1
|
Mostert I, Bester R, Burger JT, Maree HJ. Investigating Protein-Protein Interactions Between Grapevine Leafroll-Associated Virus 3 and Vitis vinifera. PHYTOPATHOLOGY 2023; 113:1994-2005. [PMID: 37311734 DOI: 10.1094/phyto-03-23-0107-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Grapevine leafroll disease (GLD) is a globally important disease that affects the metabolic composition and biomass of grapes, leading to a reduction in grape yield and quality of wine produced. Grapevine leafroll-associated virus 3 (GLRaV-3) is the main causal agent for GLD. This study aimed to identify protein-protein interactions between GLRaV-3 and its host. A yeast two-hybrid (Y2H) library was constructed from Vitis vinifera mRNA and screened against GLRaV-3 open reading frames encoding structural proteins and those potentially involved in systemic spread and silencing of host defense mechanisms. Five interacting protein pairs were identified, three of which were demonstrated in planta. The minor coat protein of GLRaV-3 was shown to interact with 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 02, a protein involved in primary carbohydrate metabolism and the biosynthesis of aromatic amino acids. Interactions were also identified between GLRaV-3 p20A and an 18.1-kDa class I small heat shock protein, as well as MAP3K epsilon protein kinase 1. Both proteins are involved in the response of plants to various stressors, including pathogen infections. Two additional proteins, chlorophyll a-b binding protein CP26 and a SMAX1-LIKE 6 protein, were identified as interacting with p20A in yeast but these interactions could not be demonstrated in planta. The findings of this study advance our understanding of the functions of GLRaV-3-encoded proteins and how the interaction between these proteins and those of V. vinifera could lead to GLD.
Collapse
Affiliation(s)
- Ilani Mostert
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Rachelle Bester
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
- Citrus Research International, Stellenbosch 7600, South Africa
| | - Johan T Burger
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Hans J Maree
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
- Citrus Research International, Stellenbosch 7600, South Africa
| |
Collapse
|
2
|
Chu B, Anane RF, Li S, Gao L, Zi S, Yan K, Ji K, Chen Z, Zhao M. Complete genome sequence analysis of Valeriana jatamansi tymovirus 1: a novel member of the genus Tymovirus infecting Valeriana jatamansi Jones. Arch Virol 2023; 168:245. [PMID: 37676512 DOI: 10.1007/s00705-023-05876-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/08/2023] [Indexed: 09/08/2023]
Abstract
A new positive-sense, single-stranded RNA virus, tentatively named "Valeriana jatamansi tymovirus 1" (VaJV1, OQ730267), was isolated from Valeriana jatamansi Jones displaying symptoms of vein-clearing in Yunnan Province, China. The complete genome of VaJV1 consists of 6,215 nucleotides and contains three open reading frames (ORFs). The genome structure of VaJV1 is typical of members of the genus Tymovirus. BLASTn analysis and multiple sequence alignments showed that the complete genome and coat protein of VaJV1 shared the most sequence similarity (65.5% nucleotides and 50.5% amino acid sequence identity) with an isolate of the tymovirus okra mosaic virus (NC_009532). Phylogenetic analysis confirmed that VaJV1 clustered most closely with other tymoviruses. We propose that Valeriana jatamansi tymovirus 1 represents a new species within the genus Tymovirus.
Collapse
Affiliation(s)
- Bifan Chu
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China
- College of Plant Protection, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China
| | - Rex Frimpong Anane
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, 23 Innovation Walk, 3800, Clayton, VIC, Australia
| | - Shangyun Li
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China
| | - Like Gao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China
- College of Plant Protection, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China
| | - Shaomei Zi
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China
- College of Plant Protection, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China
| | - Kai Yan
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China
- College of Plant Protection, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China
| | - Kaifei Ji
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China
- College of Plant Protection, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China
| | - Zeli Chen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China.
- College of Agronomy and Biotechnology, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China.
- Quality Standard and Testing Technology Research Institute, Yunnan Academy of Agricultural Sciences, No. 2238, Beijing Road, 650205, Kunming, Yunnan, China.
| | - Mingfu Zhao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China.
- College of Plant Protection, Yunnan Agricultural University, NO. 95, Jinhei Road, Panlong District, 650201, Kunming, Yunnan, China.
| |
Collapse
|
3
|
Tan FH, Ng JF, Mohamed Alitheen NB, Muhamad A, Yong CY, Lee KW. A simple and high efficiency purification of His-tagged turnip yellow mosaic virus-like particle (TYMV-VLP) by nickel ion affinity precipitation. J Virol Methods 2023; 319:114771. [PMID: 37437780 DOI: 10.1016/j.jviromet.2023.114771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/05/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
Virus-like particles (VLPs) is one of the most favourable subjects of study, especially in the field of nanobiotechnology and vaccine development because they possess good immunogenicity and self-adjuvant properties. Conventionally, VLPs can be tagged and purified using affinity chromatography or density gradient ultracentrifugation which is costly and time-consuming. Turnip yellow mosaic virus (TYMV) is a plant virus, where expression of the viral coat protein (TYMVc) in Escherichia coli (E. coli) has been shown to form VLP. In this study, we report a non-chromatographic method for VLP purification using C-terminally His-tagged TYMVc (TYMVcHis6) as a protein model. Firstly, the TYMVcHis6 was cloned and expressed in E. coli. Upon clarification of cell lysate, nickel (II) chloride [NiCl2; 15µM or equivalent to 0.0000194% (w/v)] was added to precipitate TYMVcHis6. Following centrifugation, the pellet was resuspended in buffer containing 1mM EDTA to chelate Ni2+, which is then removed via dialysis. A total of 50% of TYMVcHis6 was successfully recovered with purity above 0.90. Later, the purified TYMVcHis6 was analysed with sucrose density ultracentrifugation, dynamic light scattering (DLS), and transmission electron microscopy (TEM) to confirm VLP formation, which is comparable to TYMVcHis6 purified using the standard immobilized metal affinity chromatography (IMAC) column. As the current method omitted the need for IMAC column and beads while significantly reducing the time needed for column washing, nickel affinity precipitation represents a novel method for the purification of VLPs displaying poly-histidine tags (His-tags).
Collapse
Affiliation(s)
- Foo Hou Tan
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Jeck Fei Ng
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | | | - Azira Muhamad
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Kajang, Selangor, Malaysia
| | - Chean Yeah Yong
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Khai Wooi Lee
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia.
| |
Collapse
|
4
|
Laiton-Donato K, Guzmán C, Perdomo-Balaguera E, Sarmiento L, Torres-Fernandez O, Ruiz HA, Rosales-Munar A, Peláez-Carvajal D, Navas MC, Wong MC, Junglen S, Ajami NJ, Parra-Henao G, Usme-Ciro JA. Novel Putative Tymoviridae-like Virus Isolated from Culex Mosquitoes in Colombia. Viruses 2023; 15:v15040953. [PMID: 37112933 PMCID: PMC10143313 DOI: 10.3390/v15040953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
The family Tymoviridae comprises positive-sense RNA viruses, which mainly infect plants. Recently, a few Tymoviridae-like viruses have been found in mosquitoes, which feed on vertebrate sources. We describe a novel Tymoviridae-like virus, putatively named, Guachaca virus (GUAV), isolated from Culex pipiens and Culex quinquefasciatus species of mosquitoes and collected in the rural area of Santa Marta, Colombia. After a cytopathic effect was observed in C6/36 cells, RNA was extracted and processed through the NetoVIR next-generation sequencing protocol, and data were analyzed through the VirMAP pipeline. Molecular and phenotypic characterization of the GUAV was achieved using a 5'/3' RACE, transmission electron microscopy, amplification in vertebrate cells, and phylogenetic analysis. A cytopathic effect was observed in C6/36 cells three days post-infection. The GUAV genome was successfully assembled, and its polyadenylated 3' end was corroborated. GUAV shared only 54.9% amino acid identity with its closest relative, Ek Balam virus, and was grouped with the latter and other unclassified insect-associated tymoviruses in a phylogenetic analysis. GUAV is a new member of a family previously described as comprising plant-infecting viruses, which seem to infect and replicate in mosquitoes. The sugar- and blood-feeding behavior of the Culex spp., implies a sustained contact with plants and vertebrates and justifies further studies to unravel the ecological scenario for transmission.
Collapse
Affiliation(s)
- Katherine Laiton-Donato
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
- Grupo Genómica de Microorganismos Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Camila Guzmán
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Erik Perdomo-Balaguera
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia
- Secretaría de Salud Distrital, Programa de Enfermedades Transmitidas por Vectores, Santa Marta 470004, Colombia
| | - Ladys Sarmiento
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Orlando Torres-Fernandez
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Héctor Alejandro Ruiz
- Grupo Genómica de Microorganismos Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Alicia Rosales-Munar
- Grupo Genómica de Microorganismos Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Dioselina Peláez-Carvajal
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Maria-Cristina Navas
- Grupo de Gastrohepatología, Facultad de Medicina, Universidad de Antioquia, Medellin 050010, Colombia
| | - Matthew C Wong
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Viroworks, Houston, TX 77030, USA
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Nadim J Ajami
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Viroworks, Houston, TX 77030, USA
| | - Gabriel Parra-Henao
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia
| | - José A Usme-Ciro
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia
| |
Collapse
|
5
|
Mahillon M, Brodard J, Kellenberger I, Blouin AG, Schumpp O. A novel weevil-transmitted tymovirus found in mixed infection on hollyhock. Virol J 2023; 20:17. [PMID: 36710353 PMCID: PMC9885571 DOI: 10.1186/s12985-023-01976-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Leaves of hollyhock (Alcea rosea) exhibiting vein chlorosis and yellow mosaic symptoms were collected at public sites in Lausanne and Nyon, two cities of western Switzerland. Diagnostic methods untangled in samples from both sites the mixed infections of a novel isometric virus, tentatively named "Alcea yellow mosaic virus" (AYMV) with the carlavirus Gaillardia latent virus. A new potyvirus was also identified in samples from Nyon. A combination of Illumina, Nanopore and Sanger sequencing was necessary to assemble the full-length genome of AYMV, revealing an exceptionally high cytidine content and other features typically associated with members of the genus Tymovirus. The host range of AYMV was found to be restricted to mallows, including ornamentals as well as economically important plants. Phylogenetic analyses further showed that AYMV belongs to a Tymovirus subclade that also gathers the other mallow-infecting members. The virus was readily transmitted by sap inoculation, and the weevil species Aspidapion radiolus was evidenced as a vector. Transmission assays using another weevil or other insect species did not succeed, and seed transmission was not observed.
