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Congdon BS, Sharman M, Kehoe MA. Genetic diversity of soybean dwarf virus in two regions of mainland Australia. Arch Virol 2024; 169:216. [PMID: 39377979 PMCID: PMC11461792 DOI: 10.1007/s00705-024-06142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Accepted: 09/19/2024] [Indexed: 10/11/2024]
Abstract
Soybean dwarf virus (SbDV; family Tombusviridae, genus Luteovirus, species Luteovirus glycinis) is an RNA plant virus that is transmitted solely by aphids in a persistent, circulative and non-propagative manner. SbDV causes significant losses in cultivated Fabaceae, especially in subterranean clover (Trifolium subterraneum) pastures of mainland Australia. SbDV isolates are classified into four phenotypically distinguishable strains: YP, YS, DP, and DS. Y and D strains differ primarily in their host range, and P and S strains in their primary vector species. Genetically, Y and D strains separate into two clades in every genomic region except for the N-terminal region of the readthrough domain (N-RTD), in which P and S strains separate. SbDV diversity in Australia has yet to be investigated, so in this study, 41 isolates were collected from six different host species across two production regions of Australia: the south coast of Western Australia ('south-west') and northern New South Wales/southern Queensland ('north-east'). A near-complete genome sequence of each isolate was obtained, and together with all 50 whole-genome sequences available in the GenBank database, underwent phylogenetic analysis of the whole genome nt and the N-RTD aa sequences. At the whole-genome level, the isolates separated into D and Y clades. At the N-RTD level, most of the isolates separated into P and S clades. All south-west isolates and 11 of the 31 north-east isolates were in the Y clade, and the remaining 20 north-east isolates were in the D clade. Except for one isolate that fell outside the P and S clades, all south-west and north-east isolates were in the P clade, suggesting that they are transmitted by Acyrthosiphon pisum and Myzus persicae. Available biological data largely supported the phenotypic inferences made from the phylogenetic analysis, suggesting that genetic data can provide critical epidemiological insights, provided that sufficient biological data have been collected.
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Affiliation(s)
- B S Congdon
- Primary Industry Development, Department of Primary Industries and Regional Development, 3 Baron-Hay Court, Kensington, Western Australia, 6151, Australia.
| | - M Sharman
- Ecosciences Precinct, Queensland Department of Agriculture and Fisheries, GPO Box 46, Brisbane, Queensland, 4001, Australia
| | - M A Kehoe
- Biosecurity and Sustainability, Department of Primary Industries and Regional Development, 3 Baron-Hay Court, Kensington, Western Australia, 6151, Australia
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Stainton D, Villamor DEV, Sierra Mejia A, Srivastava A, Mollov D, Martin RR, Tzanetakis IE. Genomic analyses of a widespread blueberry virus in the United States. Virus Res 2023; 333:199143. [PMID: 37271421 PMCID: PMC10352716 DOI: 10.1016/j.virusres.2023.199143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
Screening of blueberry accessions using high throughput sequencing revealed the presence of a new virus. Genomic structure and sequence are similar to that of nectarine stem pitting associated virus (NSPaV), a member of the genus Luteovirus, family Tombusviridae. The full genome of the new luteovirus, tentatively named blueberry virus L (BlVL), was characterized and analyzed. Similar to NSPaV, BlVL does not contain readily identifiable movement proteins in any of the seven isolates sequenced. More than 600 samples collected from five states were screened and 79% were found infected, making BlVL the most widespread blueberry virus in the United States.
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Affiliation(s)
- Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA
| | - Dan E V Villamor
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA
| | - Andrea Sierra Mejia
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA
| | - Ashish Srivastava
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA
| | - Dimitre Mollov
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, 3420 NW Orchard Ave, Corvallis, OR 97330; Oregon State University, Corvallis, OR 97330, USA
| | | | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
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Miras M, Aranda MA, Truniger V. Different RNA Elements Control Viral Protein Synthesis in Polerovirus Isolates Evolved in Separate Geographical Regions. Int J Mol Sci 2022; 23:ijms232012503. [PMID: 36293360 PMCID: PMC9603980 DOI: 10.3390/ijms232012503] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 12/05/2022] Open
Abstract
Most plant viruses lack the 5′-cap and 3′-poly(A) structures, which are common in their host mRNAs, and are crucial for translation initiation. Thus, alternative translation initiation mechanisms were identified for viral mRNAs, one of these being controlled by an RNA element in their 3′-ends that is able to enhance mRNA cap-independent translation (3′-CITE). The 3′-CITEs are modular and transferable RNA elements. In the case of poleroviruses, the mechanism of translation initiation of their RNAs in the host cell is still unclear; thus, it was studied for one of its members, cucurbit aphid-borne yellows virus (CABYV). We determined that efficient CABYV RNA translation requires the presence of a 3′-CITE in its 3′-UTR. We showed that this 3′-CITE requires the presence of the 5′-UTR in cis for its eIF4E-independent activity. Efficient virus multiplication depended on 3′-CITE activity. In CABYV isolates belonging to the three phylogenetic groups identified so far, the 3′-CITEs differ, and recombination prediction analyses suggest that these 3′-CITEs have been acquired through recombination with an unknown donor. Since these isolates have evolved in different geographical regions, this may suggest that their respective 3′-CITEs are possibly better adapted to each region. We propose that translation of other polerovirus genomes may also be 3′-CITE-dependent.
