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Plug-and-Display Photo-Switchable Systems on Plant Virus Nanoparticles. BIOTECH (BASEL (SWITZERLAND)) 2022; 11:biotech11040049. [PMID: 36278561 PMCID: PMC9589989 DOI: 10.3390/biotech11040049] [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: 08/25/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Light can be used to regulate protein interactions with a high degree of spatial and temporal precision. Photo-switchable systems therefore allow the development of controllable protein complexes that can influence various cellular and molecular processes. Here, we describe a plant virus-based nanoparticle shuttle for the distribution of proteins that can be released when exposed to light. Potato virus X (PVX) is often used as a presentation system for heterologous proteins and epitopes, and has ideal properties for biomedical applications such as good tissue penetration and the ability to form hydrogels that present signaling molecules and promote cell adhesion. In this study, we describe three different systems attached to the surface of PVX particles: LOVTRAP, BphP1/QPAS1 and Dronpa145N. We demonstrated the functionality of all three photo-switchable protein complexes in vitro and the successful loading and unloading of PVX particles. The new systems provide the basis for promising applications in the biomedical and biomaterial sciences.
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Doski S, Bolus S, Grinstead S, Juszczak S, Groth-Helms D, Mollov D. Complete sequence and genome characterization of a new potexvirus isolated from Chaenostoma cordatum. Arch Virol 2022; 167:2089-2092. [PMID: 35796833 DOI: 10.1007/s00705-022-05520-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022]
Abstract
Leaves from the ornamental plant Chaenostoma cordatum (Thunb.) Benth. expressing virus-like symptoms were collected for pathogen testing. A virus with features consistent with those of members of the genus Potexvirus was identified by high-throughput sequencing. The genome sequence was confirmed and completed using RT-PCR, cloning, rapid amplification of cDNA ends kits, and Sanger sequencing, revealing a complete viral genome of 6,071 nucleotides, excluding the poly-A tail. Phylogenetic analysis of the RNA-dependent RNA polymerase sequence from the viral genome indicated that its closest relative is Plantago asiatica mosaic virus. Further analysis of the nucleotide and amino acid sequences revealed that it had diverged enough from other potexviruses to be considered a member of a new species.
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Affiliation(s)
- Shadin Doski
- USDA-ARS National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - Stephen Bolus
- USDA-ARS National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - Samuel Grinstead
- USDA-ARS National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | | | | | - Dimitre Mollov
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR, 97330, USA.
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Plchová H, Moravec T, Čeřovská N, Pobořilová Z, Dušek J, Kratochvílová K, Navrátil O, Kundu JK. A GoldenBraid-Compatible Virus-Based Vector System for Transient Expression of Heterologous Proteins in Plants. Viruses 2022; 14:1099. [PMID: 35632840 PMCID: PMC9146717 DOI: 10.3390/v14051099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/09/2022] [Accepted: 05/19/2022] [Indexed: 12/10/2022] Open
Abstract
We have developed a Potato virus X (PVX)-based vector system compatible with the GoldenBraid 2.0 (GB) cloning strategy to transiently express heterologous proteins or peptides in plants for biotechnological purposes. This vector system consists of three domestication vectors carrying three GB parts-the cauliflower mosaic virus (CaMV) 35S promoter with PVX upstream of the second subgenomic promoter of the PVX coat protein (PVX CP SGP), nopaline synthase (NOS) terminator with PVX downstream of the first PVX CP SGP and the gene of interest (GOI). The full-length PVX clone carrying the sequence encoding a green fluorescent protein (GFP) as GOI was incorporated into the binary GB vector in a one-step reaction of three GB parts using the four-nucleotide GB standard syntax. We investigated whether the obtained vector named GFP/pGBX enables systemic PVX infection and expression of GFP in Nicotiana benthamiana plants. We show that this GB-compatible vector system can be used for simple and efficient assembly of PVX-based expression constructs and that it meets the current need for interchange of standard biological parts used in different expression systems.
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Affiliation(s)
- Helena Plchová
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
| | - Tomáš Moravec
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
| | - Noemi Čeřovská
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
| | - Zuzana Pobořilová
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
| | - Jakub Dušek
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
- Department of Plant Protection, Czech University of Life Sciences, 16500 Prague, Czech Republic
| | - Kateřina Kratochvílová
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
| | - Oldřich Navrátil
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
| | - Jiban Kumar Kundu
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic
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4
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Dickmeis C, Commandeur U. Advanced Fusion Strategies for the Production of Functionalized Potato Virus X Virions. Methods Mol Biol 2022; 2480:215-239. [PMID: 35616866 DOI: 10.1007/978-1-0716-2241-4_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant virions are ideal for nanotechnology applications because they are structurally diverse and can self-assemble naturally, allowing for large-scale production in plants by molecular farming. Potato virus X (PVX) is particularly amenable due to the unique properties of its filamentous and flexible capsid, but efficient strategies are required to adapt the surface properties of PVX, such as the attachment of proteins and peptides. This chapter describes the selection and utilization of 2A ribosomal skip sequences, allowing the presentation of heterologous proteins and peptides as N-terminal fusions to the PVX coat protein at different densities. Another strategy for the rapid modification of PVX capsids is the plug-and-display module of the SpyTag/SpyCatcher system. The SpyTag can be presented on the PVX surface, allowing for the attachment of any protein fused to the SpyCatcher sequence.
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Affiliation(s)
- Christina Dickmeis
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany.
| | - Ulrich Commandeur
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
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Huang YW, Sun CI, Hu CC, Tsai CH, Meng M, Lin NS, Hsu YH. NbPsbO1 Interacts Specifically with the Bamboo Mosaic Virus (BaMV) Subgenomic RNA (sgRNA) Promoter and Is Required for Efficient BaMV sgRNA Transcription. J Virol 2021; 95:e0083121. [PMID: 34379502 PMCID: PMC8475527 DOI: 10.1128/jvi.00831-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/28/2021] [Indexed: 11/26/2022] Open
Abstract
Many positive-strand (+) RNA viruses produce subgenomic RNAs (sgRNAs) in the infection cycle through the combined activities of viral replicase and host proteins. However, knowledge about host proteins involved in direct sgRNA promoter recognition is limited. Here, in the partially purified replicase complexes from Bamboo mosaic virus (BaMV)-infected tissue, we have identified the Nicotiana benthamiana photosystem II oxygen-evolving complex protein, NbPsbO1, which specifically interacted with the promoter of sgRNA but not that of genomic RNA (gRNA). Silencing of NbPsbO1 expression suppressed BaMV accumulation in N. benthamiana protoplasts without affecting viral gRNA replication. Overexpression of wild-type NbPsbO1 stimulated BaMV sgRNA accumulation. Fluorescent microscopy examination revealed that the fluorescence associated with NbPsbO1 was redistributed from chloroplast granal thylakoids to stroma in BaMV-infected cells. Overexpression of a mislocalized mutant of NbPsbO1, dTPPsbO1-T7, inhibited BaMV RNA accumulation in N. benthamiana, whereas overexpression of an NbPsbO1 derivative, sPsbO1-T7, designed to be targeted to chloroplast stroma, upregulated the sgRNA level. Furthermore, depletion of NbPsbO1 in BaMV RdRp preparation significantly inhibited sgRNA synthesis in vitro but exerted no effect on (+) or (-) gRNA synthesis, which indicates that NbPsbO1 is required for efficient sgRNA synthesis. These results reveal a novel role for NbPsbO1 in the selective enhancement of BaMV sgRNA transcription, most likely via direct interaction with the sgRNA promoter. IMPORTANCE Production of subgenomic RNAs (sgRNAs) for efficient translation of downstream viral proteins is one of the major strategies adapted for viruses that contain a multicistronic RNA genome. Both viral genomic RNA (gRNA) replication and sgRNA transcription rely on the combined activities of viral replicase and host proteins, which recognize promoter regions for the initiation of RNA synthesis. However, compared to the cis-acting elements involved in the regulation of sgRNA synthesis, the host factors involved in sgRNA promoter recognition mostly remain to be elucidated. Here, we found a chloroplast protein, NbPsbO1, which specifically interacts with Bamboo mosaic virus (BaMV) sgRNA promoter. We showed that NbPsbO1 is relocated to the BaMV replication site in BaMV-infected cells and demonstrated that NbPsbO1 is required for efficient BaMV sgRNA transcription but exerts no effect on gRNA replication. This study provides a new insight into the regulating mechanism of viral gRNA and sgRNA synthesis.
