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Farzadfar S, Pourrahim R. Positive selection and recombination shaped the large genetic differentiation of Beet black scorch virus population. PLoS One 2019; 14:e0215574. [PMID: 31022219 PMCID: PMC6483173 DOI: 10.1371/journal.pone.0215574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 04/05/2019] [Indexed: 01/01/2023] Open
Abstract
Beet black scorch virus (BBSV) is a species in the Betanecrovirus genus, in family Tombusviridae. BBSV infection is of considerable importance, causing economic losses to sugar beet (Beta vulgaris) field crops worldwide. Phylogenetic analyses using 3'UTR sequences divided most BBSV isolates into two main groups. Group I is composed of Iranian isolates from all Iranian provinces that have been sampled. Chinese, European, one North American and some other Iranian isolates from North-Western Iran are in Group II. The division of Iranian BBSV isolates into two groups suggests numerous independent infection events have occurred in Iran, possibly from isolated sources from unknown host(s) linked through the viral vector Olpidium. The between-group diversity was higher than the within-group diversity, indicating the role of a founder effect in the diversification of BBSV isolates. The high FST among BBSV populations differentiates BBSV groups. We found no indication of frequent gene flow between populations in Mid-Eurasia, East-Asia and Europe countries. Recombination analysis indicated an intra-recombination event in the Chinese Xinjiang/m81 isolate and an inter-recombination breakpoint in the viral 3'UTR of Iranian isolates in subgroup IranA in Group I. The ω ratios (dNS/dS) were used for detecting positive selection at individual codon sites. Amino acid sequences were conserved with ω from 0.040 to 0.229 in various proteins. In addition, a small fraction of amino acids in proteins RT-ORF1 (p82), ORF4 (p7b) and ORF6 (p24) are positively selected with ω > 1. This analysis could increase the understanding of protein structure and function and Betanecrovirus epidemiology. The recombination analysis shows that genomic exchanges are associated with the emergence of new BBSV strains. Such recombinational exchange analysis may provide new information about the evolution of Betanecrovirus diversity.
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Affiliation(s)
- Shirin Farzadfar
- Plant Virus Research Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
- * E-mail:
| | - Reza Pourrahim
- Plant Virus Research Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
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Wang X, Cao X, Liu M, Zhang R, Zhang X, Gao Z, Zhao X, Xu K, Li D, Zhang Y. Hsc70-2 is required for Beet black scorch virus infection through interaction with replication and capsid proteins. Sci Rep 2018; 8:4526. [PMID: 29540800 PMCID: PMC5852052 DOI: 10.1038/s41598-018-22778-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 02/27/2018] [Indexed: 11/09/2022] Open
Abstract
Dissecting the complex molecular interplay between the host plant and invading virus improves our understanding of the mechanisms underlying viral pathogenesis. In this study, immunoprecipitation together with the mass spectrometry analysis revealed that the heat shock protein 70 (Hsp70) family homolog, Hsc70-2, was co-purified with beet black scorch virus (BBSV) replication protein p23 and coat protein (CP), respectively. Further experiments demonstrated that Hsc70-2 interacts directly with both p23 and CP, whereas there is no interaction between p23 and CP. Hsc70-2 expression is induced slightly during BBSV infection of Nicotiana benthamiana, and overexpression of Hsc70-2 promotes BBSV accumulation, while knockdown of Hsc70-2 in N. benthamiana leads to drastic reduction of BBSV accumulation. Infection experiments revealed that CP negatively regulates BBSV replication, which can be mitigated by overexpression of Hsc70-2. Further experiments indicate that CP impairs the interaction between Hsc70-2 and p23 in a dose-dependent manner. Altogether, we provide evidence that besides specific functions of Hsp70 family proteins in certain aspects of viral infection, they can serve as a mediator for the orchestration of virus infection by interacting with different viral components. Our results provide new insight into the role of Hsp70 family proteins in virus infection.
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Affiliation(s)
- Xiaoling Wang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, P. R. China
| | - Xiuling Cao
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, P. R. China
| | - Min Liu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, P. R. China
| | - Ruiqi Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, P. R. China
| | - Xin Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, P. R. China
| | - Zongyu Gao
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, P. R. China
| | - Xiaofei Zhao
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, P. R. China
| | - Kai Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, P. R. China
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, P. R. China
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, P. R. China.
