1
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Villamor DEV, Mejia AS, Martin RR, Tzanetakis IE. Genomic Analysis and Development of Infectious Clone of a Novel Carlavirus Infecting Blueberry. PHYTOPATHOLOGY 2023; 113:98-103. [PMID: 35852469 DOI: 10.1094/phyto-05-22-0186-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A new blueberry virus was discovered using high-throughput sequencing. Using sequence identity values, phylogenetics, and serological and biological properties, we propose the virus, putatively named blueberry virus S (BluVS), to be a distinct species within the genus Carlavirus (family Betaflexiviridae). The genome was analyzed in depth, and an infectious clone was developed to initiate studies on virus pathogenicity. Agroinfiltration of the binary vector construct produced severe systemic symptoms in Nicotiana occidentalis. Back-inoculation using sap from agroinfiltrated N. occidentalis produced identical symptoms to the recipient plants (N. occidentalis), and virus purification yielded flexuous carlavirus-like particles. However, unlike blueberry scorch virus (BlScV), BluVS caused symptomless infection in Chenopodium quinoa and reacted weakly to BlScV antibodies in an enzyme-linked immunosorbent assay. Collectively, the results provide evidence for the distinct speciation of BluVS. The availability of an infectious clone provides tools for future studies on the biology of the virus.
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Affiliation(s)
- D E V Villamor
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - A Sierra Mejia
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - R R Martin
- Oregon State University and U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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2
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Thekke-Veetil T, McCoppin NK, Hobbs HA, Hartman GL, Lambert KN, Lim HS, Domier LL. Discovery of a Novel Member of the Carlavirus Genus from Soybean ( Glycine max L. Merr.). Pathogens 2021; 10:pathogens10020223. [PMID: 33670683 PMCID: PMC7922177 DOI: 10.3390/pathogens10020223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/29/2022] Open
Abstract
A novel member of the Carlavirus genus, provisionally named soybean carlavirus 1 (SCV1), was discovered by RNA-seq analysis of randomly collected soybean leaves in Illinois, USA. The SCV1 genome contains six open reading frames that encode a viral replicase, triple gene block proteins, a coat protein (CP) and a nucleic acid binding protein. The proteins showed highest amino acid sequence identities with the corresponding proteins of red clover carlavirus A (RCCVA). The predicted amino acid sequence of the SCV1 replicase was only 60.6% identical with the replicase of RCCVA, which is below the demarcation criteria for a new species in the family Betaflexiviridae. The predicted replicase and CP amino acid sequences of four SCV1 isolates grouped phylogenetically with those of members of the Carlavirus genus in the family Betaflexiviridae. The features of the encoded proteins, low nucleotide and amino acid sequence identities of the replicase with the closest member, and the phylogenetic grouping suggest SCV1 is a new member of the Carlavirus genus.
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Affiliation(s)
- Thanuja Thekke-Veetil
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (T.T.-V.); (H.A.H.); (G.L.H.); (K.N.L.)
| | - Nancy K. McCoppin
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA;
| | - Houston A. Hobbs
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (T.T.-V.); (H.A.H.); (G.L.H.); (K.N.L.)
| | - Glen L. Hartman
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (T.T.-V.); (H.A.H.); (G.L.H.); (K.N.L.)
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA;
| | - Kris N. Lambert
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (T.T.-V.); (H.A.H.); (G.L.H.); (K.N.L.)
| | - Hyoun-Sub Lim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea;
| | - Leslie. L. Domier
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (T.T.-V.); (H.A.H.); (G.L.H.); (K.N.L.)
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA;
- Correspondence: ; Tel.: +1-217-333-0510
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3
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Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts. Viruses 2019; 11:v11080752. [PMID: 31416257 PMCID: PMC6722529 DOI: 10.3390/v11080752] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023] Open
Abstract
Potato virus M (PVM) is a member of the genus Carlavirus of the family Betaflexviridae and causes large economic losses of nightshade crops. Several previous studies have elucidated the population structure, evolutionary timescale and adaptive evolution of PVM. However, the synonymous codon usage pattern of PVM remains unclear. In this study, we performed comprehensive analyses of the codon usage and composition of PVM based on 152 nucleotide sequences of the coat protein (CP) gene and 125 sequences of the cysteine-rich nucleic acid binding protein (NABP) gene. We observed that the PVM CP and NABP coding sequences were GC-and AU-rich, respectively, whereas U- and G-ending codons were preferred in the PVM CP and NABP coding sequences. The lower codon usage of the PVM CP and NABP coding sequences indicated a relatively stable and conserved genomic composition. Natural selection and mutation pressure shaped the codon usage patterns of PVM, with natural selection being the most important factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analysis revealed that the greatest adaption of PVM was to pepino, followed by tomato and potato. Moreover, similarity Index (SiD) analysis showed that pepino had a greater impact on PVM than tomato and potato. Our study is the first attempt to evaluate the codon usage pattern of the PVM CP and NABP genes to better understand the evolutionary changes of a carlavirus.
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4
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Peng L, Grinstead S, Kinard G, Wu LP, Li R. Molecular characterization and detection of two carlaviruses infecting cactus. Arch Virol 2019; 164:1873-1876. [PMID: 31076911 DOI: 10.1007/s00705-019-04279-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/10/2019] [Indexed: 11/27/2022]
Abstract
Two large contigs with sequence similarities to different carlaviruses were identified by high-throughput sequencing in samples from a cactus plant. The complete genomes of the two viruses, tentatively named "cactus carlavirus 1" (CCV-1) and "cactus carlavirus 2" (CCV-2), were determined to be 8,441 and 8,396 nucleotides long, respectively, excluding the poly(A) tail. These viruses have the typical genomic organization of members of the genus Carlavirus. CCV-1 appears to be a cactus isolate of the carlavirus HSO-2016a, with 90.1% nucleotide sequence identity between the two virus genomes, whereas CCV-2 may be classified as a member of a new species. The sequences of CCV-2 and other carlaviruses are 48.9-60.0% identical at the whole-genome level.
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Affiliation(s)
- L Peng
- Key Laboratory of Poyang Lake Environment and Resource, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - S Grinstead
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - G Kinard
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - L-P Wu
- Key Laboratory of Poyang Lake Environment and Resource, School of Life Science, Nanchang University, Nanchang, 330031, China.
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA.
| | - R Li
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA.
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5
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Temporal analysis and adaptive evolution of the global population of potato virus M. INFECTION GENETICS AND EVOLUTION 2019; 73:167-174. [PMID: 31054922 DOI: 10.1016/j.meegid.2019.04.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/28/2019] [Accepted: 04/30/2019] [Indexed: 12/24/2022]
Abstract
Potato virus M (PVM), which is a member of the genus Carlavirus in the family Betaflexviridae, causes critical economic losses of nightshade crops. PVM is transmitted by aphids in a non-persistent manner, by sap inoculation and also transmitted in tubers. Previously, several reports described the genetic structure of PVM. However, the evolutionary rate, timescale, spread and adaptation evolution of the virus have not been examined. In this study, we investigated the phylodynamics of PVM using 145 nucleotide sequences of the coat protein gene and 117 sequences of the cysteine-rich nucleic acid-binding protein (NABP) gene, which were sampled between 1985 and 2013. We found that at least three lineages with isolates that were defined geographically but not by the original host were clustered. The evolutionary rate of the NABP (1.06 × 10-2) was faster than that of the CP (4.12 × 10-3). The time to the most recent common ancestors (TMRCAs) is similar between CP (CIs 31-110) and NABP (CIs 28-33) genes. Based on CP and NABP genes, PVM migrated from China to Canada, Iran, India and European countries, and it circulated within China. Our study is the first attempt to evaluate the evolutionary rates, timescales and migration dynamics of PVM.
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6
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Fujita N, Komatsu K, Ayukawa Y, Matsuo Y, Hashimoto M, Netsu O, Teraoka T, Yamaji Y, Namba S, Arie T. N-terminal region of cysteine-rich protein (CRP) in carlaviruses is involved in the determination of symptom types. MOLECULAR PLANT PATHOLOGY 2018; 19:180-190. [PMID: 27868376 PMCID: PMC6638135 DOI: 10.1111/mpp.12513] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 10/19/2016] [Accepted: 11/14/2016] [Indexed: 05/04/2023]
Abstract
Plant viruses in the genus Carlavirus include more than 65 members. Plants infected with carlaviruses exhibit various symptoms, including leaf malformation and plant stunting. Cysteine-rich protein (CRP) encoded by carlaviruses has been reported to be a pathogenicity determinant. Carlavirus CRPs contain two motifs in their central part: a nuclear localization signal (NLS) and a zinc finger motif (ZF). In addition to these two conserved motifs, carlavirus CRPs possess highly divergent, N-terminal, 34 amino acid residues with unknown function. In this study, to analyse the role of these distinct domains, we tested six carlavirus CRPs for their RNA silencing suppressor activity, ability to enhance the pathogenicity of a heterologous virus and effects on virus accumulation levels. Although all six tested carlavirus CRPs showed RNA silencing suppressor activity at similar levels, symptoms induced by the Potato virus X (PVX) heterogeneous system exhibited two different patterns: leaf malformation and whole-plant stunting. The expression of each carlavirus CRP enhanced PVX accumulation levels, which were not correlated with symptom patterns. PVX-expressing CRP with mutations in either NLS or ZF did not induce symptoms, suggesting that both motifs play critical roles in symptom expression. Further analysis using chimeric CRPs, in which the N-terminal region was replaced with the corresponding region of another CRP, suggested that the N-terminal region of carlavirus CRPs determined the exhibited symptom types. The up-regulation of a plant gene upp-L, which has been reported in a previous study, was also observed in this study; however, the expression level was not responsible for symptom types.
