in Arabidopsis thaliana. On the virus side, the potyvirus coat protein (CP) displays determinants required for long-distance movement and for RTM-based resistance breaking. However, the potyvirus CP was previously shown not to interact with the RTM proteins. We undertook the identification of Arabidopsis factors which directly interact with either the RTM proteins or the CP of lettuce mosaic virus (LMV). An Arabidopsis cDNA library generated from companion cells was screened with LMV CP and RTM proteins using the yeast two-hybrid system. Fourteen interacting proteins were identified. Two of them were shown to interact with CP and the RTM proteins suggesting that a multiprotein complex could be formed between the RTM proteins and virions or viral ribonucleoprotein complexes. Co-localization experiments in Nicotiana benthamiana showed that most of the viral and cellular protein pairs co-localized at the periphery of chloroplasts which suggests a putative role for plastids in this process.
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Affiliation(s)
- Luc Sofer
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Daniel Garcia Cabanillas
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Laval, QC, H7V 1B7, Canada
| | - Mathieu Gayral
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Rachèle Téplier
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Jérôme Pouzoulet
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Marie Ducousso
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
- UMR 0385 BGPI, Virus Insecte Plante, INRA, Campus international de Bailllarguet, Montpellier, France
| | - Laurène Dufin
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Claire Bréhélin
- UMR 5200, Laboratory of Membrane Biogenesis, CNRS, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Véronique Ziegler-Graff
- Institut de Biologie Moléculaire des Plantes, Laboratoire propre du CNRS conventionné avec l'Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, France
| | | | - Frédéric Revers
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France.
- BIOGECO, INRA, University of Bordeaux, 33615, Pessac, France.
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19
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Calil IP, Fontes EPB. Plant immunity against viruses: antiviral immune receptors in focus. ANNALS OF BOTANY 2017; 119:711-723. [PMID: 27780814 PMCID: PMC5604577 DOI: 10.1093/aob/mcw200] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 08/05/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Among the environmental limitations that affect plant growth, viruses cause major crop losses worldwide and represent serious threats to food security. Significant advances in the field of plant-virus interactions have led to an expansion of potential strategies for genetically engineered resistance in crops during recent years. Nevertheless, the evolution of viral virulence represents a constant challenge in agriculture that has led to a continuing interest in the molecular mechanisms of plant-virus interactions that affect disease or resistance. SCOPE AND CONCLUSION This review summarizes the molecular mechanisms of the antiviral immune system in plants and the latest breakthroughs reported in plant defence against viruses. Particular attention is given to the immune receptors and transduction pathways in antiviral innate immunity. Plants counteract viral infection with a sophisticated innate immune system that resembles the non-viral pathogenic system, which is broadly divided into pathogen-associated molecular pattern (PAMP)-triggered immunity and effector-triggered immunity. An additional recently uncovered virus-specific defence mechanism relies on host translation suppression mediated by a transmembrane immune receptor. In all cases, the recognition of the virus by the plant during infection is central for the activation of these innate defences, and, conversely, the detection of host plants enables the virus to activate virulence strategies. Plants also circumvent viral infection through RNA interference mechanisms by utilizing small RNAs, which are often suppressed by co-evolving virus suppressors. Additionally, plants defend themselves against viruses through hormone-mediated defences and activation of the ubiquitin-26S proteasome system (UPS), which alternatively impairs and facilitates viral infection. Therefore, plant defence and virulence strategies co-evolve and co-exist; hence, disease development is largely dependent on the extent and rate at which these opposing signals emerge in host and non-host interactions. A deeper understanding of plant antiviral immunity may facilitate innovative biotechnological, genetic and breeding approaches for crop protection and improvement.