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Jin X, Cao X, Wang X, Jiang J, Wan J, Laliberté JF, Zhang Y. Three-Dimensional Architecture and Biogenesis of Membrane Structures Associated with Plant Virus Replication. FRONTIERS IN PLANT SCIENCE 2018; 9:57. [PMID: 29441085 PMCID: PMC5797596 DOI: 10.3389/fpls.2018.00057] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/11/2018] [Indexed: 05/20/2023]
Abstract
Positive-sense (+) RNA viruses represent the most abundant group of viruses and are dependent on the host cell machinery to replicate. One remarkable feature that occurs after (+) RNA virus entry into cells is the remodeling of host endomembranes, leading to the formation of viral replication factories. Recently, rapid progress in three-dimensional (3D) imaging technologies, such as electron tomography (ET) and focused ion beam-scanning electron microscopy (FIB-SEM), has enabled researchers to visualize the novel membrane structures induced by viruses at high resolution. These 3D imaging technologies provide new mechanistic insights into the viral infection cycle. In this review, we summarize the latest reports on the cellular remodeling that occurs during plant virus infection; in particular, we focus on studies that provide 3D architectural information on viral replication factories. We also outline the mechanisms underlying the formation of these membranous structures and discuss possible future research directions.
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Affiliation(s)
- Xuejiao Jin
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiuling Cao
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xueting Wang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jun Jiang
- Institut National de la Recherche Scientifique—Institut Armand-Frappier, Laval, QC, Canada
| | - Juan Wan
- Institut National de la Recherche Scientifique—Institut Armand-Frappier, Laval, QC, Canada
| | - Jean-François Laliberté
- Institut National de la Recherche Scientifique—Institut Armand-Frappier, Laval, QC, Canada
- *Correspondence: Jean-François Laliberté
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
- Yongliang Zhang
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Atypical RNA Elements Modulate Translational Readthrough in Tobacco Necrosis Virus D. J Virol 2017; 91:JVI.02443-16. [PMID: 28148800 DOI: 10.1128/jvi.02443-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/27/2017] [Indexed: 12/13/2022] Open
Abstract
Tobacco necrosis virus, strain D (TNV-D), is a positive-strand RNA virus in the genus Betanecrovirus and family Tombusviridae The production of its RNA-dependent RNA polymerase, p82, is achieved by translational readthrough. This process is stimulated by an RNA structure that is positioned immediately downstream of the recoding site, termed the readthrough stem-loop (RTSL), and a sequence in the 3' untranslated region of the TNV-D genome, called the distal readthrough element (DRTE). Notably, a base pairing interaction between the RTSL and the DRTE, spanning ∼3,000 nucleotides, is required for enhancement of readthrough. Here, some of the structural features of the RTSL, as well as RNA sequences and structures that flank either the RTSL or DRTE, were investigated for their involvement in translational readthrough and virus infectivity. The results revealed that (i) the RTSL-DRTE interaction cannot be functionally replaced by stabilizing the RTSL structure, (ii) a novel tertiary RNA structure positioned just 3' to the RTSL is required for optimal translational readthrough and virus infectivity, and (iii) these same activities also rely on an RNA stem-loop located immediately upstream of the DRTE. Functional counterparts for the RTSL-proximal structure may also be present in other tombusvirids. The identification of additional distinct RNA structures that modulate readthrough suggests that regulation of this process by genomic features may be more complex than previously appreciated. Possible roles for these novel RNA elements are discussed.IMPORTANCE The analysis of factors that affect recoding events in viruses is leading to an ever more complex picture of this important process. In this study, two new atypical RNA elements were shown to contribute to efficient translational readthrough of the TNV-D polymerase and to mediate robust viral genome accumulation in infections. One of the structures, located close to the recoding site, could have functional equivalents in related genera, while the other structure, positioned 3' proximally in the viral genome, is likely limited to betanecroviruses. Irrespective of their prevalence, the identification of these novel RNA elements adds to the current repertoire of viral genome-based modulators of translational readthrough and provides a notable example of the complexity of regulation of this process.
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Xu J, Liu D, Zhang Y, Wang Y, Han C, Li D, Yu JL, Wang XB. Improved Pathogenicity of a Beet Black Scorch Virus Variant by Low Temperature and Co-infection with Its Satellite RNA. Front Microbiol 2016; 7:1771. [PMID: 27867378 PMCID: PMC5095503 DOI: 10.3389/fmicb.2016.01771] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/21/2016] [Indexed: 01/26/2023] Open
Abstract
Co-infection of none-coding satellite RNAs (sat-RNAs) usually inhibits replication and attenuates disease symptoms of helper viruses. However, we find that the sat-RNA of Beet black scorch virus (BBSV) and low temperature (18°C) additively enhance the systemic infection of BBSV in Nicotiana benthamiana. Northern blotting hybridization revealed a relatively reduced accumulation of BBSV-derived small interfering RNAs (siRNAs) in presence of sat-RNA as compared to that of BBSV alone. Cloning and sequencing of total small RNAs showed that more than 50% of the total small RNAs sequenced from BBSV-infected plants were BBSV-siRNAs, whereas the abundance of sat-siRNAs were higher than BBSV-siRNAs in the sat-RNA co-infected plants, indicating that the sat-RNA occupies most of the silencing components and possibly relieves the RNA silencing-mediated defense against BBSV. Interestingly, the 5' termini of siRNAs derived from BBSV and sat-RNA were dominated by Uridines (U) and Adenines (A), respectively. Besides, the infection of BBSV alone and with sat-RNA induce down-regulation of miR168 and miR403, respectively, which leads to high accumulation of their targets, Argonaute 1 (AGO1) and AGO2. Our work reveals the profiles of siRNAs of BBSV and sat-RNA and provides an additional clue to investigate the complicated interaction between the helper virus and sat-RNA.
