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Cuevas-Zuviria B, Fraile A, García-Arenal F. An Agent-Based Model Shows How Mixed Infections Drive Multiyear Pathotype Dynamics in a Plant-Virus System. PHYTOPATHOLOGY 2024; 114:1276-1288. [PMID: 38330173 DOI: 10.1094/phyto-06-23-0214-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Mathematical models are widely used to understand the evolution and epidemiology of plant pathogens under a variety of scenarios. Here, we used this approach to analyze the effects of different traits intrinsic and extrinsic to plant-virus interactions on the dynamics of virus pathotypes in genetically heterogeneous plant-virus systems. For this, we propose an agent-based epidemiological model that includes epidemiologically significant pathogen life-history traits related to virulence, transmission, and survival in the environment and allows for integrating long- and short-distance transmission, primary and secondary infections, and within-host pathogen competition in mixed infections. The study focuses on the tobamovirus-pepper pathosystem. Model simulations allowed us to integrate pleiotropic effects of resistance-breaking mutations on different virus life-history traits into the net costs of resistance breaking, allowing for predictions on multiyear pathotype dynamics. We also explored the effects of two control measures, the use of host resistance and roguing of symptomatic plants, that modify epidemiological attributes of the pathogens to understand how their populations will respond to evolutionary pressures. One major conclusion points to the importance of pathogen competition within mixed-infected hosts as a component of the overall fitness of each pathogen that, thus, drives their multiyear dynamics.
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Affiliation(s)
- Bruno Cuevas-Zuviria
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) 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 UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) 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 UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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Wendlandt T, Britz B, Kleinow T, Hipp K, Eber FJ, Wege C. Getting Hold of the Tobamovirus Particle-Why and How? Purification Routes over Time and a New Customizable Approach. Viruses 2024; 16:884. [PMID: 38932176 PMCID: PMC11209083 DOI: 10.3390/v16060884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
This article develops a multi-perspective view on motivations and methods for tobamovirus purification through the ages and presents a novel, efficient, easy-to-use approach that can be well-adapted to different species of native and functionalized virions. We survey the various driving forces prompting researchers to enrich tobamoviruses, from the search for the causative agents of mosaic diseases in plants to their increasing recognition as versatile nanocarriers in biomedical and engineering applications. The best practices and rarely applied options for the serial processing steps required for successful isolation of tobamoviruses are then reviewed. Adaptations for distinct particle species, pitfalls, and 'forgotten' or underrepresented technologies are considered as well. The article is topped off with our own development of a method for virion preparation, rooted in historical protocols. It combines selective re-solubilization of polyethylene glycol (PEG) virion raw precipitates with density step gradient centrifugation in biocompatible iodixanol formulations, yielding ready-to-use particle suspensions. This newly established protocol and some considerations for perhaps worthwhile further developments could serve as putative stepping stones towards preparation procedures appropriate for routine practical uses of these multivalent soft-matter nanorods.
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Affiliation(s)
- Tim Wendlandt
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (B.B.); (T.K.)
| | - Beate Britz
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (B.B.); (T.K.)
| | - Tatjana Kleinow
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (B.B.); (T.K.)
| | - Katharina Hipp
- Electron Microscopy Facility, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany;
| | - Fabian J. Eber
- Department of Mechanical and Process Engineering, Offenburg University of Applied Sciences, Badstr. 24, 77652 Offenburg, Germany;
| | - Christina Wege
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (B.B.); (T.K.)
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de Andrés-Torán R, Guidoum L, Zamfir AD, Mora MÁ, Moreno-Vázquez S, García-Arenal F. Tobacco Mild Green Mosaic Virus (TMGMV) Isolates from Different Plant Families Show No Evidence of Differential Adaptation to Their Host of Origin. Viruses 2023; 15:2384. [PMID: 38140625 PMCID: PMC10748040 DOI: 10.3390/v15122384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
The relevance of tobamoviruses to crop production is increasing due to new emergences, which cannot be understood without knowledge of the tobamovirus host range and host specificity. Recent analyses of tobamovirus occurrence in different plant communities have shown unsuspectedly large host ranges. This was the case of the tobacco mild green mosaic virus (TMGMV), which previously was most associated with solanaceous hosts. We addressed two hypotheses concerning TMGMV host range evolution: (i) ecological fitting, rather than genome evolution, determines TMGMV host range, and (ii) isolates are adapted to the host of origin. We obtained TMGMV isolates from non-solanaceous hosts and we tested the capacity of genetically closely related TMGMV isolates from three host families to infect and multiply in 10 hosts of six families. All isolates systemically infected all hosts, with clear disease symptoms apparent only in solanaceous hosts. TMGMV multiplication depended on the assayed host but not on the isolate's host of origin, with all isolates accumulating to the highest levels in Nicotiana tabacum. Thus, results support that TMGMV isolates are adapted to hosts in the genus Nicotiana, consistent with a well-known old virus-host association. In addition, phenotypic plasticity allows Nicotiana-adapted TMGMV genotypes to infect a large range of hosts, as encountered according to plant community composition and transmission dynamics.
