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Wrzesińska-Krupa B, Obrępalska-Stęplowska A. Small non-coding satellite RNAs - the 'game changers' at the virus-host plant interaction? Biol Rev Camb Philos Soc 2024. [PMID: 39054260 DOI: 10.1111/brv.13125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/03/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Satellite RNAs (satRNAs) are RNA molecules associated with many plant viruses and fully dependent on them for replication, encapsidation, and movement within the plant or transmission from plant to plant. Their classification is based on their length, functional protein-coding capacity, and RNA structure (whether linear or circular). They have been of interest for a long time as some of them, in particular systems, cause significant changes in the pathogenesis and epidemiology of plant viruses. The outcomes of how satRNAs affect pathogenesis depend on the components of the pathosystem: host plant species or variety, virus species or even strain, and the sequence of satRNA. These can be additionally affected by biotic and abiotic factors, for example, environmental conditions such as the presence of their vectors or ambient temperature. satRNAs may interfere with primary metabolism, signalling, plant defence [including post-transcriptional gene silencing (PTGS)], as well as the efficiency of virus transmission from plant to plant. In recent years, due to wider access to high-throughput technologies and the extension of studies on satRNAs to include the involvement of external factors in plant-virus-satRNA systems, we are gaining a broader view of the consequences of the presence of these small molecules in viral infections. This review presents the state of the art of satRNA interactions with the helper virus and host plant as well as the influence of satRNAs on the insect vector's behaviour. Moreover, areas requiring further research are identified and knowledge gaps indicated.
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Affiliation(s)
- Barbara Wrzesińska-Krupa
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection - National Research Institute, Władysława Węgorka 20, Poznań, 60-318, Poland
| | - Aleksandra Obrępalska-Stęplowska
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection - National Research Institute, Władysława Węgorka 20, Poznań, 60-318, Poland
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Molecular analysis of Greek isolates of cucumber mosaic virus from vegetables shows a low prevalence of satellite RNAs and suggests the presence of host-associated virus strains. Arch Virol 2021; 166:2199-2208. [PMID: 34057609 DOI: 10.1007/s00705-021-05115-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/06/2021] [Indexed: 01/27/2023]
Abstract
Cucumber mosaic virus (CMV) is a generalist pathogen that infects many economically important crops in Greece. The present study was designed to evaluate the genetic variability of Greek CMV isolates in combination with their satellite RNAs (satRNAs). To achieve this goal, 77 CMV isolates were collected from symptomatic Greek vegetables, mainly tomatoes and cucurbits, alongside their neighboring crops, during a four-year period from 2015 to 2018. Phylogenetic analysis of a partial coat protein (CP) gene segment revealed that all of the isolates belong to CMV subgroups IA and IB and that they are closely related to previously reported Greek isolates. It should be noted, however, that the latter mainly included tomato isolates. Network analysis of the evolutionary relationships among the CP sequences of the Greek isolates in comparison to the corresponding sequences obtained from the GenBank database indicated two predominant common ancestors and at least three differentiated peripherals, and possibly host-associated (tomatoes, legumes, cucurbits) haplogroups (strain groups). More specifically, host-adaptive evolution can be postulated regarding the tomato isolates in subgroup IB. Necrogenic or non-necrogenic satRNAs were detected in four samples from tomato and melon, and this is the first report of non-necrogenic satRNAs in CMV in Greece.
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McLeish MJ, Fraile A, García-Arenal F. Population Genomics of Plant Viruses: The Ecology and Evolution of Virus Emergence. PHYTOPATHOLOGY 2021; 111:32-39. [PMID: 33210987 DOI: 10.1094/phyto-08-20-0355-fi] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The genomics era has revolutionized studies of adaptive evolution by monitoring large numbers of loci throughout the genomes of many individuals. Ideally, the investigation of emergence in plant viruses requires examining the population dynamics of both virus and host, their interactions with each other, with other organisms and the abiotic environment. Genetic mechanisms that affect demographic processes are now being studied with high-throughput technologies, traditional genetics methods, and new computational tools for big-data. In this review, we discuss the utility of these approaches to monitor and detect changes in virus populations within cells and individuals, and over wider areas across species and communities of ecosystems. The advent of genomics in virology has fostered a multidisciplinary approach to tackling disease risk. The ability to make sense of the information now generated in this integrated setting is by far the most substantial obstacle to the ultimate goal of plant virology to minimize the threats to food security posed by disease. To achieve this goal, it is imperative to understand and forecast how populations respond to future changes in complex natural systems.