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Affiliation(s)
- Naoko Fujita
- Laboratory of Plant Pathology, Graduate School of AgricultureTokyo University of Agriculture and Technology (TUAT)183‐8509 FuchuJapan
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life SciencesThe University of Tokyo113‐8657 TokyoJapan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Graduate School of AgricultureTokyo University of Agriculture and Technology (TUAT)183‐8509 FuchuJapan
| | - Yu Ayukawa
- Laboratory of Plant Pathology, Graduate School of AgricultureTokyo University of Agriculture and Technology (TUAT)183‐8509 FuchuJapan
- United Graduate School of Agricultural ScienceTokyo University of Agriculture and TechnologyFuchu183‐8509Japan
| | - Yuki Matsuo
- Laboratory of Plant Pathology, Graduate School of AgricultureTokyo University of Agriculture and Technology (TUAT)183‐8509 FuchuJapan
| | - Masayoshi Hashimoto
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life SciencesThe University of Tokyo113‐8657 TokyoJapan
| | - Osamu Netsu
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life SciencesThe University of Tokyo113‐8657 TokyoJapan
| | - Tohru Teraoka
- Laboratory of Plant Pathology, Graduate School of AgricultureTokyo University of Agriculture and Technology (TUAT)183‐8509 FuchuJapan
| | - Yasuyuki Yamaji
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life SciencesThe University of Tokyo113‐8657 TokyoJapan
| | - Shigetou Namba
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life SciencesThe University of Tokyo113‐8657 TokyoJapan
| | - Tsutomu Arie
- Laboratory of Plant Pathology, Graduate School of AgricultureTokyo University of Agriculture and Technology (TUAT)183‐8509 FuchuJapan
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7
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Su X, Wu K, Zhang LZ, Rahman MS, Zheng K, Li T, Zhang Z, Dong J. Complete genome sequence of a new isolate of potato virus M in Yunnan, China. Arch Virol 2017; 162:2485-2488. [PMID: 28455669 DOI: 10.1007/s00705-017-3380-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/20/2017] [Indexed: 11/25/2022]
Abstract
The complete genome sequence of a new potato virus M (PVM) isolate (PVM-YN), collected from potato (Solanum tuberosum) in Yunnan, China, was determined. It was 8,530 nucleotides (nt) in length, excluding the poly(A) tail at the 3' end, and shared 71.4-72.0% nucleotide sequence identity with available PVM isolates in the NCBI database. The coat proteins (CP) of PVM-YN shared 79.0-97.4% amino acid sequence identity with that of other isolates. It is the first report of the complete genomic sequence of a new PVM isolate infecting S. tuberosum in China.
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Affiliation(s)
- Xiaoxia Su
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China
| | - Kuo Wu
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China
| | - Li Zhen Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China
| | - Mohammad Siddiqur Rahman
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China.,Bangladesh Agricultural Research Institute, Gazipur, 1701, Bangladesh
| | - Kuanyu Zheng
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China
| | - Ting Li
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China
| | - Zhongkai Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China.
| | - Jiahong Dong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China.
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8
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Deng XG, Peng XJ, Zhu F, Chen YJ, Zhu T, Qin SB, Xi DH, Lin HH. A critical domain of Sweet potato chlorotic fleck virus nucleotide-binding protein (NaBp) for RNA silencing suppression, nuclear localization and viral pathogenesis. MOLECULAR PLANT PATHOLOGY 2015; 16:365-75. [PMID: 25138489 PMCID: PMC6638403 DOI: 10.1111/mpp.12186] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
RNA silencing is an important mechanism of antiviral defence in plants. To counteract this resistance mechanism, many viruses have evolved RNA silencing suppressors. In this study, we analysed five proteins encoded by Sweet potato chlorotic fleck virus (SPCFV) for their abilities to suppress RNA silencing using a green fluorescent protein (GFP)-based transient expression assay in Nicotiana benthamiana line 16c plants. Our results showed that a putative nucleotide-binding protein (NaBp), but not other proteins encoded by the virus, could efficiently suppress local and systemic RNA silencing induced by either sense or double-stranded RNA (dsRNA) molecules. Deletion mutation analysis of NaBp demonstrated that the basic motif (an arginine-rich region) was critical for its RNA silencing suppression activity. Using confocal laser scanning microscopy imaging of transfected protoplasts expressing NaBp fused to GFP, we showed that NaBp accumulated predominantly in the nucleus. Mutational analysis of NaBp demonstrated that the basic motif represented part of the nuclear localization signal. In addition, we demonstrated that the basic motif in NaBp was a pathogenicity determinant in the Potato virus X (PVX) heterogeneous system. Overall, our results demonstrate that the basic motif of SPCFV NaBp plays a critical role in RNA silencing suppression, nuclear localization and viral pathogenesis.
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Affiliation(s)
- Xing-Guang Deng
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, 610064, China
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9
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Genetic variation in potato virus M isolates infecting pepino (Solanum muricatum) in China. Arch Virol 2014; 159:3197-210. [PMID: 25233939 DOI: 10.1007/s00705-014-2180-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 07/15/2014] [Indexed: 02/05/2023]
Abstract
Potato virus M (PVM, genus Carlavirus, family Betaflexviridae) is considered to be one of most economically important pathogens of pepino in China. However, the details and the mechanisms underlying PVM evolution are unknown. In this study, we determined and analyzed 40 TGB 1 gene sequences, 67 TGB 2 and TGB 3 gene sequences, and 88 CP and NABP gene sequences from viruses isolated from 19 samples of pepino (Solanum muricatum) and one sample of tomato (S. lycopersicum) collected from different areas of China. Recombination analysis identified only one clear recombinant in the TGB2-TGB3-CP region, but no recombinants were detected for each of the five individual genes. Phylogenetic analysis showed that all PVM isolates could be divided into at least two lineages in trees derived from the TGB 2, CP, and NABP gene sequences, and the lineages seemed to reflect geographical origin. The five PVM genes in this study were found to be under strong negative selection pressure. The PVM isolates examined showed frequent gene flow between the Chinese and European populations, and also within the Chinese population. Clear star phylogenies and the neutral equilibrium model test showed that pepino isolates of PVM appear to be experiencing a new expansion after a recent introduction into China, and these isolates display low levels of genetic diversity. To our knowledge, this study is the first report describing genetic structure, recombination, and gene flow in PVM populations, and it provides strong evolutionary evidence for the virus populations from different geographic regions of China.
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10
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Genetic structure and molecular variability of potato virus M populations. Arch Virol 2014; 159:2081-90. [DOI: 10.1007/s00705-014-2037-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 02/27/2014] [Indexed: 10/25/2022]
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11
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Li YY, Zhang RN, Xiang HY, Abouelnasr H, Li DW, Yu JL, McBeath JH, Han CG. Discovery and Characterization of a Novel Carlavirus Infecting Potatoes in China. PLoS One 2013; 8:e69255. [PMID: 23805334 PMCID: PMC3689765 DOI: 10.1371/journal.pone.0069255] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 06/12/2013] [Indexed: 11/18/2022] Open
Abstract
A new carlavirus, tentatively named Potato virus H (PVH), was found on potato plants with mild symptoms in Hohhot, Inner Mongolia Autonomous Region, China. PVH was confirmed by genome sequencing, serological reactions, electron microscopy, and host index assays. The PVH particles were filamentous and slightly curved, with a modal length of 570 nm. Complete RNA genomic sequences of two isolates of PVH were determined using reverse transcription-PCR (RT-PCR) and the 5' rapid amplification of cDNA ends (5' RACE) method. Sequence analysis revealed that PVH had the typical genomic organization of members of the genus Carlavirus, with a positive-sense single-stranded genome of 8410 nt. It shared coat protein (CP) and replicase amino acid sequence identities of 17.9-56.7% with those of reported carlaviruses. Phylogenetic analyses based on the protein-coding sequences of replicase and CP showed that PVH formed a distinct branch, which was related only distantly to other carlaviruses. Western blotting assays showed that PVH was not related serologically to other potato carlaviruses (Potato virus S, Potato virus M, and Potato latent virus). PVH systemically infected Nicotianaglutinosa but not Nicotiana tabacum, Nicotianabenthamiana, or Chenopodiumquinoa, which is in contrast with the other potato carlaviruses. These results support the classification of PVH as a novel species in the genus Carlavirus. Preliminary results also indicated that a cysteine-rich protein encoded by the smallest ORF located in the 3' proximal region of the genome suppressed local RNA silencing and enhanced the pathogenicity of the recombinant PVX.
