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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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2
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Wendlandt T, Koch C, Britz B, Liedek A, Schmidt N, Werner S, Gleba Y, Vahidpour F, Welden M, Poghossian A, Schöning MJ, Eber FJ, Jeske H, Wege C. Facile Purification and Use of Tobamoviral Nanocarriers for Antibody-Mediated Display of a Two-Enzyme System. Viruses 2023; 15:1951. [PMID: 37766357 PMCID: PMC10536799 DOI: 10.3390/v15091951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Immunosorbent turnip vein clearing virus (TVCV) particles displaying the IgG-binding domains D and E of Staphylococcus aureus protein A (PA) on every coat protein (CP) subunit (TVCVPA) were purified from plants via optimized and new protocols. The latter used polyethylene glycol (PEG) raw precipitates, from which virions were selectively re-solubilized in reverse PEG concentration gradients. This procedure improved the integrity of both TVCVPA and the wild-type subgroup 3 tobamovirus. TVCVPA could be loaded with more than 500 IgGs per virion, which mediated the immunocapture of fluorescent dyes, GFP, and active enzymes. Bi-enzyme ensembles of cooperating glucose oxidase and horseradish peroxidase were tethered together on the TVCVPA carriers via a single antibody type, with one enzyme conjugated chemically to its Fc region, and the other one bound as a target, yielding synthetic multi-enzyme complexes. In microtiter plates, the TVCVPA-displayed sugar-sensing system possessed a considerably increased reusability upon repeated testing, compared to the IgG-bound enzyme pair in the absence of the virus. A high coverage of the viral adapters was also achieved on Ta2O5 sensor chip surfaces coated with a polyelectrolyte interlayer, as a prerequisite for durable TVCVPA-assisted electrochemical biosensing via modularly IgG-assembled sensor enzymes.
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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.); (C.K.); (N.S.)
| | - Claudia Koch
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Beate Britz
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Anke Liedek
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Nora Schmidt
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Stefan Werner
- Nambawan Biotech GmbH/Now at Icon Genetics GmbH, Weinbergweg 22, 06120 Halle, Germany;
| | - Yuri Gleba
- Nomad Bioscience GmbH, Weinbergweg 22, 06120 Halle, Germany;
| | - Farnoosh Vahidpour
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany; (F.V.); (M.W.); (M.J.S.)
| | - Melanie Welden
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany; (F.V.); (M.W.); (M.J.S.)
| | | | - Michael J. Schöning
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany; (F.V.); (M.W.); (M.J.S.)
- Institute of Biological Information Processing (IBI-3), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Fabian J. Eber
- Department of Mechanical and Process Engineering, Offenburg University of Applied Sciences, 77652 Offenburg, Germany;
| | - Holger Jeske
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Christina Wege
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
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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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Tobacco Mosaic Virus Infection of Chrysanthemums in Thailand: Development of Colorimetric Reverse-Transcription Loop-Mediated Isothermal Amplification (RT–LAMP) Technique for Sensitive and Rapid Detection. PLANTS 2022; 11:plants11141788. [PMID: 35890422 PMCID: PMC9325109 DOI: 10.3390/plants11141788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/23/2022]
Abstract
We detected tobacco mosaic virus (TMV), a member of the genus Tobamovirus and one of the most significant plant-infecting viruses, for the first time in a chrysanthemum in Thailand using reverse-transcription polymerase chain reaction (RT–PCR). The TMV-infected chrysanthemum leaves exhibited mosaic symptoms. We conducted a sequence analysis of the coat protein (CP) gene and found that the TMV detected in the chrysanthemum had 98% identity with other TMV isolates in GenBank. We carried out bioassays and showed that TMV induced mosaic and stunting symptoms in inoculated chrysanthemums. We observed the rigid rod structure of TMV under a transmission electron microscope (TEM). To enhance the speed and sensitivity of detection, we developed a colorimetric RT loop-mediated isothermal amplification (LAMP) technique. We achieved LAMP detection after 30 min incubation in isothermal conditions at 65 °C, and distinguished the positive results according to the color change from pink to yellow. The sensitivity of the LAMP technique was 1000-fold greater than that of RT–PCR, and we found no cross-reactivity with other viruses or viroids. This is the first reported case of a TMV-infected chrysanthemum in Thailand, and our colorimetric RT–LAMP TMV detection method is the first of its kind.
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Park CH, Song EG, Ryu KH. A multiplex PCR assay for the simultaneous detection of five potexviruses infecting cactus plants using dual-priming oligonucleotides (DPOs) primers. J Virol Methods 2021; 298:114280. [PMID: 34592336 DOI: 10.1016/j.jviromet.2021.114280] [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: 04/11/2019] [Revised: 04/19/2021] [Accepted: 09/03/2021] [Indexed: 11/15/2022]
Abstract
Five potexviruses, namely, cactus virus X (CVX), opuntia virus X, pitaya virus X (PiVX), schlumbergera virus X (SchVX) and zygocactus virus X (ZyVX), have been reported in cactus plants. In this report, a multiplex RT-PCR assay, based on specific dual-priming oligonucleotide (DPO) primers, was developed to detect these five viruses simultaneously in field samples. Using 18 field plants comprising 16 cactus species, these viruses were detected among nine of the 18 plants, including the simultaneous detection of CVX, PiVX, SchVX and ZyVX co-infecting an Aporocactus flagelliformis and a Notocactus leninghausii f. cristatus plant. The multiplex PCR assay was thus applied successfully in the field plants and it would be useful in the diagnosis of viral infections in cactus plants.