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Affiliation(s)
- Rafael de Andrés-Torán
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM_INIA/CSIC), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.d.A.-T.); (L.G.); (A.D.Z.); (M.Á.M.)
| | - Laura Guidoum
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM_INIA/CSIC), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.d.A.-T.); (L.G.); (A.D.Z.); (M.Á.M.)
| | - Adrian D. Zamfir
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM_INIA/CSIC), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.d.A.-T.); (L.G.); (A.D.Z.); (M.Á.M.)
| | - Miguel Ángel Mora
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM_INIA/CSIC), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.d.A.-T.); (L.G.); (A.D.Z.); (M.Á.M.)
| | - Santiago Moreno-Vázquez
- Departamento de Biotecnología-Biología Vegetal, E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro 2-4, 28040 Madrid, Spain;
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM_INIA/CSIC), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.d.A.-T.); (L.G.); (A.D.Z.); (M.Á.M.)
- Departamento de Biotecnología-Biología Vegetal, E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro 2-4, 28040 Madrid, Spain;
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Zamfir AD, Babalola BM, Fraile A, McLeish MJ, García-Arenal F. Tobamoviruses Show Broad Host Ranges and Little Genetic Diversity Among Four Habitat Types of a Heterogeneous Ecosystem. PHYTOPATHOLOGY 2023; 113:1697-1707. [PMID: 36916761 DOI: 10.1094/phyto-11-22-0439-v] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Host ranges of plant viruses are poorly known, as studies have focused on pathogenic viruses in crops and adjacent wild plants. High-throughput sequencing (HTS) avoids the bias toward plant-virus interactions that result in disease. Here we study the host ranges of tobamoviruses, important pathogens of crops, using HTS analyses of an extensive sample of plant communities in four habitats of a heterogeneous ecosystem. Sequences of 17 virus operational taxonomic units (OTUs) matched references in the Tobamovirus genus, eight had narrow host ranges, and five had wide host ranges. Regardless of host range, the OTU hosts belonged to taxonomically distant families, suggesting no phylogenetic constraints in host use associated with virus adaptation, and that tobamoviruses may be host generalists. The OTUs identified as tobacco mild green mosaic virus (TMGMV), tobacco mosaic virus (TMV), pepper mild mottle virus, and Youcai mosaic virus had the largest realized host ranges that occurred across habitats and exhibited host use unrelated to the degree of human intervention. This result is at odds with assumptions that contact-transmitted viruses would be more abundant in crops than in wild plant communities and could be explained by effective seed-, contact-, or pollinator-mediated transmission or by survival in the soil. TMGMV and TMV had low genetic diversity that was not structured according to habitat or host plant taxonomy, which indicated that phenotypic plasticity allows virus genotypes to infect new hosts with no need for adaptive evolution. Our results underscore the relevance of ecological factors in host range evolution, in addition to the more often studied genetic factors. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Adrián D Zamfir
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Bisola M Babalola
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC) 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-CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - 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-CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA 5005, Australia
| | - 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-CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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Rivarez MPS, Pecman A, Bačnik K, Maksimović O, Vučurović A, Seljak G, Mehle N, Gutiérrez-Aguirre I, Ravnikar M, Kutnjak D. In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem. MICROBIOME 2023; 11:60. [PMID: 36973750 PMCID: PMC10042675 DOI: 10.1186/s40168-023-01500-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 02/20/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known. Extensive virome explorations that include both crop and diverse weed plants are therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is available through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data. RESULTS Here, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of the same species. We phylogenetically classified novel viruses and showed links between a subgroup of phylogenetically related rhabdoviruses to their taxonomically related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs and that these viruses could be exchanged between the two compartments. CONCLUSIONS We showed that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases and would serve as baseline for further post-discovery characterization studies. Video Abstract.