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MESH Headings
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Capsid Proteins/genetics
- Capsid Proteins/immunology
- Capsid Proteins/metabolism
- Carlavirus/classification
- Carlavirus/genetics
- Carlavirus/isolation & purification
- China
- DNA, Complementary/chemistry
- DNA, Complementary/metabolism
- Genome, Viral
- Microscopy, Electron
- Phylogeny
- Plant Diseases/virology
- RNA, Viral/genetics
- RNA, Viral/isolation & purification
- RNA, Viral/metabolism
- Real-Time Polymerase Chain Reaction
- Sequence Analysis, DNA
- Solanum tuberosum/virology
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Affiliation(s)
- Yuan-Yuan Li
- State Key Laboratory for Agro-biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Ru-Nan Zhang
- State Key Laboratory for Agro-biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Hai-Ying Xiang
- State Key Laboratory for Agro-biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Hesham Abouelnasr
- State Key Laboratory for Agro-biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Da-Wei Li
- State Key Laboratory for Agro-biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Jia-Lin Yu
- State Key Laboratory for Agro-biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Jenifer Huang McBeath
- Plant Pathology and Biotechnology Laboratory, Agriculture and Forestry Experiment Station, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Cheng-Gui Han
- State Key Laboratory for Agro-biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, P. R. China
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12
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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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13
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Lukhovitskaya NI, Solovieva AD, Boddeti SK, Thaduri S, Solovyev AG, Savenkov EI. An RNA virus-encoded zinc-finger protein acts as a plant transcription factor and induces a regulator of cell size and proliferation in two tobacco species. THE PLANT CELL 2013; 25:960-73. [PMID: 23482855 PMCID: PMC3634699 DOI: 10.1105/tpc.112.106476] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/29/2013] [Accepted: 02/19/2013] [Indexed: 05/03/2023]
Abstract
Plant viruses cause a variety of diseases in susceptible hosts. The disease symptoms often include leaf malformations and other developmental abnormalities, suggesting that viruses can affect plant development. However, little is known about the mechanisms underlying virus interference with plant morphogenesis. Here, we show that a C-4 type zinc-finger (ZF) protein, p12, encoded by a carlavirus (chrysanthemum virus B) can induce cell proliferation, which results in hyperplasia and severe leaf malformation. We demonstrate that the p12 protein activates expression of a regulator of cell size and proliferation, designated upp-L (upregulated by p12), which encodes a transcription factor of the basic/helix-loop-helix family sufficient to cause hyperplasia. The induction of upp-L requires translocation of the p12 protein into the nucleus and ZF-dependent specific interaction with the conserved regulatory region in the upp-L promoter. Our results establish the role of the p12 protein in modulation of host cell morphogenesis. It is likely that other members of the conserved C-4 type ZF family of viral proteins instigate reprogramming of plant development by mimicking eukaryotic transcriptional activators.
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Affiliation(s)
- Nina I. Lukhovitskaya
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Anna D. Solovieva
- Department of Virology, Biological Faculty, Moscow State University, Moscow 119992, Russia
| | - Santosh K. Boddeti
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Srinivas Thaduri
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Andrey G. Solovyev
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
- Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, 127550 Moscow, Russia
| | - Eugene I. Savenkov
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
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Abstract
Ilarviruses were among the first 16 groups of plant viruses approved by ICTV. Like Alfalfa mosaic virus (AMV), bromoviruses, and cucumoviruses they are isometric viruses and possess a single-stranded, tripartite RNA genome. However, unlike these other three groups, ilarviruses were recognized as being recalcitrant subjects for research (their ready lability is reflected in the sigla used to create the group name) and were renowned as unpromising subjects for the production of antisera. However, it was recognized that they shared properties with AMV when the phenomenon of genome activation, in which the coat protein (CP) of the virus is required to be present to initiate infection, was demonstrated to cross group boundaries. The CP of AMV could activate the genome of an ilarvirus and vice versa. Development of the molecular information for ilarviruses lagged behind the knowledge available for the more extensively studied AMV, bromoviruses, and cucumoviruses. In the past 20 years, genomic data for most known ilarviruses have been developed facilitating their detection and allowing the factors involved in the molecular biology of the genus to be investigated. Much information has been obtained using Prunus necrotic ringspot virus and the more extensively studied AMV. A relationship between some ilarviruses and the cucumoviruses has been defined with the recognition that members of both genera encode a 2b protein involved in RNA silencing and long distance viral movement. Here, we present a review of the current knowledge of both the taxonomy and the molecular biology of this genus of agronomically and horticulturally important viruses.
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Loconsole G, Onelge N, Potere O, Giampetruzzi A, Bozan O, Satar S, De Stradis A, Savino V, Yokomi RK, Saponari M. Identification and characterization of citrus yellow vein clearing virus, a putative new member of the genus Mandarivirus. PHYTOPATHOLOGY 2012; 102:1168-75. [PMID: 22913410 DOI: 10.1094/phyto-06-12-0140-r] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Molecular features and genomic organization were determined for Citrus yellow vein clearing virus (CYVCV), the putative viral causal agent of yellow vein clearing disease of lemon trees, reported in Pakistan, India, and more recently in Turkey and China. CYVCV isolate Y1 from Adana, Turkey, was used for deep sequencing analysis of the virus-induced small RNA fractions and for mechanical and graft inoculation of herbaceous and citrus indicator plants. A polyclonal antiserum was developed from CYVCV-Y1 purified from Phaseolus vulgaris and used in western blot assays to characterize the coat protein of CYVCV-Y1 and determine its serological relationship with related viruses. Contigs assembled from the Illumina sequenced short reads were used to construct the whole genome of Citrus yellow vein clearing virus (CYVCV), consisting in a positive-sense RNA of 7,529 nucleotides and containing six predicted open reading frames. The CYVCV genome organization and size resembled that of flexiviruses, and search for sequence homologies revealed that Indian citrus ringspot virus (ICRSV) (Mandarivirus, Alphaflexiviridae) is the most closely related virus. However, CYVCV had an overall nucleotide sequence identity of ≈74% with ICRSV. Although the two viruses were similar with regard to genome organization, viral particles, and herbaceous host range, CYVCV caused different symptoms in citrus and was serologically distinct from ICRSV. Primer pairs were designed and used to detect the virus by conventional and quantitative reverse transcription-polymerase chain reaction on yellow vein clearing symptomatic field trees as well as graft- and mechanically inoculated host plants. Collectively, these data suggest that CYVCV is the causal agent of yellow vein clearing disease and represents a new species in the genus Mandarivirus.
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Affiliation(s)
- G Loconsole
- Dipartimento di Scienze del Suolo, Della Pianta e Alimenti, Università di Bari "Aldo Moro", Italy
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16
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Complete genome organization of American hop latent virus and its relationship to carlaviruses. Arch Virol 2012; 157:1403-6. [PMID: 22527868 PMCID: PMC3384778 DOI: 10.1007/s00705-012-1312-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 03/17/2012] [Indexed: 11/05/2022]
Abstract
The complete genomic sequence of American hop latent virus (AHLV; genus Carlavirus) was determined. The genome consists of 8,601 nucleotides plus a 3′-polyadenylate tail. The genome encompasses six potential open reading frames (ORF) in the positive sense, and their organization is typical of other carlaviruses. Analysis of the coat protein coding sequence at both the nucleic acid level and the amino acid level indicates that AHLV is only remotely related to the other carlaviruses known to infect common hop. Polyclonal antibodies were produced against the bacterially expressed coat protein of AHLV. These antibodies differentiated between AHLV and other carlaviruses of hop.