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Affiliation(s)
- Chung Hwa Park
- Plant Virus GenBank, Department of Horticulture, Biotechnology and Landscape Architecture, Seoul Women's University, Republic of Korea
| | - Eun Gyeong Song
- Plant Virus GenBank, Department of Horticulture, Biotechnology and Landscape Architecture, Seoul Women's University, Republic of Korea
| | - Ki Hyun Ryu
- Plant Virus GenBank, Department of Horticulture, Biotechnology and Landscape Architecture, Seoul Women's University, Republic of Korea.
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New World Cactaceae Plants Harbor Diverse Geminiviruses. Viruses 2021; 13:v13040694. [PMID: 33923787 PMCID: PMC8073023 DOI: 10.3390/v13040694] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 12/15/2022] Open
Abstract
The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infects them. We previously identified a highly divergent geminivirus that is the first known to infect cacti. Recent research efforts in non-cultivated and asymptomatic plants have shown that the diversity of this viral family has been under-sampled. As a consequence, little is known about the effects and interactions of geminiviruses in many plants, such as cacti. With the objective to expand knowledge on the diversity of geminiviruses infecting cacti, we used previously acquired high-throughput sequencing results to search for viral sequences using BLASTx against a viral RefSeq protein database. We identified two additional sequences with similarity to geminiviruses, for which we designed abutting primers and recovered full-length genomes. From 42 cacti and five scale insects, we derived 42 complete genome sequences of a novel geminivirus species that we have tentatively named Opuntia virus 2 (OpV2) and 32 genomes of an Opuntia-infecting becurtovirus (which is a new strain of the spinach curly top Arizona virus species). Interspecies recombination analysis of the OpV2 group revealed several recombinant regions, in some cases spanning half of the genome. Phylogenetic analysis demonstrated that OpV2 is a novel geminivirus more closely related to viruses of the genus Curtovirus, which was further supported by the detection of three recombination events between curtoviruses and OpV2. Both OpV2 and Opuntia becurtoviruses were identified in mixed infections, which also included the previously characterized Opuntia virus 1. Viral quantification of the co-infected cactus plants compared with single infections did not show any clear trend in viral dynamics that might be associated with the mixed infections. Using experimental Rhizobium-mediated inoculations, we found that the initial accumulation of OpV2 is facilitated by co-infection with OpV1. This study shows that the diversity of geminiviruses that infect cacti is under-sampled and that cacti harbor diverse geminiviruses. The detection of the Opuntia becurtoviruses suggests spill-over events between viruses of cultivated species and native vegetation. The threat this poses to cacti needs to be further investigated.
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Fontenele RS, Salywon AM, Majure LC, Cobb IN, Bhaskara A, Avalos-Calleros JA, Argüello-Astorga GR, Schmidlin K, Khalifeh A, Smith K, Schreck J, Lund MC, Köhler M, Wojciechowski MF, Hodgson WC, Puente-Martinez R, Van Doorslaer K, Kumari S, Vernière C, Filloux D, Roumagnac P, Lefeuvre P, Ribeiro SG, Kraberger S, Martin DP, Varsani A. A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants. Viruses 2020; 12:E398. [PMID: 32260283 PMCID: PMC7232249 DOI: 10.3390/v12040398] [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: 01/15/2020] [Revised: 03/29/2020] [Accepted: 03/31/2020] [Indexed: 12/17/2022] Open
Abstract
Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensively studied, little research has focused on cactus-associated viral communities. While only single-stranded RNA viruses had ever been reported in cacti, here we report the discovery of cactus-infecting single-stranded DNA viruses. These viruses all apparently belong to a single divergent species of the family Geminiviridae and have been tentatively named Opuntia virus 1 (OpV1). A total of 79 apparently complete OpV1 genomes were recovered from 31 different cactus plants (belonging to 20 different cactus species from both the Cactoideae and Opuntioideae clades) and from nine cactus-feeding cochineal insects (Dactylopius sp.) sampled in the USA and Mexico. These 79 OpV1 genomes all share > 78.4% nucleotide identity with one another and < 64.9% identity with previously characterized geminiviruses. Collectively, the OpV1 genomes display evidence of frequent recombination, with some genomes displaying up to five recombinant regions. In one case, recombinant regions span ~40% of the genome. We demonstrate that an infectious clone of an OpV1 genome can replicate in Nicotiana benthamiana and Opuntia microdasys. In addition to expanding the inventory of viruses that are known to infect cacti, the OpV1 group is so distantly related to other known geminiviruses that it likely represents a new geminivirus genus. It remains to be determined whether, like its cactus hosts, its geographical distribution spans the globe.
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Affiliation(s)
- Rafaela S. Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Andrew M. Salywon
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
| | - Lucas C. Majure
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Ilaria N. Cobb
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Amulya Bhaskara
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- Center for Research in Engineering, Science and Technology, Paradise Valley High School, 3950 E Bell Rd, Phoenix, AZ 85032, USA
| | - Jesús A. Avalos-Calleros
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., Mexico; (J.A.A.-C.); (G.R.A.-A.)
| | - Gerardo R. Argüello-Astorga
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., Mexico; (J.A.A.-C.); (G.R.A.-A.)