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Affiliation(s)
- Manuel Miras
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Murcia, Spain
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Murcia, Spain
| | - Verónica Truniger
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Murcia, Spain
- Correspondence:
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Liu H, Wu L, Nikolaeva E, Peter K, Liu Z, Mollov D, Cao M, Li R. Characterization of a new apple luteovirus identified by high-throughput sequencing. Virol J 2018; 15:85. [PMID: 29764461 PMCID: PMC5952423 DOI: 10.1186/s12985-018-0998-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/06/2018] [Indexed: 01/05/2023] Open
Abstract
Background ‘Rapid Apple Decline’ (RAD) is a newly emerging problem of young, dwarf apple trees in the Northeastern USA. The affected trees show trunk necrosis, cracking and canker before collapse in summer. In this study, we discovered and characterized a new luteovirus from apple trees in RAD-affected orchards using high-throughput sequencing (HTS) technology and subsequent Sanger sequencing. Methods Illumina NextSeq sequencing was applied to total RNAs prepared from three diseased apple trees. Sequence reads were de novo assembled, and contigs were annotated by BLASTx. RT-PCR and 5′/3’ RACE sequencing were used to obtain the complete genome of a new virus. RT-PCR was used to detect the virus. Results Three common apple viruses and a new luteovirus were identified from the diseased trees by HTS and RT-PCR. Sequence analyses of the complete genome of the new virus show that it is a new species of the genus Luteovirus in the family Luteoviridae. The virus is graft transmissible and detected by RT-PCR in apple trees in a couple of orchards. Conclusions A new luteovirus and/or three known viruses were found to be associated with RAD. Molecular characterization of the new luteovirus provides important information for further investigation of its distribution and etiological role. Electronic supplementary material The online version of this article (10.1186/s12985-018-0998-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huawei Liu
- USDA-ARS, National Germplasm Resources Laboratory, Bldg. 004/Rm 015, Beltsville, Maryland, 20705, USA
| | - Liping Wu
- USDA-ARS, National Germplasm Resources Laboratory, Bldg. 004/Rm 015, Beltsville, Maryland, 20705, USA.,School of Life Science, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Ekaterina Nikolaeva
- Pennsylvania Department of Agriculture, Harrisburg, Pennsylvania, 17110, USA
| | - Kari Peter
- Pennsylvania State University, Biglerville, Pennsylvania, 17307, USA
| | - Zongrang Liu
- USDA-ARS, Appalachian Fruit Research Station, Kearneysville, West Virginia, 25430, USA
| | - Dimitre Mollov
- USDA-ARS, National Germplasm Resources Laboratory, Bldg. 004/Rm 015, Beltsville, Maryland, 20705, USA
| | - Mengji Cao
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Ruhui Li
- USDA-ARS, National Germplasm Resources Laboratory, Bldg. 004/Rm 015, Beltsville, Maryland, 20705, USA.
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Lotos L, Olmos A, Orfanidou C, Efthimiou K, Avgelis A, Katis NI, Maliogka VI. Insights Into the Etiology of Polerovirus-Induced Pepper Yellows Disease. PHYTOPATHOLOGY 2017; 107:1567-1576. [PMID: 28786341 DOI: 10.1094/phyto-07-16-0254-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The study of an emerging yellows disease of pepper crops (pepper yellows disease [PYD]) in Greece led to the identification of a polerovirus closely related to Pepper vein yellows virus (PeVYV). Recovery of its full genome sequence by next-generation sequencing of small interfering RNAs allowed its characterization as a new poleroviruses, which was provisionally named Pepper yellows virus (PeYV). Transmission experiments revealed its association with the disease. Sequence similarity and phylogenetic analysis highlighted the common ancestry of the three poleroviruses (PeVYV, PeYV, and Pepper yellow leaf curl virus [PYLCV]) currently reported to be associated with PYD, even though significant genetic differences were identified among them, especially in the C-terminal region of P5 and the 3' noncoding region. Most of the differences observed can be attributed to a modular type of evolution, which produces mosaic-like variants giving rise to these different poleroviruses Overall, similar to other polerovirus-related diseases, PYD is caused by at least three species (PeVYV, PeYV, and PYLCV) belonging to this group of closely related pepper-infecting viruses.
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Affiliation(s)
- Leonidas Lotos
- First, third, fourth, sixth, and seventh authors: Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; second author: Department of Virology, Plant Protection and Biotechnology Center, Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain; and fifth author: Institute of Viticulture of Heraklion, Hellenic Agricultural Organization-Demeter, 71 307 Heraklion, Crete, Greece
| | - Antonio Olmos
- First, third, fourth, sixth, and seventh authors: Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; second author: Department of Virology, Plant Protection and Biotechnology Center, Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain; and fifth author: Institute of Viticulture of Heraklion, Hellenic Agricultural Organization-Demeter, 71 307 Heraklion, Crete, Greece
| | - Chrysoula Orfanidou
- First, third, fourth, sixth, and seventh authors: Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; second author: Department of Virology, Plant Protection and Biotechnology Center, Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain; and fifth author: Institute of Viticulture of Heraklion, Hellenic Agricultural Organization-Demeter, 71 307 Heraklion, Crete, Greece
| | - Konstantinos Efthimiou
- First, third, fourth, sixth, and seventh authors: Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; second author: Department of Virology, Plant Protection and Biotechnology Center, Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain; and fifth author: Institute of Viticulture of Heraklion, Hellenic Agricultural Organization-Demeter, 71 307 Heraklion, Crete, Greece
| | - Apostolos Avgelis
- First, third, fourth, sixth, and seventh authors: Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; second author: Department of Virology, Plant Protection and Biotechnology Center, Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain; and fifth author: Institute of Viticulture of Heraklion, Hellenic Agricultural Organization-Demeter, 71 307 Heraklion, Crete, Greece
| | - Nikolaos I Katis
- First, third, fourth, sixth, and seventh authors: Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; second author: Department of Virology, Plant Protection and Biotechnology Center, Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain; and fifth author: Institute of Viticulture of Heraklion, Hellenic Agricultural Organization-Demeter, 71 307 Heraklion, Crete, Greece
| | - Varvara I Maliogka
- First, third, fourth, sixth, and seventh authors: Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; second author: Department of Virology, Plant Protection and Biotechnology Center, Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain; and fifth author: Institute of Viticulture of Heraklion, Hellenic Agricultural Organization-Demeter, 71 307 Heraklion, Crete, Greece
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Shen P, Tian X, Zhang S, Ren F, Li P, Yu YQ, Li R, Zhou C, Cao M. Molecular characterization of a novel luteovirus infecting apple by next-generation sequencing. Arch Virol 2017; 163:761-765. [DOI: 10.1007/s00705-017-3633-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/17/2017] [Indexed: 11/24/2022]
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7
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Thekke-Veetil T, McCoppin NK, Domier LL. Strain-specific association of soybean dwarf virus small subgenomic RNA with virus particles. Virus Res 2017; 242:100-105. [PMID: 28893654 DOI: 10.1016/j.virusres.2017.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
Soybean dwarf virus (SbDV) produces a large subgenomic RNA (LsgRNA) for expression of structural and movement proteins and a small subgenomic RNA (SsgRNA) that does not contain an open reading frame. Sucrose gradient-purified SbDV virions from soybean plants systemically infected with SbDV by aphids and Nicotiana benthamiana leaves agroinfiltrated with infectious clones of two red clover SbDV isolates encapsidated genomic RNA and were associated with SsgRNA in a strain-specific manner. The LsgRNA was protected from RNase degradation, but not packaged into virions as indicated by its presence primarily in ELISA-negative fractions near the tops of sucrose gradients even in mutants that did not express coat protein. Nucleotide differences in the SsgRNA region between isolates conferred differential association of SsgRNA with virions.
