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Nemchinov LG, Grinstead S. Complete genome sequence of alfalfa-associated picorna-like virus 2. Microbiol Resour Announc 2024; 13:e0105223. [PMID: 38426729 PMCID: PMC11008146 DOI: 10.1128/mra.01052-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
We have previously reported on the detection of an unknown picorna-like virus in alfalfa samples. The exact host of the virus was unclear due to its similarity to the members of Iflaviridae family, which typically infect arthropods. The virus was provisionally named alfalfa-associated picorna-like virus 2. Here, we report a complete genomic sequence of the virus.
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Affiliation(s)
- Lev G. Nemchinov
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, Maryland, USA
| | - Sam Grinstead
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, Maryland, USA
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2
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Nemchinov LG, Postnikova OA, Wintermantel WM, Palumbo JC, Grinstead S. Alfalfa vein mottling virus, a novel potyvirid infecting Medicago sativa L. Virol J 2023; 20:284. [PMID: 38037050 PMCID: PMC10690988 DOI: 10.1186/s12985-023-02250-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND We have recently identified a novel virus detected in alfalfa seed material. The virus was tentatively named alfalfa-associated potyvirus 1, as its genomic fragments bore similarities with potyvirids. In this study, we continued investigating this novel species, expanding information on its genomic features and biological characteristics. METHODS This research used a wide range of methodology to achieve end results: high throughput sequencing, bioinformatics tools, reverse transcription-polymerase chain reactions, differential diagnostics using indicator plants, virus purification, transmission electron microscopy, and others. RESULTS In this study, we obtained a complete genome sequence of the virus and classified it as a tentative species in the new genus, most closely related to the members of the genus Ipomovirus in the family Potyviridae. This assumption is based on the genome sequence and structure, phylogenetic relationships, and transmission electron microscopy investigations. We also demonstrated its mechanical transmission to the indicator plant Nicotiana benthamiana and to the natural host Medicago sativa, both of which developed characteristic symptoms therefore suggesting a pathogenic nature of the disease. CONCLUSIONS Consistent with symptomatology, the virus was renamed to alfalfa vein mottling virus. A name Alvemovirus was proposed for the new genus in the family Potyviridae, of which alfalfa vein mottling virus is a tentative member.
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Affiliation(s)
- Lev G Nemchinov
- USDA-ARS, NEA, BARC, Molecular Plant Pathology Laboratory, Beltsville, MD, USA.
| | - Olga A Postnikova
- USDA-ARS, NEA, BARC, Animal Biosciences and Biotechnology Laboratory, Beltsville, MD, USA
| | | | - John C Palumbo
- University of Arizona Yuma Agricultural Center, Yuma, AZ, USA
| | - Sam Grinstead
- USDA-ARS, NEA, BARC, Molecular Plant Pathology Laboratory, Beltsville, MD, USA
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Nemchinov LG, Irish BM, Uschapovsky IV, Grinstead S, Shao J, Postnikova OA. Composition of the alfalfa pathobiome in commercial fields. Front Microbiol 2023; 14:1225781. [PMID: 37692394 PMCID: PMC10491455 DOI: 10.3389/fmicb.2023.1225781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023] Open
Abstract
Through the recent advances of modern high-throughput sequencing technologies, the "one microbe, one disease" dogma is being gradually replaced with the principle of the "pathobiome". Pathobiome is a comprehensive biotic environment that not only includes a diverse community of all disease-causing organisms within the plant but also defines their mutual interactions and resultant effect on plant health. To date, the concept of pathobiome as a major component in plant health and sustainable production of alfalfa (Medicago sativa L.), the most extensively cultivated forage legume in the world, is non-existent. Here, we approached this subject by characterizing the biodiversity of the alfalfa pathobiome using high-throughput sequencing technology. Our metagenomic study revealed a remarkable abundance of different pathogenic communities associated with alfalfa in the natural ecosystem. Profiling the alfalfa pathobiome is a starting point to assess known and identify new and emerging stress challenges in the context of plant disease management. In addition, it allows us to address the complexity of microbial interactions within the plant host and their impact on the development and evolution of pathogenesis.
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Affiliation(s)
- Lev G. Nemchinov
- Molecular Plant Pathology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Brian M. Irish
- Plant Germplasm Introduction and Testing Research Unit, Prosser, WA, United States
| | | | - Sam Grinstead
- Molecular Plant Pathology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Jonathan Shao
- United States Department of Agriculture, Agricultural Research Service, Office of The Area Director, Beltsville, MD, United States
| | - Olga A. Postnikova
- Molecular Plant Pathology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Center, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
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Nemchinov LG, Irish BM, Grinstead S, Postnikova OA. Characterization of the seed virome of alfalfa (Medicago sativa L). Virol J 2023; 20:96. [PMID: 37208777 DOI: 10.1186/s12985-023-02063-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/05/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Seed transmission of plant viruses can be important due to the role it plays in their dissemination to new areas and subsequent epidemics. Seed transmission largely depends on the ability of a virus to replicate in reproductive tissues and survive during the seed maturation process. It occurs through the infected embryo or mechanically through the contaminated seed coat. Alfalfa (Medicago sativa L.) is an important legume forage crop worldwide, and except for a few individual seedborne viruses infecting the crop, its seed virome is poorly known. The goal of this research was to perform initial seed screenings on alfalfa germplasm accessions maintained by the USDA ARS National Plant Germplasm System in order to identify pathogenic viruses and understand their potential for dissemination. METHODS For the detection of viruses, we used high throughput sequencing combined with bioinformatic tools and reverse transcription-polymerase chain reactions. RESULTS Our results suggest that, in addition to common viruses, alfalfa seeds are infected by other potentially pathogenic viral species that could be vertically transmitted to offspring. CONCLUSIONS To the best of our knowledge, this is the first study of the alfalfa seed virome carried out by HTS technology. This initial screening of alfalfa germplasm accessions maintained by the NPGS showed that the crop's mature seeds contain a broad range of viruses, some of which were not previously considered to be seed-transmitted. The information gathered will be used to update germplasm distribution policies and to make decisions on the safety of distributing germplasm based on viral presence.
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Affiliation(s)
- Lev G Nemchinov
- Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD, 20705, USA.
| | - Brian M Irish
- Plant Germplasm Introduction and Testing Research, USDA-ARS, Prosser, WA, 99352, USA
| | - Sam Grinstead
- Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Olga A Postnikova
- Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
- Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville, MD, 20705, US
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Postnikova OA, Irish BM, Eisenback J, Nemchinov LG. Snake River alfalfa virus, a persistent virus infecting alfalfa (Medicago sativa L.) in Washington State, USA. Virol J 2023; 20:32. [PMID: 36803436 PMCID: PMC9938972 DOI: 10.1186/s12985-023-01991-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/14/2023] [Indexed: 02/21/2023] Open
Abstract
Here we report an occurrence of Snake River alfalfa virus (SRAV) in Washington state, USA. SRAV was recently identified in alfalfa (Medicago sativa L.) plants and western flower thrips in south-central Idaho and proposed to be a first flavi-like virus identified in a plant host. We argue that the SRAV, based on its prevalence in alfalfa plants, readily detectable dsRNA, genome structure, presence in alfalfa seeds, and seed-mediated transmission is a persistent new virus distantly resembling members of the family Endornaviridae.
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Affiliation(s)
- Olga A Postnikova
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville Agricultural Research Center, Beltsville, MD, USA.,School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Brian M Irish
- USDA/ARS Plant Germplasm Introduction Testing and Research Unit, Prosser, WA, USA
| | - Jonathan Eisenback
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Lev G Nemchinov
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville Agricultural Research Center, Beltsville, MD, USA.
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Vieira P, Subbotin SA, Alkharouf N, Eisenback J, Nemchinov LG. Expanding the RNA virome of nematodes and other soil-inhabiting organisms. Virus Evol 2022; 8:veac019. [PMID: 35371560 PMCID: PMC8967085 DOI: 10.1093/ve/veac019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/02/2022] [Accepted: 03/10/2022] [Indexed: 07/25/2023] Open
Abstract
In recent years, several newly discovered viruses infecting free-living nematodes, sedentary plant-parasitic nematodes, and migratory root lesion nematodes have been described. However, to the best of our knowledge, no comprehensive research focusing exclusively on metagenomic analysis of the soil nematode community virome has thus far been carried out. In this work, we have attempted to bridge this gap by investigating viral communities that are associated with soil-inhabiting organisms, particularly nematodes. This study demonstrates a remarkable diversity of RNA viruses in the natural soil environment. Over 150 viruses were identified in different soil-inhabiting hosts, of which more than 139 are potentially new virus species. Many of these viruses belong to the nematode virome, thereby enriching our understanding of the diversity and evolution of this complex part of the natural ecosystem.