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Anthony Khalifeh
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Kendal Smith
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Joshua Schreck
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Michael C. Lund
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Matias Köhler
- Departamento de BotânicaPrograma de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501970, Brazil;
| | | | - Wendy C. Hodgson
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
| | - Raul Puente-Martinez
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and UA Cancer Center, University of Arizona, Tucson, AZ 85721, USA;
| | - Safaa Kumari
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol Station, Beqa’a, Zahle, Lebanon;
| | - Christian Vernière
- CIRAD, BGPI, 34398 Montpellier, France; (C.V.); (D.F.); (P.R.)
- BGPI, INRAE, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France
| | - Denis Filloux
- CIRAD, BGPI, 34398 Montpellier, France; (C.V.); (D.F.); (P.R.)
- BGPI, INRAE, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France
| | - Philippe Roumagnac
- CIRAD, BGPI, 34398 Montpellier, France; (C.V.); (D.F.); (P.R.)
- BGPI, INRAE, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France
| | | | - Simone G. Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, CEP 70770-917, Brazil;
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
| | - Darren P. Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa;
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7925, South Africa
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Salgado-Ortíz H, De La Torre-Almaraz R, Sánchez-Navarro JÁ, Pallás V. Identification and genomic characterization of a novel tobamovirus from prickly pear cactus. Arch Virol 2020; 165:781-784. [PMID: 31980940 DOI: 10.1007/s00705-020-04528-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 12/16/2019] [Indexed: 11/30/2022]
Abstract
In this work, we describe the complete sequence and genome organization of a novel tobamovirus detected in a prickly pear plant (Opuntia sp.) by high-throughput sequencing, tentatively named "opuntia virus 2". The full genome of opuntia virus 2 is 6,453 nucleotides in length and contains four open reading frames (ORFs) coding for the two subunits of the RNA polymerase, the movement protein, and the coat protein, respectively. Phylogenetic analysis using the complete nucleotide sequence revealed that the virus belongs to the genus Tobamovirus (family Virgaviridae), showing the highest nucleotide sequence identity (49.8%) with cactus mild mottle virus (CMMoV), being indicating that it belongs in the Cactaceae subgroup of tobamoviruses.
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Affiliation(s)
- Héctor Salgado-Ortíz
- Unidad de Biotecnología y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, 54074, Tlalnepantla, Estado de México, Mexico.
| | - Rodolfo De La Torre-Almaraz
- Unidad de Biotecnología y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, 54074, Tlalnepantla, Estado de México, Mexico
| | - Jesús Ángel Sánchez-Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Ciudad Politécnica de la Innovación Ingeniero Fausto Elio, s/n, 46022, Valencia, Spain
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Ciudad Politécnica de la Innovación Ingeniero Fausto Elio, s/n, 46022, Valencia, Spain
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9
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Li Y, Tan G, Lan P, Zhang A, Liu Y, Li R, Li F. Detection of tobamoviruses by RT-PCR using a novel pair of degenerate primers. J Virol Methods 2018; 259:122-128. [PMID: 29944907 DOI: 10.1016/j.jviromet.2018.06.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/28/2018] [Accepted: 06/22/2018] [Indexed: 01/26/2023]
Abstract
A generic RT-PCR assay was developed for the universal detection of viruses of the genus Tobamovirus using a novel pair of degenerate primers designed based on conserved regions on replicase genes of 32 tobamoviruses. The assay detected nine tobamoviruses, including six Solanaceae-infecting subgroup tobamoviruses of Tobacco mosaic virus (TMV), Tomato mosaic virus (ToMV), Tomato mottle mosaic virus (ToMMV), Tobacco mottle green mosaic virus (TMGMV), Pepper mild mottle virus (PMMoV), Paprika mild mottle virus (PaMMV), one Orchidaceae-infecting tobamovirus of Odontoglossum ringspot virus (ORSV) and two Cucurbitaceae-infecting subgroup tobamoviruses of Cucumber green mottle mosaic virus (CGMMV) and Zucchini green mottle mosaic virus (ZGMMV), with high amplification efficiency, specificity and sensitivity. The assay was applied to detect tobamoviruses in pepper and tomato fields. Five tobamoviruses, PMMoV, TMV, ToMV, ToMMV and TMGMV, were detected from the pepper fields in single and mixed infections. Single infections of PMMoV, ToMV and ToMMV and mix-infection of ToMV + PMMoV were detected from the tomato fields. Among these viruses, PMMoV was first detected from tomato worldwide, while ToMMV was first detected from tomato plants in China. This generic assay is simple, cost-effective and has great potential to detect more tobamoviruses in the field.
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Affiliation(s)
- Yueyue Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Guanlin Tan
- Modern Education Technology Center, Yunnan Agricultural University, Kunming 650201, China
| | - Pingxiu Lan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Ansheng Zhang
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Ji' Nan, 250100, China
| | - Yong Liu
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ruhui Li
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD 20705, USA.
| | - Fan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.
