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Chen IH, Cheng JH, Huang YW, Lin NS, Hsu YH, Tsai CH. Characterization of the polyadenylation activity in a replicase complex from Bamboo mosaic virus-infected Nicotiana benthamiana plants. Virology 2013; 444:64-70. [PMID: 23768785 PMCID: PMC7111917 DOI: 10.1016/j.virol.2013.05.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/20/2013] [Accepted: 05/22/2013] [Indexed: 12/30/2022]
Abstract
Bamboo mosaic virus (BaMV) has a positive-sense single-stranded RNA genome with a 5' cap and a 3' poly(A) tail. To characterize polyadenylation activity in the BaMV replicase complex, we performed the in vitro polyadenylation with various BaMV templates. We conducted a polyadenylation activity assay for BaMV RNA by using a partially purified BaMV replicase complex. The results showed that approximately 200 adenylates at the 3' end of the RNA were generated on the endogenous RNA templates. Specific fractions derived from uninfected Nicotiana benthamiana plants enhanced the polyadenylation activity, implying that host factors are involved in polyadenylation. Furthermore, polyadenylation can be detected in newly synthesized plus-strand RNA in vitro when using the exogenous BaMV minus-strand minigenome. For polyadenylation on the exogenous plus-strand minigenome, the 3' end requires at least 4A to reach 22% polyadenylation activity. The results indicate that the BaMV replicase complex recognizes the 3' end of BaMV for polyadenylation.
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Affiliation(s)
- I-Hsuan Chen
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Jai-Hong Cheng
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Na-Sheng Lin
- The Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
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52
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Chen IH, Chiu MH, Cheng SF, Hsu YH, Tsai CH. The glutathione transferase of Nicotiana benthamiana NbGSTU4 plays a role in regulating the early replication of Bamboo mosaic virus. THE NEW PHYTOLOGIST 2013; 199:749-57. [PMID: 23701112 PMCID: PMC3744755 DOI: 10.1111/nph.12304] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 03/28/2013] [Indexed: 05/23/2023]
Abstract
Bamboo mosaic virus (BaMV) is a single-stranded positive-sense RNA virus. One of the plant glutathione S-transferase (GST) genes, NbGSTU4, responds as an upregulated gene in Nicotiana benthamiana post BaMV infection. In order to identify the role of NbGSTU4 in BaMV infection, the expression of NbGSTU4 was knocked down using a virus-induced gene silencing technique or was transiently expressed in N. benthamiana in BaMV inoculation. The results show a significant decrease in BaMV RNA accumulation when the expression level of NbGSTU4 is reduced; whereas the viral RNA accumulation increases when NbGSTU4 is transiently expressed. Furthermore, this study identified that the involvement of NbGSTU4 in viral RNA accumulation occurs by its participation in the viral early replication step. The findings show that the NbGSTU4 protein expressed from Escherichia coli can interact with the 3' untranslated region (UTR) of the BaMV RNA in vitro in the presence of glutathione (GSH). The addition of GSH in the in vitro replication assay shows an enhancement of minus-strand but not plus-strand RNA synthesis. The results suggest that the plant GST protein plays a role in binding viral RNA and delivering GSH to the replication complex to create a reduced condition for BaMV minus-strand RNA synthesis.
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Affiliation(s)
- I-Hsuan Chen
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, 402, Taiwan
| | - Meng-Hsuen Chiu
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, 402, Taiwan
| | - Shun-Fang Cheng
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, 402, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, 402, Taiwan
- Graduate Institute of Medical Laboratory Science and Biotechnology, China Medical UniversityTaichung, 404, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, 402, Taiwan
- Graduate Institute of Medical Laboratory Science and Biotechnology, China Medical UniversityTaichung, 404, Taiwan
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Cheng SF, Tsai MS, Huang CL, Huang YP, Chen IH, Lin NS, Hsu YH, Tsai CH, Cheng CP. Ser/Thr kinase-like protein of Nicotiana benthamiana is involved in the cell-to-cell movement of Bamboo mosaic virus. PLoS One 2013; 8:e62907. [PMID: 23646157 PMCID: PMC3639906 DOI: 10.1371/journal.pone.0062907] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 03/28/2013] [Indexed: 01/08/2023] Open
Abstract
To investigate the plant genes affected by Bamboo mosaic virus (BaMV) infection, we applied a cDNA-amplified fragment length polymorphism technique to screen genes with differential expression. A serine/threonine kinase-like (NbSTKL) gene of Nicotiana benthamiana is upregulated after BaMV infection. NbSTKL contains the homologous domain of Ser/Thr kinase. Knocking down the expression of NbSTKL by virus-induced gene silencing reduced the accumulation of BaMV in the inoculated leaves but not in the protoplasts. The spread of GFP-expressing BaMV in the inoculated leaves is also impeded by a reduced expression of NbSTKL. These data imply that NbSTKL facilitates the cell-to-cell movement of BaMV. The subcellular localization of NbSTKL is mainly on the cell membrane, which has been confirmed by mutagenesis and fractionation experiments. Combined with the results showing that active site mutation of NbSTKL does not change its subcellular localization but significantly affects BaMV accumulation, we conclude that NbSTKL may regulate BaMV movement on the cell membrane by its kinase-like activity. Moreover, the transient expression of NbSTKL does not significantly affect the accumulation of Cucumber mosaic virus (CMV) and Potato virus X (PVX); thus, NbSTKL might be a specific protein facilitating BaMV movement.