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17
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Senshu H, Yamaji Y, Minato N, Shiraishi T, Maejima K, Hashimoto M, Miura C, Neriya Y, Namba S. A dual strategy for the suppression of host antiviral silencing: two distinct suppressors for viral replication and viral movement encoded by potato virus M. J Virol 2011; 85:10269-78. [PMID: 21752911 PMCID: PMC3196401 DOI: 10.1128/jvi.05273-11] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 06/30/2011] [Indexed: 11/20/2022] Open
Abstract
Viruses encode RNA silencing suppressors to counteract host antiviral silencing. In this study, we analyzed the suppressors encoded by potato virus M (PVM), a member of the genus Carlavirus. In the conventional green fluorescent protein transient coexpression assay, the cysteine-rich protein (CRP) of PVM inhibited both local and systemic silencing, whereas the triple gene block protein 1 (TGBp1) showed suppressor activity only on systemic silencing. Furthermore, to elucidate the roles of these two suppressors during an active viral infection, we performed PVX vector-based assays and viral movement complementation assays. CRP increased the accumulation of viral RNA at the single-cell level and also enhanced viral cell-to-cell movement by inhibiting RNA silencing. However, TGBp1 facilitated viral movement but did not affect viral accumulation in protoplasts. These data suggest that CRP inhibits RNA silencing primarily at the viral replication step, whereas TGBp1 is a suppressor that acts at the viral movement step. Thus, our findings demonstrate a sophisticated viral infection strategy that suppresses host antiviral silencing at two different steps via two mechanistically distinct suppressors. This study is also the first report of the RNA silencing suppressor in the genus Carlavirus.
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Affiliation(s)
- Hiroko Senshu
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuyuki Yamaji
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Nami Minato
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takuya Shiraishi
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kensaku Maejima
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masayoshi Hashimoto
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Chihiro Miura
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yutaro Neriya
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigetou Namba
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Ji X, Qian D, Wei C, Ye G, Zhang Z, Wu Z, Xie L, Li Y. Movement protein Pns6 of rice dwarf phytoreovirus has both ATPase and RNA binding activities. PLoS One 2011; 6:e24986. [PMID: 21949821 PMCID: PMC3176798 DOI: 10.1371/journal.pone.0024986] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 08/20/2011] [Indexed: 11/18/2022] Open
Abstract
Cell-to-cell movement is essential for plant viruses to systemically infect host plants. Plant viruses encode movement proteins (MP) to facilitate such movement. Unlike the well-characterized MPs of DNA viruses and single-stranded RNA (ssRNA) viruses, knowledge of the functional mechanisms of MPs encoded by double-stranded RNA (dsRNA) viruses is very limited. In particular, many studied MPs of DNA and ssRNA viruses bind non-specifically ssRNAs, leading to models in which ribonucleoprotein complexes (RNPs) move from cell to cell. Thus, it will be of special interest to determine whether MPs of dsRNA viruses interact with genomic dsRNAs or their derivative sRNAs. To this end, we studied the biochemical functions of MP Pns6 of Rice dwarf phytoreovirus (RDV), a member of Phytoreovirus that contains a 12-segmented dsRNA genome. We report here that Pns6 binds both dsRNAs and ssRNAs. Intriguingly, Pns6 exhibits non-sequence specificity for dsRNA but shows preference for ssRNA sequences derived from the conserved genomic 5'- and 3'-terminal consensus sequences of RDV. Furthermore, Pns6 exhibits magnesium-dependent ATPase activities. Mutagenesis identified the RNA binding and ATPase activity sites of Pns6 at the N- and C-termini, respectively. Our results uncovered the novel property of a viral MP in differentially recognizing dsRNA and ssRNA and establish a biochemical basis to enable further studies on the mechanisms of dsRNA viral MP functions.
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Affiliation(s)
- Xu Ji
- State Key Laboratory of Protein and Plant Gene Research, Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Dan Qian
- State Key Laboratory of Protein and Plant Gene Research, Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Chunhong Wei
- State Key Laboratory of Protein and Plant Gene Research, Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhongkai Zhang
- Biotechnology and Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, People's Republic of China
| | - Zujian Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, People's Republic of China
| | - Lianhui Xie
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, People's Republic of China
| | - Yi Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing, People's Republic of China
- * E-mail:
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19
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Complete nucleotide sequence of the type isolate of Cowpea mild mottle virus from Ghana. Arch Virol 2010; 155:2069-73. [DOI: 10.1007/s00705-010-0821-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 09/21/2010] [Indexed: 10/19/2022]
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20
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Lin YH, Druffel KL, Whitworth J, Pavek MJ, Pappu HR. Molecular characterization of two potato virus S isolates from late-blight-resistant genotypes of potato (Solanum tuberosum). Arch Virol 2009; 154:1861-3. [DOI: 10.1007/s00705-009-0486-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Accepted: 07/28/2009] [Indexed: 11/27/2022]
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21
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Lukhovitskaya NI, Ignatovich IV, Savenkov EI, Schiemann J, Morozov SY, Solovyev AG. Role of the zinc-finger and basic motifs of chrysanthemum virus B p12 protein in nucleic acid binding, protein localization and induction of a hypersensitive response upon expression from a viral vector. J Gen Virol 2009; 90:723-733. [PMID: 19218219 DOI: 10.1099/vir.0.005025-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
The genomes of carlaviruses encode cysteine-rich proteins (CRPs) of unknown function. The 12 kDa CRP of chrysanthemum virus B (CVB), p12, has been shown previously to induce a hypersensitive response (HR) when expressed from potato virus X (PVX). This study demonstrated that a p12-induced HR was preceded by induction of a number of genes related to pathogenesis, stress and systemic acquired resistance. p12 localized predominantly to the nucleus. Interestingly, it was found that p12 bound both RNA and DNA in vitro, but notably exhibited a preference for DNA in the presence of Zn(2+) ions. Mutational analysis of the p12 conserved sequence motifs demonstrated that the basic motif is required for p12 translocation to the nucleus, thus representing part of the protein nuclear localization signal, whereas the predicted zinc finger motif is needed for both Zn(2+)-dependent DNA binding and eliciting an HR in PVX-infected leaves. Collectively, these results link, for the first time, nuclear localization of the protein encoded by a cytoplasmically replicating virus and its DNA-binding capacity with HR induction. Furthermore, these data suggest that p12 may mediate induction of the host genes by binding to the plant genomic DNA, and emphasize that CVB p12 is functionally distinct from other known nuclear-localized proteins encoded by the plant positive-stranded RNA viruses.
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Affiliation(s)
- N I Lukhovitskaya
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences (SLU), Box 7080, SE-750 07 Uppsala, Sweden
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
| | - I V Ignatovich
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
| | - E I Savenkov
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences (SLU), Box 7080, SE-750 07 Uppsala, Sweden
| | - J Schiemann
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety of Genetically Modified Plants, Messeweg 11/12, D-38104 Braunschweig, Germany
| | - S Yu Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
| | - A G Solovyev
- Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, Timiryazevskaya 42, 127550 Moscow, Russia
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
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22
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Molecular characterization of Lolium latent virus, proposed type member of a new genus in the family Flexiviridae. Arch Virol 2008; 153:1263-70. [PMID: 18509590 DOI: 10.1007/s00705-008-0108-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 04/02/2008] [Indexed: 10/22/2022]
Abstract
Lolium latent virus (LoLV) was recently detected in the USA for the first time in ryegrass hybrids (Lolium perenne x Lolium multiflorum). The genome of one USA isolate, LoLV-US1, has now been fully sequenced. The positive strand genomic RNA is 7674 nucleotides (nt) long and is organized in five open reading frames (ORFs) encoding the replication-associated protein, the movement-associated triple gene block proteins and the coat protein (CP). The genome organization is similar to that of viruses in the genera Potexvirus and Foveavirus; however, analysis of the complete LoLV genomic sequence, phylogenetic analyses of the deduced amino acid (aa) sequences of the polymerase and the CP, presence of a putative ORF 6, and the in vivo detection of two CPs in equimolar amounts, highlight features peculiar to LoLV. These characteristics indicate that LoLV forms a monotypic group separate from existing genera and unassigned species within the family Flexiviridae, for which we propose the genus name Lolavirus. One-step RT-PCR was developed for quick and reliable LoLV detection.
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23
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Ohkawa A, Yamada M, Sayama H, Sugiyama N, Okuda S, Natsuaki T. Complete nucleotide sequence of a Japanese isolate of Chrysanthemum virus B (genus Carlavirus). Arch Virol 2007; 152:2253-8. [PMID: 17726637 DOI: 10.1007/s00705-007-1039-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Accepted: 06/27/2007] [Indexed: 11/30/2022]
Abstract
The complete nucleotide sequence of a Chrysanthemum virus B isolate from Japan (CVB-S) has been determined. The genomic RNA of CVB-S is 8,990 nucleotides long, excluding the poly(A) tail and, like that of other carlaviruses, contains six open reading frames (ORFs). Multiple alignment and phylogenetic analyses indicated that the phylogenetic relationship among members of the genus Carlavirus is very diverse, with phlox virus S being the closest relative of CVB. In aphid transmission tests, CVB-S was transmitted at a very low rate by Aphis gossypii, a new vector of the virus.