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Park CH, Song EG, Ryu KH. Detection of Co-Infection of Notocactus leninghausii f. cristatus with Six Virus Species in South Korea. THE PLANT PATHOLOGY JOURNAL 2018; 34:65-70. [PMID: 29422789 PMCID: PMC5796751 DOI: 10.5423/ppj.nt.08.2017.0187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/17/2017] [Accepted: 10/29/2017] [Indexed: 06/08/2023]
Abstract
Co-infection with two virus species was previously reported in some cactus plants. Here, we showed that Notocactus leninghausii f. cristatus can be co-infected with six different viruses: cactus mild mottle virus (CMMoV)-Nl, cactus virus X (CVX)-Nl, pitaya virus X (PiVX)-Nl, rattail cactus necrosis-associated virus (RCNaV)-Nl, schlumbergera virus X (SchVX)-Nl, and zygocactus virus X (ZyVX)-Nl. The coat protein sequences of these viruses were compared with those of previously reported viruses. CMMoV-Nl, CVX-Nl, PiVX-Nl, RCNaV-Nl, SchVX-Nl, and ZyVX-Nl showed the greatest nucleotide sequence homology to CMMoV-Kr (99.8% identity, GenBank accession NC_011803), CVX-Jeju (77.5% identity, GenBank accession LC12841), PiVX-P37 (98.4% identity, GenBank accession NC_024458), RCNaV (99.4% identity, GenBank accession NC_016442), SchVX-K11 (95.7% identity, GenBank accession NC_011659), and ZyVX-B1 (97.9% identity, GenBank accession NC_006059), respectively. This study is the first report of co-infection with six virus species in N. leninghausii f. cristatus in South Korea.
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Affiliation(s)
| | | | - Ki Hyun Ryu
- Plant Virus GenBank, Department of Horticulture, Biotechnology and Landscape Architecture, Seoul Women’s University, Seoul 01797,
Korea
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11
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Dorokhov YL, Sheshukova EV, Komarova TV. Tobamovirus 3'-Terminal Gene Overlap May be a Mechanism for within-Host Fitness Improvement. Front Microbiol 2017; 8:851. [PMID: 28553276 PMCID: PMC5425575 DOI: 10.3389/fmicb.2017.00851] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/25/2017] [Indexed: 12/13/2022] Open
Abstract
Overlapping genes (OGs) are a universal phenomenon in all kingdoms, and viruses display a high content of OGs combined with a high rate of evolution. It is believed that the mechanism of gene overlap is based on overprinting of an existing gene. OGs help virus genes compress a maximum amount of information into short sequences, conferring viral proteins with novel features and thereby increasing their within-host fitness. Analysis of tobamovirus 3′-terminal genes reveals at least two modes of OG organization and mechanisms of interaction with the host. Originally isolated from Solanaceae species, viruses (referred to as Solanaceae-infecting) such as tobacco mosaic virus do not show 3′-terminal overlap between movement protein (MP) and coat protein (CP) genes but do contain open reading frame 6 (ORF6), which overlaps with both genes. Conversely, tobamoviruses, originally isolated from Brassicaceae species (referred to as Brassicaceae-infecting) and also able to infect Solanaceae plants, have no ORF6 but are characterized by overlapping MP and CP genes. Our analysis showed that the MP/CP overlap of Brassicaceae-infecting tobamoviruses results in the following: (i) genome compression and strengthening of subgenomic promoters; (ii) CP gene early expression directly from genomic and dicistronic MP subgenomic mRNA using an internal ribosome entry site (IRES) and a stable hairpin structure in the overlapping region; (iii) loss of ORF6, which influences the symptomatology of Solanaceae-infecting tobamoviruses; and (iv) acquisition of an IRES polypurine-rich region encoding an MP nuclear localization signal. We believe that MP/CP gene overlap may constitute a mechanism for host range expansion and virus adjustment to Brassicaceae plants.
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Affiliation(s)
- Yuri L Dorokhov
- N.I. Vavilov Institute of General Genetics, Russian Academy of ScienceMoscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
| | | | - Tatiana V Komarova
- N.I. Vavilov Institute of General Genetics, Russian Academy of ScienceMoscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
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12
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Li Y, Wang Y, Hu J, Xiao L, Tan G, Lan P, Liu Y, Li F. The complete genome sequence, occurrence and host range of Tomato mottle mosaic virus Chinese isolate. Virol J 2017; 14:15. [PMID: 28137291 PMCID: PMC5282660 DOI: 10.1186/s12985-016-0676-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/26/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Tomato mottle mosaic virus (ToMMV) is a recently identified species in the genus Tobamovirus and was first reported from a greenhouse tomato sample collected in Mexico in 2013. In August 2013, ToMMV was detected on peppers (Capsicum spp.) in China. However, little is known about the molecular and biological characteristics of ToMMV. METHODS Reverse transcription-polymerase chain reaction (RT-PCR) and rapid identification of cDNA ends (RACE) were carried out to obtain the complete genomic sequences of ToMMV. Sap transmission was used to test the host range and pathogenicity of ToMMV. RESULTS The full-length genomes of two ToMMV isolates infecting peppers in Yunnan Province and Tibet Autonomous Region of China were determined and analyzed. The complete genomic sequences of both ToMMV isolates consisted of 6399 nucleotides and contained four open reading frames (ORFs) encoding 126, 183, 30 and 18 kDa proteins from the 5' to 3' end, respectively. Overall similarities of the ToMMV genome sequence to those of the other tobamoviruses available in GenBank ranged from 49.6% to 84.3%. Phylogenetic analyses of the sequences of full-genome nucleotide and the amino acids of its four proteins confirmed that ToMMV was most closely related to Tomato mosaic virus (ToMV). According to the genetic structure, host of origin and phylogenetic relationships, the available 32 tobamoviruses could be divided into at least eight subgroups based on the host plant family they infect: Solanaceae-, Brassicaceae-, Cactaceae-, Apocynaceae-, Cucurbitaceae-, Malvaceae-, Leguminosae-, and Passifloraceae-infecting subgroups. The detection of ToMMV on some solanaceous, cucurbitaceous, brassicaceous and leguminous plants in Yunnan Province and other few parts of China revealed ToMMV only occurred on peppers so far. However, the host range test results showed ToMMV could infect most of the tested solanaceous and cruciferous plants, and had a high affinity for the solanaceous plants. CONCLUSIONS The complete nucleotide sequences of two Chinese ToMMV isolates from naturally infected peppers were verified. The tobamoviruses were divided into at least eight subgroups, with ToMMV belonging to the subgroup that infected plants in the Solanaceae. In China, ToMMV only occurred on peppers in the fields till now. ToMMV could infect the plants in family Solanaceae and Cucurbitaceae by sap transmission.