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Affiliation(s)
- Ying Wen Huang
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chu I Sun
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung, Taiwan
| | - Chung Chi Hu
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Ching Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Menghsiao Meng
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung, Taiwan
| | - Na Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yau Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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6
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Mei Y, Beernink BM, Ellison EE, Konečná E, Neelakandan AK, Voytas DF, Whitham SA. Protein expression and gene editing in monocots using foxtail mosaic virus vectors. PLANT DIRECT 2019; 3:e00181. [PMID: 31768497 PMCID: PMC6874699 DOI: 10.1002/pld3.181] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/08/2019] [Accepted: 10/24/2019] [Indexed: 05/03/2023]
Abstract
Plant viruses can be engineered to carry sequences that direct silencing of target host genes, expression of heterologous proteins, or editing of host genes. A set of foxtail mosaic virus (FoMV) vectors was developed that can be used for transient gene expression and single guide RNA delivery for Cas9-mediated gene editing in maize, Setaria viridis, and Nicotiana benthamiana. This was accomplished by duplicating the FoMV capsid protein subgenomic promoter, abolishing the unnecessary open reading frame 5A, and inserting a cloning site containing unique restriction endonuclease cleavage sites immediately after the duplicated promoter. The modified FoMV vectors transiently expressed green fluorescent protein (GFP) and bialaphos resistance (BAR) protein in leaves of systemically infected maize seedlings. GFP was detected in epidermal and mesophyll cells by epifluorescence microscopy, and expression was confirmed by Western blot analyses. Plants infected with FoMV carrying the bar gene were temporarily protected from a glufosinate herbicide, and expression was confirmed using a rapid antibody-based BAR strip test. Expression of these proteins was stabilized by nucleotide substitutions in the sequence of the duplicated promoter region. Single guide RNAs expressed from the duplicated promoter mediated edits in the N. benthamiana Phytoene desaturase gene, the S. viridis Carbonic anhydrase 2 gene, and the maize HKT1 gene encoding a potassium transporter. The efficiency of editing was enhanced in the presence of synergistic viruses and a viral silencing suppressor. This work expands the utility of FoMV for virus-induced gene silencing (VIGS), virus-mediated overexpression (VOX), and virus-enabled gene editing (VEdGE) in monocots.
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Affiliation(s)
- Yu Mei
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Bliss M. Beernink
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Evan E. Ellison
- Department of Genetics, Cell Biology and DevelopmentCenter for Genome EngineeringCenter for Precision Plant GenomicsUniversity of MinnesotaSt. PaulMNUSA
| | - Eva Konečná
- Department of Genetics, Cell Biology and DevelopmentCenter for Genome EngineeringCenter for Precision Plant GenomicsUniversity of MinnesotaSt. PaulMNUSA
| | | | - Daniel F. Voytas
- Department of Genetics, Cell Biology and DevelopmentCenter for Genome EngineeringCenter for Precision Plant GenomicsUniversity of MinnesotaSt. PaulMNUSA
| | - Steven A. Whitham
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
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7
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Röder J, Dickmeis C, Commandeur U. Small, Smaller, Nano: New Applications for Potato Virus X in Nanotechnology. FRONTIERS IN PLANT SCIENCE 2019; 10:158. [PMID: 30838013 PMCID: PMC6390637 DOI: 10.3389/fpls.2019.00158] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/29/2019] [Indexed: 05/08/2023]
Abstract
Nanotechnology is an expanding interdisciplinary field concerning the development and application of nanostructured materials derived from inorganic compounds or organic polymers and peptides. Among these latter materials, proteinaceous plant virus nanoparticles have emerged as a key platform for the introduction of tailored functionalities by genetic engineering and conjugation chemistry. Tobacco mosaic virus and Cowpea mosaic virus have already been developed for bioimaging, vaccination and electronics applications, but the flexible and filamentous Potato virus X (PVX) has received comparatively little attention. The filamentous structure of PVX particles allows them to carry large payloads, which are advantageous for applications such as biomedical imaging in which multi-functional scaffolds with a high aspect ratio are required. In this context, PVX achieves superior tumor homing and retention properties compared to spherical nanoparticles. Because PVX is a protein-based nanoparticle, its unique functional properties are combined with enhanced biocompatibility, making it much more suitable for biomedical applications than synthetic nanomaterials. Moreover, PVX nanoparticles have very low toxicity in vivo, and superior pharmacokinetic profiles. This review focuses on the production of PVX nanoparticles engineered using chemical and/or biological techniques, and describes current and future opportunities and challenges for the application of PVX nanoparticles in medicine, diagnostics, materials science, and biocatalysis.
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Affiliation(s)
| | | | - Ulrich Commandeur
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
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8
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Chkuaseli T, White KA. Intragenomic Long-Distance RNA-RNA Interactions in Plus-Strand RNA Plant Viruses. Front Microbiol 2018; 9:529. [PMID: 29670583 PMCID: PMC5893793 DOI: 10.3389/fmicb.2018.00529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/08/2018] [Indexed: 01/10/2023] Open
Abstract
Plant viruses that contain positive-strand RNA genomes represent an important class of pathogen. The genomes of these viruses harbor RNA sequences and higher-order RNA structures that are essential for the regulation of viral processes during infections. In recent years, it has become increasingly evident that, in addition to locally positioned RNA structures, long-distance intragenomic interactions, involving nucleotide base pairing over large distances, also contribute significantly to the control of various viral events. Viral processes that are modulated by such interactions include genome replication, translation initiation, translational recoding, and subgenomic mRNA transcription. Here, we review the structure and function of different types of long-distance RNA–RNA interactions, herein termed LDRIs, present in members of the family Tombusviridae and other plus-strand RNA plant viruses.
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Affiliation(s)
| | - K Andrew White
- Department of Biology, York University, Toronto, ON, Canada
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9
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Huang YW, Hu CC, Tsai CH, Lin NS, Hsu YH. Chloroplast Hsp70 Isoform Is Required for Age-Dependent Tissue Preference of Bamboo mosaic virus in Mature Nicotiana benthamiana Leaves. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:631-645. [PMID: 28459172 DOI: 10.1094/mpmi-01-17-0012-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Plant viruses may exhibit age-dependent tissue preference in their hosts but the underlying mechanisms are not well understood. In this study, we provide several lines of evidence to reveal the determining role of a protein of the Nicotiana benthamiana chloroplast Hsp70 (NbcpHsp70) family, NbcpHsp70-2, involved in the preference of Bamboo mosaic virus (BaMV) to infect older tissues. NbcpHsp70 family proteins were identified in complexes pulled down with BaMV replicase as the bait. Among the isoforms of NbcpHsp70, only the specific silencing of NbcpHsp70-2 resulted in the significant decrease of BaMV RNA in N. benthamiana protopalsts, indicating that NbcpHsp70-2 is involved in the efficient replication of BaMV RNA. We further identified the age-dependent import regulation signal contained in the transit peptide of NbcpHsp70-2. Deletion, overexpression, and substitution experiments revealed that the signal in the transit peptide of NbcpHsp70-2 is crucial for both the import of NbcpHsp70-2 into older chloroplasts and the preference of BaMV for infecting older leaves of N. benthamiana. Together, these data demonstrated that BaMV may exploit a cellular age-dependent transportation mechanism to target a suitable environment for viral replication.