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Affiliation(s)
- Iara P. Calil
- Departamento de Bioquímica e Biologia Molecular/National Institute of Science and Technology in Plant–Pest Interactions/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil
| | - Elizabeth P. B. Fontes
- Departamento de Bioquímica e Biologia Molecular/National Institute of Science and Technology in Plant–Pest Interactions/Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil
- For correspondence. E-mail
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20
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Tubbs E, Rieusset J. Study of Endoplasmic Reticulum and Mitochondria Interactions by In Situ Proximity Ligation Assay in Fixed Cells. J Vis Exp 2016. [PMID: 28060261 DOI: 10.3791/54899] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Structural interactions between the endoplasmic reticular (ER) and mitochondrial membranes, in domains known as mitochondria-associated membranes (MAM), are crucial hubs for cellular signaling and cell fate. Particularly, these inter-organelle contact sites allow the transfer of calcium from the ER to mitochondria through the voltage-dependent anion channel (VDAC)/glucose-regulated protein 75 (GRP75)/inositol 1,4,5-triphosphate receptor (IP3R) calcium channeling complex. While this subcellular compartment is under intense investigation in both physiological and pathological conditions, no simple and sensitive method exists to quantify the endogenous amount of ER-mitochondria contact in cells. Similarly, MAMs are highly dynamic structures, and there is no suitable approach to follow modifications of ER-mitochondria interactions without protein overexpression. Here, we report an optimized protocol based on the use of an in situ proximity ligation assay to visualize and quantify endogenous ER-mitochondria interactions in fixed cells by using the close proximity between proteins of the outer mitochondrial membrane (VDAC1) and of the ER membrane (IP3R1) at the MAM interface. Similar in situ proximity ligation experiments can also be performed with the GRP75/IP3R1 and cyclophilin D/IP3R1 pairs of antibodies. This assay provides several advantages over other imaging procedures, as it is highly specific, sensitive, and suitable to multiple-condition testing. Therefore, the use of this in situ proximity ligation assay should be helpful to better understand the physiological regulations of ER-mitochondria interactions, as well as their role in pathological contexts.
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Affiliation(s)
- Emily Tubbs
- Lund University Diabetes Centre, Lund University;
| | - Jennifer Rieusset
- INSERM UMR-1060, CarMeN Laboratory, Lyon 1 University, INRA U1235, INSA of Lyon, Rockefeller and Charles Merieux Lyon-Sud Medical Universities
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21
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Makarov VV, Kalinina NO. Structure and Noncanonical Activities of Coat Proteins of Helical Plant Viruses. BIOCHEMISTRY (MOSCOW) 2016; 81:1-18. [PMID: 26885578 DOI: 10.1134/s0006297916010016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The main function of virus coat protein is formation of the capsid that protects the virus genome against degradation. However, besides the structural function, coat proteins have many additional important activities in the infection cycle of the virus and in the defense response of host plants to viral infection. This review focuses on noncanonical functions of coat proteins of helical RNA-containing plant viruses with positive genome polarity. Analysis of data on the structural organization of coat proteins of helical viruses has demonstrated that the presence of intrinsically disordered regions within the protein structure plays an important role in implementation of nonstructural functions and largely determines the multifunctionality of coat proteins.
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Affiliation(s)
- V V Makarov
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow, 119991, Russia.
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22
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Roux F, Bergelson J. The Genetics Underlying Natural Variation in the Biotic Interactions of Arabidopsis thaliana: The Challenges of Linking Evolutionary Genetics and Community Ecology. Curr Top Dev Biol 2016; 119:111-56. [PMID: 27282025 DOI: 10.1016/bs.ctdb.2016.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the context of global change, predicting the responses of plant communities in an ever-changing biotic environment calls for a multipronged approach at the interface of evolutionary genetics and community ecology. However, our understanding of the genetic basis of natural variation involved in mediating biotic interactions, and associated adaptive dynamics of focal plants in their natural communities, is still in its infancy. Here, we review the genetic and molecular bases of natural variation in the response to biotic interactions (viruses, bacteria, fungi, oomycetes, herbivores, and plants) in the model plant Arabidopsis thaliana as well as the adaptive value of these bases. Among the 60 identified genes are a number that encode nucleotide-binding site leucine-rich repeat (NBS-LRR)-type proteins, consistent with early examples of plant defense genes. However, recent studies have revealed an extensive diversity in the molecular mechanisms of defense. Many types of genetic variants associate with phenotypic variation in biotic interactions, even among the genes of large effect that tend to be identified. In general, we found that (i) balancing selection rather than directional selection explains the observed patterns of genetic diversity within A. thaliana and (ii) the cost/benefit tradeoffs of adaptive alleles can be strongly dependent on both genomic and environmental contexts. Finally, because A. thaliana rarely interacts with only one biotic partner in nature, we highlight the benefit of exploring diffuse biotic interactions rather than tightly associated host-enemy pairs. This challenge would help to improve our understanding of coevolutionary quantitative genetics within the context of realistic community complexity.