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Affiliation(s)
- Shun-Fang Cheng
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Meng-Shan Tsai
- Department of Life Sciences, Tzu Chi University, Hualien, Taiwan
| | - Chia-Lin Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ying-Ping Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - I-Hsuan Chen
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang Taipei, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chi-Ping Cheng
- Department of Life Sciences, Tzu Chi University, Hualien, Taiwan
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Bhat S, Folimonova SY, Cole AB, Ballard KD, Lei Z, Watson BS, Sumner LW, Nelson RS. Influence of host chloroplast proteins on Tobacco mosaic virus accumulation and intercellular movement. PLANT PHYSIOLOGY 2013; 161:134-47. [PMID: 23096159 PMCID: PMC3532247 DOI: 10.1104/pp.112.207860] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 10/22/2012] [Indexed: 05/18/2023]
Abstract
Tobacco mosaic virus (TMV) forms dense cytoplasmic bodies containing replication-associated proteins (virus replication complexes [VRCs]) upon infection. To identify host proteins that interact with individual viral components of VRCs or VRCs in toto, we isolated viral replicase- and VRC-enriched fractions from TMV-infected Nicotiana tabacum plants. Two host proteins in enriched fractions, ATP-synthase γ-subunit (AtpC) and Rubisco activase (RCA) were identified by matrix-assisted laser-desorption ionization time-of-flight mass spectrometry or liquid chromatography-tandem mass spectrometry. Through pull-down analysis, RCA bound predominantly to the region between the methyltransferase and helicase domains of the TMV replicase. Tobamovirus, but not Cucumber mosaic virus or Potato virus X, infection of N. tabacum plants resulted in 50% reductions in Rca and AtpC messenger RNA levels. To investigate the role of these host proteins in TMV accumulation and plant defense, we used a Tobacco rattle virus vector to silence these genes in Nicotiana benthamiana plants prior to challenge with TMV expressing green fluorescent protein. TMV-induced fluorescent lesions on Rca- or AtpC-silenced leaves were, respectively, similar or twice the size of those on leaves expressing these genes. Silencing Rca and AtpC did not influence the spread of Tomato bushy stunt virus and Potato virus X. In AtpC- and Rca-silenced leaves TMV accumulation and pathogenicity were greatly enhanced, suggesting a role of both host-encoded proteins in a defense response against TMV. In addition, silencing these host genes altered the phenotype of the TMV infection foci and VRCs, yielding foci with concentric fluorescent rings and dramatically more but smaller VRCs. The concentric rings occurred through renewed virus accumulation internal to the infection front.
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Affiliation(s)
- Sumana Bhat
- Plant Biology Division, The Samuel Roberts Noble Foundation, Inc., Ardmore, Oklahoma 73401
| | | | | | - Kimberly D. Ballard
- Plant Biology Division, The Samuel Roberts Noble Foundation, Inc., Ardmore, Oklahoma 73401
| | - Zhentian Lei
- Plant Biology Division, The Samuel Roberts Noble Foundation, Inc., Ardmore, Oklahoma 73401
| | - Bonnie S. Watson
- Plant Biology Division, The Samuel Roberts Noble Foundation, Inc., Ardmore, Oklahoma 73401
| | - Lloyd W. Sumner
- Plant Biology Division, The Samuel Roberts Noble Foundation, Inc., Ardmore, Oklahoma 73401
| | - Richard S. Nelson
- Plant Biology Division, The Samuel Roberts Noble Foundation, Inc., Ardmore, Oklahoma 73401
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55
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Jang C, Seo EY, Nam J, Bae H, Gim YG, Kim HG, Cho IS, Lee ZW, Bauchan GR, Hammond J, Lim HS. Insights into Alternanthera mosaic virus TGB3 Functions: Interactions with Nicotiana benthamiana PsbO Correlate with Chloroplast Vesiculation and Veinal Necrosis Caused by TGB3 Over-Expression. FRONTIERS IN PLANT SCIENCE 2013; 4:5. [PMID: 23386854 PMCID: PMC3560364 DOI: 10.3389/fpls.2013.00005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 01/08/2013] [Indexed: 05/18/2023]
Abstract
Alternanthera mosaic virus (AltMV) triple gene block 3 (TGB3) protein is involved in viral movement. AltMV TGB3 subcellular localization was previously shown to be distinct from that of Potato virus X (PVX) TGB3, and a chloroplast binding domain identified; veinal necrosis and chloroplast vesiculation were observed in Nicotiana benthamiana when AltMV TGB3 was over-expressed from PVX. Plants with over-expressed TGB3 showed more lethal damage under dark conditions than under light. Yeast-two-hybrid analysis and bimolecular fluorescence complementation (BiFC) reveal that Arabidopsis thaliana PsbO1 has strong interactions with TGB3; N. benthamiana PsbO (NbPsbO) also showed obvious interaction signals with TGB3 through BiFC. These results demonstrate an important role for TGB3 in virus cell-to-cell movement and virus-host plant interactions. The Photosystem II oxygen-evolving complex protein PsbO interaction with TGB3 is presumed to have a crucial role in symptom development and lethal damage under dark conditions. In order to further examine interactions between