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Affiliation(s)
- A Ohkawa
- Faculty of Agriculture, Utsunomiya University, Utsunomiya, Japan
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Martelli GP, Adams MJ, Kreuze JF, Dolja VV. Family Flexiviridae: a case study in virion and genome plasticity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2007; 45:73-100. [PMID: 17362202 DOI: 10.1146/annurev.phyto.45.062806.094401] [Citation(s) in RCA: 199] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The plant virus family Flexiviridae includes the definitive genera Potexvirus, Mandarivirus, Allexivirus, Carlavirus, Foveavirus, Capillovirus, Vitivirus, Trichovirus, the putative genus Citrivirus, and some unassigned species. Its establishment was based on similarities in virion morphology, common features in genome type and organization, and strong phylogenetic relationships between replicational and structural proteins. In this review, we provide a brief account of the main biological and molecular properties of the members of the family, with special emphasis on the relationships within and among the genera. In phylogenetic analyses the potexvirus-like replicases were more closely related to tymoviruses than to carlaviruses. We postulate a common evolutionary ancestor for the family Tymoviridae and the two distinct evolutionary clusters of the Flexiviridae, i.e., a plant virus with a polyadenylated genome, filamentous virions, and a triple gene block of movement proteins. Subsequent recombination and gene loss would then have generated a very diverse group of plant and fungal viruses.
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Affiliation(s)
- Giovanni P Martelli
- Dipartimento di Protezione delle Piante e Microbiologia Applicata, Università degli Studi and Istituto di Virologia vegetale CNR, Sezione di Bari, 70126 Bari, Italy.
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25
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Zhou ZS, Dell'Orco M, Saldarelli P, Turturo C, Minafra A, Martelli GP. Identification of an RNA-silencing suppressor in the genome of Grapevine virus A. J Gen Virol 2006; 87:2387-2395. [PMID: 16847135 DOI: 10.1099/vir.0.81893-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Higher plants use post-transcriptional gene silencing (PTGS), an RNA-degradation system, as a defence mechanism against viral infections. To counteract this, plant viruses encode and express PTGS suppressor proteins. Four of the five proteins encoded by the Grapevine virus A (GVA) genome were screened using a green fluorescent protein (GFP)-based transient expression assay, and the expression product of ORF5 (protein p10) was identified as a suppressor of silencing. ORF5 p10 suppressed local and systemic silencing induced by a transiently expressed single-stranded sense RNA. This protein was active towards both a transgene and exogenous GFP mRNAs. Ectopic expression of GVA-ORF5 by a Potato virus X vector enhanced symptom severity. The findings that p10 markedly reduces the levels of small interfering RNAs (siRNAs) and that the recombinant protein is able to bind single-stranded and double-stranded forms of siRNAs and microRNAs, suggest the existence of a potential mechanism of suppression based on RNA sequestering.
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Affiliation(s)
- Z Sh Zhou
- Dipartimento di Protezione delle Piante e Microbiologia Applicata, Università degli Studi, Via Amendola 165/A, 70126 Bari, Italy
| | - M Dell'Orco
- Dipartimento di Protezione delle Piante e Microbiologia Applicata, Università degli Studi, Via Amendola 165/A, 70126 Bari, Italy
| | - P Saldarelli
- Istituto di Virologia Vegetale CNR, Sezione di Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - C Turturo
- Dipartimento di Protezione delle Piante e Microbiologia Applicata, Università degli Studi, Via Amendola 165/A, 70126 Bari, Italy
| | - A Minafra
- Istituto di Virologia Vegetale CNR, Sezione di Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - G P Martelli
- Dipartimento di Protezione delle Piante e Microbiologia Applicata, Università degli Studi, Via Amendola 165/A, 70126 Bari, Italy
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James D, Varga A, Croft H, Rast H, Thompson D, Hayes S. Molecular Characterization, Phylogenetic Relationships, and Specific Detection of Peach mosaic virus. PHYTOPATHOLOGY 2006; 96:137-144. [PMID: 18943916 DOI: 10.1094/phyto-96-0137] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Peach mosaic virus (PcMV) and Cherry mottle leaf virus (CMLV) are serologically related viruses that cause distinct diseases, have a different host range, and are vectored by different eriophyid mites. Sequence analysis of the genome of PcMV indicates that it is closely related genetically to CMLV but distinct, with similar genome organization and a member of the genus Trichovirus. The genome of PcMV consists of 7,988 nucleotides, excluding a poly(A) tail at the 3' end of the genome. Four putative open reading frames (ORF1 to 4) were identified coding for proteins of 216.3, 47.2, 21.7, and 15.7 kDa, respectively. Also, three noncoding regions were identified, including an intergenic region separating ORF3 and ORF4. The complete nucleotide sequence of PcMV shares 73% identity with CMLV. The CP amino acid sequence identity between isolates of PcMV ranged from 97 to 99% versus 83% identity when compared with the CP of CMLV. In vitro expression and subsequent western blot analysis confirmed ORF3 as encoding the CP gene of PcMV. Phylogenetic analysis supports classification of PcMV and CMLV as members of the genus Trichovirus. They are unique members of this genus with an extra ORF (ORF4). PcMV ORF4 appears to code for a putative nucleic acid-binding (NB) protein which has identity with the NB protein of CMLV and members of the genera Allexivirus, Carlavirus, and Vitivirus. PcMV and CMLV appear to be the products of recombination between members of the genus Trichovirus and a virus group containing the putative NB protein. Alternatively, PcMV and CMLV may represent the intact genome, with a deletion event producing members that lack ORF4. A reverse transcription-polymerase chain reaction procedure was developed for reliable and specific detection of PcMV. This will be an asset for stone fruit virus certification.
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Lukhovitskaya NI, Yelina NE, Zamyatnin AA, Schepetilnikov MV, Solovyev AG, Sandgren M, Morozov SY, Valkonen JPT, Savenkov EI. Expression, localization and effects on virulence of the cysteine-rich 8 kDa protein of Potato mop-top virus. J Gen Virol 2005; 86:2879-2889. [PMID: 16186244 DOI: 10.1099/vir.0.81099-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Potato mop-top virus (PMTV) RNA3 contains a triple gene block (TGB) encoding viral movement proteins and an open reading frame for a putative 8 kDa cysteine-rich protein (CRP). In this study, PMTV CRP was shown to be expressed in the course of virus infection, and a PMTV CRP-specific subgenomic RNA was mapped. CRP has previously been shown to be dispensable for infection of PMTV in Nicotiana benthamiana. In this study, PMTV CRP was found to increase the severity of disease symptoms when expressed from Potato virus X or Tobacco mosaic virus in N. benthamiana and Nicotiana tabacum, suggesting that the protein affects virulence of the virus or might suppress a host defence mechanism. However, PMTV CRP did not show RNA silencing suppression activity in three assays. Host responses to the PMTV CRP expression from different viral genomes ranged from an absence of response to extreme resistance at a single cell level and were dependent on the viral genome. These findings emphasized involvement of viral proteins and/or virus-induced cell components in the plant reaction to CRP. PMTV CRP was predicted to possess a transmembrane segment. CRP fused to the green fluorescent protein was associated with endoplasmic reticulum-derived membranes and induced dramatic rearrangements of the endoplasmic reticulum structure, which might account for protein functions as a virulence factor of the virus.
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Affiliation(s)
- N I Lukhovitskaya
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russian Federation
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences (SLU), Box 7080, SE-750 07 Uppsala, Sweden
| | - N E Yelina
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences (SLU), Box 7080, SE-750 07 Uppsala, Sweden
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russian Federation
| | - A A Zamyatnin
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences (SLU), Box 7080, SE-750 07 Uppsala, Sweden
| | - M V Schepetilnikov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russian Federation
| | - A G Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russian Federation
| | - M Sandgren
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences (SLU), Box 7080, SE-750 07 Uppsala, Sweden
| | - S Yu Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russian Federation
| | - J P T Valkonen
- Department of Applied Biology, University of Helsinki, Finland
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences (SLU), Box 7080, SE-750 07 Uppsala, Sweden
| | - E I Savenkov
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences (SLU), Box 7080, SE-750 07 Uppsala, Sweden
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Bragg JN, Jackson AO. The C-terminal region of the Barley stripe mosaic virusgammab protein participates in homologous interactions and is required for suppression of RNA silencing. MOLECULAR PLANT PATHOLOGY 2004; 5:465-481. [PMID: 20565621 DOI: 10.1111/j.1364-3703.2004.00246.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
SUMMARY The 17-kDa, cysteine-rich gammab protein of Barley stripe mosaic virus (BSMV) is a major contributor to viral pathogenesis, although it is dispensable for replication and movement in the ND 18 strain of the virus. Within the C-terminal region of gammab, six coiled-coil heptad repeats, structures known to mediate protein-protein interactions, are predicted between amino acids 95 and 140. In this study, we have demonstrated that gammab engages in homologous interactions and that the C-terminal 67 amino acids of the protein are required for these interactions. The gammab homologous interactions were abrogated by mutations designed to disrupt the coiled-coil motifs with substitutions of glycine residues for hydrophobic residues in the a and d positions of the heptads (gammabNC). Mutations within the gammabNC derivative were also found to destroy the silencing suppression activity of gammab in an Agrobacterium-mediated transient assay. Infectivity experiments to evaluate the gammabNC derivative revealed that this mutant developed symptoms 2 days earlier than the wild-type strain in Chenopodium amaranticolor. In barley, gammabNC elicited more severe bleaching and striping symptoms, similar to those of the previously described 'bleached' phenotype that is observed when mutations are introduced into the C1 and BM motifs. These findings collectively show that gammab interactions mediated by the coiled-coil motif are critical for the virulence and counter defence activities of BSMV in both monocot and dicot hosts.
