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Translation of Plant RNA Viruses. Viruses 2021; 13:v13122499. [PMID: 34960768 PMCID: PMC8708638 DOI: 10.3390/v13122499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/01/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022] Open
Abstract
Plant RNA viruses encode essential viral proteins that depend on the host translation machinery for their expression. However, genomic RNAs of most plant RNA viruses lack the classical characteristics of eukaryotic cellular mRNAs, such as mono-cistron, 5′ cap structure, and 3′ polyadenylation. To adapt and utilize the eukaryotic translation machinery, plant RNA viruses have evolved a variety of translation strategies such as cap-independent translation, translation recoding on initiation and termination sites, and post-translation processes. This review focuses on advances in cap-independent translation and translation recoding in plant viruses.
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Petrzik K, Přibylová J, Koloniuk I, Špak J. Molecular characterization of a novel capillovirus from red currant. Arch Virol 2016; 161:1083-6. [PMID: 26754736 DOI: 10.1007/s00705-016-2752-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/02/2016] [Indexed: 12/01/2022]
Abstract
The complete nucleotide sequence of a novel virus from red currant, provisionally named currant virus A (CuVA), was determined. The genome is 7925 nucleotides long and has a 3'-poly(A) tail. The genome organization with two overlapping open reading frames is similar to that of capilloviruses, but the CuVA genome is about 600 nucleotides longer than that of the longest known capillovirus, cherry virus A. The RNA is predicted to encode a polyprotein with domains of methyltransferase, 2OG-Fe(II) oxygenase, papain-like protease, RNA helicase, RdRp, and capsid protein. Phylogenetic analysis confirms that CuVA is a new and distinct member of the genus Capillovirus.
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Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, v.v.i., Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Jaroslava Přibylová
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, v.v.i., Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, v.v.i., Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Josef Špak
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, v.v.i., Branišovská 31, 370 05, České Budějovice, Czech Republic
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Wylie SJ, Zhang C, Long V, Roossinck MJ, Koh SH, Jones MGK, Iqbal S, Li H. Differential responses to virus challenge of laboratory and wild accessions of australian species of nicotiana, and comparative analysis of RDR1 gene sequences. PLoS One 2015; 10:e0121787. [PMID: 25822508 PMCID: PMC4379023 DOI: 10.1371/journal.pone.0121787] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 02/04/2015] [Indexed: 01/18/2023] Open
Abstract
Nicotiana benthamiana is a model plant utilised internationally in plant virology because of its apparent hyper-susceptibility to virus infection. Previously, others showed that all laboratory accessions of N. benthamiana have a very narrow genetic basis, probably originating from a single source. It is unknown if responses to virus infection exhibited by the laboratory accession are typical of the species as a whole. To test this, 23 accessions of N. benthamiana were collected from wild populations and challenged with one to four viruses. Additionally, accessions of 21 other Nicotiana species and subspecies from Australia, one from Peru and one from Namibia were tested for susceptibility to the viruses, and for the presence of a mutated RNA-dependent RNA polymerase I allele (Nb-RDR1m) described previously from a laboratory accession of N. benthamiana. All Australian Nicotiana accessions tested were susceptible to virus infections, although there was symptom variability within and between species. The most striking difference was that plants of a laboratory accession of N. benthamiana (RA-4) exhibited hypersensitivity to Yellow tailflower mild mottle tobamovirus infection and died, whereas plants of wild N. benthamiana accessions responded with non-necrotic symptoms. Plants of certain N. occidentalis accessions also exhibited initial hypersensitivity to Yellow tailflower mild mottle virus resembling that of N. benthamiana RA-4 plants, but later recovered. The mutant Nb-RDR1m allele was identified from N. benthamiana RA-4 but not from any of 51 other Nicotiana accessions, including wild accessions of N. benthamiana, demonstrating that the accession of N. benthamiana used widely in laboratories is unusual.