AtPsbO1, NbPsbO, and TGB3, and to identify the binding domain(s) in TGB3 protein, BiFC assays were performed between AtPsbO1 or NbPsbO and various mutants of TGB3. Interactions with C-terminally deleted TGB3 were significantly weaker than those with wild-type TGB3, and both N-terminally deleted TGB3 and a TGB3 mutant previously shown to lose chloroplast interactions failed to interact detectably with PsbO in BiFC. To gain additional information about TGB3 interactions in AltMV-susceptible plants, we cloned 12 natural AltMV TGB3 sequence variants into a PVX expression vector to examine differences in symptom development in N. benthamiana. Symptom differences were observed on PVX over-expression, with all AltMV TGB3 variants showing more severe symptoms than the WT PVX control, but without obvious correlation to sequence differences.
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Affiliation(s)
- Chanyong Jang
- Department of Applied Biology, Chungnam National UniversityDaejeon, South Korea
| | - Eun-Young Seo
- Department of Applied Biology, Chungnam National UniversityDaejeon, South Korea
| | - Jiryun Nam
- Department of Applied Biology, Chungnam National UniversityDaejeon, South Korea
| | - Hanhong Bae
- School of Biotechnology, Yeungnam UniversityGyeongsan, South Korea
| | - Yeong Guk Gim
- Department of Applied Biology, Chungnam National UniversityDaejeon, South Korea
| | - Hong Gi Kim
- Department of Applied Biology, Chungnam National UniversityDaejeon, South Korea
| | - In Sook Cho
- National Institute of Horticultural and Herbal Science, Rural Development AdministrationSuwon, South Korea
| | - Zee-Won Lee
- Division of Life Science, Korea Basic Science InstituteDaejeon, South Korea
| | - Gary R. Bauchan
- Electron and Confocal Microscopy Unit, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of AgricultureBeltsville, MD, USA
| | - John Hammond
- Floral and Nursery Plants Research Unit, US National Arboretum, Agricultural Research Service, United States Department of AgricultureBeltsville, MD, USA
- *Correspondence: John Hammond, Floral and Nursery Plants Research Unit, US National Arboretum, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, B-010A, Beltsville, MD 20705, USA. e-mail: ; Hyoun-Sub Lim, Department of Applied Biology, Chungnam National University, 79 Daehangno, Yuseong-gu, Daejeon 305-764, South Korea. e-mail:
| | - Hyoun-Sub Lim
- Department of Applied Biology, Chungnam National UniversityDaejeon, South Korea
- *Correspondence: John Hammond, Floral and Nursery Plants Research Unit, US National Arboretum, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, B-010A, Beltsville, MD 20705, USA. e-mail: ; Hyoun-Sub Lim, Department of Applied Biology, Chungnam National University, 79 Daehangno, Yuseong-gu, Daejeon 305-764, South Korea. e-mail:
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56
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Krenz B, Jeske H, Kleinow T. The induction of stromule formation by a plant DNA-virus in epidermal leaf tissues suggests a novel intra- and intercellular macromolecular trafficking route. FRONTIERS IN PLANT SCIENCE 2012; 3:291. [PMID: 23293643 PMCID: PMC3530832 DOI: 10.3389/fpls.2012.00291] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 12/06/2012] [Indexed: 05/20/2023]
Abstract
Stromules are dynamic thin protrusions of membrane envelope from plant cell plastids. Despite considerable progress in understanding the importance of certain cytoskeleton elements and motor proteins for stromule maintenance, their function within the cell has yet to be unraveled. Several viruses cause a remodulation of plastid structures and stromule biogenesis within their host plants. For RNA-viruses these interactions were demonstrated to be relevant to the infection process. An involvement of plastids and stromules is assumed in the DNA-virus life cycle as well, but their functional role needs to be determined. Recent findings support a participation of heat shock cognate 70 kDa protein (cpHSC70-1)-containing stromules induced by a DNA-virus infection (Abutilon mosaic virus, AbMV, Geminiviridae) in intra- and intercellular molecule exchange. The chaperone cpHSC70-1 was shown to interact with the AbMV movement protein (MP). Bimolecular fluorescence complementation confirmed the interaction of cpHSC70-1 and MP, and showed a homo-oligomerization of either protein in planta. The complexes were detected at the cellular margin and co-localized with plastids. In healthy plant tissues cpHSC70-1-oligomers occurred in distinct spots at chloroplasts and in small filaments extending from plastids to the cell periphery. AbMV-infection induced a cpHSC70-1-containing stromule network that exhibits elliptical dilations and transverses whole cells. Silencing of the cpHSC70 gene revealed an impact of cpHSC70 on chloroplast stability and restricted AbMV movement, but not viral DNA accumulation. Based on these data, a model is suggested in which these stromules function in molecule exchange between plastids and other organelles and perhaps other cells. AbMV may utilize cpHSC70-1 for trafficking along plastids and stromules into a neighboring cell or from plastids into the nucleus. Experimental approaches to investigate this hypothesis are discussed.