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Affiliation(s)
- F Roux
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France.
| | - J Bergelson
- University of Chicago, Chicago, IL, United States
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23
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Poque S, Pagny G, Ouibrahim L, Chague A, Eyquard JP, Caballero M, Candresse T, Caranta C, Mariette S, Decroocq V. Allelic variation at the rpv1 locus controls partial resistance to Plum pox virus infection in Arabidopsis thaliana. BMC PLANT BIOLOGY 2015; 15:159. [PMID: 26109391 PMCID: PMC4479089 DOI: 10.1186/s12870-015-0559-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 06/17/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Sharka is caused by Plum pox virus (PPV) in stone fruit trees. In orchards, the virus is transmitted by aphids and by grafting. In Arabidopsis, PPV is transferred by mechanical inoculation, by biolistics and by agroinoculation with infectious cDNA clones. Partial resistance to PPV has been observed in the Cvi-1 and Col-0 Arabidopsis accessions and is characterized by a tendency to escape systemic infection. Indeed, only one third of the plants are infected following inoculation, in comparison with the susceptible Ler accession. RESULTS Genetic analysis showed this partial resistance to be monogenic or digenic depending on the allelic configuration and recessive. It is detected when inoculating mechanically but is overcome when using biolistic or agroinoculation. A genome-wide association analysis was performed using multiparental lines and 147 Arabidopsis accessions. It identified a major genomic region, rpv1. Fine mapping led to the positioning of rpv1 to a 200 kb interval on the long arm of chromosome 1. A candidate gene approach identified the chloroplast phosphoglycerate kinase (cPGK2) as a potential gene underlying the resistance. A virus-induced gene silencing strategy was used to knock-down cPGK2 expression, resulting in drastically reduced PPV accumulation. CONCLUSION These results indicate that rpv1 resistance to PPV carried by the Cvi-1 and Col-0 accessions is linked to allelic variations at the Arabidopsis cPGK2 locus, leading to incomplete, compatible interaction with the virus.
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Affiliation(s)
- S Poque
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Current address: Department of Plant Pathology, National Chung Hsing University, Taichung, 402, Taiwan.
| | - G Pagny
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
| | - L Ouibrahim
- INRA-UR1052, Genetics and Breeding of Fruits and Vegetables, Dom. St Maurice, CS 60094, F-84143, Montfavet cedex, France.
| | - A Chague
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
| | - J-P Eyquard
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
| | - M Caballero
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
| | - T Candresse
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
| | - C Caranta
- INRA-UR1052, Genetics and Breeding of Fruits and Vegetables, Dom. St Maurice, CS 60094, F-84143, Montfavet cedex, France.
| | - S Mariette
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Current address: INRA, UMR 1202 Biogeco, F- 33610, Cestas, France.
- Current address: Univ. Bordeaux, UMR1202 Biogeco, F-33400, Talence, France.
| | - V Decroocq
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
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Ilardi V, Tavazza M. Biotechnological strategies and tools for Plum pox virus resistance: trans-, intra-, cis-genesis, and beyond. FRONTIERS IN PLANT SCIENCE 2015; 6:379. [PMID: 26106397 PMCID: PMC4458569 DOI: 10.3389/fpls.2015.00379] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/12/2015] [Indexed: 05/19/2023]
Abstract
Plum pox virus (PPV) is the etiological agent of sharka, the most devastating and economically important viral disease affecting Prunus species. It is widespread in most stone fruits producing countries even though eradication and quarantine programs are in place. The development of resistant cultivars and rootstocks remains the most ecologically and economically suitable approach to achieve long-term control of sharka disease. However, the few PPV resistance genetic resources found in Prunus germplasm along with some intrinsic biological features of stone fruit trees pose limits for efficient and fast breeding programs. This review focuses on an array of biotechnological strategies and tools, which have been used, or may be exploited to confer PPV resistance. A considerable number of scientific studies clearly indicate that robust and predictable resistance can be achieved by transforming plant species with constructs encoding intron-spliced hairpin RNAs homologous to conserved regions of the PPV genome. In addition, we discuss how recent advances in our understanding of PPV biology can be profitably exploited to develop viral interference strategies. In particular, genetic manipulation of host genes by which PPV accomplishes its infection cycle already permits the creation of intragenic resistant plants. Finally, we review the emerging genome editing technologies based on ZFN, TALEN and CRISPR/Cas9 engineered nucleases and how the knockout of host susceptibility genes will open up next generation of PPV resistant plants.
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Affiliation(s)
- Vincenza Ilardi
- Centro di Ricerca per la Patologia Vegetale, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Rome, Italy
| | - Mario Tavazza
- UTAGRI Centro Ricerche Casaccia, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile, Rome, Italy
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Abstract
Potyvirus is the largest genus of plant viruses causing significant losses in a wide range of crops. Potyviruses are aphid transmitted in a nonpersistent manner and some of them are also seed transmitted. As important pathogens, potyviruses are much more studied than other plant viruses belonging to other genera and their study covers many aspects of plant virology, such as functional characterization of viral proteins, molecular interaction with hosts and vectors, structure, taxonomy, evolution, epidemiology, and diagnosis. Biotechnological applications of potyviruses are also being explored. During this last decade, substantial advances have been made in the understanding of the molecular biology of these viruses and the functions of their various proteins. After a general presentation on the family Potyviridae and the potyviral proteins, we present an update of the knowledge on potyvirus multiplication, movement, and transmission and on potyvirus/plant compatible interactions including pathogenicity and symptom determinants. We end the review providing information on biotechnological applications of potyviruses.