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Affiliation(s)
- Stephen J. Wylie
- Plant Biotechnology Research Group-Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
- Plant Biotechnology Research Group—Pests, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
| | - Chao Zhang
- College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province, China
| | - Vicki Long
- Astron Environmental Services, Karratha, Western Australia, Australia
| | - Marilyn J. Roossinck
- Plant Biotechnology Research Group-Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
- Departments of Plant Pathology and Environmental Microbiology, and Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Shu Hui Koh
- Plant Biotechnology Research Group-Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
- Plant Biotechnology Research Group—Pests, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
| | - Michael G. K. Jones
- Plant Biotechnology Research Group-Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
- Plant Biotechnology Research Group—Pests, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
| | - Sadia Iqbal
- Plant Biotechnology Research Group—Pests, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
| | - Hua Li
- Plant Biotechnology Research Group-Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
- Plant Biotechnology Research Group—Pests, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
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Wu Q, Ding SW, Zhang Y, Zhu S. Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:425-44. [PMID: 26047558 DOI: 10.1146/annurev-phyto-080614-120030] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A fast, accurate, and full indexing of viruses and viroids in a sample for the inspection and quarantine services and disease management is desirable but was unrealistic until recently. This article reviews the rapid and exciting recent progress in the use of next-generation sequencing (NGS) technologies for the identification of viruses and viroids in plants. A total of four viroids/viroid-like RNAs and 49 new plant RNA and DNA viruses from 18 known or unassigned virus families have been identified from plants since 2009. A comparison of enrichment strategies reveals that full indexing of RNA and DNA viruses as well as viroids in a plant sample at single-nucleotide resolution is made possible by one NGS run of total small RNAs, followed by data mining with homology-dependent and homology-independent computational algorithms. Major challenges in the application of NGS technologies to pathogen discovery are discussed.
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Affiliation(s)
- Qingfa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 China;
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Bao Y, Chetvernin V, Tatusova T. Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification. Arch Virol 2014; 159:3293-304. [PMID: 25119676 PMCID: PMC4221606 DOI: 10.1007/s00705-014-2197-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 07/29/2014] [Indexed: 11/28/2022]
Abstract
The number of viral genome sequences in the public databases is increasing dramatically, and these sequences are playing an important role in virus classification. Pairwise sequence comparison is a sequence-based virus classification method. A program using this method calculates the pairwise identities of virus sequences within a virus family and displays their distribution, and visual analysis helps to determine demarcations at different taxonomic levels such as strain, species, genus and subfamily. Subsequent comparison of new sequences against existing ones allows viruses from which the new sequences were derived to be classified. Although this method cannot be used as the only criterion for virus classification in some cases, it is a quantitative method and has many advantages over conventional virus classification methods. It has been applied to several virus families, and there is an increasing interest in using this method for other virus families/groups. The Pairwise Sequence Comparison (PASC) classification tool was created at the National Center for Biotechnology Information. The tool's database stores pairwise identities for complete genomes/segments of 56 virus families/groups. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. The web interface of the tool ( http://www.ncbi.nlm.nih.gov/sutils/pasc/ ) makes it easy to navigate and perform analyses. Multiple new viral genome sequences can be tested simultaneously with this system to suggest the taxonomic position of virus isolates in a specific family. PASC eliminates potential discrepancies in the results caused by different algorithms and/or different data used by researchers.