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Affiliation(s)
- Björn Krenz
- Plant Pathology and Plant-Microbe Biology, Cornell UniversityIthaca, NY, USA
| | - Holger Jeske
- Molecular Biology and Plant Virology, Institute of Biology, Universität StuttgartStuttgart, Germany
| | - Tatjana Kleinow
- Molecular Biology and Plant Virology, Institute of Biology, Universität StuttgartStuttgart, Germany
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57
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Unusual roles of host metabolic enzymes and housekeeping proteins in plant virus replication. Curr Opin Virol 2012; 2:676-82. [DOI: 10.1016/j.coviro.2012.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 09/20/2012] [Accepted: 10/01/2012] [Indexed: 11/20/2022]
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58
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Sperschneider J, Datta A, Wise MJ. Predicting pseudoknotted structures across two RNA sequences. Bioinformatics 2012; 28:3058-65. [PMID: 23044552 PMCID: PMC3516145 DOI: 10.1093/bioinformatics/bts575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Motivation: Laboratory RNA structure determination is demanding and costly and thus, computational structure prediction is an important task. Single sequence methods for RNA secondary structure prediction are limited by the accuracy of the underlying folding model, if a structure is supported by a family of evolutionarily related sequences, one can be more confident that the prediction is accurate. RNA pseudoknots are functional elements, which have highly conserved structures. However, few comparative structure prediction methods can handle pseudoknots due to the computational complexity. Results: A comparative pseudoknot prediction method called DotKnot-PW is introduced based on structural comparison of secondary structure elements and H-type pseudoknot candidates. DotKnot-PW outperforms other methods from the literature on a hand-curated test set of RNA structures with experimental support. Availability: DotKnot-PW and the RNA structure test set are available at the web site http://dotknot.csse.uwa.edu.au/pw. Contact:janaspe@csse.uwa.edu.au Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jana Sperschneider
- School of Computer Science and Software Engineering, University of Western Australia, Perth, Australia.
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59
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Huang YW, Hu CC, Liou MR, Chang BY, Tsai CH, Meng M, Lin NS, Hsu YH. Hsp90 interacts specifically with viral RNA and differentially regulates replication initiation of Bamboo mosaic virus and associated satellite RNA. PLoS Pathog 2012; 8:e1002726. [PMID: 22654666 PMCID: PMC3359997 DOI: 10.1371/journal.ppat.1002726] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 04/16/2012] [Indexed: 12/22/2022] Open
Abstract
Host factors play crucial roles in the replication of plus-strand RNA viruses. In this report, a heat shock protein 90 homologue of Nicotiana benthamiana, NbHsp90, was identified in association with partially purified replicase complexes from BaMV-infected tissue, and shown to specifically interact with the 3' untranslated region (3' UTR) of BaMV genomic RNA, but not with the 3' UTR of BaMV-associated satellite RNA (satBaMV RNA) or that of genomic RNA of other viruses, such as Potato virus X (PVX) or Cucumber mosaic virus (CMV). Mutational analyses revealed that the interaction occurs between the middle domain of NbHsp90 and domain E of the BaMV 3' UTR. The knockdown or inhibition of NbHsp90 suppressed BaMV infectivity, but not that of satBaMV RNA, PVX, or CMV in N. benthamiana. Time-course analysis further revealed that the inhibitory effect of 17-AAG is significant only during the immediate early stages of BaMV replication. Moreover, yeast two-hybrid and GST pull-down assays demonstrated the existence of an interaction between NbHsp90 and the BaMV RNA-dependent RNA polymerase. These results reveal a novel role for NbHsp90 in the selective enhancement of BaMV replication, most likely through direct interaction with the 3' UTR of BaMV RNA during the initiation of BaMV RNA replication.