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Affiliation(s)
- Ying Wen Huang
- 1 Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; and
| | - Chung Chi Hu
- 1 Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; and
| | - Ching Hsiu Tsai
- 1 Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; and
| | - Na Sheng Lin
- 1 Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; and
- 2 Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yau Heiu Hsu
- 1 Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; and
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10
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Chen IH, Huang YW, Tsai CH. The Functional Roles of the Cis-acting Elements in Bamboo mosaic virus RNA Genome. Front Microbiol 2017; 8:645. [PMID: 28450857 PMCID: PMC5390519 DOI: 10.3389/fmicb.2017.00645] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/29/2017] [Indexed: 02/05/2023] Open
Abstract
Bamboo mosaic virus (BaMV), which belongs to the genus Potexvirus in the family Alphaflexiviridae, has a single-stranded positive-sense RNA genome that is approximately 6400 nucleotides (nts) in length. Positive-sense RNA viruses can use genomic RNA as a template for translation and replication after entering a suitable host cell. Furthermore, such viral RNA is recognized by capsid protein for packaging and by viral movement protein(s) or the movement protein complex for cell-to-cell and systemic movement. Hence, viral RNA must contain signals for different functions to complete the viral infection cycle. In this review, we examine various cis-acting elements in the genome of BaMV. The highly structured 3' untranslated region (UTR) of the BaMV genomic RNA plays multiple roles in the BaMV infection cycle, including targeting chloroplasts for RNA replication, providing an initiation site for the synthesis of minus-strand RNA, signaling for polyadenylation, and directing viral long-distance movement. The nt at the extreme 3' end and the structure of the 3'-terminus of minus-strand RNA are involved in the initiation of plus-strand genomic RNA synthesis. Both these regions have been mapped and reported to interact with the viral-encoded RNA-dependent RNA polymerase. Moreover, the sequences upstream of open reading frames (ORFs) 2, 3, and 5 are involved in regulating subgenomic RNA synthesis. The cis-acting elements that were identified in BaMV RNA are discussed and compared with those of other potexviruses.
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Affiliation(s)
- I-Hsuan Chen
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
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11
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Choi H, Cho WK, Kim KH. Two homologous host proteins interact with potato virus X RNAs and CPs and affect viral replication and movement. Sci Rep 2016; 6:28743. [PMID: 27353522 PMCID: PMC4926161 DOI: 10.1038/srep28743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/08/2016] [Indexed: 11/30/2022] Open
Abstract
Because viruses encode only a small number of proteins, all steps of virus infection rely on specific interactions between viruses and hosts. We previously screened several Nicotiana benthamiana (Nb) proteins that interact with the stem-loop 1 (SL1) RNA structure located at the 5' end of the potato virus X (PVX) genome. In this study, we characterized two of these proteins (NbCPIP2a and NbCPIP2b), which are homologous and are induced upon PVX infection. Electrophoretic mobility shift assay confirmed that both proteins bind to either SL1(+) or SL1(-) RNAs of PVX. The two proteins also interact with the PVX capsid protein (CP) in planta. Overexpression of NbCPIP2a positively regulated systemic movement of PVX in N. benthamiana, whereas NbCPIP2b overexpression did not affect systemic movement of PVX. Transient overexpression and silencing experiments demonstrated that NbCPIP2a and NbCPIP2b are positive regulators of PVX replication and that the effect on replication was greater for NbCPIP2a than for NbCPIP2b. Although these two host proteins are associated with plasma membranes, PVX infection did not affect their subcellular localization. Taken together, these results indicate that NbCPIP2a and NbCPIP2b specifically bind to PVX SL1 RNAs as well as to CP and enhance PVX replication and movement.
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Affiliation(s)
- Hoseong Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Won Kyong Cho
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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12
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Dickmeis C, Honickel MMA, Fischer R, Commandeur U. Production of Hybrid Chimeric PVX Particles Using a Combination of TMV and PVX-Based Expression Vectors. Front Bioeng Biotechnol 2015; 3:189. [PMID: 26636076 PMCID: PMC4653303 DOI: 10.3389/fbioe.2015.00189] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/04/2015] [Indexed: 12/30/2022] Open
Abstract
We have generated hybrid chimeric potato virus X (PVX) particles by coexpression of different PVX coat protein fusions utilizing tobacco mosaic virus (TMV) and PVX-based expression vectors. Coinfection was achieved with a modified PVX overcoat vector displaying a fluorescent protein and a TMV vector expressing another PVX fluorescent overcoat fusion protein. Coexpression of the PVX-CP fusions in the same cells was confirmed by epifluorescence microscopy. Labeling with specific antibodies and transmission electron microscopy revealed chimeric particles displaying green fluorescent protein and mCherry on the surface. These data were corroborated by bimolecular fluorescence complementation. We used split-mCherry fragments as PVX coat fusions and confirmed an interaction between the split-mCherry fragments in coinfected cells. The presence of assembled split-mCherry on the surface confirmed the hybrid character of the chimeric particles.
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Affiliation(s)
- Christina Dickmeis
- Institute for Molecular Biotechnology, RWTH Aachen University , Aachen , Germany
| | | | - Rainer Fischer
- Institute for Molecular Biotechnology, RWTH Aachen University , Aachen , Germany ; Fraunhofer Institute for Molecular Biology and Applied Ecology , Aachen , Germany
| | - Ulrich Commandeur
- Institute for Molecular Biotechnology, RWTH Aachen University , Aachen , Germany
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13
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Putlyaev EV, Smirnov AA, Karpova OV, Atabekov JG. Double Subgenomic Promoter Control for a Target Gene Superexpression by a Plant Viral Vector. BIOCHEMISTRY. BIOKHIMIIA 2015; 80:1039-46. [PMID: 26547072 DOI: 10.1134/s000629791508009x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Several new deconstructed vectors based on a potexvirus genome sequence for efficient expression of heterologous proteins in plants were designed. The first obtained vector (AltMV-single), based on the Alternanthera mosaic virus (AltMV) strain MU genome, bears a typical architecture for deconstructed plant viral vectors, i.e. a triple gene block was deleted from the viral genome and the model gene of interest was placed under control of the first viral subgenomic promoter. To enhance the efficiency of expression, maintained by the AltMV-single, another vector (AltMV-double) was designed. In AltMV-double, the gene of interest was controlled by two viral subgenomic promoters located sequentially without a gap upstream of the target gene. It was found that AltMV-double provided a significantly higher level of accumulation of the target protein in plants than AltMV-single. Moreover, our data clearly show the requirement of the presence and functioning of both the subgenomic promoters for demonstrated high level of target protein expression by AltMV-double. Taken together, our results describe an additional possible way to enhance the efficiency of transient protein expression maintained in plants by a plant viral vector.
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Affiliation(s)
- E V Putlyaev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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Dickmeis C, Fischer R, Commandeur U. Potato virus X-based expression vectors are stabilized for long-term production of proteins and larger inserts. Biotechnol J 2014; 9:1369-79. [PMID: 25171768 DOI: 10.1002/biot.201400347] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/01/2014] [Accepted: 08/27/2014] [Indexed: 12/18/2022]
Abstract
Plus-strand RNA viruses such as Potato virus X (PVX) are often used as high-yielding expression vectors in plants, because they tolerate extra transgene insertion and expression without disrupting normal virus functions. However, sequence redundancy due to promoter duplication often leads to genetic instability. Although heterologous subgenomic promoter-like sequences (SGPs) have been successfully used in Tobacco mosaic virus vectors, only homologous SGP duplications have been used in PVX vectors. We stabilized PVX-based vectors by combining heterologous SGPs from related potexviruses with an N-terminal coat protein (CP) deletion. We selected two SGPs with core sequences homologous to PVX, from Bamboo mosaic virus (BaMV) and Cassava common mosaic virus, as well as a SGP with a heterologous core sequence from Foxtail mosaic virus (FoMV). We found that only the BaMV and CsCMV SGPs were utilized by the PVX replicase. However, the transgene remained unstable, due to the presence of an additional region with strong sequence similarity at the 5' end of the cp gene. The BaMV SGP combined with an N-terminal CP deletion achieved high PVX vector stability. This new expression vector is particularly useful for long-term production of proteins and for larger inserts. The improved PVX-based vectors are suitable for the systemic expression of any gene of interest in PVX host plants. The PVX-based vector can be advantageous for the overexpression of proteins, to analyze protein functions in planta or as a system for virus-induced gene silencing.