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Affiliation(s)
- Jin Xu
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural SciencesBeijing, China
| | - Deshui Liu
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
| | - Ying Wang
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
| | - Chenggui Han
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
| | - Jia-Lin Yu
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
| | - Xian-Bing Wang
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
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Zhao X, Wang X, Dong K, Zhang Y, Hu Y, Zhang X, Chen Y, Wang X, Han C, Yu J, Li D. Phosphorylation of Beet black scorch virus coat protein by PKA is required for assembly and stability of virus particles. Sci Rep 2015; 5:11585. [PMID: 26108567 PMCID: PMC4479801 DOI: 10.1038/srep11585] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/20/2015] [Indexed: 12/22/2022] Open
Abstract
Plant virus coat proteins (CPs) play a fundamental role in protection of genomic RNAs, virion assembly, and viral movement. Although phosphorylation of several CPs during virus infection have been reported, little information is available about CP phosphorylation of the spherical RNA plant viruses. Here, we demonstrate that the CP of Beet black scorch virus (BBSV), a member of the genus Necrovirus, can be phosphorylated at threonine-41 (T41) by cAMP-dependent protein kinase (PKA)-like kinase in vivo and in vitro. Mutant viruses containing a T41A non-phosphorylatable alanine substitution, and a T41E glutamic acid substitution to mimic threonine phosphorylation were able to replicate but were unable to move systemically in Nicotiana benthamiana. Interestingly, the T41A and T41E mutants generated unstable 17 nm virus-like particles that failed to package viral genomic (g) RNA, compared with wild-type BBSV with 30 nm virions during viral infection in N. benthamiana. Further analyses showed that the T41 mutations had little effect on the gRNA-binding activity of the CP. Therefore, we propose a model whereby CP phosphorylation plays an essential role in long-distance movement of BBSV that involves formation of stable virions.
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Affiliation(s)
- Xiaofei Zhao
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoling Wang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Kai Dong
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yue Hu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xin Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xianbing Wang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Chenggui Han
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jialin Yu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Cao X, Jin X, Zhang X, Li Y, Wang C, Wang X, Hong J, Wang X, Li D, Zhang Y. Morphogenesis of Endoplasmic Reticulum Membrane-Invaginated Vesicles during Beet Black Scorch Virus Infection: Role of Auxiliary Replication Protein and New Implications of Three-Dimensional Architecture. J Virol 2015; 89:6184-95. [PMID: 25833056 PMCID: PMC4474299 DOI: 10.1128/jvi.00401-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/25/2015] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED All well-characterized positive-strand RNA viruses[(+)RNA viruses] induce the formation of host membrane-bound viral replication complexes (VRCs), yet the underlying mechanism and machinery for VRC formation remain elusive. We report here the biogenesis and topology of the Beet black scorch virus (BBSV) replication complex. Distinct cytopathological changes typical of endoplasmic reticulum (ER) aggregation and vesiculation were observed in BBSV-infected Nicotiana benthamiana cells. Immunogold labeling of the auxiliary replication protein p23 and double-stranded RNA (dsRNA) revealed that the ER-derived membranous spherules provide the site for BBSV replication. Further studies indicated that p23 plays a crucial role in mediating the ER rearrangement. Three-dimensional electron tomographic analysis revealed the formation of multiple ER-originated vesicle packets. Each vesicle packet enclosed a few to hundreds of independent spherules that were invaginations of the ER membranes into the lumen. Strikingly, these vesicle packets were connected to each other via tubules, a rearrangement event that is rare among other virus-induced membrane reorganizations. Fibrillar contents within the spherules were also reconstructed by electron tomography, which showed diverse structures. Our results provide the first, to our knowledge, three-dimensional ultrastructural analysis of membrane-bound VRCs of a plant (+)RNA virus and should help to achieve a better mechanistic understanding of the organization and microenvironment of plant (+)RNA virus replication complexes. IMPORTANCE Assembly of virus replication complexes for all known positive-strand RNA viruses depends on the extensive remodeling of host intracellular membranes. Beet black scorch virus, a necrovirus in the family Tombusviridae, invaginates the endoplasmic reticulum (ER) membranes to form spherules in infected cells. Double-stranded RNAs, the viral replication intermediate, and the viral auxiliary replication protein p23 are all localized within such viral spherules, indicating that these are the sites for generating progeny viral RNAs. Furthermore, the BBSV p23 protein could to some extent reorganize the ER when transiently expressed in N. benthamiana. Electron tomographic analysis resolves the three-dimensional (3D) architecture of such spherules, which are connected to the cytoplasm via a neck-like structure. Strikingly, different numbers of spherules are enclosed in ER-originated vesicle packets that are connected to each other via tubule-like structures. Our results have significant implications for further understanding the mechanisms underlying the replication of positive-strand RNA viruses.