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Affiliation(s)
- Paulo Vieira
- USDA-ARS Mycology & Nematology Genetic Diversity & Biology Laboratory, Beltsville, MD 20705, USA
| | - Sergei A Subbotin
- Plant Pest Diagnostics Branch, California Department of Food & Agriculture, Sacramento, CA 95832, USA
- Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow 117071, Russia
| | - Nadim Alkharouf
- Department of Computer & Information Sciences Faculty, Towson University, Towson, MD 21204, USA
| | - Jonathan Eisenback
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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Vieira P, Myers RY, Pellegrin C, Wram C, Hesse C, Maier TR, Shao J, Koutsovoulos GD, Zasada I, Matsumoto T, Danchin EGJ, Baum TJ, Eves-van den Akker S, Nemchinov LG. Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis. PLoS Pathog 2021; 17:e1010036. [PMID: 34748609 PMCID: PMC8601627 DOI: 10.1371/journal.ppat.1010036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/18/2021] [Accepted: 10/15/2021] [Indexed: 11/18/2022] Open
Abstract
The burrowing nematode, Radopholus similis, is an economically important plant-parasitic nematode that inflicts damage and yield loss to a wide range of crops. This migratory endoparasite is widely distributed in warmer regions and causes extensive destruction to the root systems of important food crops (e.g., citrus, banana). Despite the economic importance of this nematode, little is known about the repertoire of effectors owned by this species. Here we combined spatially and temporally resolved next-generation sequencing datasets of R. similis to select a list of candidates for the identification of effector genes for this species. We confirmed spatial expression of transcripts of 30 new candidate effectors within the esophageal glands of R. similis by in situ hybridization, revealing a large number of pioneer genes specific to this nematode. We identify a gland promoter motif specifically associated with the subventral glands (named Rs-SUG box), a putative hallmark of spatial and concerted regulation of these effectors. Nematode transcriptome analyses confirmed the expression of these effectors during the interaction with the host, with a large number of pioneer genes being especially abundant. Our data revealed that R. similis holds a diverse and emergent repertoire of effectors, which has been shaped by various evolutionary events, including neofunctionalization, horizontal gene transfer, and possibly by de novo gene birth. In addition, we also report the first GH62 gene so far discovered for any metazoan and putatively acquired by lateral gene transfer from a bacterial donor. Considering the economic damage caused by R. similis, this information provides valuable data to elucidate the mode of parasitism of this nematode.
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Affiliation(s)
- Paulo Vieira
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Roxana Y. Myers
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, USDA ARS, Hilo, Hawaii, United States of America
| | - Clement Pellegrin
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Catherine Wram
- USDA-ARS Horticultural Crops Research Unit, Corvallis, Oregon, United States of America
| | - Cedar Hesse
- USDA-ARS Horticultural Crops Research Unit, Corvallis, Oregon, United States of America
| | - Thomas R. Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Jonathan Shao
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | | | - Inga Zasada
- USDA-ARS Horticultural Crops Research Unit, Corvallis, Oregon, United States of America
| | - Tracie Matsumoto
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, USDA ARS, Hilo, Hawaii, United States of America
| | - Etienne G. J. Danchin
- INRAE, Université Côte d’Azur, CNRS, Institute Sophia Agrobiotech, Sophia Antipolis, France
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | | | - Lev G. Nemchinov
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
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Boutanaev AM, Nemchinov LG. Genome-wide identification of endogenous viral sequences in alfalfa (Medicago sativa L.). Virol J 2021; 18:185. [PMID: 34503524 PMCID: PMC8428138 DOI: 10.1186/s12985-021-01650-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/26/2021] [Indexed: 11/10/2022] Open
Abstract
Endogenous viral elements (EVEs) have been for the most part described in animals and to a less extent in plants. The endogenization was proposed to contribute toward evolution of living organisms via horizontal gene transfer of novel genetic material and resultant genetic diversity. During the last two decades, several full-length and fragmented EVEs of pararetroviral and non-retroviral nature have been identified in different plant genomes, both monocots and eudicots. Prior to this work, no EVEs have been reported in alfalfa (Medicago sativa L.), the most cultivated forage legume in the world. In this study, taking advantage of the most recent developments in the field of alfalfa research, we have assessed alfalfa genome on the presence of viral-related sequences. Our analysis revealed segmented EVEs resembling two dsDNA reverse-transcribing virus species: Soybean chlorotic mottle virus (family Caulimoviridae, genus Soymovirus) and Figwort mosaic virus (family Caulimoviridae, genus Caulimovirus). The EVEs appear to be stable constituents of the host genome and in that capacity could potentially acquire functional roles in alfalfa’s development and response to environmental stresses.
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Affiliation(s)
- Alexander M Boutanaev
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Lev G Nemchinov
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA.
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Vieira P, Vicente CSL, Branco J, Buchan G, Mota M, Nemchinov LG. The Root Lesion Nematode Effector Ppen10370 Is Essential for Parasitism of Pratylenchus penetrans. Mol Plant Microbe Interact 2021; 34:645-657. [PMID: 33400561 DOI: 10.1094/mpmi-09-20-0267-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The root lesion nematode Pratylenchus penetrans is a migratory species that attacks a broad range of crops. Like other plant pathogens, P. penetrans deploys a battery of secreted protein effectors to manipulate plant hosts and induce disease. Although several candidate effectors of P. penetrans have been identified, detailed mechanisms of their functions and particularly their host targets remain largely unexplored. In this study, a repertoire of candidate genes encoding pioneer effectors of P. penetrans was amplified from mixed life stages of the nematode, and candidate effectors were cloned and subjected to transient expression in a heterologous host, Nicotiana benthamiana, using potato virus X-based gene vector. Among seven analyzed genes, the candidate effector designated as Ppen10370 triggered pleiotropic phenotypes substantially different from those produced by wild type infection. Transcriptome analysis of plants expressing Ppen10370 demonstrated that observed phenotypic changes were likely related to disruption of core biological processes in the plant due to effector-originated activities. Cross-species comparative analysis of Ppen10370 identified homolog gene sequences in five other Pratylenchus species, and their transcripts were found to be localized specifically in the nematode esophageal glands by in situ hybridization. RNA silencing of the Ppen10370 resulted in a significant reduction of nematode reproduction and development, demonstrating an important role of the esophageal gland effector for parasitism.[Formula: see text] Copyright © 2021 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)
- Paulo Vieira
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Molecular Plant Pathology Laboratory, Beltsville, MD 20705-2350, U.S.A
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Cláudia S L Vicente
- NemaLab, MED-Mediterranean Institute for Agriculture, Environment and Development, Departamento de Biologia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
- INIAV, I.P.-Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - Jordana Branco
- NemaLab, MED-Mediterranean Institute for Agriculture, Environment and Development, Departamento de Biologia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Gary Buchan
- Electron & Confocal Microscopy Unit, USDA-ARS, Beltsville, MD 20705, U.S.A
| | - Manuel Mota
- NemaLab, MED-Mediterranean Institute for Agriculture, Environment and Development, Departamento de Biologia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Lev G Nemchinov
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Molecular Plant Pathology Laboratory, Beltsville, MD 20705-2350, U.S.A
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Nemchinov LG, Grinstead S. Identification of a Novel Isolate of Alfalfa virus S from China Suggests a Possible Role of Seed Contamination in the Distribution of the Virus. Plant Dis 2020; 104:3115-3117. [PMID: 33058717 DOI: 10.1094/pdis-04-20-0906-sc] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Recently, alfalfa virus S (AVS), a new species in the family Alphaflexiviridae, was identified in alfalfa samples originating from Sudan, northern Africa. Here, we report on the identification and complete genomic sequence of an AVS isolate found in 7-day-old seedlings grown from alfalfa seeds acquired from China. The Chinese isolate of AVS differed in its nucleotide sequence from the Sudanese isolate by 8.6%. The detection of AVS in alfalfa seedlings developed from the germinated seeds may indicate a potential role of seed transmission in the distribution of this virus. The results obtained suggest that AVS may be far more widespread than previously thought.
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Affiliation(s)
- Lev G Nemchinov
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD 20705
| | - Samuel Grinstead
- USDA/ARS, Beltsville Agricultural Research Center, National Germplasm Resources Laboratory, Beltsville, MD 20705
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11
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Vieira P, Shao J, Vijayapalani P, Maier TR, Pellegrin C, Eves-van den Akker S, Baum TJ, Nemchinov LG. A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans. BMC Genomics 2020; 21:738. [PMID: 33096989 PMCID: PMC7585316 DOI: 10.1186/s12864-020-07146-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/12/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The root lesion nematode Pratylenchus penetrans is a migratory plant-parasitic nematode responsible for economically important losses in a wide number of crops. Despite the importance of P. penetrans, the molecular mechanisms employed by this nematode to promote virulence remain largely unknown. RESULTS Here we generated a new and comprehensive esophageal glands-specific transcriptome library for P. penetrans. In-depth analysis of this transcriptome enabled a robust identification of a catalogue of 30 new candidate effector genes, which were experimentally validated in the esophageal glands by in situ hybridization. We further validated the expression of a multifaceted network of candidate effectors during the interaction with different plants. To advance our understanding of the "effectorome" of P. penetrans, we adopted a phylogenetic approach and compared the expanded effector repertoire of P. penetrans to the genome/transcriptome of other nematode species with similar or contrasting parasitism strategies. Our data allowed us to infer plausible evolutionary histories that shaped the effector repertoire of P. penetrans, as well as other close and distant plant-parasitic nematodes. Two remarkable trends were apparent: 1) large scale effector birth in the Pratylenchidae in general and P. penetrans in particular, and 2) large scale effector death in sedentary (endo) plant-parasitic nematodes. CONCLUSIONS Our study doubles the number of validated Pratylenchus penetrans effectors reported in the literature. The dramatic effector gene gain in P. penetrans could be related to the remarkable ability of this nematode to parasitize a large number of plants. Our data provide valuable insights into nematode parasitism and contribute towards basic understating of the adaptation of P. penetrans and other root lesion nematodes to specific host plants.
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Affiliation(s)
- Paulo Vieira
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705-2350, USA.