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Affiliation(s)
- Ying Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chung Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ming Ru Liou
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ban Yang Chang
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
| | - Ching Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Menghsiao Meng
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Na Sheng Lin
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yau Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
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60
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Prasanth KR, Huang YW, Liou MR, Wang RYL, Hu CC, Tsai CH, Meng M, Lin NS, Hsu YH. Glyceraldehyde 3-phosphate dehydrogenase negatively regulates the replication of Bamboo mosaic virus and its associated satellite RNA. J Virol 2011; 85:8829-40. [PMID: 21715476 PMCID: PMC3165797 DOI: 10.1128/jvi.00556-11] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Accepted: 06/21/2011] [Indexed: 01/24/2023] Open
Abstract
The identification of cellular proteins associated with virus replicase complexes is crucial to our understanding of virus-host interactions, influencing the host range, replication, and virulence of viruses. A previous in vitro study has demonstrated that partially purified Bamboo mosaic virus (BaMV) replicase complexes can be employed for the replication of both BaMV genomic and satellite BaMV (satBaMV) RNAs. In this study, we investigated the BaMV and satBaMV 3' untranslated region (UTR) binding proteins associated with these replicase complexes. Two cellular proteins with molecular masses of ∼35 and ∼55 kDa were specifically cross-linked with RNA elements, whereupon the ∼35-kDa protein was identified as the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Gel mobility shift assays confirmed the direct interaction of GAPDH with the 3' UTR sequences, and competition gel shift analysis revealed that GAPDH binds preferentially to the positive-strand BaMV and satBaMV RNAs over the negative-strand RNAs. It was observed that the GAPDH protein binds to the pseudoknot poly(A) tail of BaMV and stem-loop-C poly(A) tail of satBaMV 3' UTR RNAs. It is important to note that knockdown of GAPDH in Nicotiana benthamiana enhances the accumulation of BaMV and satBaMV RNA; conversely, transient overexpression of GAPDH reduces the accumulation of BaMV and satBaMV RNA. The recombinant GAPDH principally inhibits the synthesis of negative-strand RNA in exogenous RdRp assays. These observations support the contention that cytosolic GAPDH participates in the negative regulation of BaMV and satBaMV RNA replication.
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Affiliation(s)
- K. Reddisiva Prasanth
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Road, Taichung 40227, Taiwan, Republic of China
| | - Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Road, Taichung 40227, Taiwan, Republic of China
| | - Ming-Ru Liou
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Road, Taichung 40227, Taiwan, Republic of China
| | - Robert Yung-Liang Wang
- Department of Biomedical Sciences and Research Center for Emerging Viral Infections, Chang Gung University, Tao Yuan 33302, Taiwan, Republic of China
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Road, Taichung 40227, Taiwan, Republic of China
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Road, Taichung 40227, Taiwan, Republic of China
| | - Menghsiao Meng
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Road, Taichung 40227, Taiwan, Republic of China
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan, Republic of China
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Road, Taichung 40227, Taiwan, Republic of China
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Giribaldi M, Purrotti M, Pacifico D, Santini D, Mannini F, Caciagli P, Rolle L, Cavallarin L, Giuffrida MG, Marzachì C. A multidisciplinary study on the effects of phloem-limited viruses on the agronomical performance and berry quality of Vitis vinifera cv. Nebbiolo. J Proteomics 2011; 75:306-15. [PMID: 21856458 DOI: 10.1016/j.jprot.2011.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 08/03/2011] [Accepted: 08/05/2011] [Indexed: 02/08/2023]
Abstract
Viral infections are known to have a detrimental effect on grapevine yield and performance, but there is still a lack of knowledge about their effect on the quality and safety of end products. Vines of Vitis vinifera cv. Nebbiolo clone 308, affected simultaneously by Grapevine leafroll-associated virus 1 (GLRaV-1), Grapevine virus A (GVA), and Rupestris stem pitting associated virus (RSPaV), were subjected to integrated analyses of agronomical performance, grape berry characteristics, instrumental texture profile, and proteome profiling. The comparison of performance and grape quality of healthy and infected vines cultivated in a commercial vineyard revealed similar shoot fertility, number of clusters, total yield, with significant differences in titratable acidity, and resveratrol content. Also some texture parameters such as cohesiveness and resilience were altered in berries of infected plants. The proteomic analysis of skin and pulp visualized about 400 spots. The ANOVA analysis on 2D gels revealed significant differences among healthy and virus-infected grape berries for 12 pulp spots and 7 skin spots. Virus infection mainly influenced proteins involved in the response to oxidative stress in the berry skin, and proteins involved in cell structure metabolism in the pulp.