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Affiliation(s)
- Christina Dickmeis
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
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15
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Park MR, Seo JK, Kim KH. Viral and nonviral elements in potexvirus replication and movement and in antiviral responses. Adv Virus Res 2013; 87:75-112. [PMID: 23809921 DOI: 10.1016/b978-0-12-407698-3.00003-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In Potato virus X, a member of the genus Potexvirus, special sequences and structures at the 5' and 3' ends of the nontranslated region function as cis-acting elements for viral replication. These elements greatly affect interactions between viral RNAs and those between viral RNAs and host factors. The potexvirus genome encodes five open-reading frames. Viral replicase, which is required for the synthesis of viral RNA, binds viral RNA elements and host factors to form a viral replication complex at the host cellular membrane. The coat protein (CP) and three viral movement proteins (TGB1, TGB2, and TGB3) have critical roles in mediating cell-to-cell viral movement through plasmodesmata by virion formation or by nonvirion ribonucleoprotein (RNP) complex formation with viral movement proteins (TGBs). The RNP complex, like TGB1-CP-viral RNA, is associated with viral replicase and used for immediate reinitiation of viral replication in newly invaded cells. Higher plants have defense mechanisms against potexviruses such as Rx-mediated resistance and RNA silencing. The CP acts as an avirulence effector for plant defense mechanisms, while TGB1 functions as a viral suppressor of RNA silencing, which is the mechanism of innate immune resistance. Here, we describe recent findings concerning the involvement of viral and host factors in potexvirus replication and in antiviral responses to potexvirus infection.
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Affiliation(s)
- Mi-Ri Park
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
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16
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Komatsu K, Hirata H, Fukagawa T, Yamaji Y, Okano Y, Ishikawa K, Adachi T, Maejima K, Hashimoto M, Namba S. Infection of capilloviruses requires subgenomic RNAs whose transcription is controlled by promoter-like sequences conserved among flexiviruses. Virus Res 2012; 167:8-15. [DOI: 10.1016/j.virusres.2012.02.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/18/2012] [Accepted: 02/20/2012] [Indexed: 11/16/2022]
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17
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Cho SY, Cho WK, Choi HS, Kim KH. Cis-acting element (SL1) of Potato virus X controls viral movement by interacting with the NbMPB2Cb and viral proteins. Virology 2012; 427:166-76. [PMID: 22405626 DOI: 10.1016/j.virol.2012.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 01/09/2012] [Accepted: 02/04/2012] [Indexed: 01/21/2023]
Abstract
A number of candidate tobacco proteins that bind to cis-acting elements (SL1 RNAs) of Potato virus X (PVX) have been identified in previous studies. We further characterized TMV-MP30 binding protein 2C (MPB2C) homologous protein. We isolated NbMPB2Cb from Nicotiana benthamiana and confirmed the interaction of NbMPB2Cb with SL1 RNAs in vitro. The mRNA level of NbMPB2Cb was increased upon infection by PVX and Tobacco mosaic virus. The movement of PVX was reduced by overexpression of NbMPB2Cb and increased by silenced of NbMPB2Cb. In contrast, PVX RNA accumulation was not significantly altered in protoplasts. Protein-protein interaction assays showed that NbMPB2Cb interacts with PVX movement-associated proteins. PVX infection altered the subcellular localization of NbMPB2Cb from microtubules to endoplasmic reticulum. These data suggest that the NbMPB2Cb negatively affects PVX movement by interacting with SL1 RNAs and movement-associated proteins of PVX and by re-localizing in response to PVX infection.
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Affiliation(s)
- Sang-Yun Cho
- Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
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18
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Cho SY, Cho WK, Kim KH. Identification of tobacco proteins associated with the stem-loop 1 RNAs of Potato virus X. Mol Cells 2012; 33:379-84. [PMID: 22450689 PMCID: PMC3887799 DOI: 10.1007/s10059-012-2298-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 01/28/2012] [Accepted: 02/01/2012] [Indexed: 11/26/2022] Open
Abstract
Potato virus X (PVX) contains five viral proteins as well as cis-acting elements like stem-loop 1 (SL1) RNAs at the 5' region. SL1 RNAs are involved in PVX RNA replication, encapsidation, translation, and cell-to-cell movement. In this study, we performed two-dimensional electrophoresis Northwestern blot analysis and matrix-assisted laser desorption ionization time of flight mass spectrometry and identified 24 tobacco proteins that interact with SL1 RNAs. Interestingly, one-third of the identified host proteins have been shown to interact with many plant viral proteins. In addition, we demonstrated that PVX capsid protein can bind to both SL1(+/-) RNAs. We further selected three Nicotiana benthamiana proteins including NbMPB2Cb, NbMBF1, and NbCPIP2a, to confirm results of Northwestern blot analysis. Electrophoretic mobility shift assay showed that NbMPB2Cb and NbMBF1 bind to both SL1(+/-) RNAs in vitro. In contrast, NbCPIP2a interacts only SL1(+) RNA. Taken together, we provide a list of host proteins interacting with PVX SL1 RNAs, which would be good candidates for the study of viral RNA-host protein interaction.
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Affiliation(s)
- Sang-Yun Cho
- Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
| | - Won Kyong Cho
- Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
- Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
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19
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Sola I, Mateos-Gomez PA, Almazan F, Zuñiga S, Enjuanes L. RNA-RNA and RNA-protein interactions in coronavirus replication and transcription. RNA Biol 2011; 8:237-48. [PMID: 21378501 PMCID: PMC3230552 DOI: 10.4161/rna.8.2.14991] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/17/2011] [Accepted: 01/19/2011] [Indexed: 02/07/2023] Open
Abstract
Coronavirus (CoV) RNA synthesis includes the replication of the viral genome, and the transcription of sgRNAs by a discontinuous mechanism. Both processes are regulated by RNA sequences such as the 5' and 3' untranslated regions (UTRs), and the transcription regulating sequences (TRSs) of the leader (TRS-L) and those preceding each gene (TRS-Bs). These distant RNA regulatory sequences interact with each other directly and probably through protein-RNA and protein-protein interactions involving viral and cellular proteins. By analogy to other plus-stranded RNA viruses, such as polioviruses, in which translation and replication switch involves a cellular factor (PCBP) and a viral protein (3CD) it is conceivable that in CoVs the switch between replication and transcription is also associated with the binding of proteins that are specifically recruited by the replication or transcription complexes. Complexes between RNA motifs such as TRS-L and the TRS-Bs located along the CoV genome are probably formed previously to the transcription start, and most likely promote template-switch of the nascent minus RNA to the TRS-L region. Many cellular proteins interacting with regulatory CoV RNA sequences are members of the heterogeneous nuclear ribonucleoprotein (hnRNP) family of RNA-binding proteins, involved in mRNA processing and transport, which shuttle between the nucleus and the cytoplasm. In the context of CoV RNA synthesis, these cellular ribonucleoproteins might also participate in RNA-protein complexes to bring into physical proximity TRS-L and distant TRS-B, as proposed for CoV discontinuous transcription. In this review, we summarize RNA-RNA and RNA-protein interactions that represent modest examples of complex quaternary RNA-protein structures required for the fine-tuning of virus replication. Design of chemically defined replication and transcription systems will help to clarify the nature and activity of these structures.
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Affiliation(s)
- Isabel Sola
- Department of Molecular and Cell Biology, CNB, CSIC, Cantoblanco, Madrid, Spain
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20
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Park MR, Kwon SJ, Choi HS, Hemenway CL, Kim KH. Mutations that alter a repeated ACCA element located at the 5' end of the Potato virus X genome affect RNA accumulation. Virology 2008; 378:133-41. [PMID: 18589472 DOI: 10.1016/j.virol.2008.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 04/08/2008] [Accepted: 05/08/2008] [Indexed: 11/19/2022]
Abstract
The repeated ACCA or AC-rich sequence and structural (SL1) elements in the 5' non-translated region (NTR) of the Potato virus X (PVX) RNA play vital roles in the PVX life cycle by controlling translation, RNA replication, movement, and assembly. It has already been shown that the repeated ACCA or AC-rich sequence affect both gRNA and sgRNA accumulation, while not affecting minus-strand RNA accumulation, and are also required for host protein binding. The functional significance of the repeated ACCA sequence elements in the 5' NTR region was investigated by analyzing the effects of deletion and site-directed mutations on PVX replication in Nicotiana benthamiana plants and NT1 protoplasts. Substitution (ACCA into AAAA or UUUU) mutations introduced in the first (nt 10-13) element in the 5' NTR of the PVX RNA significantly affected viral replication, while mutations introduced in the second (nt 17-20) and third (nt 20-23) elements did not. The fourth (nt 29-32) ACCA element weakly affected virus replication, whereas mutations in the fifth (nt 38-41) significantly reduced virus replication due to the structure disruption of SL1 by AAAA and/or UUUU substitutions. Further characterization of the first ACCA element indicated that duplication of ACCA at nt 10-13 (nt 10-17, ACCAACCA) caused severe symptom development as compared to that of wild type, while deletion of the single element (nt 10-13), DeltaACCA) or tripling of this element caused reduced symptom development. Single- and double-nucleotide substitutions introduced into the first ACCA element revealed the importance of CC located at nt positions 11 and 12. Altogether, these results indicate that the first ACCA element is important for PVX replication.