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Affiliation(s)
- Jennifer N Bragg
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720, USA
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30
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Bragg JN, Lawrence DM, Jackson AO. The N-terminal 85 amino acids of the barley stripe mosaic virus gammab pathogenesis protein contain three zinc-binding motifs. J Virol 2004; 78:7379-91. [PMID: 15220411 PMCID: PMC434125 DOI: 10.1128/jvi.78.14.7379-7391.2004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Barley stripe mosaic virus RNAgamma encodes gammab, a cysteine-rich protein that affects pathogenesis. Nine of the eleven cysteines are concentrated in two clusters, designated C1 (residues 1 to 23) and C2 (residues 60 to 85), that are arranged in zinc finger-like motifs. A basic motif (BM) rich in lysine and arginine (residues 19 to 47) resides between the C1 and C2 clusters. We have demonstrated that gammab binds zinc and that the C1, BM, and C2 motifs have independent zinc-binding activities. To evaluate the requirements for binding, mutations were introduced into each region. Cysteine residues at positions 7, 9, 10, 19, and 23 in the C1 motif were replaced with serines. In the BM, asparagines were substituted for lysines at positions 26 and 35, glutamine for arginine at position 25, and glycines for arginines at positions 33 and 36. The C2 mutations included cysteine replacements with serines at positions 60, 64, 71, and 81, and a histidine-to-leucine change at position 85. These mutations destroyed zinc-binding activity in each of the isolated motifs. gammab derivatives containing mutations in only two of the motifs retained the ability to bind zinc, whereas a gammab derivative containing mutations inactivating all three motifs destroyed the ability to bind zinc. Plants inoculated with transcripts containing combinations of the C1, BM, and C2 mutations elicited a "null" phenotype in barley characteristic of gammab deletion mutants and also delayed the appearance and reduced the size of local lesions in Chenopodium amaranticolor. These results show that zinc binding of each of the motifs is critical for the biological activity of gammab.
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Affiliation(s)
- Jennifer N Bragg
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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31
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Galiakparov N, Tanne E, Mawassi M, Gafny R, Sela I. ORF 5 of grapevine virus A encodes a nucleic acid-binding protein and affects pathogenesis. Virus Genes 2003; 27:257-62. [PMID: 14618086 DOI: 10.1023/a:1026395815980] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A previous functional analysis of the genome of grapevine virus A (GVA) was not conclusive as to the role of open reading frame 5 (ORF 5). This ORF encodes a 10-kDa protein (p10) carrying two distinct domains: a basic, arginine-rich domain and a zinc-finger domain. P10 was cloned and expressed in Escherichia coli, and was shown by northwestern assays to interact with nucleic acids. In-frame deletion of the basic region abolished P10's nucleic acid-binding capability, whereas substitution of cysteine residues by serine in the zinc-finger domain did not affect binding. These mutations were inserted into the full-length infectious clone. It has been shown that ORF 5 mutations do not affect replication of GVA-RNA. However, plants inoculated with the aforementioned mutations did not develop symptoms, and Western blot analysis revealed markedly reduced expression of the movement protein (the product of ORF 3).
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Affiliation(s)
- Nurbol Galiakparov
- Agricultural Research Organization, The Volcani Center, Department of Virology, Tolkovski Laboratory, Bet Dagan 50250, Israel
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32
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Nicolaisen M, Nielsen SL. Analysis of the triple gene block and coat protein sequences of two strains of Kalanchoë latent carlavirus. Virus Genes 2001; 22:265-70. [PMID: 11450944 DOI: 10.1023/a:1011101904002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A region of the Kalanchoë latent carlavirus (KLV) genome, containing the coding capacity for the triple gene block and the coat protein, was cloned and sequenced for two isolates, the one infecting Chenopodium quinoa systemically whereas the other infects C. quinoa locally. The sequence confirmed the classification of KLV as a carlavirus. There was the highest identity in the amino acid sequences to the carlaviruses potato rough dwarf virus, lily latent virus, lily symptomless virus, blueberry scorch virus and potato virus S. The aminoacid sequences of proteins of the two KLV isolates had an identity between 86% and 91%.
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Affiliation(s)
- M Nicolaisen
- Department of Plant Protection, Research Centre Flakkebjerg, Danish Institute of Agricultural Sciences.
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33
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Dunoyer P, Herzog E, Hemmer O, Ritzenthaler C, Fritsch C. Peanut clump virus RNA-1-encoded P15 regulates viral RNA accumulation but is not abundant at viral RNA replication sites. J Virol 2001; 75:1941-8. [PMID: 11160693 PMCID: PMC115140 DOI: 10.1128/jvi.75.4.1941-1948.2001] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2000] [Accepted: 11/27/2000] [Indexed: 11/20/2022] Open
Abstract
RNA-1 of peanut clump pecluvirus (PCV) encodes N-terminally overlapping proteins which contain helicase-like (P131) and polymerase-like (P191) domains and is able to replicate in the absence of RNA-2 in protoplasts of tobacco BY-2 cells. RNA-1 also encodes P15, which is expressed via a subgenomic RNA. To investigate the role of P15, we analyzed RNA accumulation in tobacco BY-2 protoplasts inoculated with RNA-1 containing mutations in P15. For all the mutants, the amount of progeny RNA-1 produced was significantly lower than that obtained for wild-type RNA-1. If RNA-2 was included in the inoculum, the accumulation of both progeny RNAs was diminished, but near-normal yields of both could be recovered if the inoculum was supplemented with a small, chimeric viral replicon expressing P15, demonstrating that P15 has an effect on viral RNA accumulation. To further analyze the role of P15, transcripts were produced expressing P15 fused to enhanced green fluorescent protein (EGFP). Following inoculation to protoplasts, epifluorescence microscopy revealed that P15 accumulated as spots around the nucleus and in the cytoplasm. Intracellular sites of viral RNA synthesis were visualized by laser scanning confocal microscopy of infected protoplasts labeled with 5-bromouridine 5'-triphosphate (BrUTP). BrUTP labeling also occurred in spots distributed within the cytoplasm and around the nucleus. However, the BrUTP-labeled RNA and EGFP/P15 very rarely colocalized, suggesting that P15 does not act primarily at sites of viral replication but intervenes indirectly to control viral accumulation levels.
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Affiliation(s)
- P Dunoyer
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, 67084 Strasbourg Cedex, France
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34
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Tsai MS, Hsu YH, Lin NS. Bamboo mosaic potexvirus satellite RNA (satBaMV RNA)-encoded P20 protein preferentially binds to satBaMV RNA. J Virol 1999; 73:3032-9. [PMID: 10074153 PMCID: PMC104063 DOI: 10.1128/jvi.73.4.3032-3039.1999] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A satellite RNA of 836 nucleotides [excluding the poly(A) tail] depends on the bamboo mosaic potexvirus (BaMV) for its replication and encapsidation. The BaMV satellite RNA (satBaMV) contains a single open reading frame encoding a 20-kDa nonstructural protein (P20). The P20 protein with eight histidine residues at the C terminus was overexpressed in Escherichia coli. Experiments of gel retardation, UV cross-linking, and Northwestern hybridization demonstrated that purified P20 was a nucleic-acid-binding protein. The binding of P20 to nucleic acids was strong and highly cooperative. P20 preferred binding to satBaMV- or BaMV-related sequences rather than to nonrelated sequences. By deletion analysis, the P20 binding sites were mainly located at the 5' and 3' untranslated regions of satBaMV RNA, and the RNA-protein interactions could compete with the poly(G) and, less efficiently, with the poly(U) homopolymers. The N-terminal arginine-rich motif of P20 was the RNA binding domain, as shown by in-frame deletion analysis. This is the first report that a plant virus satellite RNA-encoded nonstructural protein preferentially binds with nucleic acids.