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Jonathan Shao
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705-2350, USA
| | | | - Thomas R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Clement Pellegrin
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | | | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Lev G Nemchinov
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705-2350, USA
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Bejerman N, Roumagnac P, Nemchinov LG. High-Throughput Sequencing for Deciphering the Virome of Alfalfa ( Medicago sativa L.). Front Microbiol 2020; 11:553109. [PMID: 33042059 PMCID: PMC7518122 DOI: 10.3389/fmicb.2020.553109] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/12/2020] [Indexed: 12/22/2022] Open
Abstract
Alfalfa (Medicago sativa L.), also known as lucerne, is a major forage crop worldwide. In the United States, it has recently become the third most valuable field crop, with an estimated value of over $9.3 billion. Alfalfa is naturally infected by many different pathogens, including viruses, obligate parasites that reproduce only inside living host cells. Traditionally, viral infections of alfalfa have been considered by breeders, growers, producers and researchers to be diseases of limited importance, although they are widespread in all major cultivation areas. However, over the past few years, due to the rapid development of high-throughput sequencing (HTS), viral metagenomics, bioinformatics tools for interpreting massive amounts of HTS data and the increasing accessibility of public data repositories for transcriptomic discoveries, several emerging viruses of alfalfa with the potential to cause serious yield losses have been described. They include alfalfa leaf curl virus (family Geminiviridae), alfalfa dwarf virus (family Rhabdoviridae), alfalfa enamovirus 1 (family Luteoviridae), alfalfa virus S (family Alphaflexiviridae) and others. These discoveries have called into question the assumed low economic impact of viral diseases in alfalfa and further suggested their possible contribution to the severity of complex infections involving multiple pathogens. In this review, we will focus on viruses of alfalfa recently described in different laboratories on the basis of the above research methodologies.
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Affiliation(s)
| | - Philippe Roumagnac
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Université Montpellier, Montpellier, France
| | - Lev G Nemchinov
- Molecular Plant Pathology Laboratory, USDA-ARS-BARC, Beltsville, MD, United States
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Vieira P, Nemchinov LG. An Expansin-Like Candidate Effector Protein from Pratylenchus penetrans Modulates Immune Responses in Nicotiana benthamiana. Phytopathology 2020; 110:684-693. [PMID: 31680651 DOI: 10.1094/phyto-09-19-0336-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The root lesion nematode (RLN) Pratylenchus penetrans is a migratory species that attacks a broad range of crops. After the RLN is initially attracted to host roots by root exudates and compounds, it releases secretions that are critical for successful parasitism. Among those secretions are nematode virulence factors or effectors that facilitate the entry and migration of nematodes through the roots and modulate plant immune defenses. The recognition of the effectors by host resistance proteins leads to effector-triggered immunity and incompatible plant-nematode interactions. Although many candidate effectors of the RLN and other plant-parasitic nematodes have been identified, the detailed mechanisms of their functions and particularly, their host targets remain largely unexplored. In this study, we sequenced and annotated genes encoding expansin-like proteins, which are major candidate effectors of P. penetrans. One of the genes, Pp-EXPB1, which was the most highly expressed during nematode infection in different plant species, was further functionally characterized via transient expression in the model plant Nicotiana benthamiana and global transcriptome profiling of gene expression changes triggered by this candidate effector in plants. As a result of this investigation, the biological roles of Pp-EXPB1 in nematode parasitism were proposed, the putative cellular targets of the proteins were identified, and the molecular mechanisms of plant responses to the nematode-secreted proteins were outlined.
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Affiliation(s)
- Paulo Vieira
- Molecular Plant Pathology Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705-2350
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
| | - Lev G Nemchinov
- Molecular Plant Pathology Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705-2350
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Vieira P, Peetz A, Mimee B, Saikai K, Mollov D, MacGuidwin A, Zasada I, Nemchinov LG. Prevalence of the root lesion nematode virus (RLNV1) in populations of Pratylenchus penetrans from North America. J Nematol 2020; 52:1-10. [PMID: 32421266 PMCID: PMC7266026 DOI: 10.21307/jofnem-2020-045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Indexed: 11/11/2022] Open
Abstract
Root lesion nematode virus 1 (RLNV1) was discovered in the migratory endoparasitic nematode species Pratylenchus penetrans. It was found in a P. penetrans population collected from soil samples in Beltsville, Maryland, USA. In this study, the distribution of the RLNV1 in 31 geographically distinct P. penetrans populations obtained from different crops was examined. The results demonstrate that RLNV1 is widespread in North American populations of P. penetrans and exhibits low genetic variability in the helicase and RNA-dependent RNA polymerase regions of the genome.
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Affiliation(s)
- Paulo Vieira
- Molecular Plant Pathology Laboratory , USDA-ARS , Beltsville, MD 20705 ; School of Plant Environmental Science , Virginia Tech , Blacksburg, VA 24061
| | - Amy Peetz
- Horticultural Crops Research Laboratory , USDA-ARS , Corvallis, OR 97330
| | - Benjamin Mimee
- St-Jean-sur-Richelieu Research and Development Center , Agriculture and Agri-Food Canada , St-Jean-sur-Richelieu , Canada
| | - Kanan Saikai
- Department of Plant Pathology, University of Wisconsin-Madison , Madison, WI 53706
| | - Dimitre Mollov
- National Germplasm Resources Laboratory , USDA-ARS , Beltsville, MD 20705
| | - Ann MacGuidwin
- Department of Plant Pathology, University of Wisconsin-Madison , Madison, WI 53706
| | - Inga Zasada
- Horticultural Crops Research Laboratory , USDA-ARS , Corvallis, OR 97330
| | - Lev G Nemchinov
- Molecular Plant Pathology Laboratory , USDA-ARS , Beltsville, MD 20705
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Jiang P, Shao J, Nemchinov LG. Identification of emerging viral genomes in transcriptomic datasets of alfalfa (Medicago sativa L.). Virol J 2019; 16:153. [PMID: 31818304 PMCID: PMC6902351 DOI: 10.1186/s12985-019-1257-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022] Open
Abstract
Background Publicly available transcriptomic datasets have become a valuable tool for the discovery of new pathogens, particularly viruses. In this study, several coding-complete viral genomes previously not found or experimentally confirmed in alfalfa were identified in the plant datasets retrieved from the NCBI Sequence Read Archive. Methods Publicly available Medicago spp. transcriptomic datasets were retrieved from the NCBI SRA database. The raw reads were first mapped to the reference genomes of Medicago sativa and Medigago truncatula followed by the alignment of the unmapped reads to the NCBI viral genome database and de novo assembly using the SPAdes tool. When possible, assemblies were experimentally confirmed using 5′/3′ RACE and RT-PCRs. Results Twenty three different viruses were identified in the analyzed datasets, of which several represented emerging viruses not reported in alfalfa prior to this study. Among them were two strains of cnidium vein yellowing virus, lychnis mottle virus and Cactus virus X, for which coding-complete genomic sequences were obtained by a de novo assembly. Conclusions The results improve our knowledge of the diversity and host range of viruses infecting alfalfa, provide essential tools for their diagnostics and characterization and demonstrate the utility of transcriptomic datasets for the discovery of new pathogens.
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Affiliation(s)
- Peng Jiang
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA
| | - Jonathan Shao
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA
| | - Lev G Nemchinov
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA.
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Vieira P, Mowery J, Eisenback JD, Shao J, Nemchinov LG. Cellular and Transcriptional Responses of Resistant and Susceptible Cultivars of Alfalfa to the Root Lesion Nematode, Pratylenchus penetrans. Front Plant Sci 2019; 10:971. [PMID: 31417588 PMCID: PMC6685140 DOI: 10.3389/fpls.2019.00971] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/11/2019] [Indexed: 05/04/2023]
Abstract
The root lesion nematode (RLN), Pratylenchus penetrans, is a migratory species that attacks a broad range of crops, including alfalfa. High levels of infection can reduce alfalfa forage yields and lead to decreased cold tolerance. Currently, there are no commercially certified varieties with RLN resistance. Little information on molecular interactions between alfalfa and P. penetrans, that would shed light on mechanisms of alfalfa resistance to RLN, is available. To advance our understanding of the host-pathogen interactions and to gain biological insights into the genetics and genomics of host resistance to RLN, we performed a comprehensive assessment of resistant and susceptible interactions of alfalfa with P. penetrans that included root penetration studies, ultrastructural observations, and global gene expression profiling of host plants and the nematode. Several gene-candidates associated with alfalfa resistance to P. penetrans and nematode parasitism genes encoding nematode effector proteins were identified for potential use in alfalfa breeding programs or development of new nematicides. We propose that preformed or constitutive defenses, such as significant accumulation of tannin-like deposits in root cells of the resistant cultivar, could be a key to nematode resistance, at least for the specific case of alfalfa-P. penetrans interaction.