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Nicaise V. Crop immunity against viruses: outcomes and future challenges. FRONTIERS IN PLANT SCIENCE 2014; 5:660. [PMID: 25484888 PMCID: PMC4240047 DOI: 10.3389/fpls.2014.00660] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/04/2014] [Indexed: 05/02/2023]
Abstract
Viruses cause epidemics on all major cultures of agronomic importance, representing a serious threat to global food security. As strict intracellular pathogens, they cannot be controlled chemically and prophylactic measures consist mainly in the destruction of infected plants and excessive pesticide applications to limit the population of vector organisms. A powerful alternative frequently employed in agriculture relies on the use of crop genetic resistances, approach that depends on mechanisms governing plant-virus interactions. Hence, knowledge related to the molecular bases of viral infections and crop resistances is key to face viral attacks in fields. Over the past 80 years, great advances have been made on our understanding of plant immunity against viruses. Although most of the known natural resistance genes have long been dominant R genes (encoding NBS-LRR proteins), a vast number of crop recessive resistance genes were cloned in the last decade, emphasizing another evolutive strategy to block viruses. In addition, the discovery of RNA interference pathways highlighted a very efficient antiviral system targeting the infectious agent at the nucleic acid level. Insidiously, plant viruses evolve and often acquire the ability to overcome the resistances employed by breeders. The development of efficient and durable resistances able to withstand the extreme genetic plasticity of viruses therefore represents a major challenge for the coming years. This review aims at describing some of the most devastating diseases caused by viruses on crops and summarizes current knowledge about plant-virus interactions, focusing on resistance mechanisms that prevent or limit viral infection in plants. In addition, I will discuss the current outcomes of the actions employed to control viral diseases in fields and the future investigations that need to be undertaken to develop sustainable broad-spectrum crop resistances against viruses.
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Affiliation(s)
- Valérie Nicaise
- Fruit Biology and Pathology, Virology Laboratory, Institut National de la Recherche Agronomique, University of BordeauxUMR 1332, Villenave d’Ornon, France
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27
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Tubbs E, Theurey P, Vial G, Bendridi N, Bravard A, Chauvin MA, Ji-Cao J, Zoulim F, Bartosch B, Ovize M, Vidal H, Rieusset J. Mitochondria-associated endoplasmic reticulum membrane (MAM) integrity is required for insulin signaling and is implicated in hepatic insulin resistance. Diabetes 2014; 63:3279-94. [PMID: 24947355 DOI: 10.2337/db13-1751] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitochondria-associated endoplasmic reticulum (ER) membranes (MAMs) are functional domains between both organelles involved in Ca(2+) exchange, through the voltage-dependent anion channel (VDAC)-1/glucose-regulated protein 75 (Grp75)/inositol 1,4,5-triphosphate receptor (IP3R)-1 complex, and regulating energy metabolism. Whereas mitochondrial dysfunction, ER stress, and altered Ca(2+) homeostasis are associated with altered insulin signaling, the implication of MAM dysfunctions in insulin resistance is unknown. Here we validated an approach based on in situ proximity ligation assay to detect and quantify VDAC1/IP3R1 and Grp75/IP3R1 interactions at the MAM interface. We demonstrated that MAM integrity is required for insulin signaling and that induction of MAM prevented palmitate-induced alterations of insulin signaling in HuH7 cells. Disruption of MAM integrity by genetic or pharmacological inhibition of the mitochondrial MAM protein, cyclophilin D (CypD), altered insulin signaling in mouse and human primary hepatocytes and treatment of CypD knockout mice with metformin improved both insulin sensitivity and MAM integrity. Furthermore, ER-mitochondria interactions are altered in liver of both ob/ob and diet-induced insulin-resistant mice and improved by rosiglitazone treatment in the latter. Finally, increasing organelle contacts by overexpressing CypD enhanced insulin action in primary hepatocytes of diabetic mice. Collectively, our data reveal a new role of MAM integrity in hepatic insulin action and resistance, providing a novel target for the modulation of insulin action.