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Affiliation(s)
- Yueyue Li
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Yang Wang
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - John Hu
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, 96822, USA
| | - Long Xiao
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Guanlin Tan
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
- Modern Education Technology Center, Yunnan Agricultural University, Kunming, 650201, China
| | - Pingxiu Lan
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Yong Liu
- Hunan Academy of Agricultural Sciences, Plant Protection Institute, Changsha, 410125, China.
| | - Fan Li
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China.
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Rhee SJ, Hong JS, Lee GP. Infectivity and complete nucleotide sequence of cucumber fruit mottle mosaic virus isolate Cm cDNA. Arch Virol 2014; 159:1807-11. [PMID: 24473709 DOI: 10.1007/s00705-014-1990-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
Abstract
Three isolates of cucumber fruit mottle mosaic virus (CFMMV) were collected from melon, cucumber, and pumpkin plants in Korea. A full-length cDNA clone of CFMMV-Cm (melon isolate) was produced and evaluated for infectivity after T7 transcription in vitro (pT7CF-Cmflc). The complete CFMMV genome sequence of the infectious clone pT7CF-Cmflc was determined. The genome of CFMMV-Cm consisted of 6,571 nucleotides and shared high nucleotide sequence identity (98.8 %) with the Israel isolate of CFMMV. Based on the infectious clone pT7CF-Cmflc, a CaMV 35S-promoter driven cDNA clone (p35SCF-Cmflc) was subsequently constructed and sequenced. Mechanical inoculation with RNA transcripts of pT7CF-Cmflc and agro-inoculation with p35SCF-Cmflc resulted in systemic infection of cucumber and melon, producing symptoms similar to those produced by CFMMV-Cm. Progeny virus in infected plants was detected by RT-PCR, western blot assay, and transmission electron microscopy.
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Affiliation(s)
- Sun-Ju Rhee
- Department of Integrative Plant Science, Chung-Ang University, Ansung, 456-756, Korea
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14
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Bae S, Kim SG, Kim YH. Biocontrol Characteristics of Bacillus Species in Suppressing Stem Rot of Grafted Cactus Caused by Bipolaris cactivora. THE PLANT PATHOLOGY JOURNAL 2013; 29:42-51. [PMID: 25288927 PMCID: PMC4174789 DOI: 10.5423/ppj.oa.07.2012.0116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/10/2012] [Accepted: 10/10/2012] [Indexed: 06/03/2023]
Abstract
One of the most important limiting factors for the production of the grafted cactus in Korea is the qualitative and quantitative yield loss derived from stem rots especially caused by Bipolaris cactivora. This study is aimed to develop microbial control agents useful for the control of the bipolaris stem rot. Two bacteria (GA1-23 and GA4-4) selected out of 943 microbial isolates because of their strong antibiotic activity against B. cactivora were identified as Bacillus subtilis and B. amyloliquefaciens, respectively, by the cultural characteristics, Biolog program and 16S rRNA sequencing analyses. Both bacterial isolates significantly inhibited the conidial germination and mycelial growth of the pathogen with no significant difference between the two, of which the inhibitory efficacies varied depending on the cultural conditions such as temperature, nutritional compositions and concentrations. Light and electron microscopy of the pathogen treated with the bacterial isolates showed the inhibition of spore germination with initial malformation of germ tubes and later formation of circle-like vesicles with no hyphal growth and hyphal disruption sometimes accompanied by hyphal swellings and shrinkages adjacent to the bacteria, suggesting their antibiotic mode of antagonistic activity. Control efficacy of B. subtilis GA1-23 and B. amyloliquefaciens GA4-4 on the cactus stem rot were not as high as but comparable to that of fungicide difenoconazole when they were treated simultaneously at the time of pathogen inoculation. All of these results suggest the two bacterial isolates have a good potential to be developed as biocontrol agents for the bipolaris stem rot of the grafted cactus.
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Affiliation(s)
- Sooil Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Sang Gyu Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Young Ho Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
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15
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Characterization of the complete genome of ribgrass mosaic virus isolated from Plantago major L. from New Zealand and Actinidia spp. from China. Arch Virol 2012; 157:1253-60. [PMID: 22456910 DOI: 10.1007/s00705-012-1292-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 02/26/2012] [Indexed: 10/28/2022]
Abstract
The complete genomes of tobamovirus isolates from Plantago major L. from New Zealand (NZ-439), Plantago sp. from Germany (Kons 1105), Actinidia chinensis (Actinidia-AC) and A. deliciosa (Actinidia-AD) from China were sequenced and compared to previously published tobamovirus genomes. Their genome organization and phylogenetic analysis of the putative replicase component, replicase readthrough component, movement protein, coat protein and complete genome placed all four isolates in subgroup 3 of the tobamoviruses. The complete genomes differed from each other by <8.5% and from published sequences of turnip vein clearing virus and youcai mosaic virus by about 12-13% and 19-20%, respectively. The aa sequences of the individual ORFs of the Plantago and Actinidia isolates differed from each other by <4% and were most similar to published (partial) sequences of ribgrass mosaic virus (RMV). We propose that these sequences constitute the first complete published sequences for RMV.