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Affiliation(s)
- Xiuling Cao
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Xuejiao Jin
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Xiaofeng Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Ying Li
- Branch of China National Center for Protein Sciences, Tsinghua University, Beijing, People's Republic of China
| | - Chunyan Wang
- Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Xianbing Wang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Jian Hong
- Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiaofeng Wang
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech University, Blacksburg, Virginia, USA
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
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Zhang X, Zhao X, Zhang Y, Niu S, Qu F, Zhang Y, Han C, Yu J, Li D. N-terminal basic amino acid residues of Beet black scorch virus capsid protein play a critical role in virion assembly and systemic movement. Virol J 2013; 10:200. [PMID: 23786675 PMCID: PMC3691604 DOI: 10.1186/1743-422x-10-200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/07/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Beet black scorch virus (BBSV) is a small single-stranded, positive-sense RNA plant virus belonging to the genus Necrovirus, family Tombusviridae. Its capsid protein (CP) contains a 13 amino acid long basic region at the N-terminus, rich in arginine and lysine residues, which is thought to interact with viral RNA to initiate virion assembly. RESULTS In the current study, a series of BBSV mutants containing amino acid substitutions as well as deletions within the N-terminal region were generated and examined for their effects on viral RNA replication, virion assembly, and long distance spread in protoplasts and whole host plants of BBSV. The RNA-binding activities of the mutated CPs were also evaluated in vitro. These experiments allowed us to identify two key basic amino acid residues in this region that are responsible for initiating virus assembly through RNA-binding. Proper assembly of BBSV particles is in turn needed for efficient viral systemic movement. CONCLUSIONS We have identified two basic amino acid residues near the N-terminus of the BBSV CP that bind viral RNA with high affinity to initiate virion assembly. We further provide evidence showing that systemic spread of BBSV in infected plants requires intact virions. This study represents the first in-depth investigation of the role of basic amino acid residues within the N-terminus of a necroviral CP.
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Affiliation(s)
- Xiaofeng Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster OH 44691, USA
| | - Xiaofei Zhao
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yanjing Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shaofang Niu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Feng Qu
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster OH 44691, USA
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Chenggui Han
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jialin Yu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Choi H, Cho WK, Yu J, Lee JS, Kim KH. Highly Specific Detection of Five Exotic Quarantine Plant Viruses using RT-PCR. THE PLANT PATHOLOGY JOURNAL 2013; 29:99-104. [PMID: 25288934 PMCID: PMC4174791 DOI: 10.5423/ppj.nt.09.2012.0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 10/03/2012] [Accepted: 10/03/2012] [Indexed: 06/03/2023]
Abstract
To detect five plant viruses (Beet black scorch virus, Beet necrotic yellow vein virus, Eggplant mottled dwarf virus, Pelargonium zonate spot virus, and Rice yellow mottle virus) for quarantine purposes, we designed 15 RT-PCR primer sets. Primer design was based on the nucleotide sequence of the coat protein gene, which is highly conserved within species. All but one primer set successfully amplified the targets, and gradient PCRs indicated that the optimal temperature for the 14 useful primer sets was 51.9°C. Some primer sets worked well regardless of annealing temperature while others required a very specific annealing temperature. A primer specificity test using plant total RNAs and cDNAs of other plant virus-infected samples demonstrated that the designed primer sets were highly specific and generated reproducible results. The newly developed RT-PCR primer sets would be useful for quarantine inspections aimed at preventing the entry of exotic plant viruses into Korea.
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Affiliation(s)
- Hoseong Choi
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Won Kyong Cho
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Jisuk Yu
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Jong-Seung Lee
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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Pu H, Li J, Li D, Han C, Yu J. Identification of an internal RNA element essential for replication and translational enhancement of tobacco necrosis virus A(C). PLoS One 2013; 8:e57938. [PMID: 23460916 PMCID: PMC3583896 DOI: 10.1371/journal.pone.0057938] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 01/30/2013] [Indexed: 12/28/2022] Open
Abstract
Different regulatory elements function are involved in plant virus gene expression and replication by long-distance RNA-RNA interactions. A cap-independent functional element of the Barley yellow dwarf virus (BYDV) - like translational enhancer (BTE) is present in Tobacco necrosis virus A (TNV-A), a Necrovirus member in the Tombusviridae family. In this paper, an RNA stretch flanking the 5' proximal end of the TNV-A(C) coat protein (CP) gene was shown to be essential for viral replication in Chenopodium amaranticolor plants and tobacco cells. This internal sequence functioned in transient expression of β-glucuronidase (GUS) when present at either the 5' or 3' sides of the GUS open reading frame. Serial deletion analyses revealed that nine nucleotides from nt 2609 to 2617 (-3 to +6 of the CP initiation site) within TNV-A(C) RNA are indispensable for viral replication in whole plants and tobacco cells. Fusion of this RNA element in mRNAs translated in tobacco cells resulted in a remarkable enhancement of luciferase expression from in vitro synthesised chimaeric RNAs or DNA expression vectors. Interestingly, the element also exhibited increased translational activity when fused downstream of the reporter genes, although the efficiency was lower than with upstream fusions. These results provide evidence that an internal RNA element in the genomic (g) RNA of TNV-A(C), ranging approximately from nt 2543 to 2617, plays a bifunctional role in viral replication and translation enhancement during infection, and that this element may use novel strategies differing from those previously reported for other viruses.