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Affiliation(s)
- Mark Paul Selda Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
- Jožef Stefan International Postgraduate School, Jamova cesta 39, Ljubljana, 1000 Slovenia
- Present Address: College of Agriculture and Agri-Industries, Caraga State University, Ampayon, Butuan City, 8600 Philippines
| | - Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
- Jožef Stefan International Postgraduate School, Jamova cesta 39, Ljubljana, 1000 Slovenia
| | - Katarina Bačnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Olivera Maksimović
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
- Jožef Stefan International Postgraduate School, Jamova cesta 39, Ljubljana, 1000 Slovenia
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Gabrijel Seljak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
- School for Viticulture and Enology, University of Nova Gorica, Dvorec Lanthieri Glavni trg 8, Vipava, 5271 Slovenia
| | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
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To Be Seen or Not to Be Seen: Latent Infection by Tobamoviruses. PLANTS 2022; 11:plants11162166. [PMID: 36015469 PMCID: PMC9415976 DOI: 10.3390/plants11162166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Tobamoviruses are among the most well-studied plant viruses and yet there is still a lot to uncover about them. On one side of the spectrum, there are damage-causing members of this genus: such as the tobacco mosaic virus (TMV), tomato brown rugose fruit virus (ToBRFV) and cucumber green mottle mosaic virus (CGMMV), on the other side, there are members which cause latent infection in host plants. New technologies, such as high-throughput sequencing (HTS), have enabled us to discover viruses from asymptomatic plants, viruses in mixed infections where the disease etiology cannot be attributed to a single entity and more and more researchers a looking at non-crop plants to identify alternative virus reservoirs, leading to new virus discoveries. However, the diversity of these interactions in the virosphere and the involvement of multiple viruses in a single host is still relatively unclear. For such host–virus interactions in wild plants, symptoms are not always linked with the virus titer. In this review, we refer to latent infection as asymptomatic infection where plants do not suffer despite systemic infection. Molecular mechanisms related to latent behavior of tobamoviruses are unknown. We will review different studies which support different theories behind latency.
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Abdelkhalek A, Aseel DG, Király L, Künstler A, Moawad H, Al-Askar AA. Induction of Systemic Resistance to Tobacco mosaic virus in Tomato through Foliar Application of Bacillus amyloliquefaciens Strain TBorg1 Culture Filtrate. Viruses 2022; 14:v14081830. [PMID: 36016452 PMCID: PMC9416369 DOI: 10.3390/v14081830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 12/26/2022] Open
Abstract
The application of microbe-derived products as natural biocontrol agents to boost systemic disease resistance to virus infections in plants is a prospective strategy to make agriculture more sustainable and environmentally friendly. In the current study, the rhizobacterium Bacillus amyloliquefaciens strain TBorg1 was identified based on 16S rRNA, rpoB, and gyrA gene sequences, and evaluated for its efficiency in conferring protection of tomato from infection by Tobacco mosaic virus (TMV). Under greenhouse circumstances, foliar sprays of TBorg1 culture filtrate (TBorg1-CF) promoted tomato growth, lowered disease severity, and significantly decreased TMV accumulation in systemically infected leaves of treated plants relative to untreated controls. TMV accumulation was reduced by 90% following the dual treatment, applied 24 h before and after TMV infection. Significant increases in levels of total soluble carbohydrates, proteins, and ascorbic acid were also found. In addition, a significant rise in activities of enzymes capable of scavenging reactive oxygen species (PPO and POX), as well as decreased levels of non-enzymatic oxidative stress markers (H2O2 and MDA) were observed, compared to untreated plants. Enhanced systemic resistance to TMV was indicated by significantly increased transcript accumulation of polyphenolic pathway (C4H, HCT, and CHI) and pathogenesis-related (PR-1 and PR-5) genes. Out of the 15 compounds identified in the GC-MS analysis, 1,2-benzenedicarboxylic acid mono(2-ethylhexyl) ester and phenol, 2,4-bis(1,1-dimethylethyl), as well as L-proline, N-valeryl-, and heptadecyl ester were present in the highest concentrations in the ethyl acetate extract of TBorg1-CF. In addition, significant amounts of n-hexadecanoic acid, pyrrolo [1,2-a] pyrazine-1,4-dione hexahydro-3-(2-methylpropyl)-, nonane, 5-butyl-, and eicosane were also detected. These compounds may act as inducers of systemic resistance to viral infection. Our findings indicate that the newly isolated B. amyloliquefaciens strain TBorg1 could be a potentially useful rhizobacterium for promoting plant growth and a possible source of biocontrol agents for combating plant virus infections.