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Affiliation(s)
- Paulo Vieira
- Molecular Plant Pathology Laboratory, United States Department of Agriculture – Agricultural Research Service, Beltsville, MD, United States
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA, United States
| | - Joseph Mowery
- Electron and Confocal Microscopy Unit, United States Department of Agriculture – Agricultural Research Service, Beltsville, MD, United States
| | - Jonathan D. Eisenback
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA, United States
| | - Jonathan Shao
- Molecular Plant Pathology Laboratory, United States Department of Agriculture – Agricultural Research Service, Beltsville, MD, United States
| | - Lev G. Nemchinov
- Molecular Plant Pathology Laboratory, United States Department of Agriculture – Agricultural Research Service, Beltsville, MD, United States
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Affiliation(s)
- Paulo Vieira
- 1Molecular Plant Pathology Laboratory, Agricultural Research Service, USA Department of Agriculture, Beltsville, USA
- 2School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, USA
| | - Lev G. Nemchinov
- 1Molecular Plant Pathology Laboratory, Agricultural Research Service, USA Department of Agriculture, Beltsville, USA
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Vicente CSL, Nemchinov LG, Mota M, Eisenback JD, Kamo K, Vieira P. Identification and characterization of the first pectin methylesterase gene discovered in the root lesion nematode Pratylenchus penetrans. PLoS One 2019; 14:e0212540. [PMID: 30794636 PMCID: PMC6386239 DOI: 10.1371/journal.pone.0212540] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/05/2019] [Indexed: 02/04/2023] Open
Abstract
Similar to other plant-parasitic nematodes, root lesion nematodes possess an array of enzymes that are involved in the degradation of the plant cell wall. Here we report the identification of a gene encoding a cell wall-degrading enzyme, pectin methylesterase PME (EC 3.1.1.11), in the root lesion nematode Pratylenchus penetrans. Both genomic and coding sequences of the gene were cloned for this species, that included the presence of four introns which eliminated a possible contamination from bacteria. Expression of the Pp-pme gene was localized in the esophageal glands of P. penetrans as determined by in situ hybridization. Temporal expression of Pp-pme in planta was validated at early time points of infection. The possible function and activity of the gene were assessed by transient expression of Pp-pme in plants of Nicotiana benthamiana plants via a Potato virus X-based vector. To our knowledge, this is the first report on identification and characterization of a PME gene within the phylum Nematoda.
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Affiliation(s)
- Cláudia S. L. Vicente
- ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Évora, Portugal
| | - Lev G. Nemchinov
- Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Manuel Mota
- Departamento de Biologia & ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Pólo da Mitra, Évora, Portugal
| | - Jonathan D. Eisenback
- School of Plant Environmental Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Kathryn Kamo
- Floral and Nursery Plants Research Unit, United States of National Arboretum, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Paulo Vieira
- Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
- School of Plant Environmental Science, Virginia Tech, Blacksburg, Virginia, United States of America
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Nemchinov LG, François S, Roumagnac P, Ogliastro M, Hammond RW, Mollov DS, Filloux D. Characterization of alfalfa virus F, a new member of the genus Marafivirus. PLoS One 2018; 13:e0203477. [PMID: 30180217 PMCID: PMC6122807 DOI: 10.1371/journal.pone.0203477] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/21/2018] [Indexed: 01/27/2023] Open
Abstract
Viral infections of alfalfa are widespread in major cultivation areas and their impact on alfalfa production may be underestimated. A new viral species, provisionally named alfalfa virus F (AVF), was identified using a virion-associated nucleic acid (VANA) metagenomics-based approach in alfalfa (Medicago sativa L.) samples collected in Southern France. The nucleotide sequence of the viral genome was determined by de-novo assembly of VANA reads and by 5'/3' RACE with viral RNA extracted from enriched viral particles or with total RNA, respectively. The virus shares the greatest degree of overall sequence identity (~78%) with Medicago sativa marafivirus 1 (MsMV1) recently deduced from alfalfa transcriptomic data. The tentative nucleotide sequence of the AVF coat protein shares ~83% identity with the corresponding region of MsMV1. A sequence search of the predicted single large ORF encoding a polyprotein of 235kDa in the Pfam database resulted in identification of five domains, characteristic of the genus Marafivirus, family Tymoviridae. The AVF genome also contains a conserved "marafibox", a 16-nt consensus sequence present in all known marafiviruses. Phylogenetic analysis of the complete nucleotide sequences of AVF and other viruses of the family Tymoviridae grouped AVF in the same cluster with MsMV1. In addition to 5' and 3' terminal extensions, the identity of the virus was confirmed by RT-PCRs with primers derived from VANA-contigs, transmission electron microscopy with virus-infected tissues and transient expression of the viral coat protein gene using a heterologous virus-based vector. Based on the criteria demarcating species in the genus Marafivirus that include overall sequence identity less than 80% and coat protein identity less than 90%, we propose that AVF represents a distinct viral species in the genus Marafivirus, family Tymoviridae.
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Affiliation(s)
- Lev G. Nemchinov
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville MD, United States of America
| | | | - Phillipe Roumagnac
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier
| | | | - Rosemarie W. Hammond
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville MD, United States of America
| | - Dimitre S. Mollov
- USDA-ARS, National Germplasm Recourses Laboratory, Beltsville MD, United States of America
| | - Denis Filloux
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier
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Nemchinov LG, Shao J, Lee MN, Postnikova OA, Samac DA. Resistant and susceptible responses in alfalfa (Medicago sativa) to bacterial stem blight caused by Pseudomonas syringae pv. syringae. PLoS One 2017; 12:e0189781. [PMID: 29244864 PMCID: PMC5731681 DOI: 10.1371/journal.pone.0189781] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/01/2017] [Indexed: 11/18/2022] Open
Abstract
Bacterial stem blight caused by Pseudomonas syringae pv. syringae is a common disease of alfalfa (Medicago sativa L). Little is known about host-pathogen interactions and host defense mechanisms. Here, individual resistant and susceptible plants were selected from cultivars Maverick and ZG9830 and used for transcript profiling at 24 and 72 hours after inoculation (hai) with the isolate PssALF3. Bioinformatic analysis revealed a number of differentially expressed genes (DEGs) in resistant and susceptible genotypes. Although resistant plants from each cultivar produced a hypersensitive response, transcriptome analyses indicated that they respond differently at the molecular level. The number of DEGs was higher in resistant plants of ZG9830 at 24 hai than in Maverick, suggesting that ZG9830 plants had a more rapid effector triggered immune response. Unique up-regulated genes in resistant ZG9830 plants included genes encoding putative nematode resistance HSPRO2-like proteins, orthologs for the rice Xa21 and soybean Rpg1-b resistance genes, and TIR-containing R genes lacking both NBS and LRR domains. The suite of R genes up-regulated in resistant Maverick plants had an over-representation of R genes in the CC-NBS-LRR family including two genes for atypical CCR domains and a putative ortholog of the Arabidopsis RPM1 gene. Resistance in both cultivars appears to be mediated primarily by WRKY family transcription factors and expression of genes involved in protein phosphorylation, regulation of transcription, defense response including synthesis of isoflavonoids, and oxidation-reduction processes. These results will further the identification of mechanisms involved in resistance to facilitate selection of parent populations and development of commercial varieties.
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Affiliation(s)
- Lev G. Nemchinov
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | - Jonathan Shao
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | - Maya N. Lee
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | - Olga A. Postnikova
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | - Deborah A. Samac
- USDA-ARS, Plant Science Research Unit, St. Paul, Minnesota, United States of America
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Abstract
A new species of the family Alphaflexiviridae provisionally named alfalfa virus S (AVS) was discovered in alfalfa samples originating from Sudan. A complete nucleotide sequence of the viral genome consisting of 8,349 nucleotides excluding the 3' poly(A) tail was determined by high throughput sequencing (HTS) on an Illumina platform. NCBI BLAST searches revealed that the virus shares the greatest degree of sequence identity with members of the family Alphaflexiviridae, genus Allexivirus. The AVS genome contains six computationally-predicted open reading frames (ORF) encoding viral replication protein, triple gene block protein 1 (TGB1), TGB2, TGB3-like protein, unknown 38.4 kDa protein resembling serine-rich 40 kDa protein characteristic for allexiviruses, and coat protein (CP). AVS lacks a clear 3' proximal ORF that encodes a nucleic acid-binding protein typical for allexiviruses. The identity of the virus was confirmed by RT-PCR with primers derived from the HTS-generated sequence, dot blot hybridization with DIG-labeled virus-specific RNA probes, and Western blot analysis with antibodies produced against a peptide derived from the CP sequence. Transmission electron microscopic observations of the infected tissues showed the presence of filamentous particles similar to allexiviruses in their length and appearance. To the best of our knowledge, this is the first report on the identification of a putative allexivirus in alfalfa (Medicago sativa). The genome sequence of AVS has been deposited in NCBI GenBank on 03/02/2016 as accession № KY696659.
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Affiliation(s)
- Lev G. Nemchinov
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | - Samuel C. Grinstead
- USDA-ARS, National Germplasm Recourses Laboratory, Beltsville, Maryland, United States of America
| | - Dimitre S. Mollov
- USDA-ARS, National Germplasm Recourses Laboratory, Beltsville, Maryland, United States of America
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Nemchinov LG, Boutanaev AM, Postnikova OA. Virus-induced gene silencing of the RPC5-like subunit of RNA polymerase III caused pleiotropic effects in Nicotiana benthamiana. Sci Rep 2016; 6:27785. [PMID: 27282827 PMCID: PMC4901293 DOI: 10.1038/srep27785] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 05/24/2016] [Indexed: 12/30/2022] Open
Abstract
In eukaryotic cells, RNA polymerase III is highly conserved and transcribes housekeeping genes such as ribosomal 5S rRNA, tRNA and other small RNAs. The RPC5-like subunit is one of the 17 subunits forming RNAPIII and its exact functional roles in the transcription are poorly understood. In this work, we report that virus-induced gene silencing of transcripts encoding a putative RPC5-like subunit of the RNA Polymerase III in a model species Nicotiana benthamiana had pleiotropic effects, including but not limited to severe dwarfing appearance, chlorosis, nearly complete reduction of internodes and abnormal leaf shape. Using transcriptomic analysis, we identified genes and pathways affected by RPC5 silencing and thus presumably related to the cellular roles of the subunit as well as to the downstream cascade of reactions in response to partial loss of RNA Polymerase III function. Our results suggest that silencing of the RPC5L in N. benthamiana disrupted not only functions commonly associated with the core RNA Polymerase III transcripts, but also more diverse cellular processes, including responses to stress. We believe this is the first demonstration that activity of the RPC5 subunit is critical for proper functionality of RNA Polymerase III and normal plant development.