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Affiliation(s)
- Heng Pu
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiang Li
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dawei Li
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chenggui Han
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jialin Yu
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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11
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Xu J, Wang X, Shi L, Zhou Y, Li D, Han C, Zhang Z, Yu J. Two distinct sites are essential for virulent infection and support of variant satellite RNA replication in spontaneous beet black scorch virus variants. J Gen Virol 2012; 93:2718-2728. [PMID: 22971822 DOI: 10.1099/vir.0.045641-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spontaneous point mutations of virus genomes are important in RNA virus evolution and often result in modifications of their biological properties. Spontaneous variants of beet black scorch virus (BBSV) and its satellite (sat) RNA were generated from cDNA clones by serial propagation in Chenopodium amaranticolor and Nicotiana benthamiana. Inoculation with recombinant RNAs synthesized in vitro revealed BBSV variants with divergent infectious phenotypes that affected either symptom expression or replication of satRNA variants. Sequence alignments showed a correlation between the phenotypes and distinct BBSV genomic loci in the 3'UTR or in the domain encoding the viral replicase. Comparative analysis between a virulent variant, BBSV-m294, and the wild-type (wt) BBSV by site-directed mutagenesis indicated that a single-nucleotide substitution of a uridine to a guanine at nt 3477 in the 3'UTR was responsible for significant increases in viral pathogenicity. Gain-of-function analyses demonstrated that the ability of the BBSV variants to support replication of variant satRNAs was mainly determined by aa 516 in the P82 replicase. In this case, an arginine substitution for a glutamine residue was essential for high levels of replication, and alterations of other residues surrounding position 516 in the wtBBSV isolate led to only minor phenotypic effects. These results provide evidence that divergence of virus functions affecting pathogenicity and supporting parasitic replication can be determined by a single genetic site, either a nucleotide or an amino acid. The results suggest that complex interactions occur between virus and associated satRNAs during virus evolution.
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Affiliation(s)
- Jin Xu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xianbing Wang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Lindan Shi
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yuan Zhou
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Chenggui Han
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Ziding Zhang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Jialin Yu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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12
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Wang X, Zhang Y, Xu J, Shi L, Fan H, Han C, Li D, Yu J. The R-rich motif of Beet black scorch virus P7a movement protein is important for the nuclear localization, nucleolar targeting and viral infectivity. Virus Res 2012; 167:207-18. [PMID: 22626884 PMCID: PMC7172424 DOI: 10.1016/j.virusres.2012.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Revised: 05/01/2012] [Accepted: 05/06/2012] [Indexed: 01/07/2023]
Abstract
Beet black scorch virus (BBSV) encodes three movement proteins (P7a, P7b and P5') that facilitate its cell-to-cell movement. An arginine-rich motif of P7a N-terminus was found to determine nuclear and nucleolar localization. Amino acids substitution or deletion of the R-rich motif interfered with P7a nuclear and nucleolar localization. Bimolecular fluorescence complementation (BiFC) assays revealed that P7a protein interacted with Nicotiana benthamiana nuclear import factor importin α, suggesting that P7a is translocated into the nucleus by the classical importin α/β-dependent pathway. Moreover, P7a also interacted with the nucleolar protein fibrillarin. Mutations in the R-rich motif of P7a diminished P7a interactions with importin α and fibrillarin, influenced viral replication in Nicotiana benthamiana protoplasts and altered the symptom phenotype and viral RNA accumulation in Chenopodium amaranticolor plants. These results demonstrate that the R-rich motif of P7a is correlated with nuclear and nucleolar localization, viral replication and virus infection.