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Affiliation(s)
- Ahmed Abdelkhalek
- Plant Protection and Biomolecular Diagnosis Department, ALCRI, City of Scientific Research and Technological Applications, New Borg El Arab City 21934, Egypt
- Correspondence: ; Tel.: +20-1007556883
| | - Dalia G. Aseel
- Plant Protection and Biomolecular Diagnosis Department, ALCRI, City of Scientific Research and Technological Applications, New Borg El Arab City 21934, Egypt
| | - Lóránt Király
- Centre for Agricultural Research, Plant Protection Institute, ELKH, P.O. Box 102, H-1022 Budapest, Hungary
| | - András Künstler
- Centre for Agricultural Research, Plant Protection Institute, ELKH, P.O. Box 102, H-1022 Budapest, Hungary
| | - Hassan Moawad
- Agriculture Microbiology Department, National Research Centre, Cairo 12622, Egypt
| | - Abdulaziz A. Al-Askar
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Complete genome sequence of a novel virga-like virus infecting Hevea brasiliensis. Arch Virol 2022; 167:965-968. [PMID: 35112201 DOI: 10.1007/s00705-021-05306-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/08/2021] [Indexed: 11/02/2022]
Abstract
Here, we report the complete genome sequence and organization of a novel virus detected in rubber trees (Hevea brasiliensis). Because the infected plants were asymptomatic, this virus was tentatively named "rubber tree latent virus 1" (RTLV1). The full genome of RTLV1 is 9,422 nt in length and contains three open reading frames with a 157-nt 5' untranslated region (UTR) and a 316-nt 3' UTR. The replicase shares the highest amino acid (aa) sequence identity (32.62%), with only 31% query coverage, with the replicase of Hubei virga-like virus 11. Phylogenetic analysis based on the aa sequence of ORF1 showed that RTLV1 clustered with unclassified members of the family Virgaviridae in a clade that was not closely related to any genus in this family.
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Koonin EV, Dolja VV, Krupovic M, Kuhn JH. Viruses Defined by the Position of the Virosphere within the Replicator Space. Microbiol Mol Biol Rev 2021; 85:e0019320. [PMID: 34468181 PMCID: PMC8483706 DOI: 10.1128/mmbr.00193-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Originally, viruses were defined as miniscule infectious agents that passed through filters that retain even the smallest cells. Subsequently, viruses were considered obligate intracellular parasites whose reproduction depends on their cellular hosts for energy supply and molecular building blocks. However, these features are insufficient to unambiguously define viruses as they are broadly understood today. We outline possible approaches to define viruses and explore the boundaries of the virosphere within the virtual space of replicators and the relationships between viruses and other types of replicators. Regardless of how, exactly, viruses are defined, viruses clearly have evolved on many occasions from nonviral replicators, such as plasmids, by recruiting host proteins to become virion components. Conversely, other types of replicators have repeatedly evolved from viruses. Thus, the virosphere is a dynamic entity with extensive evolutionary traffic across its boundaries. We argue that the virosphere proper, here termed orthovirosphere, consists of a distinct variety of replicators that encode structural proteins encasing the replicators' genomes, thereby providing protection and facilitating transmission among hosts. Numerous and diverse replicators, such as virus-derived but capsidless RNA and DNA elements, or defective viruses occupy the zone surrounding the orthovirosphere in the virtual replicator space. We define this zone as the perivirosphere. Although intense debates on the nature of certain replicators that adorn the internal and external boundaries of the virosphere will likely continue, we present an operational definition of virus that recently has been accepted by the International Committee on Taxonomy of Viruses.
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Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerian V. Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
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Zhao W, Wu S, Du L, Li T, Cheng Z, Zhou Y, Ji Y. Development of a reverse-transcription loop-mediated isothermal amplification assay for the detection of Tobacco mild green mosaic virus (TMGMV). J Virol Methods 2021; 298:114277. [PMID: 34492235 DOI: 10.1016/j.jviromet.2021.114277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 08/02/2021] [Accepted: 09/02/2021] [Indexed: 11/22/2022]
Abstract
Tobacco mild green mosaic virus (TMGMV), a member species of the genus Tobamovirus, infects pepper (Capsicum annuum) and a number of other economically important species in the Solanaceae family. TMGMV infections had seriously impacted pepper production worldwide, including China. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect TMGMV in pepper field samples and seed. This assay was based on four primers that matched to six sequences in the C-terminal region of the TMGMV genome. RT-LAMP assay could detect the presence of the virus in 3.0 × 10-7 µg of total RNA extract from pepper leaves, which was ten times more sensitive than the corresponding reverse-transcription polymerase chain reaction (RT-PCR) assay. This method specifically detected TMGMV but not the closely related species of the same genus Pepper mild mottle virus, Cucumber green mottle mosaic virus and Tomato mosaic virus. In addition, the use of SYBR Green I facilitated the detection of the TMGMV RT-LAMP products by the naked eye. These results indicated that the RT-LAMP assay was a simple, sensitive, specific and affordable diagnostic tool that has the potential to detect and monitor TMGMV infection in field samples.