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Affiliation(s)
- Lev G. Nemchinov
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville MD 20705, USA
| | - Alexander M. Boutanaev
- Institute of Basic Biological Problems, Russian Academy of Sciences, 2 Institute Street, Pushchino, Moscow Region, 142292, Russia
| | - Olga A. Postnikova
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville MD 20705, USA
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Chervyakova OV, Zaitsev VL, Iskakov BK, Tailakova ET, Strochkov VM, Sultankulova KT, Sandybayev NT, Stanbekova GE, Beisenov DK, Abduraimov YO, Mambetaliyev M, Sansyzbay AR, Kovalskaya NY, Nemchinov LG, Hammond RW. Recombinant Sheep Pox Virus Proteins Elicit Neutralizing Antibodies. Viruses 2016; 8:E159. [PMID: 27338444 PMCID: PMC4926179 DOI: 10.3390/v8060159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/24/2016] [Accepted: 05/30/2016] [Indexed: 12/24/2022] Open
Abstract
The aim of this work was to evaluate the immunogenicity and neutralizing activity of sheep pox virus (SPPV; genus Capripoxvirus, family Poxviridae) structural proteins as candidate subunit vaccines to control sheep pox disease. SPPV structural proteins were identified by sequence homology with proteins of vaccinia virus (VACV) strain Copenhagen. Four SPPV proteins (SPPV-ORF 060, SPPV-ORF 095, SPPV-ORF 117, and SPPV-ORF 122), orthologs of immunodominant L1, A4, A27, and A33 VACV proteins, respectively, were produced in Escherichia coli. Western blot analysis revealed the antigenic and immunogenic properties of SPPV-060, SPPV-095, SPPV-117 and SPPV-122 proteins when injected with adjuvant into experimental rabbits. Virus-neutralizing activity against SPPV in lamb kidney cell culture was detected for polyclonal antisera raised to SPPV-060, SPPV-117, and SPPV-122 proteins. To our knowledge, this is the first report demonstrating the virus-neutralizing activities of antisera raised to SPPV-060, SPPV-117, and SPPV-122 proteins.
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Affiliation(s)
- Olga V Chervyakova
- Research Institute for Biological Safety Problems, RK ME&S - Science Committee, Gvardeiskiy 080409, Kazakhstan.
| | - Valentin L Zaitsev
- Research Institute for Biological Safety Problems, RK ME&S - Science Committee, Gvardeiskiy 080409, Kazakhstan.
| | - Bulat K Iskakov
- M. A. Aitkhozhin's Institute of Molecular Biology and Biochemistry, RK ME&S - Science Committee, Almaty 050012, Kazakhstan.
| | - Elmira T Tailakova
- Research Institute for Biological Safety Problems, RK ME&S - Science Committee, Gvardeiskiy 080409, Kazakhstan.
| | - Vitaliy M Strochkov
- Research Institute for Biological Safety Problems, RK ME&S - Science Committee, Gvardeiskiy 080409, Kazakhstan.
| | - Kulyaisan T Sultankulova
- Research Institute for Biological Safety Problems, RK ME&S - Science Committee, Gvardeiskiy 080409, Kazakhstan.
| | - Nurlan T Sandybayev
- Research Institute for Biological Safety Problems, RK ME&S - Science Committee, Gvardeiskiy 080409, Kazakhstan.
| | - Gulshan E Stanbekova
- M. A. Aitkhozhin's Institute of Molecular Biology and Biochemistry, RK ME&S - Science Committee, Almaty 050012, Kazakhstan.
| | - Daniyar K Beisenov
- M. A. Aitkhozhin's Institute of Molecular Biology and Biochemistry, RK ME&S - Science Committee, Almaty 050012, Kazakhstan.
| | - Yergali O Abduraimov
- Research Institute for Biological Safety Problems, RK ME&S - Science Committee, Gvardeiskiy 080409, Kazakhstan.
| | - Muratbay Mambetaliyev
- Research Institute for Biological Safety Problems, RK ME&S - Science Committee, Gvardeiskiy 080409, Kazakhstan.
| | - Abylay R Sansyzbay
- Research Institute for Biological Safety Problems, RK ME&S - Science Committee, Gvardeiskiy 080409, Kazakhstan.
| | - Natalia Y Kovalskaya
- United States Department of Agriculture, Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA.
| | - Lev G Nemchinov
- United States Department of Agriculture, Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA.
| | - Rosemarie W Hammond
- United States Department of Agriculture, Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA.
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Postnikova OA, Shao J, Mock NM, Baker CJ, Nemchinov LG. Gene Expression Profiling in Viable but Nonculturable (VBNC) Cells of Pseudomonas syringae pv. syringae. Front Microbiol 2015; 6:1419. [PMID: 26733964 PMCID: PMC4683178 DOI: 10.3389/fmicb.2015.01419] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/30/2015] [Indexed: 11/30/2022] Open
Abstract
Pseudomonas syringae infects diverse crop plants and comprises at least 50 different pathovar strains with different host ranges. More information on the physiological and molecular effects of the host inhibitory environment on the pathogen is needed to develop resistant cultivars. Recently, we reported an in vitro model system that mimics the redox pulse associated with the oxidative burst in plant cells inoculated with Pseudomonas syringae pv. syringae. Using this system, we demonstrated that oxidation of acetosyringone, a major extracellular phenolic compound induced in some plants in response to bacteria, rendered Pseudomonas syringae pv. syringae to a “viable but nonculturable” (VBNC) state. Here we performed a large scale transcriptome profiling of P. s. pv. syringae in the VBNC state induced by acetosyringone treatment and identified bacterial genes and pathways presumably associated with this condition. The findings offer insight into what events occur when bacterial pathogens are first encountered and host defense responses are triggered. The acquired knowledge will improve our understanding of the molecular mechanisms of stress tolerance. We believe that this is the first work on global gene expression profiling of VBNC cells in plant pathogenic bacteria.
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Affiliation(s)
- Olga A Postnikova
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Jonathan Shao
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Norton M Mock
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Con J Baker
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Lev G Nemchinov
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
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Postnikova OA, Nemchinov LG. Natural Antisense Transcripts Associated with Salinity Response in Alfalfa. Plant Genome 2015; 8:eplantgenome2014.09.0057. [PMID: 33228296 DOI: 10.3835/plantgenome2014.09.0057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/09/2015] [Indexed: 06/11/2023]
Abstract
Natural antisense transcripts (NATs) are long noncoding RNAs (lncRNAs) complementary to the messenger (sense) RNA (Wang et al., 2014). Many of them are involved in regulation of their own sense transcripts thus playing pivotal biological roles in all processes of organismal development and responses to the environment. In our previous study, we have identified a number of differentially expressed genes (DEGs) in alfalfa plants (Medicago sativa L.) subjected to salinity stress (Postnikova et al., 2013). In this work, we selected several experimentally validated DEGs identified in response to salt and analyzed them for the presence of NAT pairs. The majority of the examined DEGs encoded NATs. Expression of some NAT pairs changed in response to salinity, suggesting their involvement in regulating the responses of alfalfa to salt.
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Affiliation(s)
- O A Postnikova
- USDA-ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Lab., 10300 Baltimore Ave., Beltsville, MD, 20705
| | - L G Nemchinov
- USDA-ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Lab., 10300 Baltimore Ave., Beltsville, MD, 20705
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Postnikova OA, Hult M, Shao J, Skantar A, Nemchinov LG. Transcriptome analysis of resistant and susceptible alfalfa cultivars infected with root-knot nematode Meloidogyne incognita. PLoS One 2015; 10:e0123157. [PMID: 25822722 PMCID: PMC4379156 DOI: 10.1371/journal.pone.0123157] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Postnikova OA, Hult M, Shao J, Skantar A, Nemchinov LG. Transcriptome analysis of resistant and susceptible alfalfa cultivars infected with root-knot nematode Meloidogyne incognita. PLoS One 2015; 10:e0118269. [PMID: 25710378 PMCID: PMC4339843 DOI: 10.1371/journal.pone.0118269] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/12/2015] [Indexed: 12/02/2022] Open
Abstract
Nematodes are one of the major limiting factors in alfalfa production. Root-knot nematodes (RKN, Meloidogyne spp.) are widely distributed and economically important sedentary endoparasites of agricultural crops and they may inflict significant damage to alfalfa fields. As of today, no studies have been published on global gene expression profiling in alfalfa infected with RKN or any other plant parasitic nematode. Very little information is available about molecular mechanisms that contribute to pathogenesis and defense responses in alfalfa against these pests and specifically against RKN. In this work, we performed root transcriptome analysis of resistant (cv. Moapa 69) and susceptible (cv. Lahontan) alfalfa cultivars infected with RKN Meloidogyne incognita, widespread root-knot nematode species and a major pest worldwide. A total of 1,701,622,580 pair-end reads were generated on an Illumina Hi-Seq 2000 platform from the roots of both cultivars and assembled into 45,595 and 47,590 transcripts in cvs Moapa 69 and Lahontan, respectively. Bioinformatic analysis revealed a number of common and unique genes that were differentially expressed in susceptible and resistant lines as a result of nematode infection. Although the susceptible cultivar showed a more pronounced defense response to the infection, feeding sites were successfully established in its roots. Characteristically, basal gene expression levels under normal conditions differed between the two cultivars as well, which may confer advantage to one of the genotypes toward resistance to nematodes. Differentially expressed genes were subsequently assigned to known Gene Ontology categories to predict their functional roles and associated biological processes. Real-time PCR validated expression changes in genes arbitrarily selected for experimental confirmation. Candidate genes that contribute to protection against M. incognita in alfalfa were proposed and alfalfa-nematode interactions with respect to resistance are discussed.