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Affiliation(s)
- Xiaohui Wang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yanjing Zhang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Jin Xu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Lindan Shi
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Huiyan Fan
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Chenggui Han
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Jialin Yu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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13
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Jiwan SD, Wu B, White KA. Subgenomic mRNA transcription in tobacco necrosis virus. Virology 2011; 418:1-11. [PMID: 21803392 DOI: 10.1016/j.virol.2011.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 06/27/2011] [Accepted: 07/07/2011] [Indexed: 12/14/2022]
Abstract
Tobacco necrosis virus-D (TNV-D), a positive-strand RNA Necrovirus in the family Tombusviridae, transcribes two subgenomic (sg) mRNAs during infections. We have investigated the strategy used by TNV-D in this process and uncovered evidence that it employs a premature termination (PT) mechanism for the transcription of its sg mRNAs. Structural and mutational analysis of the TNV-D genome identified local RNA structures upstream from transcriptional initiation sites that functioned in the plus-strand as attenuation structures and mediated the production of sg mRNA-sized minus-strands. Other evidence in support of a PT mechanism included the ability to uncouple minus-strand sg RNA production from plus-strand sg mRNA synthesis and the sequence similarities observed between the sg mRNA promoter and that for the viral genome. Accordingly, our results indicate that the necrovirus TNV-D, like several other genera in the family Tombusviridae, uses a PT mechanism for transcription of its sg mRNAs.
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Affiliation(s)
- Sadaf D Jiwan
- Department of Biology, York University, Toronto, Ontario, Canada
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14
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Zhang Y, Zhang X, Niu S, Han C, Yu J, Li D. Nuclear localization of Beet black scorch virus capsid protein and its interaction with importin α. Virus Res 2011; 155:307-15. [PMID: 21056066 DOI: 10.1016/j.virusres.2010.10.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 10/19/2010] [Accepted: 10/20/2010] [Indexed: 11/26/2022]
Abstract
Beet black scorch virus (BBSV) is a positive-sense, single-stranded RNA virus belonging to Necrovirus genus. In order to better understand the life cycle of BBSV, we have investigated the subcellular localization of BBSV capsid protein (CP) by its fusion with green fluorescent protein (GFP) agroinfiltrated into Nicotiana benthamiana leaves and by particle bombardment into onion (Allium cepa) epidermal cells. Confocal laser scanning microscopy (CLSM) showed that BBSV CP fused to GFP displayed enhanced fluorescence in nuclei and nuclear import of the CP was confirmed in BBSV-infected N. benthamiana leaves. Mutational analysis revealed that the N-terminal basic amino acid cluster (4)KRNKGGKKSR(13) of the CP is essential for nuclear localization. Bimolecular fluorescence complementation (BiFC) assays indicated that the CP could interact with the nuclear import factor importin α, suggesting that the CP is possibly imported into the nucleus via an importin α-dependent pathway. This is the first report of the nuclear localization of the CP encoded by a necrovirus.
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Affiliation(s)
- Yanjing Zhang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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15
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Zhou B, Zhang Y, Wang X, Dong J, Wang B, Han C, Yu J, Li D. Oral administration of plant-based rotavirus VP6 induces antigen-specific IgAs, IgGs and passive protection in mice. Vaccine 2010; 28:6021-7. [DOI: 10.1016/j.vaccine.2010.06.094] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 06/24/2010] [Accepted: 06/29/2010] [Indexed: 02/03/2023]
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16
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González-Vázquez M, Ayala J, García-Arenal F, Fraile A. Occurrence of Beet black scorch virus Infecting Sugar Beet in Europe. PLANT DISEASE 2009; 93:21-24. [PMID: 30764261 DOI: 10.1094/pdis-93-1-0021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In a survey of soilborne viruses infecting sugar beet in central Spain, Beet black scorch virus (BBSV) was detected in field grown sugar beets with symptoms of rhizomania disease. BBSV was found in all analyzed sugar beet producing regions from central Spain, as well as in bait plants grown in soils with a history of rhizomania from several Western European countries, thereby constituting the first report of BBSV in Europe. BBSV was transferred to Chenopodium quinoa, where it caused chlorotic local lesions from which virus particles were purified. The nucleotide sequence of the 3'-untranslated region of the genomic RNA was determined for 13 European isolates, and sequences were highly similar to those reported for Chinese and U.S. isolates. Sequence comparisons revealed three clusters of sequences, one including most European isolates, one including one European and two Chinese isolates, and the third including the U.S. isolate. BBSV was detected in a number of samples with rhizomania symptoms in which Beet necrotic yellow vein virus went undetected. However, its role in rhizomania disease in Europe, if any, remains to be established.