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Affiliation(s)
| | - Nancy K McCoppin
- United State Department of Agriculture, Agricultural Research Service, Urbana, IL, 61801, USA
| | - Leslie L Domier
- United State Department of Agriculture, Agricultural Research Service, Urbana, IL, 61801, USA.
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Zhang P, Liu Y, Liu W, Cao M, Massart S, Wang X. Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease. Front Microbiol 2017; 8:1689. [PMID: 28932215 PMCID: PMC5592212 DOI: 10.3389/fmicb.2017.01689] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/21/2017] [Indexed: 11/13/2022] Open
Abstract
To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV). The full genome of WLYaV corresponds to 5,772 nucleotides (nt), with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae. Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV), but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP) were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90%) in the family Luteoviridae. Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat.
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Affiliation(s)
- Peipei Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
- Laboratory of Phytopathology, University of Liège, Gembloux Agro-Bio TechGembloux, Belgium
| | - Yan Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China
| | - Sebastien Massart
- Laboratory of Phytopathology, University of Liège, Gembloux Agro-Bio TechGembloux, Belgium
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
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Complete nucleotide sequence of a highly divergent cherry-associated luteovirus (ChALV) isolate from peach in South Korea. Arch Virol 2017; 162:2893-2896. [PMID: 28547383 DOI: 10.1007/s00705-017-3418-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 04/12/2017] [Indexed: 10/19/2022]
Abstract
We determined the complete genome sequence of a highly divergent South Korean (SK) isolate of a cherry-associated luteovirus (ChALV) from peach. The ChALV-SK genome consists of 5,815 nucleotides, and contains five open reading frames (ORFs). A comparative analysis of the full genome showed only 73.1% nucleotide sequence identity with a recently described ChALV from the Czech Republic (CZ). Amino acid similarities of the individual ORFs between ChALV-SK and other luteoviruses range from 17.3 to 92%, which places the new isolate close to the species demarcation value for luteoviruses. Results show our ChALV-SK isolate to be highly diverged from the ChALV-CZ isolate.
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Lenz O, Přibylová J, Fránová J, Koloniuk I, Špak J. Identification and characterization of a new member of the genus Luteovirus from cherry. Arch Virol 2016; 162:587-590. [DOI: 10.1007/s00705-016-3125-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 10/15/2016] [Indexed: 11/29/2022]
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Villamor DEV, Mekuria TA, Pillai SS, Eastwell KC. High-Throughput Sequencing Identifies Novel Viruses in Nectarine: Insights to the Etiology of Stem-Pitting Disease. PHYTOPATHOLOGY 2016; 106:519-527. [PMID: 26780433 DOI: 10.1094/phyto-07-15-0168-r] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recent studies have shown the superiority of high-throughput sequencing (HTS) technology over many standard protocols for pathogen detection. HTS was initiated on fruit tree accessions from disparate sources to improve and advance virus-testing procedures. A virus with genomic features resembling most closely that of the recently described Nectarine stem-pitting-associated virus, putative member of genus Luteovirus, was found in three nectarine trees (Prunus persica cv. nectarina), each exhibiting stem-pitting symptoms on the woody cylinder above the graft union. In these samples, HTS also revealed the presence of a coinfecting virus with genome characteristics typical of members of the genus Marafivirus. The same marafivirus- and luteovirus-like viruses were detected in nonsymptomatic nectarine and peach selections, indicating only a loose relationship between these two viruses with nectarine stem-pitting disease symptoms. Two selections infected with each of these viruses had previously tested free of known virus or virus-like agents using the current biological, serological, and molecular tests employed at the Clean Plant Center Northwest. Overall, this study presents the characterization by HTS of novel marafivirus- and luteovirus-like viruses of nectarine, and provides further insights into the etiology of nectarine stem-pitting disease. The discovery of these new viruses emphasizes the ability of HTS to reveal viruses that are not detected by existing protocols.
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Affiliation(s)
- D E V Villamor
- Department of Plant Pathology, Washington State University-Irrigated Agriculture Research and Extension Center, Prosser 99350
| | - T A Mekuria
- Department of Plant Pathology, Washington State University-Irrigated Agriculture Research and Extension Center, Prosser 99350
| | - S S Pillai
- Department of Plant Pathology, Washington State University-Irrigated Agriculture Research and Extension Center, Prosser 99350
| | - K C Eastwell
- Department of Plant Pathology, Washington State University-Irrigated Agriculture Research and Extension Center, Prosser 99350
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Miller WA, Shen R, Staplin W, Kanodia P. Noncoding RNAs of Plant Viruses and Viroids: Sponges of Host Translation and RNA Interference Machinery. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:156-64. [PMID: 26900786 PMCID: PMC5410770 DOI: 10.1094/mpmi-10-15-0226-fi] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Noncoding sequences in plant viral genomes are well-known to control viral replication and gene expression in cis. However, plant viral and viroid noncoding (nc)RNA sequences can also regulate gene expression acting in trans, often acting like 'sponges' that bind and sequester host cellular machinery to favor viral infection. Noncoding sequences of small subgenomic (sg)RNAs of Barley yellow dwarf virus (BYDV) and Red clover necrotic mosaic virus (RCNMV) contain a cap-independent translation element that binds translation initiation factor eIF4G. We provide new evidence that a sgRNA of BYDV can globally attenuate host translation, probably by sponging eIF4G. Subgenomic ncRNA of RCNMV is generated via 5' to 3' degradation by a host exonuclease. The similar noncoding subgenomic flavivirus (sf)RNA, inhibits the innate immune response, enhancing viral pathogenesis. Cauliflower mosaic virus transcribes massive amounts of a 600-nt ncRNA, which is processed into small RNAs that overwhelm the host's RNA interference (RNAi) system. Viroids use the host RNAi machinery to generate viroid-derived ncRNAs that inhibit expression of host defense genes by mimicking a microRNA. More examples of plant viral and viroid ncRNAs are likely to be discovered, revealing fascinating new weaponry in the host-virus arms race.