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Affiliation(s)
- Emily Tubbs
- INSERM UMR-1060, CarMeN Laboratory, Lyon 1 University, INRA U1235, INSA of Lyon, Rockefeller and Charles Merieux Lyon-Sud Medical Universities, Lyon, France
| | - Pierre Theurey
- INSERM UMR-1060, CarMeN Laboratory, Lyon 1 University, INRA U1235, INSA of Lyon, Rockefeller and Charles Merieux Lyon-Sud Medical Universities, Lyon, France
| | - Guillaume Vial
- INSERM UMR-1060, CarMeN Laboratory, Lyon 1 University, INRA U1235, INSA of Lyon, Rockefeller and Charles Merieux Lyon-Sud Medical Universities, Lyon, France
| | - Nadia Bendridi
- INSERM UMR-1060, CarMeN Laboratory, Lyon 1 University, INRA U1235, INSA of Lyon, Rockefeller and Charles Merieux Lyon-Sud Medical Universities, Lyon, France
| | - Amélie Bravard
- INSERM UMR-1060, CarMeN Laboratory, Lyon 1 University, INRA U1235, INSA of Lyon, Rockefeller and Charles Merieux Lyon-Sud Medical Universities, Lyon, France
| | - Marie-Agnès Chauvin
- INSERM UMR-1060, CarMeN Laboratory, Lyon 1 University, INRA U1235, INSA of Lyon, Rockefeller and Charles Merieux Lyon-Sud Medical Universities, Lyon, France
| | - Jingwei Ji-Cao
- INSERM UMR-1060, CarMeN Laboratory, Lyon 1 University, INRA U1235, INSA of Lyon, Rockefeller and Charles Merieux Lyon-Sud Medical Universities, Lyon, France
| | - Fabien Zoulim
- INSERM UMR-1052, Cancer Research Center of Lyon, Lyon 1 University, Hospices Civils de Lyon, Lyon, France
| | - Birke Bartosch
- INSERM UMR-1052, Cancer Research Center of Lyon, Lyon 1 University, Hospices Civils de Lyon, Lyon, France
| | - Michel Ovize
- INSERM UMR-1060, CarMeN Laboratory, Lyon 1 University, INRA U1235, INSA of Lyon, Rockefeller and Charles Merieux Lyon-Sud Medical Universities, Lyon, France Hospices Civils de Lyon, Louis Pradel Hospital, Cardiovascular Functional Explorations Service and CIC of Lyon, Lyon, France
| | - Hubert Vidal
- INSERM UMR-1060, CarMeN Laboratory, Lyon 1 University, INRA U1235, INSA of Lyon, Rockefeller and Charles Merieux Lyon-Sud Medical Universities, Lyon, France Hospices Civils de Lyon, Lyon-Sud Hospital, Endocrinology, Diabetology, and Nutrition Service, Pierre-Bénite, France
| | - Jennifer Rieusset
- INSERM UMR-1060, CarMeN Laboratory, Lyon 1 University, INRA U1235, INSA of Lyon, Rockefeller and Charles Merieux Lyon-Sud Medical Universities, Lyon, France Hospices Civils de Lyon, Lyon-Sud Hospital, Endocrinology, Diabetology, and Nutrition Service, Pierre-Bénite, France
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de Ronde D, Butterbach P, Kormelink R. Dominant resistance against plant viruses. FRONTIERS IN PLANT SCIENCE 2014; 5:307. [PMID: 25018765 PMCID: PMC4073217 DOI: 10.3389/fpls.2014.00307] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 06/10/2014] [Indexed: 05/17/2023]
Abstract
To establish a successful infection plant viruses have to overcome a defense system composed of several layers. This review will overview the various strategies plants employ to combat viral infections with main emphasis on the current status of single dominant resistance (R) genes identified against plant viruses and the corresponding avirulence (Avr) genes identified so far. The most common models to explain the mode of action of dominant R genes will be presented. Finally, in brief the hypersensitive response (HR) and extreme resistance (ER), and the functional and structural similarity of R genes to sensors of innate immunity in mammalian cell systems will be described.