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16
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Stobbe AH, Melcher U, Palmer MW, Roossinck MJ, Shen G. Co-divergence and host-switching in the evolution of tobamoviruses. J Gen Virol 2011; 93:408-418. [PMID: 22049092 DOI: 10.1099/vir.0.034280-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The proposed phylogenetic structure of the genus Tobamovirus supports the idea that these viruses have codiverged with their hosts since radiation of the hosts from a common ancestor. The determinations of genome sequence for two strains of Passion fruit mosaic virus (PafMV), a tobamovirus from plants of the family Passifloraceae (order Malpighiales) from which only one other tobamovirus (Maracuja mosaic virus; MarMV) has been characterized, combined with the development of Bayesian analysis methods for phylogenetic inference, provided an opportunity to reassess the co-divergence hypothesis. The sequence of one PafMV strain, PfaMV-TGP, was discovered during a survey of plants of the Tallgrass Prairie Preserve for their virus content. Its nucleotides are only 73 % identical to those of MarMV. A conserved ORF not found in other tobamovirus genomes, and encoding a cysteine-rich protein, was found in MarMV and both PafMV strains. Phylogenetic tree construction, using an alignment of the nucleotide sequences of PafMV-TGP and other tobamoviruses resulted in a major clade containing isolates exclusively from rosid plants. Asterid-derived viruses were exclusively found in a second major clade that also contained an orchid-derived tobamovirus and tobamoviruses infecting plants of the order Brassicales. With a few exceptions, calibrating the virus tree with dates of host divergence at two points resulted in predictions of divergence times of family specific tobamovirus clades that were consistent with the times of divergence of the host plant orders.
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Affiliation(s)
- Anthony H Stobbe
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ulrich Melcher
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Michael W Palmer
- Department of Botany, Oklahoma State University, Stillwater, OK 74078, USA
| | - Marilyn J Roossinck
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
| | - Guoan Shen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
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17
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Kim NR, Hong JS, Song YS, Chung BN, Park JW, Ryu KH. The complete genome sequence of a member of a new species of tobamovirus (rattail cactus necrosis-associated virus) isolated from Aporcactus flagelliformis. Arch Virol 2011; 157:185-7. [PMID: 22006045 DOI: 10.1007/s00705-011-1142-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 10/06/2011] [Indexed: 11/28/2022]
Abstract
In this study, we identified a new tobamovirus from diseased Aporcactus flagelliformis cactus plants, named it rattail cactus necrosis-associated virus (RCNaV), and determined its complete genome sequence. The full RCNaV genome consisted of 6,506 nucleotides and contained four open reading frames coding for proteins of M(r) 128 kDa (3,441 nt), 185 kDa (4,929 nt), 55 kDa (1452 nt), 36 kDa (1,005 nt) and 19 kDa (513 nt) from the 5' to 3' end, respectively. The overall similarities for the four ORFs of RCNaV were from 32.5% to 64.1% and from 17.0% to 67.3% to those of the other tobamoviruses, at the nucleotide and amino acid level, respectively. Comparison of the coding and non-coding regions of the virus with those of other tobamoviruses showed that RCNaV is the most closely related to cactus mild mottle virus.
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Affiliation(s)
- N R Kim
- Department of Horticulture, Biotechnology and Landscape Architecture, Plant Virus GenBank, Seoul Women's University, Seoul 139-774, Korea
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18
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The complete genome sequence and genome structure of passion fruit mosaic virus. Arch Virol 2011; 156:1093-5. [PMID: 21547441 DOI: 10.1007/s00705-011-0961-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 02/25/2011] [Indexed: 10/18/2022]
Abstract
In this study, we determined the complete sequence of the genomic RNA of a Florida isolate of maracuja mosaic virus (MarMV-FL) and compared it to that of a Peru isolate of the virus (MarMV-P) and those of other known tobamoviruses. Complete sequence analysis revealed that the isolate should be considered a member of a new species and named passion fruit mosaic virus (PafMV). The genomic RNA of PafMV consists of 6,791 nucleotides and encodes four open reading frames (ORFs) coding for proteins of 125 kDa (1,101 aa), 184 kDa (1,612 aa), 34 kDa (311 aa) and 18 kDa (164 aa) in consecutive order from the 5' to the 3' end. The sequence homologies of the four ORFs of PafMV were from 78.8% to 81.6% to those of MarMV-P at the amino acid level. The sequence homologies of the four ORFs of PafMV ranged from 36.0% to 77.9% and from 21.7% to 81.6% to those of other tobamoviruses, at the nucleotide and amino acid level, respectively. Phylogenetic analysis revealed that these PafMV-encoded proteins are closely related to those of MarMV-P. In conclusion, the results indicate that PafMV and MarMV-P belong to different species within the genus Tobamovirus.