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Affiliation(s)
- W. Allen Miller
- Interdepartmental Genetics & Genomics Program, Iowa State University, Ames, IA 50011 USA
- Corresponding author:
| | - Ruizhong Shen
- Interdepartmental Genetics & Genomics Program, Iowa State University, Ames, IA 50011 USA
| | | | - Pulkit Kanodia
- Interdepartmental Genetics & Genomics Program, Iowa State University, Ames, IA 50011 USA
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Bag S, Al Rwahnih M, Li A, Gonzalez A, Rowhani A, Uyemoto JK, Sudarshana MR. Detection of a New Luteovirus in Imported Nectarine Trees: A Case Study to Propose Adoption of Metagenomics in Post-Entry Quarantine. PHYTOPATHOLOGY 2015; 105:840-846. [PMID: 25775105 DOI: 10.1094/phyto-09-14-0262-r] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In spring 2013, 5-year-old nectarine (Prunus persica) trees, grafted on peach rootstock Nemaguard, were found stunted in a propagation block in California. These trees had been propagated from budwood of three nectarine cultivars imported from France and cleared through the post-entry quarantine procedure. Examination of the canopy failed to reveal any obvious symptoms. However, examination of the trunks, after stripping the bark, revealed extensive pitting on the woody cylinder. To investigate the etiological agent, double-stranded RNA was extracted from bark scrapings from the scion and rootstock portions, and a cDNA library was prepared and sequenced using the Illumina platform. BLAST analysis of the contigs generated by the de novo assembly of sequence reads indicated the presence of a novel luteovirus. Complete sequence of the viral genome was determined by sequencing of three overlapping cDNA clones generated by reverse transcription-polymerase chain reaction (RT-PCR) and by rapid amplification of the 5'- and 3'-termini. The virus genome was comprised of 4,991 nucleotides with a gene organization similar to members of the genus Luteovirus (family Luteoviridae). The presence of the virus, tentatively named Nectarine stem pitting-associated virus, was confirmed in symptomatic trees by RT-PCR. Discovery of a new virus in nectarine trees after post-entry quarantine indicates the importance of including (i) metagenomic analysis by next-generation sequencing approach as an essential tool to assess the plant health status, and (ii) examination of the woody cylinders as part of the indexing process.
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Affiliation(s)
- Sudeep Bag
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
| | - Maher Al Rwahnih
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
| | - Ashley Li
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
| | - Asaul Gonzalez
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
| | - Adib Rowhani
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
| | - Jerry K Uyemoto
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
| | - Mysore R Sudarshana
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
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14
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Miller WA, Jackson J, Feng Y. Cis- and trans-regulation of luteovirus gene expression by the 3' end of the viral genome. Virus Res 2015; 206:37-45. [PMID: 25858272 DOI: 10.1016/j.virusres.2015.03.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 10/23/2022]
Abstract
Translation of the 5.7 kb luteovirus genome is controlled by the 3' untranslated region (UTR). Base pairing between regions of the 3' UTR and sequences kilobases upstream is required for cap-independent translation and ribosomal frameshifting needed to synthesize the viral replicase. Luteoviruses produce subgenomic RNAs, which can serve as mRNA, but one sgRNA also regulates translation initiation in trans. As on all viruses, the 3' and 5' ends contain structures that are presumed to facilitate RNA synthesis. This review describes the structures and interactions of barley yellow dwarf virus RNA that facilitate the complex interplay between the above events and result in a successful virus infection. We also present surprising results on the apparent lack of need for some subgenomic RNAs for the virus to infect cells or whole plants. In summary, the UTRs of luteoviruses are highly complex entities that control and fine-tune many key events of the virus replication cycle.
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Affiliation(s)
- W Allen Miller
- Plant Pathology & Microbiology Department, Iowa State University, Ames, IA 50011, United States; Interdepartmental Genetics & Genomics Program, Iowa State University, Ames, IA 50011, United States; Bioinformatics & Computational Biology Program, Iowa State University, Ames, IA 50011, United States.
| | - Jacquelyn Jackson
- Plant Pathology & Microbiology Department, Iowa State University, Ames, IA 50011, United States; Interdepartmental Genetics & Genomics Program, Iowa State University, Ames, IA 50011, United States
| | - Ying Feng
- Plant Pathology & Microbiology Department, Iowa State University, Ames, IA 50011, United States; Bioinformatics & Computational Biology Program, Iowa State University, Ames, IA 50011, United States
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15
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Moureau G, Cook S, Lemey P, Nougairede A, Forrester NL, Khasnatinov M, Charrel RN, Firth AE, Gould EA, de Lamballerie X. New insights into flavivirus evolution, taxonomy and biogeographic history, extended by analysis of canonical and alternative coding sequences. PLoS One 2015; 10:e0117849. [PMID: 25719412 PMCID: PMC4342338 DOI: 10.1371/journal.pone.0117849] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 01/02/2015] [Indexed: 12/20/2022] Open
Abstract
To generate the most diverse phylogenetic dataset for the flaviviruses to date, we determined the genomic sequences and phylogenetic relationships of 14 flaviviruses, of which 10 are primarily associated with Culex spp. mosquitoes. We analyze these data, in conjunction with a comprehensive collection of flavivirus genomes, to characterize flavivirus evolutionary and biogeographic history in unprecedented detail and breadth. Based on the presumed introduction of yellow fever virus into the Americas via the transatlantic slave trade, we extrapolated a timescale for a relevant subset of flaviviruses whose evolutionary history, shows that different Culex-spp. associated flaviviruses have been introduced from the Old World to the New World on at least five separate occasions, with 2 different sets of factors likely to have contributed to the dispersal of the different viruses. We also discuss the significance of programmed ribosomal frameshifting in a central region of the polyprotein open reading frame in some mosquito-associated flaviviruses.