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Affiliation(s)
- Mi-Ri Park
- Department of Agricultural Biotechnology and Center for Plant Molecular Genetics and Breeding Research, Seoul National University, Seoul 151-921, Korea
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21
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Nucleotide sequence and phylogenetic analysis of a new potexvirus: Malva Mosaic Virus. INFECTION GENETICS AND EVOLUTION 2008; 8:83-93. [DOI: 10.1016/j.meegid.2007.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Revised: 10/10/2007] [Accepted: 10/19/2007] [Indexed: 11/18/2022]
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Hu B, Pillai-Nair N, Hemenway C. Long-distance RNA-RNA interactions between terminal elements and the same subset of internal elements on the potato virus X genome mediate minus- and plus-strand RNA synthesis. RNA (NEW YORK, N.Y.) 2007; 13:267-80. [PMID: 17185361 PMCID: PMC1781375 DOI: 10.1261/rna.243607] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Potexvirus genomes contain conserved terminal elements that are complementary to multiple internal octanucleotide elements. Both local sequences and structures at the 5' terminus and long-distance interactions between this region and internal elements are important for accumulation of potato virus X (PVX) plus-strand RNA in vivo. In this study, the role of the conserved hexanucleotide motif within SL3 of the 3' NTR and internal conserved octanucleotide elements in minus-strand RNA synthesis was analyzed using both a template-dependent, PVX RNA-dependent RNA polymerase (RdRp) extract and a protoplast replication system. Template analyses in vitro indicated that 3' terminal templates of 850 nucleotides (nt), but not 200 nt, supported efficient, minus-strand RNA synthesis. Mutational analyses of the longer templates indicated that optimal transcription requires the hexanucleotide motif in SL3 within the 3' NTR and the complementary CP octanucleotide element 747 nt upstream. Additional experiments to disrupt interactions between one or more internal conserved elements and the 3' hexanucleotide element showed that long-distance interactions were necessary for minus-strand RNA synthesis both in vitro and in vivo. Additionally, multiple internal octanucleotide elements could serve as pairing partners with the hexanucleotide element in vivo. These cis-acting elements and interactions correlate in several ways to those previously observed for plus-strand RNA accumulation in vivo, suggesting that dynamic interactions between elements at both termini and the same subset of internal octanucleotide elements are required for both minus- and plus-strand RNA synthesis and potentially other aspects of PVX replication.
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Affiliation(s)
- Bin Hu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh 27695-7622, USA
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23
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Li W, Wong SM. Analyses of subgenomic promoters of Hibiscus chlorotic ringspot virus and demonstration of 5' untranslated region and 3'-terminal sequences functioning as subgenomic promoters. J Virol 2006; 80:3395-405. [PMID: 16537607 PMCID: PMC1440410 DOI: 10.1128/jvi.80.7.3395-3405.2006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hibiscus chlorotic ringspot virus (HCRSV), which belongs to the genus Carmovirus, generates two 3'-coterminal subgenomic RNAs (sgRNAs) of 1.4 kb and 1.7 kb. Transcription start sites of the two sgRNAs were identified at nucleotides (nt) 2178 and 2438, respectively. The full promoter of sgRNA1, a 118-base sequence, is localized between positions +6 and -112 relative to its transcription start site (+1). Similarly, a 132-base sequence, from +6 to -126, defines the sgRNA2 promoter. Computer analysis revealed that both sgRNA promoters share a similar two-stem-loop (SL1 + SL2) structure, immediately upstream of the transcription start site. Mutational analysis of the primary sequence and secondary structures showed further similarities between the two subgenomic promoters. The basal portion of SL2, encompassing the transcription start site, was essential for transcription activity in each promoter, while SL1 and the upper portion of SL2 played a role in transcription enhancement. Both the 5' untranslated region (UTR) and the last 87 nt at the 3' UTR of HCRSV genomic RNA are likely to be the putative genomic plus-strand and minus-strand promoters, respectively. They function well as individual sgRNA promoters to produce ectopic subgenomic RNAs in vivo but not to the same levels of the actual sgRNA promoters. This suggests that HCRSV sgRNA promoters share common features with the promoters for genomic plus-strand and minus-strand RNA synthesis. To our knowledge, this is the first demonstration that both the 5' UTR and part of the 3' UTR can be duplicated and function as sgRNA promoters within a single viral genome.
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Affiliation(s)
- Weimin Li
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore
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24
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Komatsu K, Kagiwada S, Takahashi S, Mori T, Yamaji Y, Hirata H, Ozeki J, Yoshida A, Suzuki M, Ugaki M, Namba S. Phylogenetic characteristics, genomic heterogeneity and symptomatic variation of five closely related Japanese strains of Potato virus X. Virus Genes 2005; 31:99-105. [PMID: 15965614 DOI: 10.1007/s11262-005-2205-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Revised: 12/28/2004] [Accepted: 02/17/2005] [Indexed: 11/24/2022]
Abstract
To elucidate the genomic determinants of Potato virus X (PVX) strains, which cause diverse responses in host plants, we determined the complete genomic RNA sequences of four Japanese PVX strains: PVX-BS, -BH, -OG, and -TO. These four strains, plus the previously sequenced PVX-OS strain, differ in their pathogenicity in wild potato (Solanum demissum) and tobacco (Nicotiana tabacum cv. Samsun NN). The genomic sequences of these five PVX strains were highly homologous (i.e., the nucleotide sequence identity ranged from 95.4 to 98.5%). Phylogenetic analysis indicated that the Japanese PVX strains originated from an ancestral PVX strain in the European group, and that the virulence of these strains in both S. demissum and tobacco is not correlated with their phylogenetic relationships, suggesting that the pathogenicity of each strain in these host plants is determined by a relatively small number of nucleotides and can easily be altered independent of phylogenetic relationships. Particularly, OS, BH, and BS, which respectively produce markedly contrasting ringspot, mosaic, and asymptomatic infections in tobacco leaves, were the most closely related, suggesting that these three strains are an attractive model for analyzing the genetic determinants causing these symptoms. A possible correlation between the genomic and biological differences of these strains is discussed.
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Affiliation(s)
- Ken Komatsu
- Laboratory of Bioresource Technology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba, Kashiwa, 277-8562, Japan
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25
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Kagiwada S, Yamaji Y, Komatsu K, Takahashi S, Mori T, Hirata H, Suzuki M, Ugaki M, Namba S. A single amino acid residue of RNA-dependent RNA polymerase in the Potato virus X genome determines the symptoms in Nicotiana plants. Virus Res 2005; 110:177-82. [PMID: 15845269 DOI: 10.1016/j.virusres.2004.12.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2004] [Revised: 12/07/2004] [Accepted: 12/23/2004] [Indexed: 11/24/2022]
Abstract
A Potato virus X (PVX) strain, PVX-OS, causes a necrotic mosaic in Nicotiana benthamiana and ring spot mosaic in N. tabacum cv. SamsunNN. By contrast, strain PVX-BS causes a mild mosaic in N. benthamiana and systemic asymptomatic infection in N. tabacum cv. SamsunNN. To investigate the viral determinant of this difference, we produced various infectious cDNA clones chimeric between these PVX genomes and clones with point mutations introduced by site-directed mutagenesis. Inoculation tests with these clones mapped the symptom determinant in Nicotiana plants to the 1422 amino acid residue in the region of the C-terminus of RNA-dependent RNA polymerase (RdRp). Western blot analysis and local lesion assay indicated that virus accumulation in the infected leaves was similar for these PVX strains, suggesting that the symptom difference was not due to virus accumulation.