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Affiliation(s)
- Dryas de Ronde
- Laboratory of Virology, Department of Plant Sciences, Wageningen University Wageningen, Netherlands
| | - Patrick Butterbach
- Laboratory of Virology, Department of Plant Sciences, Wageningen University Wageningen, Netherlands
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University Wageningen, Netherlands
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29
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Zambrano JL, Jones MW, Brenner E, Francis DM, Tomas A, Redinbaugh MG. Genetic analysis of resistance to six virus diseases in a multiple virus-resistant maize inbred line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:867-80. [PMID: 24500307 DOI: 10.1007/s00122-014-2263-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 01/03/2014] [Indexed: 05/11/2023]
Abstract
Novel and previously known resistance loci for six phylogenetically diverse viruses were tightly clustered on chromosomes 2, 3, 6 and 10 in the multiply virus-resistant maize inbred line, Oh1VI. Virus diseases in maize can cause severe yield reductions that threaten crop production and food supplies in some regions of the world. Genetic resistance to different viruses has been characterized in maize populations in diverse environments using different screening techniques, and resistance loci have been mapped to all maize chromosomes. The maize inbred line, Oh1VI, is resistant to at least ten viruses, including viruses in five different families. To determine the genes and inheritance mechanisms responsible for the multiple virus resistance in this line, F1 hybrids, F2 progeny and a recombinant inbred line (RIL) population derived from a cross of Oh1VI and the virus-susceptible inbred line Oh28 were evaluated. Progeny were screened for their responses to Maize dwarf mosaic virus, Sugarcane mosaic virus, Wheat streak mosaic virus, Maize chlorotic dwarf virus, Maize fine streak virus, and Maize mosaic virus. Depending on the virus, dominant, recessive, or additive gene effects were responsible for the resistance observed in F1 plants. One to three gene models explained the observed segregation of resistance in the F2 generation for all six viruses. Composite interval mapping in the RIL population identified 17 resistance QTLs associated with the six viruses. Of these, 15 were clustered in specific regions of chr. 2, 3, 6, and 10. It is unknown whether these QTL clusters contain single or multiple virus resistance genes, but the coupling phase linkage of genes conferring resistance to multiple virus diseases in this population could facilitate breeding efforts to develop multi-virus resistant crops.
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Affiliation(s)
- Jose Luis Zambrano
- Department of Horticulture and Crop Science, The Ohio State University-Ohio Agriculture Research and Development Center (OSU-OARDC), Wooster, OH, 44691, USA
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30
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Cosson P, Decroocq V, Revers F. Development and characterization of 96 microsatellite markers suitable for QTL mapping and accession control in an Arabidopsis core collection. PLANT METHODS 2014; 10:2. [PMID: 24447639 PMCID: PMC3899612 DOI: 10.1186/1746-4811-10-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 01/20/2014] [Indexed: 05/14/2023]
Abstract
BACKGROUND To identify plant genes involved in various key traits, QTL mapping is a powerful approach. This approach is based on the use of mapped molecular markers to identify genomic regions controlling quantitative traits followed by a fine mapping and eventually positional cloning of candidate genes. Mapping technologies using SNP markers are still rather expensive and not feasible in every laboratory. In contrast, microsatellite (also called SSR for Simple Sequence Repeat) markers are technologically less demanding and less costly for any laboratory interested in genetic mapping. RESULTS In this study, we present the development and the characterization of a panel of 96 highly polymorphic SSR markers along the Arabidopsis thaliana genome allowing QTL mapping among accessions of the Versailles 24 core collection that covers a high percentage of the A. thaliana genetic diversity. These markers can be used for any QTL mapping analysis involving any of these accessions. We optimized the use of these markers in order to reveal polymorphism using standard PCR conditions and agarose gel electrophoresis. In addition, we showed that the use of only three of these markers allows differentiating all 24 accessions which makes this set of markers a powerful tool to control accession identity or any cross between any of these accessions. CONCLUSION The set of SSR markers developed in this study provides a simple and efficient tool for any laboratory focusing on QTL mapping in A. thaliana and a simple means to control seed stock or crosses between accessions.
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Affiliation(s)
- Patrick Cosson
- INRA, UMR 1332 de Biologie du fruit et Pathologie, Villenave d’Ornon, F-33140, France
- Univ Bordeaux, UMR 1332 de Biologie du fruit et Pathologie, Villenave d’Ornon, F-33140, France
| | - Véronique Decroocq
- INRA, UMR 1332 de Biologie du fruit et Pathologie, Villenave d’Ornon, F-33140, France
- Univ Bordeaux, UMR 1332 de Biologie du fruit et Pathologie, Villenave d’Ornon, F-33140, France
| | - Frédéric Revers
- INRA, UMR 1332 de Biologie du fruit et Pathologie, Villenave d’Ornon, F-33140, France
- Univ Bordeaux, UMR 1332 de Biologie du fruit et Pathologie, Villenave d’Ornon, F-33140, France
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31
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Ouibrahim L, Caranta C. Exploitation of natural genetic diversity to study plant-virus interactions: what can we learn from Arabidopsis thaliana? MOLECULAR PLANT PATHOLOGY 2013; 14:844-54. [PMID: 23790151 PMCID: PMC6638744 DOI: 10.1111/mpp.12052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The development and use of cultivars that are genetically resistant to viruses is an efficient strategy to tackle the problems of virus diseases. Over the past two decades, the model plant Arabidopsis thaliana has been documented as a host for a broad range of viral species, providing access to a large panel of resources and tools for the study of viral infection processes and resistance mechanisms. Exploration of its natural genetic diversity has revealed a wide range of genes conferring virus resistance. The molecular characterization of some of these genes has unveiled resistance mechanisms distinct from those described in crops. In these respects, Arabidopsis represents a rich and largely untapped source of new genes and mechanisms involved in virus resistance. Here, we review the current status of our knowledge concerning natural virus resistance in Arabidopsis. We also address the impact of environmental conditions on Arabidopsis-virus interactions and resistance mechanisms, and discuss the potential of applying the knowledge gained from the study of Arabidopsis natural diversity for crop improvement.