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Affiliation(s)
- Gregory Moureau
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 Emergence des Pathologies Virales, Marseille, France
| | - Shelley Cook
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Antoine Nougairede
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 Emergence des Pathologies Virales, Marseille, France
| | - Naomi L. Forrester
- Institute for Human Infections and Immunity and Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, United States of America
| | - Maxim Khasnatinov
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh, Gifford, Wallingford, Oxfordshire, OX10, United Kingdom
| | - Remi N. Charrel
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 Emergence des Pathologies Virales, Marseille, France
| | - Andrew E. Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Ernest A. Gould
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 Emergence des Pathologies Virales, Marseille, France
| | - Xavier de Lamballerie
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 Emergence des Pathologies Virales, Marseille, France
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16
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Miras M, Sempere RN, Kraft JJ, Miller WA, Aranda MA, Truniger V. Interfamilial recombination between viruses led to acquisition of a novel translation-enhancing RNA element that allows resistance breaking. THE NEW PHYTOLOGIST 2014; 202:233-246. [PMID: 24372390 PMCID: PMC4337425 DOI: 10.1111/nph.12650] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/19/2013] [Indexed: 05/04/2023]
Abstract
Many plant viruses depend on functional RNA elements, called 3'-UTR cap-independent translation enhancers (3'-CITEs), for translation of their RNAs. In this manuscript we provide direct proof for the existing hypothesis that 3'-CITEs are modular and transferable by recombination in nature, and that this is associated with an advantage for the created virus. By characterizing a newly identified Melon necrotic spot virus (MNSV; Tombusviridae) isolate, which is able to overcome eukaryotic translation initiation factor 4E (eIF4E)-mediated resistance, we found that it contains a 55 nucleotide insertion in its 3'-UTR. We provide strong evidence that this insertion was acquired by interfamilial recombination with the 3'-UTR of an Asiatic Cucurbit aphid-borne yellows virus (CABYV; Luteoviridae). By constructing chimeric viruses, we showed that this recombined sequence is responsible for resistance breaking. Analysis of the translational efficiency of reporter constructs showed that this sequence functions as a novel 3'-CITE in both resistant and susceptible plants, being essential for translation control in resistant plants. In conclusion, we showed that a recombination event between two clearly identified viruses from different families led to the transfer of exactly the sequence corresponding to a functional RNA element, giving rise to a new isolate with the capacity to infect an otherwise nonsusceptible host.
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Affiliation(s)
- Manuel Miras
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
| | - Raquel N. Sempere
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
| | - Jelena J. Kraft
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey Hall, Ames, IA 50011, USA
| | - W. Allen Miller
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey Hall, Ames, IA 50011, USA
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
| | - Veronica Truniger
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
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17
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Lotos L, Efthimiou K, Maliogka VI, Katis NI. Generic detection of poleroviruses using an RT-PCR assay targeting the RdRp coding sequence. J Virol Methods 2013; 198:1-11. [PMID: 24374125 DOI: 10.1016/j.jviromet.2013.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 11/22/2013] [Accepted: 12/14/2013] [Indexed: 10/25/2022]
Abstract
In this study a two-step RT-PCR assay was developed for the generic detection of poleroviruses. The RdRp coding region was selected as the primers' target, since it differs significantly from that of other members in the family Luteoviridae and its sequence can be more informative than other regions in the viral genome. Species specific RT-PCR assays targeting the same region were also developed for the detection of the six most widespread poleroviral species (Beet mild yellowing virus, Beet western yellows virus, Cucurbit aphid-borne virus, Carrot red leaf virus, Potato leafroll virus and Turnip yellows virus) in Greece and the collection of isolates. These isolates along with other characterized ones were used for the evaluation of the generic PCR's detection range. The developed assay efficiently amplified a 593bp RdRp fragment from 46 isolates of 10 different Polerovirus species. Phylogenetic analysis using the generic PCR's amplicon sequence showed that although it cannot accurately infer evolutionary relationships within the genus it can differentiate poleroviruses at the species level. Overall, the described generic assay could be applied for the reliable detection of Polerovirus infections and, in combination with the specific PCRs, for the identification of new and uncharacterized species in the genus.
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Affiliation(s)
- Leonidas Lotos
- Aristotle University of Thessaloniki, School of Agriculture, Laboratory of Plant Pathology, 54124 Thessaloniki, Greece
| | - Konstantinos Efthimiou
- Aristotle University of Thessaloniki, School of Agriculture, Laboratory of Plant Pathology, 54124 Thessaloniki, Greece
| | - Varvara I Maliogka
- Aristotle University of Thessaloniki, School of Agriculture, Laboratory of Plant Pathology, 54124 Thessaloniki, Greece.
| | - Nikolaos I Katis
- Aristotle University of Thessaloniki, School of Agriculture, Laboratory of Plant Pathology, 54124 Thessaloniki, Greece
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18
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Hwang YT, Kalischuk M, Fusaro AF, Waterhouse PM, Kawchuk L. Small RNA sequencing of Potato leafroll virus-infected plants reveals an additional subgenomic RNA encoding a sequence-specific RNA-binding protein. Virology 2013; 438:61-9. [DOI: 10.1016/j.virol.2012.12.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 10/28/2012] [Accepted: 12/25/2012] [Indexed: 10/27/2022]
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19
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Abstract
In the Mediterranean region, pea, bean, and faba bean production is affected by around 17 major viruses. These viruses do not have the same ecology and consequently require a variety of different preventive measures to control them. Some of these viruses have a narrow host range, such as Faba bean necrotic yellows virus (FBNYV), and others, such as Alfalfa mosaic virus (AMV) and Cucumber mosaic virus (CMV), a very wide host range. Such features are important when identifying sources of virus inoculum in a region, and the vectors can transmit viruses from natural reservoirs to the crop plants. Some of these viruses are seed borne and, consequently, can be disseminated long distances through infected seeds. Crop losses caused by these viruses are variable, depending on the sensitivity and susceptibility of the crop to infection. Host resistance genes have been identified for some of these viruses, but in others, such as FBNYV, no resistance genes in faba bean have been identified yet. Significant progress was made in developing precise methods for the identification of these viruses, and new virus problems are being identified every year. This chapter is not intended to be a review for pea, bean, and faba bean viruses, but rather focuses on the major viruses which affect these crops in the Mediterranean basin with focus on the progress made over the past two decades.