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Affiliation(s)
- Olga A. Postnikova
- USDA-ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | - Maria Hult
- USDA-ARS, Beltsville Agricultural Research Center, Nematology Laboratory, Beltsville, Maryland, United States of America
| | - Jonathan Shao
- USDA-ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | - Andrea Skantar
- USDA-ARS, Beltsville Agricultural Research Center, Nematology Laboratory, Beltsville, Maryland, United States of America
| | - Lev G. Nemchinov
- USDA-ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
- * E-mail:
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Postnikova OA, Shao J, Nemchinov LG. Analysis of the Alfalfa Root Transcriptome in Response to Salinity Stress. ACTA ACUST UNITED AC 2013; 54:1041-55. [DOI: 10.1093/pcp/pct056] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Postnikova OA, Nemchinov LG. Comparative analysis of microarray data in Arabidopsis transcriptome during compatible interactions with plant viruses. Virol J 2012; 9:101. [PMID: 22643110 PMCID: PMC3430556 DOI: 10.1186/1743-422x-9-101] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 04/23/2012] [Indexed: 01/21/2023] Open
Abstract
Background At the moment, there are a number of publications describing gene expression profiling in virus-infected plants. Most of the data are limited to specific host-pathogen interactions involving a given virus and a model host plant – usually Arabidopsis thaliana. Even though several summarizing attempts have been made, a general picture of gene expression changes in susceptible virus-host interactions is lacking. Methods To analyze transcriptome response to virus infection, we have assembled currently available microarray data on changes in gene expression levels in compatible Arabidopsis-virus interactions. We used the mean r (Pearson’s correlation coefficient) for neighboring pairs to estimate pairwise local similarity in expression in the Arabidopsis genome. Results Here we provide a functional classification of genes with altered expression levels. We also demonstrate that responsive genes may be grouped or clustered based on their co-expression pattern and chromosomal location. Conclusions In summary, we found that there is a greater variety of upregulated genes in the course of viral pathogenesis as compared to repressed genes. Distribution of the responsive genes in combined viral databases differed from that of the whole Arabidopsis genome, thus underlining a role of the specific biological processes in common mechanisms of general resistance against viruses and in physiological/cellular changes caused by infection. Using integrative platforms for the analysis of gene expression data and functional profiling, we identified overrepresented functional groups among activated and repressed genes. Each virus-host interaction is unique in terms of the genes with altered expression levels and the number of shared genes affected by all viruses is very limited. At the same time, common genes can participate in virus-, fungi- and bacteria-host interaction. According to our data, non-homologous genes that are located in close proximity to each other on the chromosomes, and whose expression profiles are modified as a result of the viral infection, occupy 12% of the genome. Among them 5% form co-expressed and co-regulated clusters.
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Affiliation(s)
- Olga A Postnikova
- USDA/ARS, Plant Sciences Institute, Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA
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Boutanaev AM, Nemchinov LG. Are clustered genes in the genomes of Arabidopsis and Drosophila regulated differently? Gene 2012; 491:284-8. [PMID: 22008664 DOI: 10.1016/j.gene.2011.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 09/22/2011] [Accepted: 09/24/2011] [Indexed: 10/16/2022]
Abstract
In the eukaryotic genome, genes with similar functions tend to co-localize in close proximity. Such gene clusters together with non-clustered genes constitute a chromatin domain which is a higher order regulatory unit. On a lower level co-expressed genes are regulated by differential activity of transcription factors (TF). We compared genome-wide distributions of TF in gene clusters in the genomes of Drosophila melanogaster and Arabidopsis thaliana. This revealed a significant excess of TF genes in gene clusters of the Arabidopsis genome, whereas in the genome of Drosophila distribution of TF in gene clusters did not differ from stochastic. We speculate that these alternatives could lead to different pathways of regulation of clustered genes in two species and to evolutionary-progressive changes in architecture of regulatory networks, governing the activity of clustered genes in the animal kingdom.
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Affiliation(s)
- Alexander M Boutanaev
- USDA/ARS, Plant Sciences Institute, Molecular Plant Pathology Laboratory, Beltsville MD 20705, USA.
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Abstract
Previously, we used heterologous expressed sequence tag (EST) mapping to generate a profile of 4 935 pathogen-response genes of Arabidopsis thaliana. In this work, we performed a computer analysis of this profile, revealing 1 594 non-homologous clustered genes distributed among all A. thaliana chromosomes, whose co-regulation may be related to host responses to pathogens. To supplement computer data, we arbitrarily selected two clusters and analyzed their expression levels in A. thaliana ecotypes Col-0 and C24 during infection with the yellow strain of Cucumber mosaic virus CMV(Y). Ecotype Col-0 is susceptible to CMV(Y), whereas C24 contains the dominant resistance gene RCY1. Upon infection with CMV(Y), all clustered genes were significantly activated in the resistant ecotype C24. In addition, we demonstrated that posttranslational histone modifications associated with trimethylation of histone H3 lysine 27 are most likely involved in regulation of several cluster genes described in this study. Overall, our experiments indicated that pathogen-response genes in the genome of A. thaliana may be clustered and co-regulated.
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Affiliation(s)
- Olga A Postnikova
- United States Department of Agriculture, Agricultural Research Service, Plant Sciences Institute, Molecular Plant Pathology Laboratory, Beltsville 20705, USAInstitute of Basic Biological Problems, Russian Academy of Sciences, Pushchino 142292, Russia
| | - Natalia Y Minakova
- United States Department of Agriculture, Agricultural Research Service, Plant Sciences Institute, Molecular Plant Pathology Laboratory, Beltsville 20705, USAInstitute of Basic Biological Problems, Russian Academy of Sciences, Pushchino 142292, Russia
| | - Alexander M Boutanaev
- United States Department of Agriculture, Agricultural Research Service, Plant Sciences Institute, Molecular Plant Pathology Laboratory, Beltsville 20705, USAInstitute of Basic Biological Problems, Russian Academy of Sciences, Pushchino 142292, Russia
| | - Lev G Nemchinov
- United States Department of Agriculture, Agricultural Research Service, Plant Sciences Institute, Molecular Plant Pathology Laboratory, Beltsville 20705, USAInstitute of Basic Biological Problems, Russian Academy of Sciences, Pushchino 142292, Russia
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Shabala S, Bækgaard L, Shabala L, Fuglsang AT, Cuin TA, Nemchinov LG, Palmgren MG. Endomembrane Ca2+-ATPases play a significant role in virus-induced adaptation to oxidative stress. Plant Signal Behav 2011; 6:1053-6. [PMID: 21633195 PMCID: PMC3257794 DOI: 10.4161/psb.6.7.15634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 03/24/2011] [Indexed: 05/04/2023]
Abstract
Although the role of Ca2+ influx channels in oxidative stress signaling and cross-tolerance in plants is well established, little is known about the role of active Ca2+ efflux systems in this process. In our recent paper, we reported Potato Virus X (PVX)-induced acquired resistance to oxidative stress in Nicotiana benthamiana and showed the critical role of plasma membrane Ca2+/H+ exchangers in this process. The current study continues this research. Using biochemical and electrophysiological approaches, we reveal that both endomembrane P2A and P2B Ca2+-ATPases play significant roles in adaptive responses to oxidative stress by removing excessive Ca2+ from the cytosol, and that their functional expression is significantly altered in PVX-inoculated plants. These findings highlight the crucial role of Ca2+ efflux systems in acquired tolerance to oxidative stress and open up prospects for practical applications in agriculture, after in-depth comprehension of the fundamental mechanisms involved in common responses to environmental factors at the genomic, cellular and organismal levels.
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Affiliation(s)
- Sergey Shabala
- School of Agricultural Science, University of Tasmania, Hobart, TAS, Australia.
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Shabala S, Baekgaard L, Shabala L, Fuglsang A, Babourina O, Palmgren MG, Cuin TA, Rengel Z, Nemchinov LG. Plasma membrane Ca²+ transporters mediate virus-induced acquired resistance to oxidative stress. Plant Cell Environ 2011; 34:406-17. [PMID: 21062316 DOI: 10.1111/j.1365-3040.2010.02251.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This paper reports the phenomenon of acquired cross-tolerance to oxidative stress in plants and investigates the activity of specific Ca²+ transport systems mediating this phenomenon. Nicotiana benthamiana plants were infected with Potato virus X (PVX) and exposed to oxidative [either ultraviolet (UV-C) or H₂O₂] stress. Plant adaptive responses were assessed by the combined application of a range of electrophysiological (non-invasive microelectrode ion flux measurements), biochemical (Ca²+- and H+-ATPase activity), imaging (fluorescence lifetime imaging measurements of changes in intracellular Ca²+ concentrations), pharmacological and cytological transmission electrone microscopy techniques. Virus-infected plants had a better ability to control UV-induced elevations in cytosolic-free Ca²+ and prevent structural and functional damage of chloroplasts. Taken together, our results suggest a high degree of crosstalk between UV and pathogen-induced oxidative stresses, and highlight the crucial role of Ca²+ efflux systems in acquired resistance to oxidative stress in plants.