Collapse
Affiliation(s)
- Mathieu Mahillon
- grid.417771.30000 0004 4681 910XResearch Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland
| | - Justine Brodard
- grid.417771.30000 0004 4681 910XResearch Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland
| | - Isabelle Kellenberger
- grid.417771.30000 0004 4681 910XResearch Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland
| | - Arnaud G. Blouin
- grid.417771.30000 0004 4681 910XResearch Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Research Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland.
| |
Collapse
|
6
|
Powell JD, Dreher TW. The generation of empty Turnip yellow mosaic virus capsids through depletion of virion-associated divalent cations. J Virol Methods 2022; 309:114595. [PMID: 35931228 DOI: 10.1016/j.jviromet.2022.114595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022]
Abstract
Turnip yellow mosaic virus (TYMV) is a well-studied icosahedral plant virus that has attractive properties for nanoscience applications. Stable empty particles devoid of viral genomic RNA have historically been generated from virions by: 1. high pressure; 2. extreme alkaline pH; and 3. freeze-thaw using liquid nitrogen. Herein we report a fourth and more convenient avenue for empty particle formation through EDTA treatment, implicating chelation of virion-associated cations. We present findings that confirm TYMV virions purified in an EDTA-based buffer are converted to 94 % empty on average during purification. Additional experimentation revealed TYMV virions purified through CsCl vs. sucrose gradients are more readily converted to empty particles after freeze thaw. These studies are novel as they show a purification method through EDTA-treatment that can generate stable empty particles devoid of viral genome. The convenience of this method should prove suitable for scientists seeking to use TYMV capsids in nanoscience-inspired applications. Importantly, these findings provide insight into historical discrepancies in creating empty particles after freeze-thaw, as the method in which TYMV virions are purified influences the downstream virion-to-empty conversion process.
Collapse
Affiliation(s)
- Joshua D Powell
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA.
| | - Theo W Dreher
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| |
Collapse
|
7
|
Xu M, Risse J, Kormelink R. Cap-snatching as a possible contributor to photosynthesis shut-off. J Gen Virol 2022; 103. [PMID: 35947091 DOI: 10.1099/jgv.0.001763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cap-snatching is a mechanism applied by segmented, negative strand (-) RNA viruses (NSVs) to initiate genome transcription. So far, the cap donor source of cytoplasmic-replicating NSVs has remained elusive. Recently, studies pointed to processing body (P body, PB) as the potential source for providing capped RNAs but conclusive evidence is still lacking. To attempt identifying these sources, here the 5' non-viral leader sequences of Tomato spotted wilt virus (TSWV) N mRNAs were analysed by high-throughput sequencing (HTS) from plants subjected to normal and heat-stress conditions, and subsequently mapped on host donor transcripts. The majority of non-viral heterogenous, host-derived leader sequences ranged in size between ~10-20 nt and contained A or AG residues at the cleavage site and the presence of certain sequence motifs. Mapping the capped-leader sequences to the 5' UTR region of genes encoded by the Nicotiana tabacum genome, identified 348 donor genes and which were specifically enriched in cellular photosynthesis pathway. Nineteen of those were clearly expressed differentially at normal condition versus heat-stress conditions. Although the results did not point towards snatching of capped-RNA leader sequences from certain cytoplasmic RNA granules in particular, they indicated photosynthesis downregulation (and development of disease symptoms) partially result from cap-snatching.
Collapse
Affiliation(s)
- Min Xu
- Laboratory of Virology, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Judith Risse
- Laboratory of Bioinformatics, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| |
Collapse
|
8
|
Yuan B, Liu T, Cheng Y, Gao S, Li L, Cai L, Yang J, Chen J, Zhong K. Comprehensive Proteomic Analysis of Lysine Acetylation in Nicotiana benthamiana After Sensing CWMV Infection. Front Microbiol 2021; 12:672559. [PMID: 34084157 PMCID: PMC8166574 DOI: 10.3389/fmicb.2021.672559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/15/2021] [Indexed: 11/13/2022] Open
Abstract
Protein lysine acetylation (Kac) is an important post-translational modification mechanism in eukaryotes that is involved in cellular regulation. To investigate the role of Kac in virus-infected plants, we characterized the lysine acetylome of Nicotiana benthamiana plants with or without a Chinese wheat mosaic virus (CWMV) infection. We identified 4,803 acetylated lysine sites on 1,964 proteins. A comparison of the acetylation levels of the CWMV-infected group with those of the uninfected group revealed that 747 sites were upregulated on 422 proteins, including chloroplast localization proteins and histone H3, and 150 sites were downregulated on 102 proteins. Nineteen conserved motifs were extracted and 51 percent of the acetylated proteins located on chloroplast. Nineteen Kac sites were located on histone proteins, including 10 Kac sites on histone 3. Bioinformatics analysis results indicated that lysine acetylation occurs on a large number of proteins involved in biological processes, especially photosynthesis. Furthermore, we found that the acetylation level of chloroplast proteins, histone 3 and some metabolic pathway-related proteins were significantly higher in CWMV-infected plants than in uninfected plants. In summary, our results reveal the regulatory roles of Kac in response to CWMV infection.
Collapse
Affiliation(s)
- Bowen Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tingting Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Ye Cheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shiqi Gao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China.,Yantai Academy of Agricultural Science, Yantai, China
| | - Linzhi Li
- Yantai Academy of Agricultural Science, Yantai, China
| | - Linna Cai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Kaili Zhong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| |
Collapse
|
9
|
Aljabali AAA, Al Zoubi MS, Al-Batayneh KM, Pardhi DM, Dua K, Pal K, Tambuwala MM. Innovative Applications of Plant Viruses in Drug Targeting and Molecular Imaging- A Review. Curr Med Imaging 2021; 17:491-506. [PMID: 33030133 DOI: 10.2174/1573405616666201007160243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/13/2020] [Accepted: 08/06/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nature had already engineered various types of nanoparticles (NPs), especially viruses, which can deliver their cargo to the host/targeted cells. The ability to selectively target specific cells offers a significant advantage over the conventional approach. Numerous organic NPs, including native protein cages, virus-like particles, polymeric saccharides, and liposomes, have been used for the preparation of nanoparticles. Such nanomaterials have demonstrated better performance as well as improved biocompatibility, devoid of side effects, and stable without any deterioration. OBJECTIVE This review discusses current clinical and scientific research on naturally occurring nanomaterials. It also illustrates and updates the tailor-made approaches for selective delivery and targeted medications that require a high-affinity interconnection to the targeted cells. METHODS A comprehensive search was performed using keywords for viral nanoparticles, viral particles for drug delivery, viral nanoparticles for molecular imaging, theranostics applications of viral nanoparticles and plant viruses in nanomedicine. We searched on Google Scholar, PubMed, Springer, Medline, and Elsevier from 2000 till date and by the bibliographic review of all identified articles. RESULTS The findings demonstrated that structures dependent on nanomaterials might have potential applications in diagnostics, cell marking, comparing agents (computed tomography and magnetic resonance imaging), and antimicrobial drugs, as well as drug delivery structures. However, measures should be taken in order to prevent or mitigate, in pharmaceutical or medical applications, the toxic impact or incompatibility of nanoparticle-based structures with biological systems. CONCLUSION The review provided an overview of the latest advances in nanotechnology, outlining the difficulties and the advantages of in vivo and in vitro structures that are focused on a specific subset of the natural nanomaterials.
Collapse
Affiliation(s)
- Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University - Faculty of Pharmacy, Irbid, Jordan
| | - Mazhar S Al Zoubi
- Department of Basic Medical Sciences, Yarmouk University - Faculty of Medicine, Irbid, Jordan
| | - Khalid M Al-Batayneh
- Department of Biological Sciences, Yarmouk University - Faculty of Science, Irbid, Jordan
| | - Dinesh M Pardhi
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, FL-70211, Kuopio, Finland
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology, Sydney, Australia
| | - Kaushik Pal
- Federal University of Rio de Janeiro, Cidade Universitaria, Rio de Janeiro-RJ, 21941-901, Brazil
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, County Londonderry, BT52 1SA, Northern Ireland, United Kingdom
| |
Collapse
|
10
|
In vitro translation of virally-encoded replication polyproteins to recapitulate polyprotein maturation processes. Protein Expr Purif 2020; 175:105694. [PMID: 32681958 DOI: 10.1016/j.pep.2020.105694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 11/21/2022]
Abstract
Single-stranded, positive-sense RNA viruses encode essential replication polyproteins which are composed of several domains. They are usually subjected to finely regulated proteolytic maturation processes to generate cleavage intermediates and end-products. Both polyproteins and maturation products play multiple key roles that ultimately allow synthesis of viral genome progeny. Despite the importance of these proteins in the course of viral replication, their structural properties, including the conformational changes regulating their numerous functions, are poorly described at the structural level. This lack of information is mainly due to the extreme difficulty to express large, membrane-bound, multi-domain proteins with criteria suitable for structural biology methods. To tackle this challenge, we have used a wheat-germ cell-free expression system. We firstly establish that this approach allows to synthesize viral polyproteins encoded by two unrelated positive-sense RNA viruses, a human norovirus and a plant tymovirus. Then, we demonstrate that these polyproteins are fully functional and are spontaneously auto-cleaved by their active protease domain, giving rise to natural maturation products. Moreover, we show that introduction of point mutations in polyproteins allows to inhibit the proteolytic maturation process of each virus. This allowed us to express and partially purify the uncleaved full-length norovirus polyprotein and the tymoviral RNA-dependent RNA polymerase. Thus, this study provides a powerful tool to obtain soluble viral polyproteins and their maturation products in order to conduct challenging structural biology projects and therefore solve unanswered questions.