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Affiliation(s)
- Marzia Giribaldi
- Istituto di Scienze delle Produzioni Alimentari, National Research Council, Grugliasco (TO), Italy
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Nadar M, Chan MY, Huang SW, Huang CC, Tseng JT, Tsai CH. HuR binding to AU-rich elements present in the 3' untranslated region of Classical swine fever virus. Virol J 2011; 8:340. [PMID: 21729330 PMCID: PMC3144019 DOI: 10.1186/1743-422x-8-340] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 07/06/2011] [Indexed: 02/01/2023] Open
Abstract
Background Classical swine fever virus (CSFV) is the member of the genus Pestivirus under the family Flaviviridae. The 5' untranslated region (UTR) of CSFV contains the IRES, which is a highly structured element that recruits the translation machinery. The 3' UTR is usually the recognition site of the viral replicase to initiate minus-strand RNA synthesis. Adenosine-uridine rich elements (ARE) are instability determinants present in the 3' UTR of short-lived mRNAs. However, the presence of AREs in the 3' UTR of CSFV conserved in all known strains has never been reported. This study inspects a possible role of the ARE in the 3' UTR of CSFV. Results Using RNA pull-down and LC/MS/MS assays, this study identified at least 32 possible host factors derived from the cytoplasmic extracts of PK-15 cells that bind to the CSFV 3' UTR, one of which is HuR. HuR is known to bind the AREs and protect the mRNA from degradation. Using recombinant GST-HuR, this study demonstrates that HuR binds to the ARE present in the 3' UTR of CSFV in vitro and that the binding ability is conserved in strains irrespective of virulence. Conclusions This study identified one of the CSFV 3' UTR binding proteins HuR is specifically binding to in the ARE region.
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Affiliation(s)
- Muthukumar Nadar
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
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63
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Cheng SF, Huang YP, Wu ZR, Hu CC, Hsu YH, Tsai CH. Identification of differentially expressed genes induced by Bamboo mosaic virus infection in Nicotiana benthamiana by cDNA-amplified fragment length polymorphism. BMC PLANT BIOLOGY 2010; 10:286. [PMID: 21184690 PMCID: PMC3024324 DOI: 10.1186/1471-2229-10-286] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 12/27/2010] [Indexed: 05/03/2023]
Abstract
BACKGROUND The genes of plants can be up- or down-regulated during viral infection to influence the replication of viruses. Identification of these differentially expressed genes could shed light on the defense systems employed by plants and the mechanisms involved in the adaption of viruses to plant cells. Differential gene expression in Nicotiana benthamiana plants in response to infection with Bamboo mosaic virus (BaMV) was revealed using cDNA-amplified fragment length polymorphism (AFLP). RESULTS Following inoculation with BaMV, N. benthamiana displayed differential gene expression in response to the infection. Isolation, cloning, and sequencing analysis using cDNA-AFLP furnished 90 cDNA fragments with eight pairs of selective primers. Fifteen randomly selected genes were used for a combined virus-induced gene silencing (VIGS) knockdown experiment, using BaMV infection to investigate the roles played by these genes during viral infection, specifically addressing the means by which these genes influence the accumulation of BaMV protein. Nine of the 15 genes showed either a positive or a negative influence on the accumulation of BaMV protein. Six knockdown plants showed an increase in the accumulation of BaMV, suggesting that they played a role in the resistance to viral infection, while three plants showed a reduction in coat protein, indicating a positive influence on the accumulation of BaMV in plants. An interesting observation was that eight of the nine plants showing an increase in BaMV coat protein were associated with cell rescue, defense, death, aging, signal transduction, and energy production. CONCLUSIONS This study reports an efficient and straightforward method for the identification of host genes involved in viral infection. We succeeded in establishing a cDNA-AFLP system to help track changes in gene expression patterns in N. benthamiana plants when infected with BaMV. The combination of both DNA-AFLP and VIGS methodologies made it possible to screen a large number of genes and identify those associated with infections of plant viruses. In this report, 9 of the 15 analyzed genes exhibited either a positive or a negative influence on the accumulation of BaMV in N. benthamiana plants.
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Affiliation(s)
- Shun-Fang Cheng
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Ying-Ping Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Zi-Rong Wu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
- Graduate Institute of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 404, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
- Graduate Institute of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 404, Taiwan
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64
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Verchot-Lubicz J, Torrance L, Solovyev AG, Morozov SY, Jackson AO, Gilmer D. Varied movement strategies employed by triple gene block-encoding viruses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:1231-47. [PMID: 20831404 DOI: 10.1094/mpmi-04-10-0086] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Several RNA virus genera belonging to the Virgaviridae and Flexiviridae families encode proteins organized in a triple gene block (TGB) that facilitate cell-to-cell and long-distance movement. The TGB proteins have been traditionally classified as hordei-like or potex-like based on phylogenetic comparisons and differences in movement mechanisms of the Hordeivirus and Potexvirus spp. However, accumulating data from other model viruses suggests that a revised framework is needed to accommodate the profound differences in protein interactions occurring during infection and ancillary capsid protein requirements for movement. The goal of this article is to highlight common features of the TGB proteins and salient differences in movement properties exhibited by individual viruses encoding these proteins. We discuss common and divergent aspects of the TGB transport machinery, describe putative nucleoprotein movement complexes, highlight recent data on TGB protein interactions and topological properties, and review membrane associations occurring during subcellular targeting and cell-to-cell movement. We conclude that the existing models cannot be used to explain all TGB viruses, and we propose provisional Potexvirus, Hordeivirus, and Pomovirus models. We also suggest areas that might profit from future research on viruses harboring this intriguing arrangement of movement proteins.