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Affiliation(s)
- Laurence Ouibrahim
- Laboratoire de Génétique et Biophysique des Plantes, UMR 7265, CEA/CNRS, Aix Marseille Université, Faculté des Sciences de Luminy, 163 Avenue de Luminy, Marseille, France
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32
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Zuriaga E, Soriano JM, Zhebentyayeva T, Romero C, Dardick C, Cañizares J, Badenes ML. Genomic analysis reveals MATH gene(s) as candidate(s) for Plum pox virus (PPV) resistance in apricot (Prunus armeniaca L.). MOLECULAR PLANT PATHOLOGY 2013; 14:663-77. [PMID: 23672686 PMCID: PMC6638718 DOI: 10.1111/mpp.12037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Sharka disease, caused by Plum pox virus (PPV), is the most important viral disease affecting Prunus species. A major PPV resistance locus (PPVres) has been mapped to the upper part of apricot (Prunus armeniaca) linkage group 1. In this study, a physical map of the PPVres locus in the PPV-resistant cultivar 'Goldrich' was constructed. Bacterial artificial chromosome (BAC) clones belonging to the resistant haplotype contig were sequenced using 454/GS-FLX Titanium technology. Concurrently, the whole genome of seven apricot varieties (three PPV-resistant and four PPV-susceptible) and two PPV-susceptible apricot relatives (P. sibirica var. davidiana and P. mume) were obtained using the Illumina-HiSeq2000 platform. Single nucleotide polymorphisms (SNPs) within the mapped interval, recorded from alignments against the peach genome, allowed us to narrow down the PPVres locus to a region of ∼196 kb. Searches for polymorphisms linked in coupling with the resistance led to the identification of 68 variants within 23 predicted transcripts according to peach genome annotation. Candidate resistance genes were ranked combining data from variant calling and predicted functions inferred from sequence homology. Together, the results suggest that members of a cluster of meprin and TRAF-C homology domain (MATHd)-containing proteins are the most likely candidate genes for PPV resistance in apricot. Interestingly, MATHd proteins are hypothesized to control long-distance movement (LDM) of potyviruses in Arabidopsis, and restriction for LDM is also a major component of PPV resistance in apricot. Although the PPV resistance gene(s) remains to be unambiguously identified, these results pave the way to the determination of the underlying mechanism and to the development of more accurate breeding strategies.
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Affiliation(s)
- Elena Zuriaga
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial, 46113 Moncada, Valencia, Spain
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Molecular cloning and differential expression of sHSP gene family members from the resurrection plant Boea hygrometrica in response to abiotic stresses. Biologia (Bratisl) 2013. [DOI: 10.2478/s11756-013-0204-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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34
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Hipper C, Brault V, Ziegler-Graff V, Revers F. Viral and cellular factors involved in Phloem transport of plant viruses. FRONTIERS IN PLANT SCIENCE 2013; 4:154. [PMID: 23745125 PMCID: PMC3662875 DOI: 10.3389/fpls.2013.00154] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 05/05/2013] [Indexed: 05/03/2023]
Abstract
Phloem transport of plant viruses is an essential step in the setting-up of a complete infection of a host plant. After an initial replication step in the first cells, viruses spread from cell-to-cell through mesophyll cells, until they reach the vasculature where they rapidly move to distant sites in order to establish the infection of the whole plant. This last step is referred to as systemic transport, or long-distance movement, and involves virus crossings through several cellular barriers: bundle sheath, vascular parenchyma, and companion cells for virus loading into sieve elements (SE). Viruses are then passively transported within the source-to-sink flow of photoassimilates and are unloaded from SE into sink tissues. However, the molecular mechanisms governing virus long-distance movement are far from being understood. While most viruses seem to move systemically as virus particles, some viruses are transported in SE as viral ribonucleoprotein complexes (RNP). The nature of the cellular and viral factors constituting these RNPs is still poorly known. The topic of this review will mainly focus on the host and viral factors that facilitate or restrict virus long-distance movement.