Collapse
|
11
|
Yang X, Lu Y, Wang F, Chen Y, Tian Y, Jiang L, Peng J, Zheng H, Lin L, Yan C, Taliansky M, MacFarlane S, Wu Y, Chen J, Yan F. Involvement of the chloroplast gene ferredoxin 1 in multiple responses of Nicotiana benthamiana to Potato virus X infection. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2142-2156. [PMID: 31872217 PMCID: PMC7094082 DOI: 10.1093/jxb/erz565] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/20/2019] [Indexed: 05/14/2023]
Abstract
The chloroplast protein ferredoxin 1 (FD1), with roles in the chloroplast electron transport chain, is known to interact with the coat proteins (CPs) of Tomato mosaic virus and Cucumber mosaic virus. However, our understanding of the roles of FD1 in virus infection remains limited. Here, we report that the Potato virus X (PVX) p25 protein interacts with FD1, whose mRNA and protein levels are reduced by PVX infection or by transient expression of p25. Silencing of FD1 by Tobacco rattle virus-based virus-induced gene silencing (VIGS) promoted the local and systemic infection of plants by PVX. Use of a drop-and-see (DANS) assay and callose staining revealed that the permeability of plasmodesmata (PDs) was increased in FD1-silenced plants together with a consistently reduced level of PD callose deposition. After FD1 silencing, quantitative reverse transcription-real-time PCR (qRT-PCR) analysis and LC-MS revealed these plants to have a low accumulation of the phytohormones abscisic acid (ABA) and salicylic acid (SA), which contributed to the decreased callose deposition at PDs. Overexpression of FD1 in transgenic plants manifested resistance to PVX infection, but the contents of ABA and SA, and the PD callose deposition were not increased in transgenic plants. Overexpression of FD1 interfered with the RNA silencing suppressor function of p25. These results demonstrate that interfering with FD1 function causes abnormal plant hormone-mediated antiviral processes and thus enhances PVX infection.
Collapse
Affiliation(s)
- Xue Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Department of Plant Protection, Shenyang Agriculture University, Shenyang, China
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Fang Wang
- Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Ying Chen
- Department of Plant Protection, Shenyang Agriculture University, Shenyang, China
| | - Yanzhen Tian
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liangliang Jiang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Lin Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Chengqi Yan
- Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Michael Taliansky
- The James Hutton Institute, Cell and Molecular Sciences Group, Invergowrie, Dundee, UK
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow, Russia
| | - Stuart MacFarlane
- The James Hutton Institute, Cell and Molecular Sciences Group, Invergowrie, Dundee, UK
| | - Yuanhua Wu
- Department of Plant Protection, Shenyang Agriculture University, Shenyang, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Department of Plant Protection, Shenyang Agriculture University, Shenyang, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| |
Collapse
|
12
|
Morina F, Mishra A, Mijovilovich A, Matoušková Š, Brückner D, Špak J, Küpper H. Interaction Between Zn Deficiency, Toxicity and Turnip Yellow Mosaic Virus Infection in Noccaea ochroleucum. FRONTIERS IN PLANT SCIENCE 2020; 11:739. [PMID: 32582260 PMCID: PMC7290001 DOI: 10.3389/fpls.2020.00739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/08/2020] [Indexed: 05/08/2023]
Abstract
Zinc is essential for the functioning of numerous proteins in plants. To investigate how Zn homeostasis interacts with virus infection, Zn-tolerant Noccaea ochroleucum plants exposed to deficient (Zn'0'), optimal (Zn10), and excess Zn (Zn100) concentrations, as well as Cd amendment, were infected with Turnip yellow mosaic virus (TYMV). Imaging analysis of fluorescence kinetics from the μs (OJIP) to the minutes (Kautsky effect, quenching analysis) time domain revealed strong patchiness of systemic virus-induced photosystem II (PSII) inhibition. That was more pronounced in Zn-deficient plants, while Zn excess acted synergistically with TYMV, in both cases resulting in reduced PSII reaction centers. Infected Cd-treated plants, already severely stressed, showed inhibited non-photochemical quenching and PSII activity. Quantitative in situ hybridization at the cellular level showed increased gene expression of ZNT5 and downregulation of HMA4 in infected Zn-deficient leaves. In Zn10 and Zn100 infected leaves, vacuolar sequestration of Zn increased by activation of HMA3 (mesophyll) and MTP1 (epidermis). This correlated with Zn accumulation in the mesophyll and formation of biomineralization dots in the cell wall (Zn100) visible by micro X-ray fluorescence tomography. The study reveals the importance of adequate Zn supply and distribution in the maintenance of photosynthesis under TYMV infection, achieved by tissue-targeted activation of metal transporter gene expression.
Collapse
Affiliation(s)
- Filis Morina
- Department of Plant Biophysics and Biochemistry, Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czechia
| | - Archana Mishra
- Department of Plant Biophysics and Biochemistry, Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czechia
| | - Ana Mijovilovich
- Department of Plant Biophysics and Biochemistry, Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czechia
| | - Šárka Matoušková
- Department of Geological Processes, Czech Academy of Sciences, Institute of Geology, Rozvojová, Czechia
| | - Dennis Brückner
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Department of Physics, University of Hamburg, Hamburg, Germany
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Josef Špak
- Department of Plant Virology, Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czechia
| | - Hendrik Küpper
- Department of Plant Biophysics and Biochemistry, Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czechia
- Department of Experimental Plant Biology, University of South Bohemia, České Budějovice, Czechia
- *Correspondence: Hendrik Küpper,
| |
Collapse
|
13
|
Sokullu E, Soleymani Abyaneh H, Gauthier MA. Plant/Bacterial Virus-Based Drug Discovery, Drug Delivery, and Therapeutics. Pharmaceutics 2019; 11:E211. [PMID: 31058814 PMCID: PMC6572107 DOI: 10.3390/pharmaceutics11050211] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
Viruses have recently emerged as promising nanomaterials for biotechnological applications. One of the most important applications of viruses is phage display, which has already been employed to identify a broad range of potential therapeutic peptides and antibodies, as well as other biotechnologically relevant polypeptides (including protease inhibitors, minimizing proteins, and cell/organ targeting peptides). Additionally, their high stability, easily modifiable surface, and enormous diversity in shape and size, distinguish viruses from synthetic nanocarriers used for drug delivery. Indeed, several plant and bacterial viruses (e.g., phages) have been investigated and applied as drug carriers. The ability to remove the genetic material within the capsids of some plant viruses and phages produces empty viral-like particles that are replication-deficient and can be loaded with therapeutic agents. This review summarizes the current applications of plant viruses and phages in drug discovery and as drug delivery systems and includes a discussion of the present status of virus-based materials in clinical research, alongside the observed challenges and opportunities.
Collapse
Affiliation(s)
- Esen Sokullu
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
| | - Hoda Soleymani Abyaneh
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
| | - Marc A Gauthier
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
| |
Collapse
|
14
|
Das PP, Lin Q, Wong SM. Comparative proteomics of Tobacco mosaic virus-infected Nicotiana tabacum plants identified major host proteins involved in photosystems and plant defence. J Proteomics 2019; 194:191-199. [PMID: 30503828 DOI: 10.1016/j.jprot.2018.11.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/29/2018] [Accepted: 11/16/2018] [Indexed: 11/18/2022]
Abstract
Tobacco mosaic virus (TMV) is a positive single-stranded RNA virus. Its 5' end ORF codes for the replicase proteins, namely 126 kDa and 183 kDa, respectively. These proteins interact with many host proteins to form a virus replication complex (VRC). This study aims to dissect the proteome profile of TMV-infected Nicotiana tabacum in host cellular and molecular pathways. We used the isobaric tags for relative and absolute quantification (iTRAQ) technique to analyse the differential global proteomic profile of TMV infected and mock infected plants. Out of 1897 total proteins, we identified 407 differentially abundant proteins and grouped them into three functional categories, namely metabolism, cellular processes and signalling processing. Our results showed that photosynthesis, carbon metabolism, plant defence, protein synthesis, and protein processing in the endoplasmic reticulum were significantly altered. Carbon metabolism and photosynthesis were present in very low abundance, whereas accumulation of reactive oxygen species and misfolded proteins lead to the accumulation of thioredoxin H-type 1. In conclusion, we identified several key host proteins that are involved in TMV infection/replication in N. tabacum plants. SIGNIFICANCE OF THE STUDY: TMV is one of the most widely studied plant virus. It is used as a tool to study host-virus interaction. There are several host proteins reported that facilitate VRC formation and replication of TMV. However, there is limited knowledge in the expression regulation of these host proteins upon TMV infection. This study is the first report that investigates the response of host protein expression involved in TMV infection through a quantitative proteomics technique iTRAQ, combined with LC-MS/MS analysis. We used TMV-infected Nicotiana tabacum plants to investigate the effects of TMV infection on host proteins. Our results revealed differential abundance of proteins involving various pathways in protein translation, protein processing, photosynthesis and plant defence. There was a high abundance of thioredoxin H-type 1, a protein that counters oxidative stress and accelerated regulation of fatty acid synthesis to provide additional lipid molecules for VRC formation. There was a significant reduction in abundance of psaA and psbB proteins in the photosynthetic pathways. Our results identified key candidate host proteins involved in TMV-infected N. tabacum for functional studies in future.
Collapse
Affiliation(s)
- Prem Prakash Das
- Department of Biological Sciences, National University of Singapore (NUS), 14 Science Drive 4, 117543, Singapore.
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore (NUS), 14 Science Drive 4, 117543, Singapore.
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore (NUS), 14 Science Drive 4, 117543, Singapore; Temasek Life Sciences Laboratory, 1 Research Link, 117604, Singapore; National University of Singapore Suzhou Research Institute, Suzhou, Jiangsu 215123, China.
| |
Collapse
|
15
|
Hartwick EW, Costantino DA, MacFadden A, Nix JC, Tian S, Das R, Kieft JS. Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels. Nat Commun 2018; 9:5074. [PMID: 30498211 PMCID: PMC6265322 DOI: 10.1038/s41467-018-07542-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 11/07/2018] [Indexed: 12/22/2022] Open
Abstract
Structured RNA elements, programmed RNA conformational changes, and interactions between different RNA domains underlie many modes of regulating gene expression, mandating studies to understand the foundational principles that govern these phenomena. Exploring the structured 3' untranslated region (UTR) of a viral RNA, we discovered that different contexts of the 3'-UTR confer different abilities to enhance translation of an associated open reading frame. In one context, ribosome-induced conformational changes in a 'sensor' RNA domain affect a separate RNA 'functional' domain, altering translation efficiency. The structure of the entire 3'-UTR reveals that structurally distinct domains use a spine of continuously stacked bases and a strut-like linker to create a conduit for communication within the higher-order architecture. Thus, this 3'-UTR RNA illustrates how RNA can use programmed conformational changes to sense the translation status of an upstream open reading frame, then create a tuned functional response by communicating that information to other RNA elements.