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Affiliation(s)
- Michael J McLeish
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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Gallet R, Michalakis Y, Blanc S. Vector-transmission of plant viruses and constraints imposed by virus–vector interactions. Curr Opin Virol 2018; 33:144-150. [DOI: 10.1016/j.coviro.2018.08.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/01/2018] [Accepted: 08/08/2018] [Indexed: 11/26/2022]
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Giakountis A, Tsarmpopoulos I, Chatzivassiliou EK. Cucumber mosaic virus Isolates from Greek Legumes are Associated with Satellite RNAs that are Necrogenic for Tomato. PLANT DISEASE 2018; 102:2268-2276. [PMID: 30189158 DOI: 10.1094/pdis-08-17-1259-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Worldwide, Cucumber mosaic virus (CMV) is the causal agent of many economically important diseases. Based on immunological or molecular analysis, three distinct subgroups of CMV isolates can be identified (IA, IB, and II). In addition, some CMV isolates are associated with satellite RNAs (satRNAs), a type of noncoding transcript that may alter the symptoms of CMV infections. This study presents an analysis of CMV isolates occurring in legumes in Greece in respect to their genetic diversity, and the presence and diversity of their satRNA. Phylogenetic analysis of the CMV coat protein sequence of 18 legume and 5 tomato CMV isolates collected throughout Greece classified them within subgroups IA and IB, with a limited genetic diversity. The CMV satRNAs found in nine field legumes exhibiting mild symptoms and in one tomato with a necrotic syndrome contained a functional necrogenic motif; therefore, they were grouped within the necrogenic group of CMV-satRNAs. The necrotic phenotype was expressed in all legume CMV isolates containing necrogenic satRNAs when mechanically inoculated onto tomato plants. To our knowledge, this is the first observation that legumes host necrogenic CMV-satRNAs. The possible role of legumes in the epidemiology of CMV and necrogenic satRNA complex is discussed.
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Affiliation(s)
- Antonis Giakountis
- Agricultural University of Athens, School of Agricultural Production, Infrastructure and Environment, Department of Crop Science, Plant Pathology Laboratory, Iera Odos 75, Votanikos, 11855 Athens, Greece
| | - Iason Tsarmpopoulos
- Agricultural University of Athens, School of Agricultural Production, Infrastructure and Environment, Department of Crop Science, Plant Pathology Laboratory, Iera Odos 75, Votanikos, 11855 Athens, Greece
| | - Elisavet K Chatzivassiliou
- Agricultural University of Athens, School of Agricultural Production, Infrastructure and Environment, Department of Crop Science, Plant Pathology Laboratory, Iera Odos 75, Votanikos, 11855 Athens, Greece
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Lucía-Sanz A, Aguirre J, Manrubia S. Theoretical approaches to disclosing the emergence and adaptive advantages of multipartite viruses. Curr Opin Virol 2018; 33:89-95. [PMID: 30121469 DOI: 10.1016/j.coviro.2018.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/19/2018] [Accepted: 07/31/2018] [Indexed: 01/02/2023]
Abstract
Multipartite viruses have a segmented genome encapsidated in different viral particles that, in principle, propagate independently. Current empirical knowledge on the molecular, ecological and evolutionary features underlying the very existence of multipartitism is fragmented and puzzling. Although it is generally assumed that multipartitism is viable only when propagation occurs at high multiplicity of infection, evidence indicates that severe population bottlenecks are common. Mathematical models aimed at describing the dynamics of multipartite viruses typically assign an advantage to the multipartite form to compensate for the cost of high multiplicity of infection. Since progress in the theoretical understanding of the evolutionary ecology of multipartitism is strongly conditioned by empirical advances, both aspects are jointly revised in this contribution.
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Affiliation(s)
- Adriana Lucía-Sanz
- Spanish National Centre for Biotechnology (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| | - Jacobo Aguirre
- Spanish National Centre for Biotechnology (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| | - Susanna Manrubia
- Spanish National Centre for Biotechnology (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
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Boissot N, Schoeny A, Vanlerberghe-Masutti F. Vat, an Amazing Gene Conferring Resistance to Aphids and Viruses They Carry: From Molecular Structure to Field Effects. FRONTIERS IN PLANT SCIENCE 2016; 7:1420. [PMID: 27725823 PMCID: PMC5035753 DOI: 10.3389/fpls.2016.01420] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/06/2016] [Indexed: 05/20/2023]
Abstract
We review half a century of research on Cucumis melo resistance to Aphis gossypii from molecular to field levels. The Vat gene is unique in conferring resistance to both A. gossypii and the viruses it transmits. This double phenotype is aphid clone-dependent and has been observed in 25 melon accessions, mostly from Asia. It is controlled by a cluster of genes including CC-NLR, which has been characterized in detail. Copy-number polymorphisms (for the whole gene and for a domain that stands out in the LLR region) and single-nucleotide polymorphisms have been identified in the Vat cluster. The role of these polymorphisms in plant/aphid interactions remains unclear. The Vat gene structure suggests a functioning with separate recognition and response phases. During the recognition phase, the VAT protein is thought to interact (likely indirectly) with an aphid effector introduced during cell puncture by the aphid. A few hours later, several miRNAs are upregulated in Vat plants. Peroxidase activity increases, and callose and lignin are deposited in the walls of the cells adjacent to the stylet path, disturbing aphid behavior. In aphids feeding on Vat plants, Piwi-interacting RNA-like sequences are abundant and the levels of other miRNAs are modified. At the plant level, resistance to aphids is quantitative (aphids escape the plant and display low rates of reproduction). Resistance to viruses is qualitative and local. Durability of NLR genes is highly variable. A. gossypii clones are adapted to Vat resistance, either by introducing a new effector that interferes with the deployment of plant defenses, or by adapting to the defenses it triggered. Viruses transmitted in a non-persistent manner cannot adapt to Vat resistance. At population level, Vat reduces aphid density and genetic diversity. The durability of Vat resistance to A. gossypii populations depends strongly on the agro-ecosystem, including, in particular, the presence of other cucurbit crops serving as alternative hosts for adapted clones in fall and winter. At the crop level, Vat resistance decreases the intensity of virus epidemics when A. gossypii is the main aphid vector in the crop environment.
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Affiliation(s)
- Nathalie Boissot
- Génétique et Amélioration des Fruits et Légumes, INRAMontfavet, France
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