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Affiliation(s)
- Satoshi Kagiwada
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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26
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Kwon SJ, Park MR, Kim KW, Plante CA, Hemenway CL, Kim KH. cis-Acting sequences required for coat protein binding and in vitro assembly of Potato virus X. Virology 2005; 334:83-97. [PMID: 15749125 DOI: 10.1016/j.virol.2005.01.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2004] [Revised: 11/17/2004] [Accepted: 01/14/2005] [Indexed: 10/25/2022]
Abstract
The 5' region of Potato virus X (PVX) RNA containing an AC-rich single-stranded region and stem-loop 1 (SL1) has been shown to be important for PVX replication (Miller, E.D., Plante, C.A., Kim, K.-H., Brown, J.W., Hemenway, C., 1998. Stem-loop structure in the 5' region of potato virus X genome required for plus-strand RNA accumulation. J. Mol. Biol. 284, 591-608.). Here, we describe the involvement of SL1 for binding to the PVX coat protein (CP) using an in vitro assembly system and various deletion mutants of the 5' region of PVX RNA. Internal and 5' terminal deletions of the 5'-nontranslated region of PVX RNA were assessed for their effects on formation of assembled virus-like particles (VLPs). Mutant RNAs that contain the top region of SL1 or sequences therein bound to CP to form VLPs. In contrast, transcripts of mutants that disrupt SL1 RNA structure were unable to form VLPs. SELEX was used to further confirm the specific RNA recognition of PVX CP using RNA transcripts containing randomized sequences of the upper portion of SL1. Wild-type (wt) sequences along with many other sequences that resemble SL1 structure were selected after fourth and fifth rounds of SELEX (27.0% and 44.4%, respectively). RNA transcripts from several SELEX winners that are predicted to form stable stem-loop structures very closely resembling wt PVX SL1 VLPs. RNA transcripts not predicted to form secondary structures similar to SL1 did not form VLPs in vitro. Taken together, our results suggest that RNA secondary structural elements within SL1 and/or sequences therein are crucial for formation of VLPs and are required for the specific recognition by the CP subunit.
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Affiliation(s)
- Sun-Jung Kwon
- School of Agricultural Biotechnology and Center for Plant Molecular Genetics and Breeding Research, Seoul National University, Seoul 151-921, Korea
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27
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Ayllón MA, Gowda S, Satyanarayana T, Karasev AV, Adkins S, Mawassi M, Guerri J, Moreno P, Dawson WO. Effects of modification of the transcription initiation site context on citrus tristeza virus subgenomic RNA synthesis. J Virol 2003; 77:9232-43. [PMID: 12915539 PMCID: PMC187412 DOI: 10.1128/jvi.77.17.9232-9243.2003] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Citrus tristeza virus (CTV), a member of the Closteroviridae, has a positive-sense RNA genome of about 20 kb organized into 12 open reading frames (ORFs). The last 10 ORFs are expressed through 3'-coterminal subgenomic RNAs (sgRNAs) regulated in both amounts and timing. Additionally, relatively large amounts of complementary sgRNAs are produced. We have been unable to determine whether these sgRNAs are produced by internal promotion from the full-length template minus strand or by transcription from the minus-stranded sgRNAs. Understanding the regulation of 10 sgRNAs is a conceptual challenge. In analyzing commonalities of a replicase complex in producing so many sgRNAs, we examined initiating nucleotides of the sgRNAs. We mapped the 5' termini of intermediate- (CP and p13) and low- (p18) produced sgRNAs that, like the two highly abundant sgRNAs (p20 and p23) previously mapped, all initiate with an adenylate. We then examined modifications of the initiation site, which has been shown to be useful in defining mechanisms of sgRNA synthesis. Surprisingly, mutation of the initiating nucleotide of the CTV sgRNAs did not prevent sgRNA accumulation. Based on our results, the CTV replication complex appears to initiate sgRNA synthesis with purines, preferably with adenylates, and is able to initiate synthesis using a nucleotide a few positions 5' or 3' of the native initiation nucleotide. Furthermore, the context of the initiation site appears to be a regulatory mechanism for levels of sgRNA production. These data do not support either of the established mechanisms for synthesis of sgRNAs, suggesting that CTV sgRNA production utilizes a different mechanism.
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Affiliation(s)
- María A Ayllón
- Department of Plant Pathology, University of Florida, Citrus Research and Education Center, Lake Alfred, Florida 33850, USA
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28
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Batten JS, Yoshinari S, Hemenway C. Potato virus X: a model system for virus replication, movement and gene expression. MOLECULAR PLANT PATHOLOGY 2003; 4:125-31. [PMID: 20569372 DOI: 10.1046/j.1364-3703.2003.00156.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
SUMMARY Considerable research has focused on the cis- and trans-acting components required for various aspects of the potato virus X (PVX) infection process. In addition, the development of PVX-based vectors has facilitated analyses of the PVX infection process and provided diverse technological applications. As a result, the PVX system will continue to serve as a model for analyses of processes such as virus movement, RNA replication, and gene silencing, and as a tool for protein expression.
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Affiliation(s)
- Jeffrey S Batten
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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29
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Kim KH, Kwon SJ, Hemenway C. Cellular protein binds to sequences near the 5' terminus of potato virus X RNA that are important for virus replication. Virology 2002; 301:305-12. [PMID: 12359432 DOI: 10.1006/viro.2002.1559] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The sequences in the 5'-nontranslated region (NTR) of Potato virus X (PVX) genomic RNA were previously reported to contain several regulatory elements that are required for genomic and subgenomic RNA accumulation. To investigate whether cellular proteins bind to these elements, we conducted electrophoretic mobility shift assays (EMSA) with protoplast protein extracts and RNA sequences from the PVX 5'-NTR. These analyses showed that the 5' region of PVX positive-strand RNA formed complexes with cellular proteins. UV cross-linking studies of complexes formed with various deletions of the PVX RNA indicated that a 54-kDa cellular protein (p54) was bound to nt 1-46 at the 5' terminus of PVX RNA. Site-directed mutations introduced within this 46-nt region further indicated that an ACCA sequence element located at nt 10-13 was important for optimal binding. In addition, mutations that decreased the affinity of the template RNA for the cellular factor decreased PVX plus-strand RNA accumulation in protoplasts. These studies suggest that the p54 may function in PVX RNA replication by binding to the 5' terminus of the viral genomic RNA.
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Affiliation(s)
- Kook-Hyung Kim
- School of Agricultural Biotechnology, Center for Plant Molecular Genetics and Breeding Research, Seoul National University, Suwon, 441-744, Korea.
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30
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Choi IR, White KA. An RNA activator of subgenomic mRNA1 transcription in tomato bushy stunt virus. J Biol Chem 2002; 277:3760-6. [PMID: 11714712 DOI: 10.1074/jbc.m109067200] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many (+)-strand RNA viruses transcribe small subgenomic (sg) mRNAs that allow for regulated expression of a subset of their genes. Tomato bushy stunt virus (TBSV) transcribes two such messages and here we report the identification of a long-distance RNA*RNA interaction that is essential for the efficient accumulation of capsid protein-encoding sg mRNA1. The relevant base pairing interaction occurs within the TBSV RNA genome between a 7-nucleotide (nt) long sequence, separated by just 3 nt from the downstream sg mRNA1 initiation site, and a complementary sequence positioned some approximately 1000 nt further upstream. Analyses of this interaction indicate that it (i) functions in the (+)-strand, (ii) modulates both (+)- and (-)-strand sg mRNA1 accumulation, (iii) specifically regulates the accumulation of sg mRNA1 (-)-strands, (iv) controls sg mRNA1 expression from an ectopic transcriptional initiation site, (v) may occur in cis and, and (vi) could nucleate the formation of a more complex RNA structure. These data are most consistent with a role for this interaction in regulating sg mRNA1 accumulation at the level of transcription.