Collapse
Affiliation(s)
- Erik W Hartwick
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, 80045, USA.,RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO, 80045, USA
| | - David A Costantino
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, 80045, USA
| | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, 80045, USA
| | - Jay C Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Siqi Tian
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, 80045, USA. .,RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO, 80045, USA.
| |
Collapse
|
16
|
Hily JM, Candresse T, Garcia S, Vigne E, Tannière M, Komar V, Barnabé G, Alliaume A, Gilg S, Hommay G, Beuve M, Marais A, Lemaire O. High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member. Front Microbiol 2018; 9:1782. [PMID: 30210456 PMCID: PMC6123372 DOI: 10.3389/fmicb.2018.01782] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/16/2018] [Indexed: 12/20/2022] Open
Abstract
In the past decade, high-throughput sequencing (HTS) has had a major impact on virus diversity studies as well as on diagnosis, providing an unbiased and more comprehensive view of the virome of a wide range of organisms. Rather than the serological and molecular-based methods, with their more "reductionist" view focusing on one or a few known agents, HTS-based approaches are able to give a "holistic snapshot" of the complex phytobiome of a sample of interest. In grapevine for example, HTS is powerful enough to allow for the assembly of complete genomes of the various viral species or variants infecting a sample of known or novel virus species. In the present study, a total RNAseq-based approach was used to determine the full genome sequences of various grapevine fanleaf virus (GFLV) isolates and to analyze the eventual presence of other viral agents. From four RNAseq datasets, a few complete grapevine-infecting virus and viroid genomes were de-novo assembled: (a) three GFLV genomes, 11 grapevine rupestris stem-pitting associated virus (GRSPaV) and six viroids. In addition, a novel viral genome was detected in all four datasets, consisting of a single-stranded, positive-sense RNA molecule of 6033 nucleotides. This genome displays an organization similar to Tymoviridae family members in the Tymovirales order. Nonetheless, the new virus shows enough differences to be considered as a new species defining a new genus. Detection of this new agent in the original grapevines proved very erratic and was only consistent at the end of the growing season. This virus was never detected in the spring period, raising the possibility that it might not be a grapevine-infecting virus, but rather a virus infecting a grapevine-associated organism that may be transiently present on grapevine samples at some periods of the year. Indeed, the Tymoviridae family comprises isometric viruses infecting a wide range of hosts in different kingdoms (Plantae, Fungi, and Animalia). The present work highlights the fact that even though HTS technologies produce invaluable data for the description of the sanitary status of a plant, in-depth biological studies are necessary before assigning a new virus to a particular host in such metagenomic approaches.
Collapse
Affiliation(s)
- Jean-Michel Hily
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, Bordeaux, France
| | - Shahinez Garcia
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Emmanuelle Vigne
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Mélanie Tannière
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Véronique Komar
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Guillaume Barnabé
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Antoine Alliaume
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Sophie Gilg
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Gérard Hommay
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Monique Beuve
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, Bordeaux, France
| | - Olivier Lemaire
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| |
Collapse
|
17
|
Empty Turnip yellow mosaic virus capsids as delivery vehicles to mammalian cells. Virus Res 2018; 252:13-21. [DOI: 10.1016/j.virusres.2018.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/26/2018] [Accepted: 05/02/2018] [Indexed: 11/19/2022]
|
18
|
Budziszewska M, Obrępalska-Stęplowska A. The Role of the Chloroplast in the Replication of Positive-Sense Single-Stranded Plant RNA Viruses. FRONTIERS IN PLANT SCIENCE 2018; 9:1776. [PMID: 30542365 PMCID: PMC6278097 DOI: 10.3389/fpls.2018.01776] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/15/2018] [Indexed: 05/20/2023]
Abstract
Positive-sense single-stranded plant RNA viruses are obligate intracellular parasites that infect many agriculturally important crops. Most known plant RNA viruses are characterized by small genomes encoding a limited number of multifunctional viral proteins. Viral pathogens are considered to be absolutely dependent on their hosts, and viruses must recruit numerous host proteins and other factors for genomic RNA replication. Overall, the replication process depends on virus-plant protein-protein, RNA-protein and protein-lipid interactions. Recent publications provide strong evidence for the important role of chloroplasts in viral RNA synthesis. The chloroplast is considered to be a multifunctional organelle responsible for photosynthesis and for the generation of plant defense signaling molecules. High-throughput technologies (genomics and proteomics), and electron microscopy, including three-dimensional tomography, have revealed that several groups of plant RNA viruses utilize chloroplast membranes to assemble viral replication complexes (VRCs). Moreover, some chloroplast-related proteins reportedly interact with both viral proteins and their genomic RNAs and participate in trafficking these molecules to the chloroplast, where replication occurs. Here, we present the current knowledge on the important role of chloroplasts in the viral replication process.
Collapse
|
19
|
Geng C, Yan ZY, Cheng DJ, Liu J, Tian YP, Zhu CX, Wang HY, Li XD. Tobacco vein banding mosaic virus 6K2 Protein Hijacks NbPsbO1 for Virus Replication. Sci Rep 2017; 7:43455. [PMID: 28230184 PMCID: PMC5322494 DOI: 10.1038/srep43455] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/23/2017] [Indexed: 01/18/2023] Open
Abstract
Chloroplast-bound vesicles are key components in viral replication complexes (VRCs) of potyviruses. The potyviral VRCs are induced by the second 6 kDa protein (6K2) and contain at least viral RNA and nuclear inclusion protein b. To date, no chloroplast protein has been identified to interact with 6K2 and involve in potyvirus replication. In this paper, we showed that the Photosystem II oxygen evolution complex protein of Nicotiana benthamiana (NbPsbO1) was a chloroplast protein interacting with 6K2 of Tobacco vein banding mosaic virus (TVBMV; genus Potyvirus) and present in the VRCs. The first 6 kDa protein (6K1) was recruited to VRCs by 6K2 but had no interaction with NbPSbO1. Knockdown of NbPsbO1 gene expression in N. benthamiana plants through virus-induced gene silencing significantly decreased the accumulation levels of TVBMV and another potyvirus Potato virus Y, but not Potato virus X of genus Potexvirus. Amino acid substitutions in 6K2 that disrupted its interaction with NbPsbO1 also affected the replication of TVBMV. NbPsbP1 and NbPsbQ1, two other components of the Photosystem II oxygen evolution complex had no interaction with 6K2 and no effect on TVBMV replication. To conclude, 6K2 recruits 6K1 to VRCs and hijacks chloroplast protein NbPsbO1 to regulate potyvirus replication.
Collapse
Affiliation(s)
- Chao Geng
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Zhi-Yong Yan
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - De-Jie Cheng
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Jin Liu
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Yan-Ping Tian
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Chang-Xiang Zhu
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
- Shandong Provincial Key laboratory for Agricultural Microbiology, Tai’an, Shandong, 271018, China
| | - Hong-Yan Wang
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Xiang-Dong Li
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
- Shandong Provincial Key laboratory for Agricultural Microbiology, Tai’an, Shandong, 271018, China
| |
Collapse
|
20
|
Cantara WA, Olson ED, Musier-Forsyth K. Analysis of RNA structure using small-angle X-ray scattering. Methods 2017; 113:46-55. [PMID: 27777026 PMCID: PMC5253320 DOI: 10.1016/j.ymeth.2016.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/10/2016] [Accepted: 10/20/2016] [Indexed: 11/22/2022] Open
Abstract
In addition to their role in correctly attaching specific amino acids to cognate tRNAs, aminoacyl-tRNA synthetases (aaRS) have been found to possess many alternative functions and often bind to and act on other nucleic acids. In contrast to the well-defined 3D structure of tRNA, the structures of many of the other RNAs recognized by aaRSs have not been solved. Despite advances in the use of X-ray crystallography (XRC), nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (cryo-EM) for structural characterization of biomolecules, significant challenges to solving RNA structures still exist. Recently, small-angle X-ray scattering (SAXS) has been increasingly employed to characterize the 3D structures of RNAs and RNA-protein complexes. SAXS is capable of providing low-resolution tertiary structure information under physiological conditions and with less intensive sample preparation and data analysis requirements than XRC, NMR and cryo-EM. In this article, we describe best practices involved in the process of RNA and RNA-protein sample preparation, SAXS data collection, data analysis, and structural model building.
Collapse
Affiliation(s)
- William A Cantara
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
| | - Erik D Olson
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States.
| |
Collapse
|
21
|
Moriceau L, Jomat L, Bressanelli S, Alcaide-Loridan C, Jupin I. Identification and Molecular Characterization of the Chloroplast Targeting Domain of Turnip yellow mosaic virus Replication Proteins. FRONTIERS IN PLANT SCIENCE 2017; 8:2138. [PMID: 29312393 PMCID: PMC5742235 DOI: 10.3389/fpls.2017.02138] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/04/2017] [Indexed: 05/20/2023]
Abstract
Turnip yellow mosaic virus (TYMV) is a positive-strand RNA virus infecting plants. The TYMV 140K replication protein is a key organizer of viral replication complex (VRC) assembly, being responsible for recruitment of the viral polymerase and for targeting the VRCs to the chloroplast envelope where viral replication takes place. However, the structural requirements determining the subcellular localization and membrane association of this essential viral protein have not yet been defined. In this study, we investigated determinants for the in vivo chloroplast targeting of the TYMV 140K replication protein. Subcellular localization studies of deletion mutants identified a 41-residue internal sequence as the chloroplast targeting domain (CTD) of TYMV 140K; this sequence is sufficient to target GFP to the chloroplast envelope. The CTD appears to be located in the C-terminal extension of the methyltransferase domain-a region shared by 140K and its mature cleavage product 98K, which behaves as an integral membrane protein during infection. We predicted the CTD to fold into two amphipathic α-helices-a folding that was confirmed in vitro by circular dichroism spectroscopy analyses of a synthetic peptide. The importance for subcellular localization of the integrity of these amphipathic helices, and the function of 140K/98K, was demonstrated by performing amino acid substitutions that affected chloroplast targeting, membrane association and viral replication. These results establish a short internal α-helical peptide as an unusual signal for targeting proteins to the chloroplast envelope membrane, and provide new insights into membrane targeting of viral replication proteins-a universal feature of positive-strand RNA viruses.