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Affiliation(s)
- M S Tsai
- Graduate Institute of Life Science, National Defence Medical Center, Taipei, Taiwan 100
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35
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Prüfer D, Kawchuk L, Monecke2 M, Nowok S, Fischer R, Rohde W. Immunological analysis of potato leafroll luteovirus (PLRV) P1 expression identifies a 25 kDa RNA-binding protein derived via P1 processing. Nucleic Acids Res 1999; 27:421-5. [PMID: 9862960 PMCID: PMC148195 DOI: 10.1093/nar/27.2.421] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mono- and polyclonal antibodies directed against different domains of the potato leafroll luteovirus (PLRV) P1 (ORF1) protein were applied to the analysis of P1 expression during PLRV replication in planta. Western analyses detected P1 and a protein of approximately 25 kDa (P1-C25) that accumulated to readily detectable amounts in PLRV-infected plants, but was not detected by in vitro cell-free translation of P1. P1-C25 represents the C-terminus of P1 and is a proteolytic cleavage product produced during P1 processing. On the basis of its molecular weight, the N-terminus of P1-C25 is either identical to or located adjacent to the previously identified PLRV genome-linked protein, VPg. P1-C25 is not associated with virus particles, and subcellular localization experiments detected P1-C25, but not P1, in the membrane and cytoplasmic fractions of PLRV-infected cells. In addition, P1-C25 exhibits nucleic acid-binding properties. On the basis of its biosynthesis, localization and biochemical properties, P1-C25 may facilitate the formation of P1/PLRV RNA complexes in which the spatial proximity allows for covalent bond formation between PLRV RNA and VPg.
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Affiliation(s)
- D Prüfer
- Max-Planck-Institut für Züchtungsforschung, Carl-von-Linné Weg 10, 50829 Köln, Germany.
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36
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López C, Ayllón MA, Navas-Castillo J, Guerri J, Moreno P, Flores R. Molecular variability of the 5'- and 3'-terminal regions of citrus tristeza virus RNA. PHYTOPATHOLOGY 1998; 88:685-691. [PMID: 18944941 DOI: 10.1094/phyto.1998.88.7.685] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Isolates of citrus tristeza virus (CTV) differ widely in their biological properties. These properties may depend on the structure of viral RNA populations comprising the different isolates. As a first approach to study the molecular basis of the biological variability, we have compared the sequences of multiple cDNA clones of the two terminal regions of the RNA from different CTV isolates. The polymorphism of the 5' untranslated region (UTR) allowed the classification of the sequences into three groups, with intragroup sequence identity higher than 88% and intergroup sequence identity as low as 44%. The variability of an open reading frame (ORF) 1a segment adjacent to the 5' UTR supports the same grouping. Some CTV isolates contained sequences of more than one group. Most sequences from Spanish isolates belonged to group III, whereas a Japanese isolate was composed mostly of sequences of groups I and II. The mildest isolates contained only sequences of group III, whereas the most severe isolates also contained sequences of groups I, II, or both. The most stable secondary structure predicted for the 5' UTR was composed of two stem-loops and remained essentially unchanged as a result of compensatory mutations in the stems and accommodation of most of the variability in the loops. In contrast to the 5'-terminal region, the variability of the 3'-terminal region of CTV RNA was very much restricted, with nucleotide identity values higher than 90%. The presence of a conserved putative "zinc-finger" domain adjacent to a basic region in p23, the predicted product of ORF 11, suggests that this protein might act as a regulatory factor during virus replication.
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37
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Xu H, Li Y, Mao Z, Li Y, Wu Z, Qu L, An C, Ming X, Schiemann J, Casper R, Chen Z. Rice dwarf phytoreovirus segment S11 encodes a nucleic acid binding protein. Virology 1998; 240:267-72. [PMID: 9454700 DOI: 10.1006/viro.1997.8945] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The function of rice dwarf virus segment 11 and the corresponding segments of other phytoreoviruses is not yet determined. The amino acid sequence of Pns11, encoded by segment 11, contains a putative zinc finger and five flanking basic regions at the C-terminus. The full-length Pns11 protein and three truncated derivatives, which lack the N-terminus, the zinc-finger or the C-terminal five basic regions were expressed in Escherichia coli and their nucleic acid binding properties were studied. Pns11 interacts with single- and double-stranded forms of DNA and RNA in a sequence-nonspecific manner. The truncated derivative which contains both the zinc-finger and the C-terminal basic regions has the same binding properties as the full-length Pns11. However, removal of either of these domains prevents binding activity. The binding activity of Pns11 was drastically reduced when the blots were treated with a high concentration of EDTA. Moreover, Pns11 extracted from infected rice also binds to single-stranded RNA. These data suggest that RDV Pns11 binding activity is structure-dependent and it may play an important role in virus replication and/or genome assortment.
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Affiliation(s)
- H Xu
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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38
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Ashoub A, Rohde W, Prüfer D. In planta transcription of a second subgenomic RNA increases the complexity of the subgroup 2 luteovirus genome. Nucleic Acids Res 1998; 26:420-6. [PMID: 9421494 PMCID: PMC147298 DOI: 10.1093/nar/26.2.420] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The genetic information of potato leafroll virus (PLRV), a typical member of the subgroup 2 luteoviruses, is contained in a single-stranded (+) sense RNA of approximately 5.9 kb. A single subgenomic RNA (sgRNA1) of approximately 2.3 kb has been characterized as the mRNA for the 3' clustered viral open reading frames ORF3, ORF3/5 and ORF4. Here we demonstrate by Northern blot analyses of polysomal RNAs from PLRV-infected Solanum tuberosum and Physalis floridana plants that, as with luteoviruses belonging to subgroup 1, in planta synthesis of a second 0.8 kb subgenomic RNA (sgRNA2) increases the complexity of subgroup 2 luteoviral genomes significantly. PLRV-specific hybridization probes as well as primer extension experiments map sgRNA2 to the 3'-end of the PLRV RNA genome (positions 5190-5987). Similarly, for the closely related cucurbit aphid-borne yellows virus (CABYV) a sgRNA2 of similar size and position (positions 4888-5669) was identified. PLRV sgRNA2 may code for two viral proteins of 7.1 (ORF6) and 14 kDa (ORF7) respectively, while the CABYV proteins are 8.7 (ORF6) and 8.3 kDa (ORF7) in size, with PLRV ORF7 displaying nucleic acid binding activity. In vivo experiments by transient expression of chimeric GUS fusions in potato protoplasts demonstrated that sgRNA2 functions as a bicistronic mRNA with high expression of ORF6 and low translational efficiency for synthesis of ORF7.
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Affiliation(s)
- A Ashoub
- Max-Planck-Institut für Züchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Köln, Germany
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39
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Cavileer TD, Clarke RC, Corsini DL, Berger PH. A New Strain of Potato Carlavirus M. PLANT DISEASE 1998; 82:98-102. [PMID: 30857078 DOI: 10.1094/pdis.1998.82.1.98] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In 1994, potato samples for certification from Idaho seed fields reacted in enzyme-linked immunosorbent assay (ELISA) tests to a polyclonal potato carlavirus M (PVM) antiserum. Sample affinity to the antiserum was lower than control samples. Furthermore, ELISA-positive samples were obtained from both symptomatic as well as asymptomatic plants. A complementary DNA library was prepared using both reverse transcription-polymerase chain reaction and primers based on published PVM sequences, or oligo d(T) primed reverse transcribed sequences. The nucleotide sequence was determined for the 3'-terminus of the genome. Putative coat protein amino acid sequence was compared to published PVM and potato virus S coat protein sequences. While this new isolate is likely a strain of PVM, it is significantly different from known PVM coat protein sequences in the amino terminus region. These differences may explain the poor reactivity to other PVM antisera and suggest that it is a new strain of PVM, which we have designated PVM-ID.
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Affiliation(s)
- T D Cavileer
- Department of Plant, Soil, and Entomological Sciences, University of Idaho, Moscow, ID 83844-2339
| | - R C Clarke
- formerly with Idaho Crop Improvement Association, Idaho Falls, ID 83405-1139
| | | | - P H Berger
- Department of Plant, Soil, and Entomological Sciences, University of Idaho
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40
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Kalinina NO, Fedorkin ON, Samuilova OV, Maiss E, Korpela T, Atabekov JG. Expression and biochemical analyses of the recombinant potato virus X 25K movement protein. FEBS Lett 1996; 397:75-8. [PMID: 8941717 DOI: 10.1016/s0014-5793(96)01138-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The 25K movement protein (MP) of potato virus X (PVX) is encoded by the 5'-proximal gene of three overlapping MP genes forming a 'triple gene block'. The PVX 25K MP (putative NTPase-helicase) has been synthesized in Escherichia coli as a recombinant containing a six-histidine tag at the amino terminus. The His-tagged 25K protein was purified in a one-column Ni-chelate affinity chromatography procedure. In the absence of any other viral factors, this protein had obvious Mg2+-dependent ATPase activity, which was stimulated slightly (1.7-1.9-fold) by various polynucleotides. Like other viral proteins possessing ATPase-helicase motifs and many plant viral movement proteins, the PVX 25K MP was able to bind nucleic acids in vitro. The RNA binding activity of the 25K MP was pronounced only at very low salt concentrations and was independent of its ATPase activity.