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Affiliation(s)
- Magali González-Vázquez
- Departamento de Biotecnología and Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Julián Ayala
- Asociación de Investigación y Mejora del Cultivo de la Remolacha Azucarera, Ctra. De Villabañez Km 2.7, 47012 Valladolid, Spain
| | - Fernando García-Arenal
- Departamento de Biotecnología and Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Aurora Fraile
- Departamento de Biotecnología and Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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17
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Molecular and serological characterization of an Iranian isolate of Beet black scorch virus. Arch Virol 2008; 153:1397-400. [PMID: 18548319 DOI: 10.1007/s00705-008-0121-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Accepted: 05/19/2008] [Indexed: 10/22/2022]
Abstract
An isolate of Beet black scorch virus (BBSV) was obtained from Iranian sugar beet roots. Its genome organization closely resembles that of the previously described Chinese and North American isolates, but the nucleotide sequences of the three isolates differ considerably. Most of the nucleotide exchanges, however, are silent, and the Iranian and the Chinese isolates were serologically indistinguishable. Beets infected by the Iranian BBSV did not show black scorch symptoms, but severe root beardedness. This might have been caused by BBSV or the simultaneously present beet necrotic yellow vein virus, or both together.
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18
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Jiang L, Min L, Cui L, Yang G, DaWei L, ChengGui H, JiaLin Y. Effects on the local symptoms of subgenomic RNAs expressions and their translational products of Tobacco necrosis virus A Chinese isolate. Sci Bull (Beijing) 2008. [DOI: 10.1007/s11434-008-0204-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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Xi D, Li J, Han C, Li D, Yu J, Zhou X. Complete nucleotide sequence of a new strain of Tobacco necrosis virus A infecting soybean in China and infectivity of its full-length cDNA clone. Virus Genes 2008; 36:259-66. [PMID: 18071890 DOI: 10.1007/s11262-007-0185-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Accepted: 11/28/2007] [Indexed: 10/22/2022]
Abstract
The complete nucleotide sequence of a virus isolated from soybean (Glycine max (L.) Merr.) in China, previously identified as a new strain of Tobacco necrosis virus A (TNV-A) based on its biological, serological properties, and coat protein (CP) sequence and named as TNV-A C, was determined and compared with that of TNV-A and other closely related Necroviruses and Carmoviruses. The viral RNA genome consists of 3,682 nucleotides and contains five open reading frames (ORFs). TNV-A C showed 86.4% overall nucleotide sequence identity to TNV-A. The CP and putative RNA-dependent RNA polymerase (RdRp) showed 88.8 and 95.9% amino acid identity, respectively, to that of TNV-A. The greatest difference between TNV-A C and TNV-A was in the 3' terminal region: the p7K ORF region present in TNV-A was absent in TNV-A C. Phylogenetic analysis of RdRp, CP, and small ORF regions of Necroviruses confirmed TNV-A C as a new strain of TNV-A. A full-length cDNA clone of TNV-A C was constructed and used as template for run-off transcription based on the obtained sequence. The results indicate that the in vitro-synthesized viral RNA faithfully represented the biological activity of wild-type TNV-A C.
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Affiliation(s)
- Dehui Xi
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, PR China
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20
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Weiland JJ, Van Winkle D, Edwards MC, Larson RL, Shelver WL, Freeman TP, Liu HY. Characterization of a U.S. Isolate of Beet black scorch virus. PHYTOPATHOLOGY 2007; 97:1245-54. [PMID: 18943682 DOI: 10.1094/phyto-97-10-1245] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
ABSTRACT The first reported U.S. isolate of Beet black scorch necrovirus (BBSV) was obtained and characterized. Host range of the virus for localized and occasionally systemic infection included the Chenopodiaceae and Tetragonia expansa; Nicotiana benthamiana supported symptomless systemic infection by the virus. The complete nucleotide sequence of the genomic RNA of the virus, designated BBSV-Co, exhibits 93% similarity to the genome of the 'Ningxia' isolate of BBSV from China. Amino acid sequence similarity in predicted genes ranged from 95% in the p4 gene to 97% in the p82 and coat protein genes. A potential additional gene exists within the U.S. isolate of BBSV that is absent from Chinese isolates of BBSV due to nucleotide differences between these isolates within the coat protein gene. Coat protein analysis by isoelectric focusing and by mass spectroscopy indicated the presence of phosphorylated residues. Using primer extension analysis of the 5' end of the genome and site-directed mutants of genomic clones of BBSV-Co from which infectious RNA was produced, the native 5' end of the BBSV-Co genome was determined to be 5'-GAAACCTAACC...3', lacking the two terminal adenosine nucleotides in the published sequences of BBSV from China.