Collapse
Affiliation(s)
- Lucille Moriceau
- Laboratory of Molecular Virology, Institut Jacques Monod, CNRS, Université Paris-Diderot, Paris, France
- Université Paris-Sud – Université Paris-Saclay, Orsay, France
| | - Lucile Jomat
- Laboratory of Molecular Virology, Institut Jacques Monod, CNRS, Université Paris-Diderot, Paris, France
| | - Stéphane Bressanelli
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud – Université Paris-Saclay, Gif-sur-Yvette, France
| | - Catherine Alcaide-Loridan
- Laboratory of Molecular Virology, Institut Jacques Monod, CNRS, Université Paris-Diderot, Paris, France
| | - Isabelle Jupin
- Laboratory of Molecular Virology, Institut Jacques Monod, CNRS, Université Paris-Diderot, Paris, France
- *Correspondence: Isabelle Jupin,
| |
Collapse
|
22
|
Zhao J, Zhang X, Hong Y, Liu Y. Chloroplast in Plant-Virus Interaction. Front Microbiol 2016; 7:1565. [PMID: 27757106 PMCID: PMC5047884 DOI: 10.3389/fmicb.2016.01565] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/20/2016] [Indexed: 11/16/2022] Open
Abstract
In plants, the chloroplast is the organelle that conducts photosynthesis. It has been known that chloroplast is involved in virus infection of plants for approximate 70 years. Recently, the subject of chloroplast-virus interplay is getting more and more attention. In this article we discuss the different aspects of chloroplast-virus interaction into three sections: the effect of virus infection on the structure and function of chloroplast, the role of chloroplast in virus infection cycle, and the function of chloroplast in host defense against viruses. In particular, we focus on the characterization of chloroplast protein-viral protein interactions that underlie the interplay between chloroplast and virus. It can be summarized that chloroplast is a common target of plant viruses for viral pathogenesis or propagation; and conversely, chloroplast and its components also can play active roles in plant defense against viruses. Chloroplast photosynthesis-related genes/proteins (CPRGs/CPRPs) are suggested to play a central role during the complex chloroplast-virus interaction.
Collapse
Affiliation(s)
- Jinping Zhao
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua UniversityBeijing, China
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Xian Zhang
- Research Centre for Plant RNA Signaling, School of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, School of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua UniversityBeijing, China
| |
Collapse
|
23
|
Li Y, Cui H, Cui X, Wang A. The altered photosynthetic machinery during compatible virus infection. Curr Opin Virol 2016; 17:19-24. [DOI: 10.1016/j.coviro.2015.11.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 10/22/2015] [Accepted: 11/09/2015] [Indexed: 01/09/2023]
|
24
|
ORF43 of maize rayado fino virus is dispensable for systemic infection of maize and transmission by leafhoppers. Virus Genes 2016; 52:303-7. [PMID: 26837893 DOI: 10.1007/s11262-016-1287-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/02/2016] [Indexed: 10/22/2022]
Abstract
Maize rayado fino virus (MRFV) possesses an open reading frame (ORF43) predicted to encode a 43 kDa protein (p43) that has been postulated to be a viral movement protein. Using a clone of MRFV (pMRFV-US) from which infectious RNA can be produced, point mutations were introduced to either prevent initiation from three potential AUG initiation codons near the 5'-end of ORF43 or prematurely terminate translation of ORF43. Inoculation of maize seed via vascular puncture inoculation (VPI) resulted in plants exhibiting symptoms typical of MRFV infection for all mutants tested. Furthermore, corn leafhoppers (Dalbulus maidis) transmitted the virus mutants to healthy plants at a frequency similar to that for wild-type MRFV-US. Viral RNA recovered from plants infected with mutants both prior to and after leafhopper transmission retained mutations blocking ORF43 expression. The results indicate that ORF43 of MRFV is dispensable for both systemic infection of maize and transmission by leafhoppers.
Collapse
|
25
|
Chae KH, Kim D, Cho TJ. N-terminal Extension of Coat Protein of Turnip Yellow Mosaic Virus has Variable Effects on Replication, RNA Packaging, and Virion Assembly Depending on the Inserted Sequence. ACTA ACUST UNITED AC 2016. [DOI: 10.4167/jbv.2016.46.1.13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Kwang-Hee Chae
- Department of Biochemistry, Chungbuk National University, Cheongju, Korea
| | - Doyeong Kim
- Department of Biochemistry, Chungbuk National University, Cheongju, Korea
| | - Tae-Ju Cho
- Department of Biochemistry, Chungbuk National University, Cheongju, Korea
| |
Collapse
|
26
|
Abstract
In plants, the chloroplast is the organelle that conducts photosynthesis. It has been known that chloroplast is involved in virus infection of plants for approximate 70 years. Recently, the subject of chloroplast-virus interplay is getting more and more attention. In this article we discuss the different aspects of chloroplast-virus interaction into three sections: the effect of virus infection on the structure and function of chloroplast, the role of chloroplast in virus infection cycle, and the function of chloroplast in host defense against viruses. In particular, we focus on the characterization of chloroplast protein-viral protein interactions that underlie the interplay between chloroplast and virus. It can be summarized that chloroplast is a common target of plant viruses for viral pathogenesis or propagation; and conversely, chloroplast and its components also can play active roles in plant defense against viruses. Chloroplast photosynthesis-related genes/proteins (CPRGs/CPRPs) are suggested to play a central role during the complex chloroplast-virus interaction.
Collapse
Affiliation(s)
- Jinping Zhao
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua UniversityBeijing, China; State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Xian Zhang
- Research Centre for Plant RNA Signaling, School of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, School of Life and Environmental Sciences, Hangzhou Normal University Hangzhou, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University Beijing, China
| |
Collapse
|
27
|
Li P, Lin Y, Zhang H, Wang S, Qiu D, Guo L. Molecular characterization of a novel mycovirus of the family Tymoviridae isolated from the plant pathogenic fungus Fusarium graminearum. Virology 2015; 489:86-94. [PMID: 26744993 DOI: 10.1016/j.virol.2015.12.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/05/2015] [Accepted: 12/13/2015] [Indexed: 11/16/2022]
Abstract
We isolated a novel mycovirus, Fusarium graminearum mycotymovirus 1 (FgMTV1/SX64), which is related to members of the family Tymoviridae, from the plant pathogenic fungus F. graminearum strain SX64. The complete 7863 nucleotide sequence of FgMTV1/SX64, excluding the poly (A) tail, was determined. The genome of FgMTV1/SX64 is predicted to contain four open reading frames (ORFs). The largest ORF1 is 6723 nucleotides (nt) in length and encodes a putative polyprotein of 2242 amino acids (aa), which contains four conserved domains, a methyltransferase (Mtr), tymovirus endopeptidase (Pro), viral RNA helicase (Hel), and RNA-dependent RNA polymerase (RdRp), of the replication-associated proteins (RPs) of the positive-strand RNA viruses. ORFs 2-4 putatively encode three putative small hypothetical proteins, but their functions are still unknown. Sequence alignments and phylogenetic analyses based on the putative RP protein and the three conserved domains (Mtr, Hel and RdRp) showed that FgMTV1/SX64 is most closely related to, but distinctly branched from, the viruses from the family Tymoviridae. Although FgMTV1/SX64 infection caused mild or no effect on conidia production, biomass and virulence of its host F. graminearum strain SX64, its infection had significant effects on the growth rate, colony diameter and deoxynivalenol (DON) production. This is the first molecular characterization of a tymo-like mycovirus isolated from a plant pathogenic fungus. It is proposed that the mycovirus FgMTV1/SX64 is a representative member of new proposed lineage Mycotymovirus in the family Tymoviridae.
Collapse
Affiliation(s)
- Pengfei Li
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
| | - Yanhong Lin
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
| | - Hailong Zhang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
| | - Shuangchao Wang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
| | - Dewen Qiu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
| | - Lihua Guo
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China.
| |
Collapse
|
28
|
Edwards MC, Weiland JJ, Todd J, Stewart LR. Infectious Maize rayado fino virus from Cloned cDNA. PHYTOPATHOLOGY 2015; 105:833-839. [PMID: 25651051 DOI: 10.1094/phyto-09-14-0250-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A full-length cDNA clone was produced from a U.S. isolate of Maize rayado fino virus (MRFV), the type member of the genus Marafivirus within the family Tymoviridae. Infectivity of transcripts derived from cDNA clones was demonstrated by infection of maize plants and protoplasts, as well as by transmission via the known leafhopper vectors Dalbulus maidis and Graminella nigrifrons that transmit the virus in a persistent-propagative manner. Infection of maize plants through vascular puncture inoculation of seed with transcript RNA resulted in the induction of fine stipple stripe symptoms typical of those produced by wild-type MRFV and a frequency of infection comparable with that of the wild type. Northern and Western blotting confirmed the production of MRFV-specific RNAs and proteins in infected plants and protoplasts. An unanticipated increase in subgenomic RNA synthesis over levels in infected plants was observed in protoplasts infected with either wild-type or cloned virus. A conserved cleavage site motif previously demonstrated to function in both Oat blue dwarf virus capsid protein and tymoviral nonstructural protein processing was identified near the amino terminus of the MRFV replicase polyprotein, suggesting that cleavage at this site also may occur.