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Affiliation(s)
- Khaled Makkouk
- National Council for Scientific Research, Beirut, Lebanon
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20
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Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome. Proc Natl Acad Sci U S A 2011; 108:E1111-9. [PMID: 22025686 DOI: 10.1073/pnas.1102932108] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The genus Cardiovirus (family Picornaviridae) currently comprises the species Encephalomyocarditis virus (EMCV) and Theilovirus. Cardioviruses have a positive-sense, single-stranded RNA genome that encodes a large polyprotein (L-1ABCD-2ABC-3ABCD) that is cleaved to produce approximately 12 mature proteins. We report on a conserved ORF that overlaps the 2B-encoding sequence of EMCV in the +2 reading frame. The ORF is translated as a 128-129 amino acid transframe fusion (2B*) with the N-terminal 11-12 amino acids of 2B, via ribosomal frameshifting at a conserved GGUUUUY motif. Mutations that knock out expression of 2B* result in a small-plaque phenotype. Curiously, although theilovirus sequences lack a long ORF in the +2 frame at this genomic location, they maintain a conserved GGUUUUU motif just downstream of the 2A-2B junction, and a highly localized peak in conservation at polyprotein-frame synonymous sites suggests that theiloviruses also utilize frameshifting here, albeit into a very short +2-frame ORF. Unlike previous cases of programmed -1 frameshifting, here frameshifting is modulated by virus infection, thus suggesting a novel regulatory role for frameshifting in these viruses.
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21
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Cilia M, Tamborindeguy C, Rolland M, Howe K, Thannhauser TW, Gray S. Tangible benefits of the aphid Acyrthosiphon pisum genome sequencing for aphid proteomics: Enhancements in protein identification and data validation for homology-based proteomics. JOURNAL OF INSECT PHYSIOLOGY 2011; 57:179-190. [PMID: 21070785 DOI: 10.1016/j.jinsphys.2010.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 10/28/2010] [Accepted: 11/01/2010] [Indexed: 05/30/2023]
Abstract
Homology-driven proteomics promises to reveal functional biology in insects with sparse genome sequence information. A proteomics study comparing plant virus transmission competent and refractive genotypes of the aphid Schizaphis graminum isolated numerous candidate proteins involved in virus transmission, but limited genome sequence information hampered their identification. The complete genome of the pea aphid, Acyrthosiphon pisum, released in 2008, enabled us to double the number of protein identifications beyond what was possible using available EST libraries and other insect sequences. This was concomitant with a dramatic increase of the number of MS and MS/MS peptide spectra matching the genome-derived protein sequence. LC-MS/MS proved to be the most robust method of peptide detection. Cross-matching spectral data to multiple EST sequences and error tolerant searching to identify amino acid substitutions enhanced the percent coverage of the Schizaphis graminum proteins. 2-D electrophoresis provided the protein pI and MW which enabled the refinement of the candidate protein selection and provided a measure of protein abundance when coupled to the spectral data. Thus, the homology-based proteomics pipeline for insects should include efforts to maximize the number of peptide matches to the protein to increase certainty in protein identification and relative protein abundance.
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Affiliation(s)
- M Cilia
- Robert W. Holley Center for Agriculture and Health, Cornell University, Tower Road, Ithaca, NY 14853, USA
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22
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Sztuba-Solińska J, Urbanowicz A, Figlerowicz M, Bujarski JJ. RNA-RNA recombination in plant virus replication and evolution. ANNUAL REVIEW OF PHYTOPATHOLOGY 2011; 49:415-43. [PMID: 21529157 DOI: 10.1146/annurev-phyto-072910-095351] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
RNA-RNA recombination is one of the strongest forces shaping the genomes of plant RNA viruses. The detection of recombination is a challenging task that prompted the development of both in vitro and in vivo experimental systems. In the divided genome of Brome mosaic virus system, both inter- and intrasegmental crossovers are described. Other systems utilize satellite or defective interfering RNAs (DI-RNAs) of Turnip crinkle virus, Tomato bushy stunt virus, Cucumber necrosis virus, and Potato virus X. These assays identified the mechanistic details of the recombination process, revealing the role of RNA structure and proteins in the replicase-mediated copy-choice mechanism. In copy choice, the polymerase and the nascent RNA chain from which it is synthesized switch from one RNA template to another. RNA recombination was found to mediate the rearrangement of viral genes, the repair of deleterious mutations, and the acquisition of nonself sequences influencing the phylogenetics of viral taxa. The evidence for recombination, not only between related viruses but also among distantly related viruses, and even with host RNAs, suggests that plant viruses unabashedly test recombination with any genetic material at hand.
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Affiliation(s)
- Joanna Sztuba-Solińska
- Plant Molecular Biology Center, Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
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23
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A novel strain of Beet western yellows virus infecting sugar beet with two distinct genotypes differing in the 5′-terminal half of genome. Virus Genes 2010; 42:141-9. [DOI: 10.1007/s11262-010-0553-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 11/08/2010] [Indexed: 11/26/2022]
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24
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Vemulapati B, Druffel KL, Eigenbrode SD, Karasev A, Pappu HR. Molecular characterization of pea enation mosaic virus and bean leafroll virus from the Pacific Northwest, USA. Arch Virol 2010; 155:1713-5. [PMID: 20697921 DOI: 10.1007/s00705-010-0767-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 07/20/2010] [Indexed: 11/24/2022]
Abstract
The family Luteoviridae consists of eight viruses assigned to three different genera, Luteovirus, Polerovirus and Enamovirus. The complete genomic sequences of pea enation mosaic virus (genus Enamovirus) and bean leafroll virus (genus Luteovirus) from the Pacific Northwest, USA, were determined. Annotation, sequence comparisons, and phylogenetic analysis of selected genes together with those of known polero- and enamoviruses were conducted.
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Affiliation(s)
- B Vemulapati
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
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25
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Salem NM, Miller WA, Rowhani A, Golino DA, Moyne AL, Falk BW. Rose spring dwarf-associated virus has RNA structural and gene-expression features like those of Barley yellow dwarf virus. Virology 2008; 375:354-60. [PMID: 18329064 PMCID: PMC4324725 DOI: 10.1016/j.virol.2008.01.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Revised: 11/29/2007] [Accepted: 01/27/2008] [Indexed: 11/29/2022]
Abstract
We determined the complete nucleotide sequence of the Rose spring dwarf-associated virus (RSDaV) genomic RNA (GenBank accession no. EU024678) and compared its predicted RNA structural characteristics affecting gene expression. A cDNA library was derived from RSDaV double-stranded RNAs (dsRNAs) purified from infected tissue. Nucleotide sequence analysis of the cloned cDNAs, plus for clones generated by 5'- and 3'-RACE showed the RSDaV genomic RNA to be 5808 nucleotides. The genomic RNA contains five major open reading frames (ORFs), and three small ORFs in the 3'-terminal 800 nucleotides, typical for viruses of genus Luteovirus in the family Luteoviridae. Northern blot hybridization analysis revealed the genomic RNA and two prominent subgenomic RNAs of approximately 3 kb and 1 kb. Putative 5' ends of the sgRNAs were predicted by identification of conserved sequences and secondary structures which resembled the Barley yellow dwarf virus (BYDV) genomic RNA 5' end and subgenomic RNA promoter sequences. Secondary structures of the BYDV-like ribosomal frameshift elements and cap-independent translation elements, including long-distance base pairing spanning four kb were identified. These contain similarities but also informative differences with the BYDV structures, including a strikingly different structure predicted for the 3' cap-independent translation element. These analyses of the RSDaV genomic RNA show more complexity for the RNA structural elements for members of the Luteoviridae.