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Affiliation(s)
- Yiming Bao
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA,
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Hassan M. Genome sequence of two isolates of Yellow oatgrass mosaic virus, a new grass-infecting Tritimovirus. Virus Genes 2014; 49:116-23. [PMID: 24818694 DOI: 10.1007/s11262-014-1073-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/29/2014] [Indexed: 10/25/2022]
Abstract
Complete genome sequences of two Yellow oatgrass mosaic virus (YOgMV) isolates have been determined to be 9,292 nucleotides excluding the 3' polyadenylated tail. The viral RNA encodes a large putative open reading frame (ORF) of a single polyprotein consisting of 3,002 amino acids with typical genome organization of monopartite potyvirids. A small overlapping ORF encoding a pretty interesting Potyviridae ORF of 122 amino acids is found in the P3 cistron of both YOgMV isolates. The nucleotide and amino acid identities between the two YOgMV isolates are 90 and 97 %, respectively. Pairwise comparison of YOgMV putative mature proteins and proteinase cleavage sites with those of representative members of the family Potyviridae indicated that YOgMV is more closely related to members of the genus Tritimovirus. In phylogenetic trees constructed with sequences of putative polyprotein, YOgMV consistently groups with members of the genus Tritimovirus. These results suggest that YOgMV should be classified as a distinct species in the genus Tritimovirus in the family Potyviridae.
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Affiliation(s)
- Mohamed Hassan
- Department of Agricultural Botany, Faculty of Agriculture, Fayoum University, Fayoum, Egypt,
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Wylie SJ, Li H, Jones MGK. Donkey orchid symptomless virus: a viral 'platypus' from Australian terrestrial orchids. PLoS One 2013; 8:e79587. [PMID: 24223974 PMCID: PMC3818234 DOI: 10.1371/journal.pone.0079587] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 10/02/2013] [Indexed: 11/19/2022] Open
Abstract
Complete and partial genome sequences of two isolates of an unusual new plant virus, designated Donkey orchid symptomless virus (DOSV) were identified using a high-throughput sequencing approach. The virus was identified from asymptomatic plants of Australian terrestrial orchid Diuris longifolia (Common donkey orchid) growing in a remnant forest patch near Perth, western Australia. DOSV was identified from two D. longifolia plants of 264 tested, and from at least one plant of 129 Caladenia latifolia (pink fairy orchid) plants tested. Phylogenetic analysis of the genome revealed open reading frames (ORF) encoding seven putative proteins of apparently disparate origins. A 69-kDa protein (ORF1) that overlapped the replicase shared low identity with MPs of plant tymoviruses (Tymoviridae). A 157-kDa replicase (ORF2) and 22-kDa coat protein (ORF4) shared 32% and 40% amino acid identity, respectively, with homologous proteins encoded by members of the plant virus family Alphaflexiviridae. A 44-kDa protein (ORF3) shared low identity with myosin and an autophagy protein from Squirrelpox virus. A 27-kDa protein (ORF5) shared no identity with described proteins. A 14-kDa protein (ORF6) shared limited sequence identity (26%) over a limited region of the envelope glycoprotein precursor of mammal-infecting Crimea-Congo hemorrhagic fever virus (Bunyaviridae). The putative 25-kDa movement protein (MP) (ORF7) shared limited (27%) identity with 3A-like MPs of members of the plant-infecting Tombusviridae and Virgaviridae. Transmissibility was shown when DOSV systemically infected Nicotiana benthamiana plants. Structure and organization of the domains within the putative replicase of DOSV suggests a common evolutionary origin with ‘potexvirus-like’ replicases of viruses within the Alphaflexiviridae and Tymoviridae, and the CP appears to be ancestral to CPs of allexiviruses (Alphaflexiviridae). The MP shares an evolutionary history with MPs of dianthoviruses, but the other putative proteins are distant from plant viruses. DOSV is not readily classified in current lower order virus taxa.
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Affiliation(s)
- Stephen J. Wylie
- Australian Plant Virology Laboratory, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Australia
- * E-mail:
| | - Hua Li
- Australian Plant Virology Laboratory, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Australia
| | - Michael G. K. Jones
- Australian Plant Virology Laboratory, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Australia
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Wylie SJ, Li H, Dixon KW, Richards H, Jones MG. Exotic and indigenous viruses infect wild populations and captive collections of temperate terrestrial orchids (Diuris species) in Australia. Virus Res 2013; 171:22-32. [DOI: 10.1016/j.virusres.2012.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 10/02/2012] [Accepted: 10/03/2012] [Indexed: 01/01/2023]
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