Collapse
Affiliation(s)
- Michael C Edwards
- First and second authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Crops Research Unit, Fargo, ND 58102-2765; third and fourth authors: USDA-ARS Corn, Soybean, and Wheat Quality Research Unit, Wooster, OH 44691
| | - John J Weiland
- First and second authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Crops Research Unit, Fargo, ND 58102-2765; third and fourth authors: USDA-ARS Corn, Soybean, and Wheat Quality Research Unit, Wooster, OH 44691
| | - Jane Todd
- First and second authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Crops Research Unit, Fargo, ND 58102-2765; third and fourth authors: USDA-ARS Corn, Soybean, and Wheat Quality Research Unit, Wooster, OH 44691
| | - Lucy R Stewart
- First and second authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Crops Research Unit, Fargo, ND 58102-2765; third and fourth authors: USDA-ARS Corn, Soybean, and Wheat Quality Research Unit, Wooster, OH 44691
| |
Collapse
|
29
|
Ruščić J, Gutiérrez-Aguirre I, Tušek Žnidarič M, Kolundžija S, Slana A, Barut M, Ravnikar M, Krajačić M. A new application of monolithic supports: The separation of viruses from one another. J Chromatogr A 2015; 1388:69-78. [DOI: 10.1016/j.chroma.2015.01.097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/30/2015] [Accepted: 01/30/2015] [Indexed: 11/29/2022]
|
30
|
Kim HB, Kim DY, Cho TJ. Replication and packaging of Turnip yellow mosaic virus RNA containing Flock house virus RNA1 sequence. BMB Rep 2014; 47:330-5. [PMID: 24286326 PMCID: PMC4163869 DOI: 10.5483/bmbrep.2014.47.6.187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 09/17/2013] [Accepted: 09/26/2013] [Indexed: 11/20/2022] Open
Abstract
Turnip yellow mosaic virus (TYMV) is a spherical plant virus that has a single 6.3 kb positive strand RNA as a genome. In this study, RNA1 sequence of Flock house virus (FHV) was inserted into the TYMV genome to test whether TYMV can accommodate and express another viral entity. In the resulting construct, designated TY-FHV, the FHV RNA1 sequence was expressed as a TYMV subgenomic RNA. Northern analysis of the Nicotiana benthamiana leaves agroinfiltrated with the TY-FHV showed that both genomic and subgenomic FHV RNAs were abundantly produced. This indicates that the FHV RNA1 sequence was correctly expressed and translated to produce a functional FHV replicase. Although these FHV RNAs were not encapsidated, the FHV RNA having a TYMV CP sequence at the 3'-end was efficiently encapsidated. When an eGFP gene was inserted into the B2 ORF of the FHV sequence, a fusion protein of B2-eGFP was produced as expected.
Collapse
Affiliation(s)
| | | | - Tae-Ju Cho
- Department of Biochemistry, Chungbuk National University, Cheongju 361-763, Korea
| |
Collapse
|
31
|
Shin HI, Chae KH, Cho TJ. Modification of Turnip yellow mosaic virus coat protein and its effect on virion assembly. BMB Rep 2013; 46:495-500. [PMID: 24148770 PMCID: PMC4133836 DOI: 10.5483/bmbrep.2013.46.10.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 03/09/2013] [Accepted: 03/11/2013] [Indexed: 11/20/2022] Open
Abstract
Turnip yellow mosaic virus (TYMV) is a positive strand RNA virus. We have modified TYMV coat protein (CP) by inserting a c-Myc epitope peptide at the N- or C-terminus of the CP, and have examined its effect on assembly. We introduced the recombinant CP constructs into Nicotiana benthamiana leaves by agroinfiltration. Examination of the leaf extracts by agarose gel electrophoresis and Western blot analysis showed that the CP modified at the N-terminus produced a band co-migrating with wild-type virions. With C-terminal modification, however, the detected bands moved faster than the wild-type virions. To further examine the effect, TYMV constructs producing the modified CPs were prepared. With N-terminal modification, viral RNAs were protected from RNase A. In contrast, the viral RNAs were not protected with C-terminal modification. Overall, the results suggest that virion assembly and RNA packaging occur properly when the N-terminus of CP is modified, but not when the C-terminus is modified.
Collapse
Affiliation(s)
- Hyun-Il Shin
- Department of Biochemistry, Chungbuk National University, Cheongju 361-763, Korea
| | | | | |
Collapse
|
32
|
Wei T, Zhang C, Hou X, Sanfaçon H, Wang A. The SNARE protein Syp71 is essential for turnip mosaic virus infection by mediating fusion of virus-induced vesicles with chloroplasts. PLoS Pathog 2013; 9:e1003378. [PMID: 23696741 PMCID: PMC3656112 DOI: 10.1371/journal.ppat.1003378] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 04/05/2013] [Indexed: 11/18/2022] Open
Abstract
All positive-strand RNA viruses induce the biogenesis of cytoplasmic membrane-bound virus factories for viral genome multiplication. We have previously demonstrated that upon plant potyvirus infection, the potyviral 6K2 integral membrane protein induces the formation of ER-derived replication vesicles that subsequently target chloroplasts for robust genome replication. Here, we report that following the trafficking of the Turnip mosaic potyvirus (TuMV) 6K2 vesicles to chloroplasts, 6K2 vesicles accumulate at the chloroplasts to form chloroplast-bound elongated tubular structures followed by chloroplast aggregation. A functional actomyosin motility system is required for this process. As vesicle trafficking and fusion in planta are facilitated by a superfamily of proteins known as SNAREs (soluble N-ethylmaleimide-sensitive-factor attachment protein receptors), we screened ER-localized SNARES or SNARE-like proteins for their possible involvement in TuMV infection. We identified Syp71 and Vap27-1 that colocalize with the chloroplast-bound 6K2 complex. Knockdown of their expression using a Tobacco rattle virus (TRV)-based virus-induced gene silencing vector showed that Syp71 but not Vap27-1 is essential for TuMV infection. In Syp71-downregulated plant cells, the formation of 6K2-induced chloroplast-bound elongated tubular structures and chloroplast aggregates is inhibited and virus accumulation is significantly reduced, but the trafficking of the 6K2 vesicles from the ER to chloroplast is not affected. Taken together, these data suggest that Syp71 is a host factor essential for successful virus infection by mediating the fusion of the virus-induced vesicles with chloroplasts during TuMV infection.
Collapse
Affiliation(s)
- Taiyun Wei
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
- Department of Biology, The University of Western Ontario, London, Ontario, Canada
| | - Changwei Zhang
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
- Department of Biology, The University of Western Ontario, London, Ontario, Canada
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing , People's Republic of China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing , People's Republic of China
| | - Hélène Sanfaçon
- Pacific Agri-Food Research Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
| | - Aiming Wang
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
- Department of Biology, The University of Western Ontario, London, Ontario, Canada
| |
Collapse
|
33
|
Characterization of a novel tymovirus on tomato plants in Brazil. Virus Genes 2012; 46:190-4. [DOI: 10.1007/s11262-012-0830-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 09/20/2012] [Indexed: 11/25/2022]
|
34
|
Genomic characterization of a novel virus of the family Tymoviridae isolated from mosquitoes. PLoS One 2012; 7:e39845. [PMID: 22848363 PMCID: PMC3407206 DOI: 10.1371/journal.pone.0039845] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 06/01/2012] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The family Tymoviridae comprises three plant virus genera, including Tymovirus, Marafivirus, and Maculavirus, which are found in most parts of the world and cause severe agricultural losses. We describe a putatively novel member of the family Tymoviridae, which is isolated from mosquitoes (Culex spp.), referred to as CuTLV. METHODS AND RESULTS The CuTLV was isolated by cell culture, which replicates and causes cytopathic effects in Aedes albopictus C6/36 cells, but not in mammalian BHK-21 or Vero cells. The complete 6471 nucleotide sequence of CuTLV was determined. The genome of CuTLV is predicted to contain three open reading frames (ORFs). The largest ORF1 is 5307 nucleotides (nt) in length and encodes a putative polypeptide of 1769 amino acids (aa), which contains the conserved motifs for the methyltransferase (MTR), Tymovirus endopeptidase (PRO), helicase (HEL), and RNA-dependent RNA polymerase (RdRp) of the replication-associated proteins (RPs) of positive-stranded RNA viruses. In contrast, the ORF1 sequence does not contain the so-called "tymobox" or "marafibox", the conserved subgenomic RNA promoter present in all tymoviruses or marafiviruses, respectively. ORF2 and ORF3 putatively encode a 248-aa coat protein (CP) and a proline-rich 149-aa polypeptide. The whole genomic nucleotide identity of CuTLV with other members of family Tymoviridae ranged from 46.2% (ChiYMV) to 52.4% (GFkV). Phylogenetic analysis based on the putative RP and CP genes of CuTLV demonstrated that the virus is most closely related to viruses in the genus Maculavirus. CONCLUSIONS The CuTLV is a novel virus related to members of the family Tymoviridae, with molecular characters that are distinct from those of tymoviruses, marafiviruses, and other maculaviruses or macula-like viruses. This is the first report of the isolation of a Tymoviridae-like virus from mosquitoes. Further investigations are required to clarify the origin, replication strategy, and the public health or agricultural importance of the CuTLV.
Collapse
|
35
|
Nicolini C, Pio-Ribeiro G, Andrade GP, Melo FL, Oliveira VC, Guimarães FC, Resende RO, Kitajima EW, Rezende JAM, Nagata T. A distinct tymovirus infecting Cassia hoffmannseggii in Brazil. Virus Genes 2012; 45:190-4. [PMID: 22528644 DOI: 10.1007/s11262-012-0750-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 04/11/2012] [Indexed: 11/29/2022]
Abstract
Leaves of Cassia hoffmannseggii, a wild fabaceous species found in the Atlantic Forest, with a severe mosaic symptom were collected in Pernambuco State, Brazil. By transmission electron microscopy, two types of virus particles were found: the first was recognized as particles of a potyvirus, which was later identified as Cowpea aphid-borne mosaic virus; and the second was isometric and present in high concentration. The observation of vesicles at the periphery of chloroplasts suggested a tymovirus infection, which was confirmed by subsequent assays. A serological assay against several tymovirus antisera resulted in positive reaction of this tymo-like virus with an antiserum of Passion fruit yellow mosaic virus. By means of RT-PCR and using degenerated primers for the conserved region of RNA-dependent RNA polymerase (RdRp) gene of tymoviruses, a specific DNA fragment was amplified and sequenced. Based on this sequence, a specific forward primer was synthesized and successfully used to amplify the 3' terminal genome region, containing the partial RdRp gene and the complete coat protein (CP) sequences. The CP was 188 amino acids (aa) long, and the highest CP aa identity was observed with Kennedya yellow mosaic virus (61 %). Based on the current ICTV demarcation criterion, this isolate was considered as a distinct tymovirus and tentatively named as Cassia yellow mosaic-associated virus.