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Affiliation(s)
- N O Kalinina
- Department of Virology of Moscow State University, Russian Federation
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41
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Maia IG, Séron K, Haenni AL, Bernardi F. Gene expression from viral RNA genomes. PLANT MOLECULAR BIOLOGY 1996; 32:367-391. [PMID: 8980488 DOI: 10.1007/bf00039391] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
This review is centered on the major strategies used by plant RNA viruses to produce the proteins required for virus multiplication. The strategies at the level of transcription presented here are synthesis of mRNA or subgenomic RNAs from viral RNA templates, and 'cap-snatching'. At the level of translation, several strategies have been evolved by viruses at the steps of initiation, elongation and termination. At the initiation step, the classical scanning mode is the most frequent strategy employed by viruses; however in a vast number of cases, leaky scanning of the initiation complex allows expression of more than one protein from the same RNA sequence. During elongation, frameshift allows the formation of two proteins differing in their carboxy terminus. At the termination step, suppression of termination produces a protein with an elongated carboxy terminus. The last strategy that will be described is co- and/or post-translational cleavage of a polyprotein precursor by virally encoded proteinases. Most (+)-stranded RNA viruses utilize a combination of various strategies.
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Affiliation(s)
- I G Maia
- Institut Jacques Monod, Paris, France
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42
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Sung YK, Coutts RH. Potato yellow mosaic geminivirus AC2 protein is a sequence non-specific DNA binding protein. FEBS Lett 1996; 383:51-4. [PMID: 8612789 DOI: 10.1016/0014-5793(96)00217-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The AC2 protein of potato yellow mosaic geminivirus (PYMV) is by analogy with related geminiviruses thought to be a transcriptional activator protein. We have over-expressed the AC2 open reading frame in E. coli and purified the protein from bacterial extracts to near homogeneity. We have studied the interaction of the AC2 protein with DNA and from gel retardation assays shown that it binds both double-stranded (ds) and single-stranded (ss) DNA non-specifically. The binding to PYMV intergenic region ds DNA appeared to be independent of the presence of zinc ions and did not require the protein to be phosphorylated.
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Affiliation(s)
- Y K Sung
- Biology Department, Imperial College of Science, Technology and Medicine, London, UK
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43
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Gramstat A, Prüfer D, Rohde W. The nucleic acid-binding zinc finger protein of potato virus M is translated by internal initiation as well as by ribosomal frameshifting involving a shifty stop codon and a novel mechanism of P-site slippage. Nucleic Acids Res 1994; 22:3911-7. [PMID: 7937111 PMCID: PMC308388 DOI: 10.1093/nar/22.19.3911] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The genes for the capsid protein CP and the nucleic acid-binding 12K protein (pr12) of potato virus M (PVM) constitute the 3' terminal gene cluster of the PVM RNA genome. Both proteins are presumably translated from a single subgenomic RNA. We have identified two translational strategies operating in pr12 gene expression. Internal initiation at the first and the second AUG codon of the pr12 coding sequence results in the synthesis of the 12K protein. In addition the protein is produced as a CP/12K transframe protein by ribosomal frameshifting. For these studies parts of the CP and pr12 coding sequences including the putative frameshift region were introduced into an internal position of the beta-glucuronidase gene. Mutational analyses in conjunction with in vitro translation experiments identified a homopolymeric string of four adenosine nucleotides which together with a 3' flanking UGA stop codon were required for efficient frameshifting. The signal AAAAUGA is the first frameshift signal with a shifty stop codon to be analyzed in the eukaryotic system. Substitution of the four consecutive adenosine nucleotides by UUUU increased the efficiency of frameshifting, while substitution by GGGG or CCCC dramatically reduced the synthesis of the transframe protein. Also, UAA and UAG could replace the opal stop codon without effect on the frameshifting event, but mutation of UGA to the sense codon UGG inhibited transframe protein formation. These findings suggest that the mechanism of ribosomal frameshifting at the PVM signal is different from the one described by the 'simultaneous slippage' model in that only the string of four adenosine nucleotides represents the slippery sequence involved in a -1 P-site slippage.
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Affiliation(s)
- A Gramstat
- Max-Planck-Institut für Züchtungsforschung, Köln, Germany
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44
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Minafra A, Saldarelli P, Grieco F, Martelli GP. Nucleotide sequence of the 3' terminal region of the RNA of two filamentous grapevine viruses. Arch Virol 1994; 137:249-61. [PMID: 7944948 DOI: 10.1007/bf01309473] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The 3' terminal region of grapevine virus A (GVA) and grapevine virus B (GVB), encompassing 1883 and 2136 nucleotides, respectively, was sequenced by the deoxynucleotide chain termination method. Three putative open reading frames (ORF) were identified in both genomic viral RNAs, denoted 1 to 3 in the 5' to 3' direction. ORF 1 encoded a polypeptide with estimated M(r) of 31 kDa (GVA) and 36.5 kDa (GVB), possessing the G/D motif of the "30 K superfamily" movement proteins, and showing good alignments with putative movement proteins of trichoviruses and capilloviruses. ORF 2 was identified as the coat protein (CP) cistron, coding for polypeptides with an estimated M(r) of 21.5 kDa (GVA) and 21.6 kDa (GVB). These CPs showed substantial sequence homology with one another and with CPs of tricho- and capilloviruses, but not of closteroviruses. ORF 3 potentially coded for two small polypeptides with estimated M(r) of 10 kDa (GVA) and 14 kDa (GVB). The ORF 3 product of GVB (14 K), but not that of GVA, shared some homology with the 3' terminal polypeptides of different plant viruses that exhibit the "zinc finger domain" of proteins with nucleic acid-binding properties. GVA and GVB have many properties in common with trichoviruses but possess an extra open reading frame (ORF 3). Whether this finding may have a bearing on the classification of these viruses is unclear. However, until the taxonomic significance of this difference in genome structure is established, it seems plausible to include GVA and GVB as tentative species in the Trichovirus genus.
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Affiliation(s)
- A Minafra
- Dipartimento di Protezione delle Piante, Università degli Studi, Bari, Italy
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45
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Abstract
The sequence of 1346 nucleotides of the 3'-terminal region of an ordinary strain of potato virus S was determined from cloned cDNA. This portion of the viral RNA contains two major open reading frames (ORFs), encoding the coat protein of M(r)33K and a protein of M(r)11K 3' to the coat protein, both of which showed high homology, 93% and 79%, respectively, with the equivalent proteins of the Andean strain. A major block of amino acids that differ between the ordinary and Andean strains was present in both the coat protein and the 11K. These blocks may be responsible for the substantial differences between the ordinary and Andean strains at the symptom and aphid transmissibility levels.
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Affiliation(s)
- G D Foster
- Botany Department, University of Leicester, UK
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46
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Prüfer D, Tacke E, Schmitz J, Kull B, Kaufmann A, Rohde W. Ribosomal frameshifting in plants: a novel signal directs the -1 frameshift in the synthesis of the putative viral replicase of potato leafroll luteovirus. EMBO J 1992. [PMID: 1547775 PMCID: PMC556553 DOI: 10.1002/j.1460-2075.1992.tb05151.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The 5.8 kb RNA genome of potato leafroll luteovirus (PLRV) contains two overlapping open reading frames, ORF2a and ORF2b, which are characterized by helicase and RNA polymerase motifs, respectively, and possibly represent the viral replicase. Within the overlap, ORF2b lacks an AUG translational start codon and is therefore presumably translated by -1 ribosomal frameshifting as a transframe protein with ORF2a. This hypothesis was studied by introducing the putative frameshift region into an internal position of the beta-glucuronidase (GUS) gene and testing for the occurrence of frameshifting in vivo by transient expression of GUS activity in potato protoplasts as well as in vitro by translation in the reticulocyte system. Both experimental approaches demonstrate that a -1 frameshift occurs at a frequency of approximately 1%. Site-directed mutagenesis identified the frameshift region and the involvement of the novel heptanucleotide motif UUUAAAU in conjunction with an adjacent stem-loop structure. Part of this stem-loop encodes a basic region in the ORF2b moiety of the transframe protein which was shown by binding experiments with PLRV RNA to represent a nucleic acid-binding domain. These data support a possible biological significance of the frameshift to occur at this position of the large overlap by including the putative RNA template-binding site of the PLRV replicase in the ORF2a/ORF2b transframe protein.
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Affiliation(s)
- D Prüfer
- Max-Planck-Institut für Züchtungsforschung, Köln, FRG
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Affiliation(s)
- G D Foster
- Botany Department, University of Leicester, UK
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