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Affiliation(s)
- Jeanmarie Verchot-Lubicz
- Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK 74078, USA.
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Chiu MH, Chen IH, Baulcombe DC, Tsai CH. The silencing suppressor P25 of Potato virus X interacts with Argonaute1 and mediates its degradation through the proteasome pathway. MOLECULAR PLANT PATHOLOGY 2010; 11:641-9. [PMID: 20696002 PMCID: PMC6640501 DOI: 10.1111/j.1364-3703.2010.00634.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Previous evidence has indicated that the P25 protein encoded by Potato virus X (PVX) inhibits either the assembly or function of the effector complexes in the RNA silencing-based antiviral defence system (Bayne et al., Cell-to-cell movement of Potato Potexvirus X is dependent on suppression of RNA silencing. Plant J.44, 471-482). This finding prompted us to investigate the possibility that P25 targets the Argonaute (AGO) effector nuclease of RNA silencing. Co-immunoprecipitation and Western blot analysis indicated that there is a strong interaction between P25 and AGO1 of Arabidopsis when these proteins are transiently co-expressed in Nicotiana benthamiana. P25 also interacts with AGO1, AGO2, AGO3 and AGO4, but not with AGO5 and AGO9. As an effective suppressor, the amount of AGO1 accumulated in the presence of P25 was dramatically lower than that infiltrated with HcPro, but was restored when treated with a proteasome inhibitor MG132. These findings are consistent with the idea that RNA silencing is an antiviral defence mechanism and that the counter-defence role of P25 is through the degradation of AGO proteins via the proteasome pathway. Further support for this idea is provided by the observation that plants treated with MG132 are less susceptible to PVX and its relative Bamboo mosaic virus.
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Affiliation(s)
- Meng-Hsuen Chiu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
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66
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Cheng CW, Hsiao YY, Wu HC, Chuang CM, Chen JS, Tsai CH, Hsu YH, Wu YC, Lee CC, Meng M. Suppression of bamboo mosaic virus accumulation by a putative methyltransferase in Nicotiana benthamiana. J Virol 2009; 83:5796-805. [PMID: 19297487 PMCID: PMC2681968 DOI: 10.1128/jvi.02471-08] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 03/10/2009] [Indexed: 12/12/2022] Open
Abstract
Bamboo mosaic virus (BaMV) is a 6.4-kb positive-sense RNA virus belonging to the genus Potexvirus of the family Flexiviridae. The 155-kDa viral replicase, the product of ORF1, comprises an N-terminal S-adenosyl-l-methionine (AdoMet)-dependent guanylyltransferase, a nucleoside triphosphatase/RNA 5'-triphosphatase, and a C-terminal RNA-dependent RNA polymerase (RdRp). To search for cellular factors potentially involved in the regulation of replication and/or transcription of BaMV, the viral RdRp domain was targeted as bait to screen against a leaf cDNA library of Nicotiana benthamiana using a yeast two-hybrid system. A putative methyltransferase (PNbMTS1) of 617 amino acid residues without an established physiological function was identified. Cotransfection of N. benthamiana protoplasts with a BaMV infectious clone and the PNbMTS1-expressing plasmid showed a PNbMTS1 dosage-dependent inhibitory effect on the accumulation of BaMV coat protein. Deletion of the N-terminal 36 amino acids, deletion of a predicted signal peptide or transmembrane segment, or mutations in the putative AdoMet-binding motifs of PNbMTS1 abolished the inhibitory effect. In contrast, suppression of PNbMTS1 by virus-induced gene silencing in N. benthamiana increased accumulation of the viral coat protein as well as the viral genomic RNA. Collectively, PNbMTS1 may function as an innate defense protein against the accumulation of BaMV through an uncharacterized mechanism.