Collapse
Affiliation(s)
- C Nicolini
- Laboratório de Fitovirologia, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Turnip yellow mosaic virus forms infectious particles without the native beta-annulus structure and flexible coat protein N-terminus. Virology 2012; 422:165-73. [DOI: 10.1016/j.virol.2011.10.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/20/2011] [Accepted: 10/19/2011] [Indexed: 11/22/2022]
|
37
|
Chenon M, Camborde L, Cheminant S, Jupin I. A viral deubiquitylating enzyme targets viral RNA-dependent RNA polymerase and affects viral infectivity. EMBO J 2011; 31:741-53. [PMID: 22117220 PMCID: PMC3273391 DOI: 10.1038/emboj.2011.424] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 11/03/2011] [Indexed: 01/17/2023] Open
Abstract
Turnip Yellow Mosaic Virus protects its replicative polymerase from degradation by the host cell ubiquitin-proteasome system, employing deubiquitination activity of a processing protease with resemblance to OTU domain DUBs. Selective protein degradation via the ubiquitin-proteasome system (UPS) plays an essential role in many major cellular processes, including host–pathogen interactions. We previously reported that the tightly regulated viral RNA-dependent RNA polymerase (RdRp) of the positive-strand RNA virus Turnip yellow mosaic virus (TYMV) is degraded by the UPS in infected cells, a process that affects viral infectivity. Here, we show that the TYMV 98K replication protein can counteract this degradation process thanks to its proteinase domain. In-vitro assays revealed that the recombinant proteinase domain is a functional ovarian tumour (OTU)-like deubiquitylating enzyme (DUB), as is the 98K produced during viral infection. We also demonstrate that 98K mediates in-vivo deubiquitylation of TYMV RdRp protein—its binding partner within replication complexes—leading to its stabilization. Finally, we show that this DUB activity contributes to viral infectivity in plant cells. The identification of viral RdRp as a specific substrate of the viral DUB enzyme thus reveals the intricate interplay between ubiquitylation, deubiquitylation and the interaction between viral proteins in controlling levels of RdRp and viral infectivity.
Collapse
Affiliation(s)
- Mélanie Chenon
- Laboratoire de Virologie Moléculaire, CNRS-Univ Paris Diderot, Institut Jacques Monod, Cell Biology Department, UMR 7592, Paris, France
| | | | | | | |
Collapse
|
38
|
Camborde L, Planchais S, Tournier V, Jakubiec A, Drugeon G, Lacassagne E, Pflieger S, Chenon M, Jupin I. The ubiquitin-proteasome system regulates the accumulation of Turnip yellow mosaic virus RNA-dependent RNA polymerase during viral infection. THE PLANT CELL 2010; 22:3142-52. [PMID: 20823192 PMCID: PMC2965540 DOI: 10.1105/tpc.109.072090] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Revised: 08/01/2010] [Accepted: 08/22/2010] [Indexed: 05/19/2023]
Abstract
Replication of positive-strand RNA viruses, the largest group of plant viruses, is initiated by viral RNA-dependent RNA polymerase (RdRp). Given its essential function in viral replication, understanding the regulation of RdRp is of great importance. Here, we show that Turnip yellow mosaic virus (TYMV) RdRp (termed 66K) is degraded by the proteasome at late time points during viral infection and that the accumulation level of 66K affects viral RNA replication in infected Arabidopsis thaliana cells. We mapped the cis-determinants responsible for 66K degradation within its N-terminal noncatalytic domain, but we conclude that 66K is not a natural N-end rule substrate. Instead, we show that a proposed PEST sequence within 66K functions as a transferable degradation motif. In addition, several Lys residues that constitute target sites for ubiquitylation were mapped; mutation of these Lys residues leads to stabilization of 66K. Altogether, these results demonstrate that TYMV RdRp is a target of the ubiquitin-proteasome system in plant cells and support the idea that proteasomal degradation may constitute yet another fundamental level of regulation of viral replication.
Collapse
|
39
|
Shin HI, Kim HY, Cho TJ. The Pro/Hel region is indispensable for packaging non-replicating turnip yellow mosaic virus RNA, but not replicating viral RNA. Mol Cells 2010; 29:463-9. [PMID: 20396967 DOI: 10.1007/s10059-010-0057-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 10/19/2022] Open
Abstract
Turnip yellow mosaic virus (TYMV) is a spherical plant virus that has a single 6.3 kb positive strand RNA. The genomic RNA has a tRNA-like structure (TLS) at the 3'-end. The 3'-TLS and hairpins in the 5'-untranslated region supposedly serve as packaging signals; however, recent studies have shown that they do not play a role in TYMV RNA packaging. In this study, we focused on packaging signals by examining a series of deletion mutants of TYMV. Analysis of encapsidated viral RNA after agroinfiltration of the deletion constructs into Nicotiana benthamiana showed that the mutant RNA lacking the protease (Pro)/helicase (Hel) region was not encapsidated by the coat proteins provided in trans, implicating that a packaging signal lies in the Pro/Hel region. Examination of two Pro(-)Hel(-) mutants showed that protein activity from the Pro/Hel domains was dispensable for the packaging of the non-replicating TYMV RNA. In contrast, the mutant TYMV RNA lacking the Pro/Hel region was efficiently encapsidated when the mutant TYMV was co-introduced with a wild-type TYMV, suggesting that packaging mechanisms might differ depending on whether the virus is replicating or not.
Collapse
Affiliation(s)
- Hyun-Il Shin
- Department of Biochemistry, Chungbuk National University, Cheongju, 361-763, Korea
| | | | | |
Collapse
|
40
|
Shin HI, Tzanetakis IE, Dreher TW, Cho TJ. The 5′-UTR of Turnip yellow mosaic virus does not include a critical encapsidation signal. Virology 2009; 387:427-35. [DOI: 10.1016/j.virol.2009.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Revised: 01/19/2009] [Accepted: 02/04/2009] [Indexed: 10/21/2022]
|
41
|
Shin HI, Cho NJ, Cho TJ. Role of 5'-UTR hairpins of the Turnip yellow mosaic virus RNA in replication and systemic movement. BMB Rep 2009; 41:778-83. [PMID: 19017489 DOI: 10.5483/bmbrep.2008.41.11.778] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Turnip yellow mosaic virus (TYMV) RNA has two hairpins in its 5' untranslated region (5'-UTR). To investigate the role of the hairpins in replication of TYMV, mutants lacking one or both of the two hairpins were constructed. The TYMV constructs were introduced into Chinese cabbage by an Agrobacterium-mediated T-DNA transfer method, called agroinfiltration. Analysis of total RNA from agroinfiltrated leaves showed that replication of the mutant TYMV RNA lacking both hairpins was about 1/100 of wild type. This mutant was also impaired in systemic spread. Deletion analysis of each hairpin revealed that both hairpins were needed for maximal replication. The deletion analysis along with sequence modification of the hairpin structure indicates that the second hairpin plays a role in efficient long-distance systemic movement of TYMV.
Collapse
Affiliation(s)
- Hyun-Il Shin
- Division of Life Sciences, Chungbuk National University, Cheongju, Korea
| | | | | |
Collapse
|
42
|
Shin HI, Kim IC, Cho TJ. Replication and encapsidation of recombinant Turnip yellow mosaic virus RNA. BMB Rep 2008; 41:739-44. [DOI: 10.5483/bmbrep.2008.41.10.739] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
43
|
Segwagwe AT, Putnam ML, Druffel KL, Pappu HR, Eastwell KC. Molecular characterization of a new tymovirus from Diascia ornamental plants. Arch Virol 2008; 153:1495-503. [PMID: 18600295 DOI: 10.1007/s00705-008-0149-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2008] [Accepted: 05/21/2008] [Indexed: 10/21/2022]
Abstract
Two tymoviruses were identified in plants of Diascia x hybrida 'Sun Chimes Coral' that exhibited chlorotic mottling and reduced growth. A strain of Nemesia ring necrosis virus (NeRNV) designated NeRNV-WA was detected in symptomatic plants; the deduced amino acid sequence is virtually identical to that of the previously reported NeRNV-Nf from Nemesia fruticosa. Sequence analysis also revealed the presence of a new tymovirus, and the entire genomic sequence of this virus was determined. The genome of 6,290 nucleotides was organized into three potential open reading frames (ORFs) typical of viruses in the genus Tymovirus. Based on sequence identity to tymovirus sequences, ORFs I to III encoded the replicase, movement protein and coat protein, respectively. Amino acid sequence identities to those of NeRNV-Nf were 84.8, 50.3 and 94.8%, respectively. The 5'-untranslated region could potentially form four hairpin structures. Secondary structure analysis of the 3'-terminus showed that the RNA can form a transfer-RNA-like structure that has an anticodon specific for histidine. Only 77.9% nucleotide identity was found when complete genomic sequences of this tymovirus from diascia and NeRNV-Nf were compared. The name Diascia yellow mottle virus (DiaYMV) is proposed for this new tymovirus.
Collapse
Affiliation(s)
- A T Segwagwe
- Department of Crop Science and Production, Botswana College of Agriculture, Gaborone, Botswana
| | | | | | | | | |
Collapse
|
44
|
Stephan D, Siddiqua M, Ta Hoang A, Engelmann J, Winter S, Maiss E. Complete nucleotide sequence and experimental host range of Okra mosaic virus. Virus Genes 2007; 36:231-40. [PMID: 18049886 DOI: 10.1007/s11262-007-0181-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 11/21/2007] [Indexed: 12/12/2022]
Abstract
Okra mosaic virus (OkMV) is a tymovirus infecting members of the family Malvaceae. Early infections in okra (Abelmoschus esculentus) lead to yield losses of 12-19.5%. Besides intensive biological characterizations of OkMV only minor molecular data were available. Therefore, we determined the complete nucleotide sequence of a Nigerian isolate of OkMV. The complete genomic RNA (gRNA) comprises 6,223 nt and its genome organization showed three major ORFs coding for a putative movement protein (MP) of M r 73.1 kDa, a large replication-associated protein (RP) of M r 202.4 kDa and a coat protein (CP) of M r 19.6 kDa. Prediction of secondary RNA structures showed three hairpin structures with internal loops in the 5'-untranslated region (UTR) and a 3'-terminal tRNA-like structure (TLS) which comprises the anticodon for valine, typical for a member of the genus Tymovirus. Phylogenetic comparisons based on the RP, MP and CP amino acid sequences showed the close relationship of OkMV not only to other completely sequenced tymoviruses like Kennedya yellow mosaic virus (KYMV), Turnip yellow mosaic virus (TYMV) and Erysimum latent virus (ErLV), but also to Calopogonium yellow vein virus (CalYVV), Clitoria yellow vein virus (CYVV) and Desmodium yellow mottle virus (DYMoV). This is the first report of a complete OkMV genome sequence from one of the various OkMV isolates originating from West Africa described so far. Additionally, the experimental host range of OkMV including several Nicotiana species was determined.