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21
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Yuan X, Cao Y, Xi D, Guo L, Han C, Li D, Zhai Y, Yu J. Analysis of the subgenomic RNAs and the small open reading frames of Beet black scorch virus. J Gen Virol 2006; 87:3077-3086. [PMID: 16963767 DOI: 10.1099/vir.0.81928-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A full-length cDNA of the genome of Beet black scorch virus (BBSV), isolate Ningxia, was constructed and modified by site-directed mutagenesis to permit in vitro transcription of mutant viral RNAs. Two subgenomic (sg) RNAs (sgRNA1 and sgRNA2) appeared during BBSV replication. Mutagenesis revealed that sgRNA1 transcription was initiated at G2209 within the P82 polymerase subunit open reading frame (ORF) and that transcription of sgRNA2 began at G2526 within the nested p7b/p5' ORF. Initiation-codon shifting or premature termination of translation of the three ORFs (P7a, P7b and P5') encoded by sgRNA1 indicated that each of the genes was required for localized movement, accumulation of viral RNAs and formation of local lesions on the leaves of Chenopodium amaranticolor. Microscopic observations of the distribution of green fluorescent protein fused to the N-terminal portion of the capsid protein provided additional evidence that the P7a, P7b and P5' proteins are each required for cell-to-cell movement. In contrast, elimination of sgRNA2 showed that the BBSV coat protein was not required for viral RNA accumulation or the appearance of local lesions on C. amaranticolor. In addition, disruption of the small P5 ORF previously predicted by computer analysis to originate at the C terminus of the P82 ORF had no effect on disease phenotype, suggesting that this ORF may represent a cryptic, non-essential gene. These results show that BBSV has a novel cell-to-cell movement protein organization that differs in size and sequence from that of other viruses.
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Affiliation(s)
- Xuefeng Yuan
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, PR China
| | - Yunhe Cao
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, PR China
| | - Dehui Xi
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, PR China
| | - Lihua Guo
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, PR China
| | - Chenggui Han
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, PR China
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, PR China
| | - Yafeng Zhai
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, PR China
| | - Jialin Yu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, PR China
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22
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Stuart GW, Moffett PK, Bozarth RF. A comprehensive open reading frame phylogenetic analysis of isometric positive strand ssRNA plant viruses. Arch Virol 2006; 151:1159-77. [PMID: 16385397 DOI: 10.1007/s00705-005-0692-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Accepted: 11/02/2005] [Indexed: 11/26/2022]
Abstract
Rigorous large-scale whole genome comparisons are capable of providing more comprehensive and potentially more accurate descriptions of viral relationships, allowing for the effective validation and modification of current taxonomy. Using a set of 5 togaviruses as an outgroup, a comprehensive phylogeny for 115 isometric positive ssRNA plant viruses was generated based on the simultaneous comparison of over 480 ORFs found within completely sequenced genomes. With the exception of a diverse group of viruses representing the family Comoviridae, the single tree generated contained well supported branches corresponding to well established groups of viruses, including Bromoviridae, Umbravirus, Sobemovirus, and Tymoviridae. In addition, evidence for specific relationships between groups were also observed, specifically Tombusviridae + Umbravirus, and Luteoviridae + Sobemovirus. Various well established subgroups of viruses were also well resolved within the tree. In addition, some recent proposals involving the creation of new genera or the inclusion of newly described viruses into established genera were supported, while others were not. The evidence for frequent gene sharing and the potential consequences to viral taxonomy are discussed.
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Affiliation(s)
- G W Stuart
- Department of Life Sciences, Indiana State University, Terre Haute, Indiana 47809, USA.
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23
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Guo LH, Cao YH, Li DW, Niu SN, Cai ZN, Han CG, Zhai YF, Yu JL. Analysis of nucleotide sequences and multimeric forms of a novel satellite RNA associated with beet black scorch virus. J Virol 2005; 79:3664-74. [PMID: 15731260 PMCID: PMC1075689 DOI: 10.1128/jvi.79.6.3664-3674.2005] [Citation(s) in RCA: 19] [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
The full-length sequence of a satellite RNA (sat-RNA) of Beet black scorch virus isolate X (BBSV-X) was determined. This agent is 615 nucleotides long and lacks extensive sequence homology with its helper virus or with other reported viruses. Purified virus particles contained abundant single-stranded plus-sense monomers and smaller amounts of dimers. Single-stranded RNAs from total plant RNA extracts also included primarily monomers and smaller amounts of dimers that could be revealed by hybridization, and preparations of purified double-stranded RNAs also contained monomers and dimers. Coinoculation of in vitro transcripts of sat-RNA to Chenopodium amaranticolor with BBSV RNAs was used to assess the replication and accumulation of various forms of sat-RNA, including monomers, dimers, and tetramers. Dimeric sat-RNAs with 5- or 10-base deletions or 15-base insertions within the junction regions accumulated preferentially. In contrast, the replication of monomeric sat-RNA was severely inhibited by five-nucleotide deletions in either the 5' or the 3' termini. Therefore, sequences at both the 5' and the 3' ends of the monomers or the presence of intact juxtaposed multimers is essential for the replication of sat-RNA and for the predomination of monomeric progeny. Comparisons of the time courses of replication initiated by in vitro-synthesized monomeric or multimeric sat-RNAs raised the possibility that the dimeric form has an intermediate role in replication. We propose that replication primarily involves multimers, possibly as dimeric forms. These forms may revert to monomers by a termination of replication at 5' end sequences and/or by internal initiation at the 3' ends of multimeric junctions.
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Affiliation(s)
- Li-Hua Guo
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100094, China
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