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Affiliation(s)
- Wenhao Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Shuhua Wu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Linlin Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Tingfang Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Zhaobang Cheng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Yijun Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Yinghua Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China.
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11
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Bera S, Blundell R, Liang D, Crowder DW, Casteel CL. The Oxylipin Signaling Pathway Is Required for Increased Aphid Attraction and Retention on Virus-Infected Plants. J Chem Ecol 2020; 46:771-781. [PMID: 32065342 DOI: 10.1007/s10886-020-01157-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/19/2020] [Accepted: 01/27/2020] [Indexed: 11/26/2022]
Abstract
Many studies have shown that virus infection alters phytohormone signaling and insect vector contact with hosts. Increased vector contact and movement among plants should increase virus survival and host range. In this study we examine the role of virus-induced changes in phytohormone signaling in plant-aphid interactions, using Pea enation mosaic virus (PEMV), pea aphids (Acyrthosiphon pisum), and pea (Pisum sativum) as a model. We observed that feeding by aphids carrying PEMV increases salicylic acid and jasmonic acid accumulation in pea plants compared to feeding by virus-free aphids. To determine if induction of the oxylipin jasmonic acid is critical for aphid settling, attraction, and retention on PEMV-infected plants, we conducted insect bioassays using virus-induced gene silencing (VIGS), an oxylipin signaling inducer, methyl jasmonate (MeJA), and a chemical inhibitor of oxylipin signaling, phenidone. Surprisingly, there was no impact of phenidone treatment on jasmonic acid or salicylic acid levels in virus-infected plants, though aphid attraction and retention were altered. These results suggest that the observed impacts of phenidone on aphid attraction to and retention on PEMV-infected plants are independent of the jasmonic acid and salicylic acid pathway but may be mediated by another component of the oxylipin signaling pathway. These results shed light on the complexity of viral manipulation of phytohormone signaling and vector-plant interactions.
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Affiliation(s)
- S Bera
- School of Integrative Plant Science, Plant-Microbe Biology and Plant Pathology Section, Cornell University, Ithaca, NY, 14853, USA
| | - R Blundell
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - D Liang
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - D W Crowder
- Department of Entomology, Washington State University, Pullman, WA, 99164, USA
| | - C L Casteel
- School of Integrative Plant Science, Plant-Microbe Biology and Plant Pathology Section, Cornell University, Ithaca, NY, 14853, USA.
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12
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Chen J, Liu H, Xia Z, Zhao X, Wu Y, An M. Purification and Structural Analysis of the Effective Anti-TMV Compound ε-Poly-l-lysine Produced by Streptomyces ahygroscopicus. Molecules 2019; 24:molecules24061156. [PMID: 30909546 PMCID: PMC6471872 DOI: 10.3390/molecules24061156] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 02/07/2023] Open
Abstract
Microbial secondary metabolites produced by actinomycetes are important natural products widely applied to control plant diseases. A variety of actinomycetes were isolated from soil samples collected from Tianzhu Mountain in Shenyang, China. A Streptomyces strain Shenyang Tianzhu (STZ) exhibits effective antiviral activity against Tobacco mosaic virus (TMV). The isolate was identified as Streptomyces ahygroscopicus based on its cultural, morphological, physiological, biochemical characteristics as well as the phylogenetic analysis using 16S rRNA sequences. To obtain the pure anti-TMV compound from Streptomyces STZ, the culture broth was subjected to Amberlite IRC-50 ion-exchange resin, SX-8 macroporous adsorption resin and Sephadex G-25 gel column chromatography. The purified active compound was confirmed to be ε-poly-l-lysine (ε-PL), with molecular mass in the range of 3454⁻4352 Da by structural analysis with infrared (IR), matrix-assisted laser desorption ionization-time-of-flight MS (MALDI-TOF), thin-layer chromatography (TLC) and high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR). The protective and curative effects of the purified compound ε-PL were tested and the results showed that the compound exhibited significant protective and curative activity against TMV. The potential application of ε-PL as an efficient anti-plant virus agent was expected.
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Affiliation(s)
- Jianguang Chen
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
| | - He Liu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
| | - Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
| | - Xiuxiang Zhao
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
| | - Mengnan An
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
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