Collapse
Affiliation(s)
- Dirk Stephan
- Institute of Plant Diseases and Plant Protection, Leibniz University Hannover, Herrenhaeuser Str. 2, 30419 Hannover, Germany.
| | | | | | | | | | | |
Collapse
|
45
|
Jakubiec A, Drugeon G, Camborde L, Jupin I. Proteolytic processing of turnip yellow mosaic virus replication proteins and functional impact on infectivity. J Virol 2007; 81:11402-12. [PMID: 17686855 PMCID: PMC2045563 DOI: 10.1128/jvi.01428-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Turnip yellow mosaic virus (TYMV), a positive-strand RNA virus belonging to the alphavirus-like supergroup, encodes its nonstructural replication proteins as a 206K precursor with domains indicative of methyltransferase (MT), proteinase (PRO), NTPase/helicase (HEL), and polymerase (POL) activities. Subsequent processing of 206K generates a 66K protein encompassing the POL domain and uncharacterized 115K and 85K proteins. Here, we demonstrate that TYMV proteinase mediates an additional cleavage between the PRO and HEL domains of the polyprotein, generating the 115K protein and a 42K protein encompassing the HEL domain that can be detected in plant cells using a specific antiserum. Deletion and substitution mutagenesis experiments and sequence comparisons indicate that the scissile bond is located between residues Ser879 and Gln880. The 85K protein is generated by a host proteinase and is likely to result from nonspecific proteolytic degradation occurring during protein sample extraction or analysis. We also report that TYMV proteinase has the ability to process substrates in trans in vivo. Finally, we examined the processing of the 206K protein containing native, mutated, or shuffled cleavage sites and analyzed the effects of cleavage mutations on viral infectivity and RNA synthesis by performing reverse-genetics experiments. We present evidence that PRO/HEL cleavage is critical for productive virus infection and that the impaired infectivity of PRO/HEL cleavage mutants is due mainly to defective synthesis of positive-strand RNA.
Collapse
Affiliation(s)
- Anna Jakubiec
- Institut Jacques Monod, 2 Place Jussieu, 75251 Paris Cedex 05, France
| | | | | | | |
Collapse
|
46
|
Camborde L, Tournier V, Noizet M, Jupin I. A Turnip yellow mosaic virus infection system in Arabidopsis suspension cell culture. FEBS Lett 2007; 581:337-41. [PMID: 17222410 DOI: 10.1016/j.febslet.2006.12.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 11/06/2006] [Accepted: 12/21/2006] [Indexed: 12/11/2022]
Abstract
Turnip yellow mosaic virus (TYMV) is a positive-strand RNA virus able to infect Arabidopsis thaliana. To establish a TYMV infection system in Arabidopsis cell culture, TYMV replicons with the capsid protein gene replaced by a reporter gene expressing the Sh ble protein conferring zeocin resistance were used to transfect Arabidopsis cells. Zeocin-resistant Arabidopsis calli were used to generate a suspension cell culture. Detection of viral proteins and RNAs after 18 months in culture demonstrated persistent replication of the replicon. The Arabidopsis cell culture yielded soluble, active replication complexes, providing a useful tool to study host factors involved in TYMV replication.
Collapse
Affiliation(s)
- Laurent Camborde
- Laboratoire de Virologie Moléculaire, Institut Jacques Monod, UMR 7592 CNRS, Universités Paris 6, Paris 7, 2 place Jussieu, 75251 Paris Cedex 05, France
| | | | | | | |
Collapse
|
47
|
Matsuda D, Dreher TW. Cap- and initiator tRNA-dependent initiation of TYMV polyprotein synthesis by ribosomes: evaluation of the Trojan horse model for TYMV RNA translation. RNA (NEW YORK, N.Y.) 2007; 13:129-37. [PMID: 17095542 PMCID: PMC1705754 DOI: 10.1261/rna.244407] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Turnip yellow mosaic virus (TYMV) RNA directs the translation of two overlapping open reading frames. Competing models have been previously published to explain ribosome access to the downstream polyprotein cistron. The Trojan horse model, based on cell-free experiments, proposes noncanonical cap-independent initiation in which the 3'-terminal tRNA-like structure (TLS) functionally replaces initiator tRNA, and the valine bound to the TLS becomes cis-incorporated into viral protein. The initiation coupling model, based on in vivo expression and ribosome toe-printing studies, proposes a variation of canonical leaky scanning. Here, we have re-examined the wheat germ extract experiments that led to the Trojan horse model, incorporating a variety of controls. We report that (1) translation in vitro from the polyprotein AUG of TYMV RNA is unchanged after removal of the 3' TLS but is stimulated by the presence of a 5'-cap; (2) the presence of free cap analog or edeine (which interferes with initiation at the ribosomal P site and its tRNA(i) (Met) involvement) inhibits translation from the polyprotein AUG; (3) the toe-prints of immediately post-initiation ribosomes on TYMV RNA are similar with and without an intact TLS; and (4) significant deacylation of valyl-TYMV RNA in wheat germ extract can complicate the detection of cis-incorporation. These results favor the initiation coupling model.
Collapse
Affiliation(s)
- Daiki Matsuda
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804, USA
| | | |
Collapse
|
48
|
Cho TJ, Dreher TW. Encapsidation of genomic but not subgenomic Turnip yellow mosaic virus RNA by coat protein provided in trans. Virology 2006; 356:126-35. [PMID: 16942786 DOI: 10.1016/j.virol.2006.06.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 06/02/2006] [Accepted: 06/07/2006] [Indexed: 11/17/2022]
Abstract
We have studied the encapsidation requirements of Turnip yellow mosaic virus (TYMV) genomic and subgenomic RNA using an "agroinfiltration" procedure involving transient expression of RNAs and coat protein (CP) in Nicotiana benthamiana leaves. Although N. benthamiana is a nonhost, expression of TYMV RNA in its leaves by agroinfiltration resulted in efficient local infection and production of the expected virions containing genomic and subgenomic RNAs together with empty capsids. A nonreplicating genomic RNA with a mutation in the polymerase domain was efficiently encapsidated by CP provided in trans, even though RNA levels were a thousand-fold lower than in normal infections. In contrast, encapsidation of CP mRNA was not observed under these conditions, even when the CP mRNA had authentic 5'- and 3'-termini. Deletion of the 3'-tRNA-like structure from the genomic RNA did not alter the encapsidation behavior, suggesting that this feature does not play a role in the encapsidation of TYMV RNA. Our results indicate differences in the encapsidation process between genomic and subgenomic RNAs, and suggest an interaction between RNA replication and the packaging of subgenomic RNA.
Collapse
Affiliation(s)
- Tae-Ju Cho
- Division of Life Sciences, Chungbuk National University, Cheongju 361-763, Korea
| | | |
Collapse
|
49
|
Matsuda D, Dreher TW. Close spacing of AUG initiation codons confers dicistronic character on a eukaryotic mRNA. RNA (NEW YORK, N.Y.) 2006; 12:1338-49. [PMID: 16682564 PMCID: PMC1484435 DOI: 10.1261/rna.67906] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2006] [Accepted: 03/30/2006] [Indexed: 05/08/2023]
Abstract
TYMV RNA supports the translation of two proteins, p69 and p206, from AUG initiation codons 7 nucleotides apart. We have studied the translation of this overlapping dicistronic mRNA with luciferase reporter RNAs electroporated into cowpea protoplasts and in toe-printing studies that map ribosomes stalled during initiation in wheat germ extracts. Agreement between these two assays indicates that the observed effects reflect ribosome initiation events. The robust expression from the downstream AUG206 codon was dependent on its closeness to the upstream AUG69 codon. Stepwise separation of these codons resulted in a gradual increase in upstream initiation and decrease in downstream initiation, and expression was converted from dicistronic to monocistronic. Selection by ribosomes for initiation between the nearby AUG codons was responsive to the sequence contexts that govern leaky scanning, but the normally strong position effect favoring upstream initiation was greatly diminished. Similar dicistronic expression was supported for RNAs with altered initiation sequences and for RNAs devoid of flanking viral sequences. Closely spaced AUG codons may thus represent an under-recognized strategy for bicistronic expression from eukaryotic mRNAs. The initiation behavior observed in these studies suggests that 5'-3' ribosome scanning involves backward excursions averaging about 15 nucleotides.
Collapse
Affiliation(s)
- Daiki Matsuda
- Department of Microbiology, Oregon State University, Corvallis, OR 97331-3804, USA
| | | |
Collapse
|
50
|
Jakubiec A, Tournier V, Drugeon G, Pflieger S, Camborde L, Vinh J, Héricourt F, Redeker V, Jupin I. Phosphorylation of viral RNA-dependent RNA polymerase and its role in replication of a plus-strand RNA virus. J Biol Chem 2006; 281:21236-21249. [PMID: 16717096 DOI: 10.1074/jbc.m600052200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Central to the process of plus-strand RNA virus genome amplification is the viral RNA-dependent RNA polymerase (RdRp). Understanding its regulation is of great importance given its essential function in viral replication and the common architecture and catalytic mechanism of polymerases. Here we show that Turnip yellow mosaic virus (TYMV) RdRp is phosphorylated, when expressed both individually and in the context of viral infection. Using a comprehensive biochemical approach, including metabolic labeling and mass spectrometry analyses, phosphorylation sites were mapped within an N-terminal PEST sequence and within the highly conserved palm subdomain of RNA polymerases. Systematic mutational analysis of the corresponding residues in a reverse genetic system demonstrated their importance for TYMV infectivity. Upon mutation of the phosphorylation sites, distinct steps of the viral cycle appeared affected, but in contrast to other plus-strand RNA viruses, the interaction between viral replication proteins was unaltered. Our results also highlighted the role of another TYMV-encoded replication protein as an antagonistic protein that may prevent the inhibitory effect of RdRp phosphorylation on viral infectivity. Based on these data, we propose that phosphorylation-dependent regulatory mechanisms are essential for viral RdRp function and virus replication.
Collapse
Affiliation(s)
| | | | | | | | | | - Joëlle Vinh
- Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, 75005 Paris, France
| | | | - Virginie Redeker
- Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, 75005 Paris, France
| | | |
Collapse
|