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Affiliation(s)
- Sergey Shabala
- School of Agricultural Science, Menzies Research Institute, University of Tasmania, Private Bag 54, Hobart, Tas 7001, Australia.
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Shabala S, Babourina O, Rengel Z, Nemchinov LG. Non-invasive microelectrode potassium flux measurements as a potential tool for early recognition of virus-host compatibility in plants. Planta 2010; 232:807-15. [PMID: 20623138 DOI: 10.1007/s00425-010-1213-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 06/20/2010] [Indexed: 05/18/2023]
Abstract
Diseases caused by plant viruses are widespread, resulting in severe economic losses worldwide. Understanding the cellular basis of defense responses and developing efficient diagnostic tools for early recognition of host specificity to viral infection is, therefore, of great importance. In this work, non-invasive ion selective microelectrodes (the MIFE technique) were used to measure net ion fluxes in mesophyll tissue of host (potato, tomato, tobacco) and non-host (sugar beet and periwinkle) plants in response to infection with Potato virus X (PVX). These results were complemented by FLIM (Fluorescence Lifetime Imaging) measurements of PVX-induced changes in intracellular Ca(2+) concentrations. Our results demonstrate that, unlike in other plant-pathogen interactions, Ca(2+) signaling appears to be non-essential in recognition of the early stages of viral infection. Instead, we observed significant changes in K(+) fluxes as early as 10 min after inoculation. Results of pharmacological experiments and membrane potential measurements pointed out that a significant part of these fluxes may be mediated by depolarization-activated outward-rectifying K(+) channels. This may suggest that viral infections trigger a different mechanism of plant defense signaling as compared to signals derived from other microbial pathogens; hence, altered Ca(2+) fluxes across the plasma membrane may not be a prerequisite for all elicitor-activated defense reactions. Clearly pronounced host specificity in K(+) flux responses suggests that the MIFE technique can be effectively used as a screening tool for the early diagnostics of virus-host compatibility.
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Affiliation(s)
- Sergey Shabala
- School of Agricultural Science, University of Tasmania, Hobart, Tasmania, Australia.
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Abstract
Plant-derived biologicals for use in animal health are becoming an increasingly important target for research into alternative, improved methods for disease control. Although there are no commercial products on the market yet, the development and testing of oral, plant-based vaccines is now beyond the proof-of-principle stage. Vaccines, such as those developed for porcine transmissible gastroenteritis virus, have the potential to stimulate both mucosal and systemic, as well as, lactogenic immunity as has already been seen in target animal trials. Plants are a promising production system, but they must compete with existing vaccines and protein production platforms. In addition, regulatory hurdles will need to be overcome, and industry and public acceptance of the technology are important in establishing successful products.
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Affiliation(s)
- R W Hammond
- USDA-ARS, BARC-West, Rm.252, Bldg. 011, Beltsville, MD 20705, USA.
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Boutanaev AM, Postnikova OA, Nemchinov LG. Mapping of heterologous expressed sequence tags as an alternative to microarrays for study of defense responses in plants. BMC Genomics 2009; 10:273. [PMID: 19538747 PMCID: PMC2706895 DOI: 10.1186/1471-2164-10-273] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Accepted: 06/18/2009] [Indexed: 11/19/2022] Open
Abstract
Background Microarray technology helped to accumulate an immense pool of data on gene expression changes in response to different environmental factors. Yet, computer- generated gene profiling using expressed sequence tags (EST) represents a valuable alternative to microarrays, which allows efficient discovery of homologous sequences in evolutionarily different species and comparison of gene sets on the whole genome scale. In this study, we used publicly available EST database derived from different plant species infected with a variety of pathogens, to generate an expression profile of homologous genes involved in defense response of a model organism, Arabidopsis thaliana. Results EST-driven prediction identified 4,935 genes (16% of the total Arabidopsis genome) which, according to the origin of EST sets, were associated with defense responses in the reference genome. Profiles of defense-related genes, obtained by mapping of heterologous EST, represent putative Arabidopsis homologs of the corresponding species. Comparison of these profiles in pairs and locating common genes allowed estimating similarity between defense-related gene sets of different plant species. To experimentally support computer data, we arbitrarily selected a number of transcription factor genes (TF) detected by EST mapping. Their expression levels were examined by real-time polymerase chain reaction during infection with yellow strain of Cucumber mosaic virus, a compatible virus systemically infecting Arabidopsis. We observed that 65% of the designated TF were upregulated in accordance with the EST-generated profile. Conclusion We demonstrated that heterologous EST mapping may be efficiently used to reveal genes involved in host defense responses to pathogens. Upregulated genes identified in this study substantially overlap with those previously obtained by microarrays.
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Affiliation(s)
- Alexander M Boutanaev
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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Natilla A, Nemchinov LG. Improvement of PVX/CMV CP expression tool for display of short foreign antigens. Protein Expr Purif 2008; 59:117-21. [PMID: 18280751 DOI: 10.1016/j.pep.2008.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Revised: 01/14/2008] [Accepted: 01/15/2008] [Indexed: 11/24/2022]
Abstract
We have previously reported that Potato virus X-expressed coat protein of Cucumber mosaic virus (CMV) formed virus-like particles (VLPs), which served as carriers for display of different neutralizing epitopes of Newcastle disease virus (NDV). In this work, we further modified the purification protocol of recombinant VLPs carrying short neutralizing epitopes of the NDV proteins and demonstrated that self-contained capsid protein subunits of CMV transiently expressed from heterologous virus packaged into individual virions morphologically resembling and/or indistinguishable from wild type CMV particles. Homogeneity of the final preparation represents an advance over our previous study, where VLPs were found to be of variable size. Chickens immunized with purified VLPs developed antigen-specific response.
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Affiliation(s)
- Angela Natilla
- Molecular Plant Pathology Laboratory, Plant Sciences Institute, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
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Nemchinov LG, Shabala L, Shabala S. Calcium efflux as a component of the hypersensitive response of Nicotiana benthamiana to Pseudomonas syringae. Plant Cell Physiol 2008; 49:40-6. [PMID: 18048411 DOI: 10.1093/pcp/pcm163] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Using a model plant Nicotiana benthamiana, we have demonstrated that initial calcium uptake in response to the HR (hypersensitive response)-causing pathogen Pseudomonas syringae pv syringae 61 is followed by net calcium efflux initiated at about 12 h after the bacterial challenge and sustained for at least 48 h. Our data suggest that calcium not only acts as an important second messenger in the activation of resistance responses but may also be a downstream mediator of later cell death acceleration and completion of the defense reaction. Accordingly, we propose that the existing model of HR should be amended to include a PM Ca(2+) ATP pump as an important component of the HR to pathogens in plants.
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Affiliation(s)
- Lev G Nemchinov
- USDA/ARS, Plant Sciences Institute, Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA.
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Shabala S, Cuin TA, Prismall L, Nemchinov LG. Expression of animal CED-9 anti-apoptotic gene in tobacco modifies plasma membrane ion fluxes in response to salinity and oxidative stress. Planta 2007; 227:189-97. [PMID: 17712568 DOI: 10.1007/s00425-007-0606-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2007] [Accepted: 07/29/2007] [Indexed: 05/16/2023]
Abstract
Apoptosis, one form of programmed cell death (PCD), plays an important role in mediating plant adaptive responses to the environment. Recent studies suggest that expression of animal anti-apoptotic genes in transgenic plants may significantly improve a plant's ability to tolerate a variety of biotic and abiotic stresses. The underlying cellular mechanisms of this process remain unexplored. In this study, we investigated specific ion flux "signatures" in Nicotiana benthamiana plants transiently expressing CED-9 anti-apoptotic gene and undergoing salt- and oxidative stresses. Using a range of electrophysiological techniques, we show that expression of CED-9 increased plant salt and oxidative stress tolerance by altering K(+) and H(+) flux patterns across the plasma membrane. Our data shows that PVX/CED-9 plants are capable of preventing stress-induced K(+) efflux from mesophyll cells, so maintaining intracellular K(+) homeostasis. We attribute these effects to the ability of CED-9 to control at least two types of K(+)-permeable channels; outward-rectifying depolarization-activating K(+) channels (KOR) and non-selective cation channels (NSCC). A possible scenario linking CED-9 expression and ionic relations in plant cell is suggested. To the best of our knowledge, this study is the first to link "ion flux signatures" and mechanisms involved in regulation of PCD in plants.
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Affiliation(s)
- Sergey Shabala
- School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart, TAS, 7001, Australia.