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Lim MA, Hong JS, Song YS, Ryu KH. The complete genome sequence and genome structure of frangipani mosaic virus. Arch Virol 2010; 155:1543-6. [PMID: 20668892 DOI: 10.1007/s00705-010-0766-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 07/19/2010] [Indexed: 10/19/2022]
Abstract
In this study, the complete sequence of the genomic RNA of frangipani mosaic virus (FrMV) has been determined and compared to those of other known tobamoviruses. The complete genome sequence of FrMV consisted of 6,643 nucleotides. The FrMV genomic RNA encoded four open reading frames (ORFs), for proteins of M(r) 128 kDa (1,147 aa), 186 kDa (1,651 aa), 30 kDa (257 aa) and 18 kDa (175 aa) from the 5' to the 3' end. Overall similarities for the four ORFs of FrMV-P ranged from 26.8 to 53.0% at the amino acid level when compared to those of 24 other tobamoviruses. Phylogenetic analysis of the FrMV replicase (186 kDa) and MP revealed that FrMV is closely related to SHMV and CMMoV, while the FrMV replicase (128 kDa) is more closely related to cucurbit-infecting and malvaceous-infecting tobamoviruses, and the FrMV CP is closely related to that of CMMoV and solanaceous-infecting tobamoviruses.
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Affiliation(s)
- M A Lim
- Plant Virus GenBank, Department of Horticultural and Landscape Architecture, Division of Environmental and Life Sciences, Seoul Women's University, Seoul, Korea
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20
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Min BE, Song YS, Ryu KH. Complete sequence and genome structure of cactus mild mottle virus. Arch Virol 2009; 154:1371-4. [PMID: 19562252 DOI: 10.1007/s00705-009-0435-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2009] [Accepted: 06/16/2009] [Indexed: 11/30/2022]
Abstract
We have completed the genomic sequence of a tobamovirus, cactus mild mottle virus (CMMoV), and compared it to those of other known tobamoviruses. The complete genome sequence of CMMoV consists of 6,449 nucleotides. The genome RNA of the virus contains four open reading frames, encoding, from the 5' to the 3' end, the 120-kDa viral replicase, the 186-kDa viral polymerase, the 33-kDa movement protein and the 18-kDa coat protein. Overall amino acid similarities for the four viral proteins of CMMoV ranged from 16.3 to 44.4% compared to those of 20 other tobamoviruses. Phylogenetic analysis of the viral replicases and MP revealed that CMMoV is closely related to cucurbit-infecting tobamoviruses, while the CMMoV CP is more closely related to brassica- and solanaceous-infecting tobamoviruses.
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Affiliation(s)
- B E Min
- Plant Virus GenBank, Division of Environmental and Life Sciences, Seoul Women's University, Seoul 139-774, Korea
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21
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Biological and molecular characterization of a crucifer Tobamovirus infecting oilseed rape. Biochem Genet 2009; 47:451-61. [PMID: 19449162 DOI: 10.1007/s10528-009-9244-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Accepted: 04/24/2009] [Indexed: 10/20/2022]
Abstract
In China, the tobamovirus that infects oilseed rape has been misdiagnosed as Tobacco mosaic virus (TMV) based on its morphological similarity and serological relatedness. Recently, a tobamovirus has been isolated from oilseed rape in China, which we named Youcai mosaic virus Br (YoMV-Br), according to its biological and molecular characteristics. It had strong infectivity to Cruciferae but less to Solanaceae, Leguminosae, and Cucurbitaceae, and its virion morphology was consistent with that of the tobamoviruses. At high concentrations, it serologically cross reacted with TMV antiserum. The 3' terminal sequence (2,283 nucleotides) of YoMV-Br was determined, including the 3' noncoding region, the CP and MP genes, and the C-terminal part of the replicase gene. Between the MP and CP genes, 77 nucleotides overlapped. Compared with homologous regions of 21 recognized species of Tobamovirus, YoMV-Br had a much higher identity to crucifer species than to other tobamoviruses. Phylogenetic analysis demonstrated that YoMV-Br was closely related to the YoMV cluster of tobamoviruses and distantly to TMV, so that they likely belong to different strains of the same species.
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Lockhart BE, Swenson AS, Olszewski NE, Voth P. Characterization of a Strain of Turnip vein-clearing virus Causing Red Ringspot of Penstemon. PLANT DISEASE 2008; 92:725-729. [PMID: 30769585 DOI: 10.1094/pdis-92-5-0725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A disease of penstemon (Penstemon digitalis) occurring in commercial nurseries in Minnesota in 2004 to 2006 and characterized by red foliar ringspots, leaf deformation, and plant stunting was found to be caused by a strain of Turnip vein-clearing virus (TVCV) that was named Penstemon ringspot virus (PenRSV). This is the first report of a viral disease of penstemon. The genome organization of PenRSV was similar to that of the crucifer-infecting tobamoviruses. The nucleotide sequence of PenRSV was almost identical (99%) to that of TVCV, but the two viruses differed importantly in host range and symptoms induced. The only sequence difference between PenRSV and TVCV occurred at the 3' end of open reading frame I, where the amino acid sequence FRDSNL in TVCV is replaced by FRGQQL in PenRSV. The experimental host range of PenRSV included species in the families Brassicaceae (Cruciferae), Cactaceae, Cucurbitaceae, Leguminosae, Malvaceae, and Solanaceae. This virus poses a potential threat to commercial nursery and bedding plant production because of its wide host range and because it will escape detection by immunoenzymatic screening procedures for tobamoviruses based on use of antibodies to Tobacco mosaic virus (TMV).