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Affiliation(s)
- Nida’ M. Salem
- Department of Plant Pathology, One Shields Ave., University of California, Davis, CA 95616, USA
| | - W. Allen Miller
- Plant Pathology Department and Biochemistry, Biophysics & Molecular Biology Department, Iowa State University, Ames, Iowa 50011, USA
| | - Adib Rowhani
- Department of Plant Pathology, One Shields Ave., University of California, Davis, CA 95616, USA
| | - Deborah A. Golino
- Department of Plant Pathology, One Shields Ave., University of California, Davis, CA 95616, USA
| | - Anne-Laure Moyne
- Department of Plant Pathology, One Shields Ave., University of California, Davis, CA 95616, USA
| | - Bryce W. Falk
- Department of Plant Pathology, One Shields Ave., University of California, Davis, CA 95616, USA
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26
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Beuve M, Stevens M, Liu HY, Wintermantel WM, Hauser S, Lemaire O. Biological and Molecular Characterization of an American Sugar Beet-Infecting Beet western yellows virus Isolate. PLANT DISEASE 2008; 92:51-60. [PMID: 30786380 DOI: 10.1094/pdis-92-1-0051] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Three aphid-transmitted viruses belonging to the Polerovirus genus, Beet mild yellowing virus (BMYV), Beet chlorosis virus (BChV), and Beet western yellows virus (BWYV), have been described as pathogens of sugar beet. We present the complete biological, serological, and molecular characterization of an American isolate of Beet western yellows virus (BWYV-USA), collected from yellow beet leaves. The biological data suggested that BWYV-USA displayed a host range similar to that of BMYV, but distinct from those of BChV and the lettuce and rape isolates of Turnip yellows virus. The complete genomic RNA sequence of BWYV-USA showed a genetic organization and expression typical of other Polerovirus members. Comparisons of deduced amino acid sequences showed that P0 and the putative replicase complex (P1-P2) of BWYV-USA are more closely related to Cucurbit aphid-borne yellows virus (CABYV) than to BMYV, whereas alignments of P3, P4, and P5 showed the highest homology with BMYV. Intraspecific and interspecific phylogenetic analyses have suggested that the BWYV-USA genome may be the result of recombination events between a CABYV-like ancestor contributing open reading frame (ORF) 0, ORF 1, and ORF 2, and a beet Polerovirus progenitor providing the 3' ORFs, with a similar mechanism of speciation occurring for BMYV in Europe. Results demonstrate that BWYV-USA is a distinct species in the Polerovirus genus, clarifying the nomenclature of this important group of viruses.
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Affiliation(s)
- Monique Beuve
- Institut National de la Recherche Agronomique (INRA), UMR Santé de la Vigne et Qualité du Vin (SVQV), Laboratoire Virologie & Vection, 68021 Colmar cedex, France, and Université L. Pasteur, 67000 Strasbourg, France
| | - Mark Stevens
- Broom's Barn Research Center, Higham, Bury St. Edmunds, Suffolk, IP28 6 NP, UK
| | - Hsing-Yeh Liu
- United States Department of Agriculture-Agricultural Research Station, Salinas, CA 93905
| | - William M Wintermantel
- United States Department of Agriculture-Agricultural Research Station, Salinas, CA 93905
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27
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Shen R, Rakotondrafara AM, Miller WA. trans regulation of cap-independent translation by a viral subgenomic RNA. J Virol 2006; 80:10045-54. [PMID: 17005682 PMCID: PMC1617300 DOI: 10.1128/jvi.00991-06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many positive-strand RNA viruses generate 3'-coterminal subgenomic mRNAs to allow translation of 5'-distal open reading frames. It is unclear how viral genomic and subgenomic mRNAs compete with each other for the cellular translation machinery. Translation of the uncapped Barley yellow dwarf virus genomic RNA (gRNA) and subgenomic RNA1 (sgRNA1) is driven by the powerful cap-independent translation element (BTE) in their 3' untranslated regions (UTRs). The BTE forms a kissing stem-loop interaction with the 5' UTR to mediate translation initiation at the 5' end. Here, using reporter mRNAs that mimic gRNA and sgRNA1, we show that the abundant sgRNA2 inhibits translation of gRNA, but not sgRNA1, in vitro and in vivo. This trans inhibition requires the functional BTE in the 5' UTR of sgRNA2, but no translation of sgRNA2 itself is detectable. The efficiency of translation of the viral mRNAs in the presence of sgRNA2 is determined by proximity to the mRNA 5' end of the stem-loop that kisses the 3' BTE. Thus, the gRNA and sgRNA1 have "tuned" their expression efficiencies via the site in the 5' UTR to which the 3' BTE base pairs. We conclude that sgRNA2 is a riboregulator that switches off translation of replication genes from gRNA while permitting translation of structural genes from sgRNA1. These results reveal (i) a new level of control of subgenomic-RNA gene expression, (ii) a new role for a viral subgenomic RNA, and (iii) a new mechanism for RNA-mediated regulation of translation.