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Affiliation(s)
- Il-Ryong Choi
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
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31
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Qiu W, Scholthof HB. Effects of inactivation of the coat protein and movement genes of Tomato bushy stunt virus on early accumulation of genomic and subgenomic RNAs. J Gen Virol 2001; 82:3107-3114. [PMID: 11714989 DOI: 10.1099/0022-1317-82-12-3107] [Citation(s) in RCA: 15] [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
Accumulation of RNA of Tomato bushy stunt virus (TBSV) was examined within the first few hours after infection of Nicotiana benthamiana protoplasts to determine the influence of the coat protein (CP), the movement-associated proteins P22 and P19 and RNA sequences at very early stages of replication. The results showed that P19 had no effect on early RNA replication, whereas the absence of CP and/or P22 expression delayed RNA accumulation only marginally. Removal of CP-coding sequences had no added negative effects, but when the deletion extended into the downstream p22 gene, it not only eliminated synthesis of subgenomic RNA2 but also delayed accumulation of genomic RNA by 10 h. At times beyond 20 h post-transfection, RNA accumulated to normal high levels for all mutants. This illustrates that TBSV RNA sequences that have negligible impact on overall RNA levels observed late in infection can actually have pronounced effects at very early stages.
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Affiliation(s)
- Wenping Qiu
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843-2132, USA1
| | - Herman B Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843-2132, USA1
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Choi IR, Ostrovsky M, Zhang G, White KA. Regulatory activity of distal and core RNA elements in Tombusvirus subgenomic mRNA2 transcription. J Biol Chem 2001; 276:41761-8. [PMID: 11546813 DOI: 10.1074/jbc.m106727200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Positive-strand RNA viruses that encode multiple cistrons often mediate expression of 3'-encoded open reading frames via RNA-templated transcription of subgenomic (sg) mRNAs. Tomato bushy stunt virus (TBSV) is a positive-strand RNA virus that transcribes two such sg mRNAs during infections. We have previously identified a distal element (DE), located approximately 1100 nucleotides upstream from the initiation site of sg mRNA2 transcription, part of which must base pair with a portion of a core element (CE), located just 5' to the initiation site, for efficient transcription to occur (Zhang, G., Slowinski, V., and White, K. A. (1999) RNA 5, 550-561). Here we have analyzed further this long distance RNA-RNA interaction and have investigated the regulatory roles of other subelements within the DE and CE. Our results indicate that (i) the functional base-pairing interaction between these elements occurs in the positive strand and that the interaction likely acts to properly position other subelements, (ii) two previously undefined subelements within the DE and CE are important and essential, respectively, for efficient sg mRNA2 accumulation, and (iii) the production of (-)-strand sg mRNA2 can be uncoupled from the synthesis of its (+)-strand complement. These data provide important insight into the mechanism of sg mRNA2 transcription.
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Affiliation(s)
- I R Choi
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
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Hemenway CL, Lommel SA. Manipulating plant viral RNA transcription signals. GENETIC ENGINEERING 2001; 22:171-95. [PMID: 11501376 DOI: 10.1007/978-1-4615-4199-8_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- C L Hemenway
- Departments of Biochemistry Box 7622 & Plant Pathology Box 7616, North Carolina State University, Raleigh, NC 27695, USA
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Huang P, Lai MM. Heterogeneous nuclear ribonucleoprotein a1 binds to the 3'-untranslated region and mediates potential 5'-3'-end cross talks of mouse hepatitis virus RNA. J Virol 2001; 75:5009-17. [PMID: 11333880 PMCID: PMC114904 DOI: 10.1128/jvi.75.11.5009-5017.2001] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2000] [Accepted: 03/06/2001] [Indexed: 11/20/2022] Open
Abstract
The 3'-untranslated region (3'-UTR) of mouse hepatitis virus (MHV) RNA regulates the replication of and transcription from the viral RNA. Several host cell proteins have previously been shown to interact with this regulatory region. By immunoprecipitation of UV-cross-linked cellular proteins and in vitro binding of the recombinant protein, we have identified the major RNA-binding protein species as heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1). A strong hnRNP A1-binding site was located 90 to 170 nucleotides from the 3' end of MHV RNA, and a weak binding site was mapped at nucleotides 260 to 350 from the 3' end. These binding sites are complementary to the sites on the negative-strand RNA that bind another cellular protein, polypyrimidine tract-binding protein (PTB). Mutations that affect PTB binding to the negative strand of the 3'-UTR also inhibited hnRNP A1 binding on the positive strand, indicating a possible relationship between these two proteins. Defective-interfering RNAs containing a mutated hnRNP A1-binding site have reduced RNA transcription and replication activities. Furthermore, hnRNP A1 and PTB, both of which also bind to the complementary strands at the 5' end of MHV RNA, together mediate the formation of an RNP complex involving the 5'- and 3'-end fragments of MHV RNA in vitro. These studies suggest that hnRNP A1-PTB interactions provide a molecular mechanism for potential 5'-3' cross talks in MHV RNA, which may be important for RNA replication and transcription.
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Affiliation(s)
- P Huang
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, California 90033-1054, USA
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Schirawski J, Voyatzakis A, Zaccomer B, Bernardi F, Haenni AL. Identification and functional analysis of the turnip yellow mosaic tymovirus subgenomic promoter. J Virol 2000; 74:11073-80. [PMID: 11070002 PMCID: PMC113187 DOI: 10.1128/jvi.74.23.11073-11080.2000] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Most plant viruses rely on the production of subgenomic RNAs (sgRNAs) for the expression of their genes and survival in the plant. Although this is a widely adopted strategy among viruses, the mechanism(s) whereby sgRNA production occurs remains poorly defined. Turnip yellow mosaic tymovirus (TYMV) is a positive-stranded RNA virus that produces an sgRNA for the expression of its coat protein. Here we report that the subgenomic promoter sequence of TYMV is located on a 494-nucleotide fragment, containing previously identified highly conserved sequence elements, which are shown here to be essential for promoter function. After duplication, the subgenomic promoter can be inserted into the coat protein open reading frame, giving rise to the in vivo production of a second sgRNA. It is suggested that this promoter can function when contained on a different molecule than viral genomic RNA. This interesting trait may be of general use for plant and plant virus research.
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Affiliation(s)
- J Schirawski
- Institut Jacques Monod, 75251 Paris Cedex 05, France.
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Lee YS, Hsu YH, Lin NS. Generation of subgenomic RNA directed by a satellite RNA associated with bamboo mosaic potexvirus: analyses of potexvirus subgenomic RNA promoter. J Virol 2000; 74:10341-8. [PMID: 11044078 PMCID: PMC110908 DOI: 10.1128/jvi.74.22.10341-10348.2000] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2000] [Accepted: 08/15/2000] [Indexed: 11/20/2022] Open
Abstract
Satellite RNA of bamboo mosaic potexvirus (satBaMV), a single-stranded positive-sense RNA encoding a nonstructural protein of 20 kDa (P20), depends on bamboo mosaic potexvirus (BaMV) for replication and encapsidation. A full-length cDNA clone of satBaMV was used to examine the sequences required for the synthesis of potexvirus subgenomic RNAs (sgRNAs). Subgenomic promoter-like sequences (SGPs), 107 nucleotides (nt) upstream from the capsid protein (CP) gene of BaMV-V, were inserted upstream of the start codon of the P20 gene of satBaMV. Insertion of SGPs gave rise to the synthesis of sgRNA of satBaMV in protoplasts of Nicotiana benthamiana and leaves of Chenopodium quinoa when coinoculated with BaMV-V genomic RNA. Moreover, both the satBaMV cassette and its sgRNA were encapsidated. From analysis of the SGPs by deletion mutation, we concluded that an SGP contains one core promoterlike sequence (nt -30 through +16), two upstream enhancers (nt -59 through -31 and -91 through -60), and one downstream enhancer (nt +17 through +52), when the transcription initiation site is taken as +1. Site-directed mutagenesis and compensatory mutation to disrupt and restore potential base pairing in the core promoter-like sequence suggest that the stem-loop structure is important for the function of SGP in vivo. Likewise, the insertion of a putative SGP of the BaMV open reading frame 2 gene or a heterologous SGP of potato virus X resulted in generation of an sgRNA. The satBaMV cassette should be a useful tool to gain insight into sequences required for the synthesis of potexvirus sgRNAs.