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Affiliation(s)
| | | | | | - Peter Voth
- Plant Biological Sciences Graduate Group, University of Minnesota, St. Paul 55108
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Rhie MJ, Min BE, Hong JS, Song YS, Ryu KH. Complete genome sequence supports bell pepper mottle virus as a species of the genus Tobamovirus. Arch Virol 2007; 152:1401-7. [PMID: 17334946 DOI: 10.1007/s00705-007-0950-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Accepted: 01/26/2007] [Indexed: 10/23/2022]
Abstract
Biological properties and the complete genome sequence of bell pepper mottle virus (BPeMV) were determined. The full genome of BPeMV consists of 6375 nucleotides. The BPeMV genomic RNA has four open reading frames (ORFs) encoding proteins of M(r) 126, 181, 30 and 18 kDa from the 5' to the 3' end, respectively. The lengths of the 5' nontranslated region (NTR) and the 3' NTR are 71 and 198 nucleotides, respectively. Overall identities for the four ORFs of BpeMV, at the nucleotide and amino acid levels, respectively, ranged from 36.0 to 80.6% and from 32.1 to 90.9%, compared to those of 22 other tobamoviruses. The CP gene of BPeMV displayed 43.5-73.5% and 32.1-82.4% identity to those of 22 other tobamoviruses at the nucleotide and amino acid levels, respectively. Phylogenetic analyses of four viral proteins clearly supported the conclusion that BPeMV-encoded proteins were related to those of members of the Solanaceae-infecting tobamoviruses. BPeMV was closely related to tomato mosaic virus, and tobacco mosaic virus and different from other tobamoviruses. Western blot analysis showed that BPeMV cross-reacted strongly with antibodies against members of Solanaceae-infecting tobamoviruses. These data represent the first molecular evidence supporting BPeMV as a separate species of the genus Tobamovirus.
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Affiliation(s)
- M J Rhie
- Plant Virus GenBank, Division of Environmental and Life Sciences, Seoul Women's University, Seoul, Republic of Korea
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Adkins S, Kamenova I, Rosskopf EN, Lewandowski DJ. Identification and Characterization of a Novel Tobamovirus from Tropical Soda Apple in Florida. PLANT DISEASE 2007; 91:287-293. [PMID: 30780562 DOI: 10.1094/pdis-91-3-0287] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Foliar symptoms suggestive of virus infection were recently observed on the noxious weed tropical soda apple (Solanum viarum) in Florida. An agent was mechanically transmitted to Nicotiana benthamiana, and virions were isolated from systemically infected leaves. Rod-shaped particles ~300 nm in length were observed in the partially purified preparations by electron microscopy. The host range determined by mechanical inoculation with purified virions included all tested plants in the Solanaceae (16 species including the important vegetable crops, pepper and tomato) and Chenopodiaceae (2 species) but excluded all tested plants in the Ama-ranthaceae, Apocynaceae, Brassicaceae, Caryophyllaceae, Cucurbitaceae, Fabaceae, Lamiaceae, Malvaceae, and Tropaeolaceae, including several common virus indicator hosts. Comparisons of the coat and movement protein nucleotide and deduced amino acid sequences of this putative tobamovirus with recognized members of this genus, indicate that it is a novel tobamovirus that shares the highest level of sequence identity with Pepper mild mottle virus followed by other members of the Solanaceae-infecting subgroup of tobamoviruses. The virus, for which the name Tropical soda apple mosaic virus (TSAMV) is proposed, was found to be widespread in tropical soda apple in peninsular Florida during an initial survey. TSAMV contamination of seed from infected tropical soda apple plants was found, suggesting that seed transmission may be important for TSAMV dissemination and epidemiology.
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Affiliation(s)
- Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, Fort Pierce, FL 34945
| | - Ivanka Kamenova
- United States Department of Agriculture, Agricultural Research Service, Fort Pierce, FL 34945
| | - Erin N Rosskopf
- United States Department of Agriculture, Agricultural Research Service, Fort Pierce, FL 34945
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Song YS, Min BE, Hong JS, Rhie MJ, Kim MJ, Ryu KH. Molecular evidence supporting the confirmation of maracuja mosaic virus as a species of the genus Tobamovirus and production of an infectious cDNA transcript. Arch Virol 2006; 151:2337-48. [PMID: 16862384 DOI: 10.1007/s00705-006-0823-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2006] [Accepted: 06/19/2006] [Indexed: 10/24/2022]
Abstract
The complete genome sequence of maracuja mosaic virus (MarMV) was determined and analyzed. The full MarMV genome consisted of 6794 nucleotides, and this is the largest genome size among known tobamoviruses. The MarMV genome RNA contained four open reading frames (ORFs) coding for proteins of M(r) 126, 181, 34 and 18 kDa from the 5' to 3' end, respectively. The lengths of the 5' nontranslated region (NTR) and the 3' NTR were 54 and 177 nucleotides, respectively. Phylogenetic tree analysis revealed that these MarMV-encoded proteins are related to members of the Malvaceae- and Cucurbitaceae-infecting tobamoviruses. MarMV is different from other tobamoviruses and forms a new Passifloraceae-infecting subgroup. Western blot analysis showed that MarMV cross-reacted strongly with antibodies against Kyuri green mottle mosaic virus and Hibiscus latent Singapore virus. Synthesized capped transcripts from full-length cDNA of MarMV were infectious. These data clearly indicate that MarMV belongs to a separate species of the genus Tobamovirus.
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Affiliation(s)
- Y S Song
- Plant Virus GenBank, Division of Environmental and Life Sciences, Seoul Women's University, Seoul, Republic of Korea
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