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Nemchinov LG, Natilla A. Transient expression of the ectodomain of matrix protein 2 (M2e) of avian influenza A virus in plants. Protein Expr Purif 2007; 56:153-9. [PMID: 17644356 DOI: 10.1016/j.pep.2007.05.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 05/04/2007] [Accepted: 05/04/2007] [Indexed: 11/15/2022]
Abstract
We have previously reported an expression system based on the capsid protein gene (CP) of cucumber mosaic virus (CMV) placed under transcriptional control of a potato virus X (PVX)-based vector. PVX-expressed CMV CP formed virus-like particles, which served as carriers for heterologous antigens of the Newcastle disease virus (NDV). In this work, we applied our expression tool toward the development of plant-derived vaccine candidate against avian influenza A virus. Twenty-three amino acid-long extracellular domain of the viral M2 protein (M2e) was engineered into the internal motif 5 of CMV CP and the recombinant gene then was transiently expressed in plants through a PVX vector. Chimeric CMV capsids reacted with specific antibodies produced to synthetic M2e epitope of the H5N1 strain of the virus. In addition, CMV CP-M2e protein was expressed to high levels in Escherichia coli bacterial cells and was recognized by antibodies to both CMV and M2e. This initial study demonstrates the feasibility of using plant virus-based vectors for expression of antigenic epitopes of H5N1 avian influenza in plants.
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Affiliation(s)
- Lev G Nemchinov
- Molecular Plant Pathology Laboratory, Plant Sciences Institute, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD 20705, USA.
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Natilla A, Hammond RW, Nemchinov LG. Epitope presentation system based on cucumber mosaic virus coat protein expressed from a potato virus X-based vector. Arch Virol 2006; 151:1373-86. [PMID: 16489509 DOI: 10.1007/s00705-005-0711-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Accepted: 12/14/2005] [Indexed: 11/25/2022]
Abstract
The Cucumber mosaic virus Ixora isolate (CMV) coat protein gene (CP) was placed under the transcriptional control of the duplicated subgenomic CP promoter of a Potato virus X (PVX)-based vector. In vitro RNA transcripts were inoculated onto Nicotiana benthamiana plants and recombinant CMV capsid proteins were identified on Western blots probed with CMV antibodies 5-7 days post-inoculation. PVX-produced CMV CP subunits were capable of assembling into virus-like particles (VLPs), which were visualized by electron microscopy. We further used the PVX/CMVCP system for transient expression of recombinant CMV CP constructs containing different neutralizing epitopes of Newcastle disease virus (NDV) engineered into the internal betaH-betaI (motif 5) loop. Both crude plant extracts and purified VLPs were immunoreactive with CMV antibodies as well as with epitope-specific antibodies to NDV, thus confirming the surface display of the engineered NDV epitope. Our study demonstrates the potential of PVX/CMVCP as an expression tool and as a presentation system for promising epitopes.
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Affiliation(s)
- A Natilla
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland 20705, USA
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Nemchinov LG, Paape MJ, Sohn EJ, Bannerman DD, Zarlenga DS, Hammond RW. Bovine CD14 receptor produced in plants reduces severity of intramammary bacterial infection. FASEB J 2006; 20:1345-51. [PMID: 16816109 DOI: 10.1096/fj.05-5295com] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
CD14 is a high-affinity receptor protein for the complex of bacterial LPS (LPS) and LPS binding protein in animals. Binding of the soluble form of CD14 (sCD14) to LPS, found in the outer membrane of Escherichia coli and other Gram-negative bacteria, enhances host innate immune responses, reduces the severity of mastitis, and facilitates clearance and neutralization of LPS, thus protecting against an excessive immune response to LPS and development of endotoxic shock. A truncated form of sCD14, carrying a histidine residue affinity tag for purification, was incorporated into Potato virus X for transient expression in Nicotiana benthamiana plants. Western blots probed with CD14-specific antibodies demonstrated that crude plant extracts and affinity-purified samples contained immunoreactive sCD14. Biological activity of plant-derived recombinant bovine sCD14 (PrbosCD14) was demonstrated in vitro by LPS-induced apoptosis and interleukin (IL) -8 production in bovine endothelial cells, and in vivo by enhancement of LPS-induced neutrophil recruitment. Finally, in PrbosCD14-infused glands subsequently infected with E. coli, lower numbers of viable bacteria were recovered and there was an absence of clinical symptoms, demonstrating prophylactic efficacy of PrbosCD14. This is the first report of a functionally active animal receptor protein made in plants and the prophylactic use of a plant-derived protein to reduce the severity of bacterial infections in animals.
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Affiliation(s)
- Lev G Nemchinov
- USDA, ARS, Beltsville Agricultural Research Center, Beltsville, Maryland 20705, USA
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Nemchinov LG, Hammond J, Jordan R, Hammond RW. The complete nucleotide sequence, genome organization, and specific detection of Beet mosaic virus. Arch Virol 2004; 149:1201-14. [PMID: 15168206 DOI: 10.1007/s00705-003-0278-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2003] [Accepted: 11/20/2003] [Indexed: 11/30/2022]
Abstract
Beet mosaic virus (BtMV) was identified almost five decades ago but has not been fully characterized at the molecular level. In this study, we have determined for the first time the complete nucleotide sequence of BtMV genomic RNA and have developed a specific molecular means for its diagnosis. The viral genome of BtMV comprises 9591 nucleotides, excluding the 3' terminal poly (A) sequence, and contains a single open reading frame (ORF) that begins at nt 166 and terminates at nt 9423, encoding a single polyprotein of 3086 amino acid residues. A 3' untranslated region of 168 nucleotides follows the ORF. The deduced genome organization is typical for a member of the family Potyviridae and includes 10 proteins: P1, HC-Pro, P3, 6K1, CI, 6K2, NIa-VPg, NIa-Pro, NIb and coat protein (CP). Nine putative protease cleavage sites were predicted computationally and by analogy with genome arrangements of other potyviruses. Conserved sequence motifs of homologous proteins of other potyviruses were found in corresponding positions of BtMV. BtMV is a distinct species of the genus Potyvirus with the most closely related species being Peanut mottle virus ( approximately 55% amino acid identity). Based on the nucleotide sequence obtained, we have developed a virus-specific RT-PCR assay for accurate diagnosis and differentiation of BtMV.
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Affiliation(s)
- L G Nemchinov
- USDA-ARS Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Agricultural Research Service,Building 004, BARC-West, 10300 Baltimore Avenue, Beltsville, MD 20705, U.S.A
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Nemchinov LG, Liang TJ, Rifaat MM, Mazyad HM, Hadidi A, Keith JM. Development of a plant-derived subunit vaccine candidate against hepatitis C virus. Arch Virol 2001; 145:2557-73. [PMID: 11205105 DOI: 10.1007/s007050070008] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hepatitis C virus (HCV) is a major cause of acute and chronic hepatitis with over 180 million cases worldwide. Vaccine development for HCV has been difficult. Presently, the virus cannot be grown in tissue culture and there is no vaccine or effective therapy against this virus. In this research, we describe the development of an experimental plant-derived subunit vaccine against HCV. A tobamoviral vector was engineered to encode a consensus sequence of hypervariable region 1 (HVR1), a potential neutralizing epitope of HCV, genetically fused to the C-terminal of the B subunit of cholera toxin (CTB). This epitope was selected from among the amino acid sequences of HVR1 "mimotopes" previously derived by phage display technology. The nucleotide sequence encoding this epitope was designed utilizing optimal plant codons. This mimotope is capable of inducing cross-neutralizing antibodies against different variants of the virus. Plants infected with recombinant tobacco mosaic virus (TMV) engineered to express the HVR1/CTB chimeric protein, contained intact TMV particles and produced the HVR1 consensus peptide fused to the functionally active, pentameric B subunit of cholera toxin. Plant-derived HVR1/CTB reacted with HVR1-specific monoclonal antibodies and immune sera from individuals infected with virus from four of the major genotypes of HCV. Intranasal immunization of mice with a crude plant extract containing the recombinant HVR1/CTB protein elicited both anti-CTB serum antibody and anti-HVR1 serum antibody which specifically bound to HCV virus-like particles. Using plant-virus transient expression to produce this unique chimeric antigen will facilitate the development and production of an experimental HCV vaccine. A plant-derived recombinant HCV vaccine can potentially reduce expenses normally associated with production and delivery of conventional vaccines.
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Affiliation(s)
- L G Nemchinov
- Vaccine and Therapeutic Development Section, Oral Infection and Immunity Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892-4350, USA
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Abstract
Extraction of viral double-stranded RNA from peach leaves infected with Apricot latent virus (ALV) followed by molecular cloning of synthesized cDNA and its sequencing, suggested that ALV is a new virus, whose coat protein (CP) coding region contains Apple stem pitting virus (ASPV)-related sequences. The sequenced portion of the ALV genome (1,444 nt) includes the putative CP gene and the 3' non-translated region. The 5' portion of this fragment (1-651 nt) is highly distinct whereas the 3' portion is 77% identical to the corresponding region of ASPV. Molecular hybridization experiments using a cRNA probe to ASPV with ALV-infected leaf tissue extracts also revealed that the genome of ALV contains nucleotide sequences related to that of ASPV. Western blots of tissue extracts indicated that ALV coat protein reacted with polyclonal antiserum against ASPV; however, the ALV CP differs in size from that of ASPV. ALV was graft-transmitted to several Prunus rootstocks. Based on the available sequence data, serological observations and bioassays we propose that ALV is a new species in the genus Foveavirus, typified by ASPV. ALV-specific PCR-primers and viral-specific cRNA probes developed in this investigation may be useful for detecting the virus and for studying its epidemiology and geographical distribution.
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Affiliation(s)
- L G Nemchinov
- Vaccine and Therapeutic Development Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA
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