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Affiliation(s)
- Chun-Wei Cheng
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
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67
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Seay M, Hayward AP, Tsao J, Dinesh-Kumar SP. Something old, something new: plant innate immunity and autophagy. Curr Top Microbiol Immunol 2009; 335:287-306. [PMID: 19802571 DOI: 10.1007/978-3-642-00302-8_14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Autophagy performs a variety of established functions during plant growth and development. Recently, autophagy has been further implicated in the regulation of programmed cell death induced during the plant innate immune response. In this chapter we describe specific mechanisms through which autophagy may contribute to a successful defense against pathogen invasion. Accumulating evidence shows that the plant immune system utilizes the chloroplasts as primary sites for the regulation of cell death programs. Viruses also appear to utilize the chloroplast as a site of replication and accumulation, potentially inactivating chloroplast defense signaling in the process. Autophagy-like mechanisms have been observed to target the chloroplast, which we refer to as "chlorophagy," potentially targeting invasive viruses for degradation or regulating chloroplast-based signaling during the immune response. We hypothesize that chlorophagy is significant for the execution of plant immune defenses, during both basal and effector-triggered immunity.
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Affiliation(s)
- Montrell Seay
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
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Huang YW, Hu CC, Lin NS, Tsai CH, Hsu YH. In vitro replication of Bamboo mosaic virus satellite RNA. Virus Res 2008; 136:98-106. [PMID: 18538884 DOI: 10.1016/j.virusres.2008.04.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 04/13/2008] [Accepted: 04/28/2008] [Indexed: 01/17/2023]
Abstract
An in vitro system was applied to analyze the replication of a satellite RNA of Bamboo mosaic virus (BaMV), designated satBaMV RNA, using solubilized membrane-bound RNA-dependent RNA polymerase (RdRp) complexes isolated from BaMV-infected Nicotiana benthamiana. After removal of endogenous templates, the RdRp complexes of BaMV catalyzed RNA synthesis upon the addition of the full-length positive (+)- or negative (-)-strand satBaMV RNA transcripts used as templates. Both (+)- and (-)-satBaMV RNA products were detected when only the (+)-satBaMV RNA was used as a template in the in vitro RdRp assays, which further demonstrated the capability of the RdRp preparation to complete the replication cycles of satBaMV RNAs. In addition, use of 5' rapid amplification of cDNA ends and DNA sequencing showed that the BaMV RdRp preparation could specifically recognize the promoter sequences in the (-)-satBaMV RNA for accurate initiation of (+)-satBaMV RNA synthesis. The results suggested that the same enzyme complexes could be used for the replication of both BaMV genomic and satBaMV RNAs. The soluble and template-dependent RdRp could be further used in mechanistic studies, such as those analyzing the cis-elements and candidate host factors required for satBaMV RNA replication in vitro.
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Affiliation(s)
- Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuokuang Road, Taichung 40227, Taiwan, ROC
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Verchot-Lubicz J, Ye CM, Bamunusinghe D. Molecular biology of potexviruses: recent advances. J Gen Virol 2007; 88:1643-1655. [PMID: 17485523 DOI: 10.1099/vir.0.82667-0] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Recent advances in potexvirus research have produced new models describing virus replication, cell-to-cell movement, encapsidation, R gene-mediated resistance and gene silencing. Interactions between distant RNA elements are a central theme in potexvirus replication. The 5′ non-translated region (NTR) regulates genomic and subgenomic RNA synthesis and encapsidation, as well as virus plasmodesmal transport. The 3′ NTR regulates both plus- and minus-strand RNA synthesis. How the triple gene-block proteins interact for virus movement is still elusive. As the potato virus X (PVX) TGBp1 protein gates plasmodesmata, regulates virus translation and is a suppressor of RNA silencing, further research is needed to determine how these properties contribute to propelling virus through the plasmodesmata. Specifically, TGBp1 suppressor activity is required for virus movement, but how the silencing machinery relates to plasmodesmata is not known. The TGBp2 and TGBp3 proteins are endoplasmic reticulum (ER)-associated proteins required for virus movement. TGBp2 associates with ER-derived vesicles that traffic along the actin network. Future research will determine whether the virus-induced vesicles are cytopathic structures regulating events along the ER or are vehicles carrying virus to the plasmodesmata for transfer into neighbouring cells. Efforts to assemble virions in vitro identified a single-tailed particle (STP) comprising RNA, coat protein (CP) and TGBp1. It has been proposed that TGBp1 aids in transport of virions or STP between cells and ensures translation of RNA in the receiving cells. PVX is also a tool for studying Avr–R gene interactions and gene silencing in plants. The PVX CP is the elicitor for the Rx gene. Recent reports of the PVX CP reveal how CP interacts with the Rx gene product.
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Affiliation(s)
- Jeanmarie Verchot-Lubicz
- Oklahoma State University, Department of Entomology and Plant Pathology, 127 Noble Research Center, Stillwater, OK 74078, USA
| | - Chang-Ming Ye
- Oklahoma State University, Department of Entomology and Plant Pathology, 127 Noble Research Center, Stillwater, OK 74078, USA
| | - Devinka Bamunusinghe
- Oklahoma State University, Department of Entomology and Plant Pathology, 127 Noble Research Center, Stillwater, OK 74078, USA
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