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Affiliation(s)
- Ruizhong Shen
- Plant Pathology Department, 351 Bessey Hall, Iowa State University, Ames, IA 50011, USA
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28
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Stuart GW, Moffett PK, Bozarth RF. A comprehensive open reading frame phylogenetic analysis of isometric positive strand ssRNA plant viruses. Arch Virol 2006; 151:1159-77. [PMID: 16385397 DOI: 10.1007/s00705-005-0692-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Accepted: 11/02/2005] [Indexed: 11/26/2022]
Abstract
Rigorous large-scale whole genome comparisons are capable of providing more comprehensive and potentially more accurate descriptions of viral relationships, allowing for the effective validation and modification of current taxonomy. Using a set of 5 togaviruses as an outgroup, a comprehensive phylogeny for 115 isometric positive ssRNA plant viruses was generated based on the simultaneous comparison of over 480 ORFs found within completely sequenced genomes. With the exception of a diverse group of viruses representing the family Comoviridae, the single tree generated contained well supported branches corresponding to well established groups of viruses, including Bromoviridae, Umbravirus, Sobemovirus, and Tymoviridae. In addition, evidence for specific relationships between groups were also observed, specifically Tombusviridae + Umbravirus, and Luteoviridae + Sobemovirus. Various well established subgroups of viruses were also well resolved within the tree. In addition, some recent proposals involving the creation of new genera or the inclusion of newly described viruses into established genera were supported, while others were not. The evidence for frequent gene sharing and the potential consequences to viral taxonomy are discussed.
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Affiliation(s)
- G W Stuart
- Department of Life Sciences, Indiana State University, Terre Haute, Indiana 47809, USA.
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Pettit Kneller EL, Rakotondrafara AM, Miller WA. Cap-independent translation of plant viral RNAs. Virus Res 2005; 119:63-75. [PMID: 16360925 PMCID: PMC1880899 DOI: 10.1016/j.virusres.2005.10.010] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 09/01/2005] [Accepted: 10/19/2005] [Indexed: 11/29/2022]
Abstract
The RNAs of many plant viruses lack a 5' cap and must be translated by a cap-independent mechanism. Here, we discuss the remarkably diverse cap-independent translation elements that have been identified in members of the Potyviridae, Luteoviridae, and Tombusviridae families, and genus Tobamovirus. Many other plant viruses have uncapped RNAs but their translation control elements are uncharacterized. Cap-independent translation elements of plant viruses differ strikingly from those of animal viruses: they are smaller (<200 nt), some are located in the 3' untranslated region, some require ribosome scanning from the 5' end of the mRNA, and the 5' UTR elements are much less structured than those of animal viruses. We discuss how these elements may interact with host translation factors, and speculate on their mechanism of action and their roles in the virus replication cycle. Much remains to be learned about how these elements enable plant viruses to usurp the host translational machinery.
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Affiliation(s)
- Elizabeth L. Pettit Kneller
- Interdepartmental Plant Physiology Program, Department of Plant Pathology, 351 Bessey Hall, Iowa State University, Ames, IA 50011, USA
| | - Aurélie M. Rakotondrafara
- Molecular, Cellular and Developmental Biology Program, Department of Plant Pathology, 351 Bessey Hall, Iowa State University, Ames, IA 50011, USA
| | - W. Allen Miller
- Molecular, Cellular and Developmental Biology Program, Department of Plant Pathology, 351 Bessey Hall, Iowa State University, Ames, IA 50011, USA
- * Corresponding author. Tel.: +1 515 294 2436; fax: +1 515 294 9420. E-mail address: (W.A. Miller)
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Huang LF, Naylor M, Pallett DW, Reeves J, Cooper JI, Wang H. The complete genome sequence, organization and affinities of carrot red leaf virus. Arch Virol 2005; 150:1845-55. [PMID: 15883658 DOI: 10.1007/s00705-005-0537-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2004] [Accepted: 02/28/2005] [Indexed: 10/25/2022]
Abstract
A sequence of 5723 nucleotides (GenBank accession number: AY695933) is reported for the RNA genome of an isolate of Carrot red leaf virus (CtRLV). The sequence is predicted to contain six large open reading frames and non coding sequences of 28 nucleotides at the 5' end, 110 nucleotides at the 3' end, and 215 nucleotides between the two main blocks of coding sequences. The 5' coding region encodes two polypeptides with calculated molecular masses (Mr) of 28.6 kDa (P0) and 68.2 kDa (P1) that overlap in different reading frames. Circumstantially, the third ORF in the 5' block is putatively translated by frameshift read-through to yield a polypeptide (P1 + P2) with a calculated Mr of 116.9 kDa. Frameshifting is predicted at a "shifty" sequence (GGGAAAC; nt 1523-1529) also found in most members of the genus Polerovirus. The C-terminal region of the 116.9 kDa polypeptide includes the consensus sequence for the viral RNA-directed RNA polymerase. The 3' block of coding sequence defines three putative polypeptides of: 23.0 kDa (P3), 21.3 kDa (P4, in a different reading frame) and 77.2 kDa (P3 + P5, by read-through of P3) respectively. From the genome structure of CtRLV, it is suggested that this virus belongs to the genus Polerovirus, rather than either the genus Luteovirus or the genus Enamovirus.
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Affiliation(s)
- L F Huang
- NERC/Centre for Ecology and Hydrology-Oxford, Oxford, UK
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Shen R, Miller WA. Subgenomic RNA as a riboregulator: negative regulation of RNA replication by Barley yellow dwarf virus subgenomic RNA 2. Virology 2004; 327:196-205. [PMID: 15351207 DOI: 10.1016/j.virol.2004.06.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2004] [Accepted: 06/15/2004] [Indexed: 10/26/2022]
Abstract
Barley yellow dwarf virus (BYDV) generates three 3'-coterminal subgenomic RNAs (sgRNAs) in infected cells. Translation of BYDV genomic RNA (gRNA) and sgRNA1 is mediated by the BYDV cap-independent translation element (BTE) in the 3' untranslated region. sgRNAs 2 and 3 are unlikely to be mRNAs. We proposed that accumulation of sgRNA2, which contains the BTE in its 5' UTR, regulates BYDV replication by trans-inhibiting translation of the viral polymerase from genomic RNA (gRNA). Here, we tested this hypothesis and found that: (i) co-inoculation of the BTE or sgRNA2 with BYDV RNA inhibits BYDV RNA accumulation in protoplasts; (ii) Brome mosaic virus (BMV), engineered to contain the BTE, trans-inhibits BYDV replication; and (iii) sgRNA2 generated during BYDV infection trans-inhibits both GFP expression from BMV RNA and translation of a non-viral reporter mRNA. We conclude that sgRNA2, via its BTE, functions as a riboregulator to inhibit translation of gRNA. This may make gRNA available as a replicase template and for encapsidation. Thus, BYDV sgRNA2 joins a growing list of trans-acting regulatory RNAs.
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Affiliation(s)
- Ruizhong Shen
- Interdepartmental Genetics Program and Department of Plant Pathology, Iowa State University, Ames, IA 50011, USA
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