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Affiliation(s)
| | | | - Véronique Ziegler-Graff
- Laboratoire Propre du CNRS (UPR 2357), Virologie Végétale, Institut de Biologie Moléculaire des Plantes, Université de StrasbourgStrasbourg, France
| | - Frédéric Revers
- UMR 1332 de Biologie du Fruit et Pathologie, INRA, Université de BordeauxVillenave d’Ornon, France
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35
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Contreras-Paredes CA, Silva-Rosales L, Daròs JA, Alejandri-Ramírez ND, Dinkova TD. The absence of eukaryotic initiation factor eIF(iso)4E affects the systemic spread of a Tobacco etch virus isolate in Arabidopsis thaliana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:461-70. [PMID: 23252462 DOI: 10.1094/mpmi-09-12-0225-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Translation initiation factor eIF4E exerts an important role during infection of viral species in the family Potyviridae. Particularly, a eIF(iso)4E family member is required for Arabidopsis thaliana susceptibility to Turnip mosaic virus, Lettuce mosaic virus, and Tobacco etch virus (TEV). In addition, a resistance mechanism named restriction of TEV movement (RTM) in A. thaliana controls the systemic spread of TEV in Col-0 ecotype. Here, we describe that TEV-TAMPS, a Mexican isolate, overcomes the RTM resistance mechanism reported for TEV-7DA infection of the Col-0 ecotype but depends on eIF(iso)4E for its systemic spread. To understand at which level eIF(iso)4E participates in A. thaliana TEV-TAMPS infection, the viral RNA replication and translation were measured. The absence or overexpression of eIF(iso)4E did not affect viral translation, and replication was still observed in the absence of eIF(iso)4E. However, the TEV-TAMPS systemic spread was completely abolished in the null mutant. The viral protein genome-linked (VPg) precursor NIa was found in coimmunoprecipitated complexes with both, eIF(iso)4E and eIF4E. However, the viral coat protein (CP) was only present in the eIF(iso)4E complexes. Since both the VPg and the CP proteins are needed for systemic spread, we propose a role of A. thaliana eIF(iso)4E in the movement of TEV-TAMPS within this host.
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Jones MW, Boyd EC, Redinbaugh MG. Responses of maize (Zea mays L.) near isogenic lines carrying Wsm1, Wsm2, and Wsm3 to three viruses in the Potyviridae. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:729-740. [PMID: 21667271 DOI: 10.1007/s11032-012-9789-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Accepted: 05/14/2011] [Indexed: 05/29/2023]
Abstract
Genes on chromosomes six (Wsm1), three (Wsm2) and ten (Wsm3) in the maize (Zea mays L.) inbred line Pa405 control resistance to Wheat streak mosaic virus (WSMV), and the same or closely linked genes control resistance to Maize dwarf mosaic virus (MDMV) and Sugarcane mosaic virus (SCMV). Near isogenic lines (NIL) carrying one or two of the genes were developed by introgressing regions of the respective chromosomes into the susceptible line Oh28 and tested for their responses to WSMV, MDMV, and SCMV in the field and greenhouse. F(1) progeny from NIL × Oh28 were also tested. Wsm1, or closely linked genes, provided resistance to all three viruses, as determined by symptom incidence and severity. Wsm2 and Wsm3 provided resistance to WSMV. Wsm2 and/or Wsm3 provided no resistance to MDMV, but significantly increased resistance in plants with one Wsm1 allele. NIL carrying Wsm1, Wsm2, or Wsm3 had similar SCMV resistance in the field, but NIL with Wsm2 and Wsm3 were not resistant in the greenhouse. Addition of Wsm2 to Wsm1 increased SCMV resistance in the field. For all viruses, symptom incidence was higher in the greenhouse than in the field, and relative disease severity was higher in the greenhouse for WSMV and MDMV. An Italian MDMV isolate and the Ohio SCMV infected the Wsm1 NIL, while the Ohio MDMV and Seehausen SCMV isolates did not. Our results indicate that the three genes, or closely linked loci, provide virus resistance. Resistance conferred by the three genes is influenced by interactions among the genes, the virus species, the virus isolate, and the environment.
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Affiliation(s)
- Mark W Jones
- Corn and Soybean Research Unit, USDA, Agricultural Research Service, Wooster, OH 44691, USA
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