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Affiliation(s)
- Y S Lee
- Institute of Botany, Academia Sinica, Taipei, Taiwan
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Plante CA, Kim KH, Pillai-Nair N, Osman TA, Buck KW, Hemenway CL. Soluble, template-dependent extracts from Nicotiana benthamiana plants infected with potato virus X transcribe both plus- and minus-strand RNA templates. Virology 2000; 275:444-51. [PMID: 10998342 DOI: 10.1006/viro.2000.0512] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have developed a method to convert membrane-bound replication complexes isolated from Nicotiana benthamiana plants infected with potato virus X (PVX) to a soluble, template-dependent system for analysis of RNA synthesis. Analysis of RNA-dependent RNA polymerase activity in the membrane-bound, endogenous template extracts indicated three major products, which corresponded to double-stranded versions of PVX genomic RNA and the two predominant subgenomic RNAs. The endogenous templates were removed from the membrane-bound complex by treatment with BAL 31 nuclease in the presence of Nonidet P-40 (NP-40). Upon the addition of full-length plus- or minus- strand PVX transcripts, the corresponding-size products were detected. Synthesis was not observed when red clover necrotic mosaic dianthovirus (RCNMV) RNA 2 templates were added, indicating template specificity for PVX transcripts. Plus-strand PVX templates lacking the 3' terminal region were not copied, suggesting that elements in the 3' region were required for initiation of RNA synthesis. Extracts that supported RNA synthesis from endogenous templates could also be solublized using sodium taurodeoxycholate and then rendered template-dependent by BAL 31 nuclease/NP-40 treatment. The solubilized preparations copied both plus- and minus-strand PVX transcripts, but did not support synthesis from RCNMV RNA 2. These membrane-bound and soluble template-dependent systems will facilitate analyses of viral and host components required for PVX RNA synthesis.
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Affiliation(s)
- C A Plante
- Department of Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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Hagiwara Y, Peremyslov VV, Dolja VV. Regulation of closterovirus gene expression examined by insertion of a self-processing reporter and by northern hybridization. J Virol 1999; 73:7988-93. [PMID: 10482546 PMCID: PMC112813 DOI: 10.1128/jvi.73.10.7988-7993.1999] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A reporter open reading frame (ORF) coding for a fusion of bacterial beta-glucuronidase (GUS) with a proteinase domain (Pro) derived from tobacco etch potyvirus was utilized for tagging individual genes of beet yellows closterovirus (BYV). Insertion of this reporter ORF between the first and second codons of the BYV ORFs encoding the HSP70 homolog (HSP70h), a major capsid protein (CP), and a 20-kDa protein (p20) resulted in the expression of the processed GUS-Pro reporter from corresponding subgenomic RNAs. The high sensitivity of GUS assays permitted temporal analysis of reporter accumulation, revealing early expression from the HSP70h promoter, followed by the CP promoter and later the p20 promoter. The kinetics of transcription of the remaining BYV genes encoding a 64-kDa protein (p64), a minor capsid protein (CPm), and a 21-kDa protein (p21) were examined via Northern blot analysis. Taken together, the data indicated that the temporal regulation of BYV gene expression includes early (HSP70h, CPm, CP, and p21 promoters) and late (p64 and p20 promoters) phases. It was also demonstrated that the deletion of six viral genes that are nonessential for RNA amplification resulted in a dramatic increase in the level of transcription from one of the two remaining subgenomic promoters. Comparison with other positive-strand RNA viruses producing multiple subgenomic RNAs showed the uniqueness of the pattern of closterovirus transcriptional regulation.
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Affiliation(s)
- Y Hagiwara
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
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Miller ED, Plante CA, Kim KH, Brown JW, Hemenway C. Stem-loop structure in the 5' region of potato virus X genome required for plus-strand RNA accumulation. J Mol Biol 1998; 284:591-608. [PMID: 9826501 DOI: 10.1006/jmbi.1998.2174] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Computer-generated thermodynamic predictions and solution structure probing indicated two stem-loop structures, stem-loop 1 (SL1; nt 32-106) and stem-loop 2 (SL2; nt 143-183), within the 5' 230 nt of potato virus X (PVX) RNA. Because the existence of SL1 was further supported by covariation analysis of several PVX strains, the functional significance of this structure was investigated by site-directed mutational analysis in a tobacco protoplast system. In general, mutations that reduced genomic plus-strand RNA accumulation similarly affected coat protein accumulation, indicating that subgenomic plus-strand RNA was also affected. In contrast, minus-strand RNA levels remained relatively unchanged. Mutational analysis of the stem C (SC) region of SL1 indicated that pairing was more important than sequence, which was consistent with the covariation analysis. Alterations that increased length and stability of either SC or stem D (SD) were deleterious to plus-strand RNA accumulation. The formation of internal loop C between SC and SD, as well as specific nucleotides within this loop, were also required. Several modifications were made to the terminal GAAA tetraloop, a motif known for enhanced RNA stability. Both GANA and GAAG motifs resulted in wild-type levels of RNA accumulation. However, a UUCG tetraloop was detrimental, indicating that the sequence of this element was important beyond just providing stabilization of the structure. These data indicate that multiple features of SL1 are critical for accumulation of PVX plus-strand RNA.
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Affiliation(s)
- E D Miller
- Department of Biochemistry, North Carolina State University, Raleigh, 27695, USA
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Siegel RW, Bellon L, Beigelman L, Kao CC. Moieties in an RNA promoter specifically recognized by a viral RNA-dependent RNA polymerase. Proc Natl Acad Sci U S A 1998; 95:11613-8. [PMID: 9751714 PMCID: PMC21689 DOI: 10.1073/pnas.95.20.11613] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNAs 33 nucleotides in length can direct accurate initiation of subgenomic RNA synthesis by the brome mosaic virus RNA-dependent RNA polymerase (RdRp), provided that the native sequences are maintained at five positions: -17, -14, -13, -11, and the +1 initiation site. The functional groups in the bases of these essential nucleotides required to interact with RdRp were examined by using chemically synthesized RNAs containing base analogs at each of the five positions. Analysis using a template competition assay revealed that the mode of recognition for the initiation nucleotide (+1) is distinct from that of the other essential nucleotides in the promoter. Competition experiments also determined that three template nucleotides are sufficient for stable interaction with RdRp. These results identify base moieties in the brome mosaic virus subgenomic promoter required for efficient RNA synthesis and support the hypothesis that the recognition of a RNA promoter by a viral RdRp is analogous to the recognition of DNA promoters by DNA-dependent RNA polymerases.
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Affiliation(s)
- R W Siegel
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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41
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Siegel RW, Adkins S, Kao CC. Sequence-specific recognition of a subgenomic RNA promoter by a viral RNA polymerase. Proc Natl Acad Sci U S A 1997; 94:11238-43. [PMID: 9326593 PMCID: PMC23427 DOI: 10.1073/pnas.94.21.11238] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
RNA templates of 33 nucleotides containing the brome mosaic virus (BMV) core subgenomic promoter were used to determine the promoter elements recognized by the BMV RNA-dependent RNA polymerase (RdRp) to initiate RNA synthesis. Nucleotides at positions -17, -14, -13, and -11 relative to the subgenomic initiation site must be maintained for interaction with the RdRp. Changes to every other nucleotide at these four positions allow predictions for the base-specific functional groups required for RdRp recognition. RdRp contact of the nucleotide at position -17 was suggested with a template competition assay. Comparison of the BMV subgenomic promoter to those from other plant and animal alphaviruses shows a remarkable degree of conservation of the nucleotides required for BMV subgenomic RNA synthesis. We show that the RdRp of the plant-infecting BMV is capable of accurately, albeit inefficiently, initiating RNA synthesis from the subgenomic promoter of the animal-infecting Semliki Forest virus. The sequence-specific recognition of RNA by the BMV RdRp is analogous to the recognition of DNA promoters by DNA-dependent RNA polymerases.
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Affiliation(s)
- R W Siegel
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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