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Villar-Álvarez D, Navarro JA, Pallas V, Sanchez-Navarro JÁ. Engineering VIGS Vectors by Modifying Movement Proteins of the 30K Family. Biotechnol J 2024; 19:e202400584. [PMID: 39711101 DOI: 10.1002/biot.202400584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 12/04/2024] [Accepted: 12/09/2024] [Indexed: 12/24/2024]
Abstract
Virus-induced gene silencing (VIGS) represents a particularly relevant tool in agricultural species for studying gene functionality. This study presents a novel approach for utilizing viruses belonging to the 30K family of movement proteins (MPs) as VIGS vectors. The method described here employs smaller inserts (54 bp or less) than those commonly used (100-500 bp). The developed strategy involves modifying 30K family MPs to introduce heterologous sequences of the gene of interest into their coding sequence. This approach enabled the successful induction of gene silencing in Nicotiana tabacum and Nicotiana benthamiana. Three representative viruses of the MP 30K family, alfalfa mosaic virus (AMV), cucumber mosaic virus (CMV), and tobacco mosaic virus (TMV) were employed. The capacity to induce gene silencing of small inserts (18-54 bp) was investigated, enabling to establish a correlation between insert size and silencing efficacy. This allowed the system to be calibrated to achieve partial silencing levels. The relationship between viral encapsidation and the level of gene silencing was also investigated, revealing that a high efficiency of viral encapsidation results in a reduction in the level of gene silencing achieved. Considering these findings, it can be concluded that the approach carried out with AMV, CMV, and TMV could be applied to other members of the MP 30K family. The MP 30K family comprises 20 viral genera and over 500 viral species, which can infect all agronomically significant plant species. Consequently, the strategy presented in this work could be applied to a wide range of relevant hosts.
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Affiliation(s)
- David Villar-Álvarez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Jesús Ángel Sanchez-Navarro
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
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Palukaitis P, Akbarimotlagh M, Astaraki S, Shams-Bakhsh M, Yoon JY. The Forgotten Tobamovirus Genes Encoding the 54 kDa Protein and the 4-6 kDa Proteins. Viruses 2024; 16:1680. [PMID: 39599795 PMCID: PMC11599109 DOI: 10.3390/v16111680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 10/14/2024] [Accepted: 10/25/2024] [Indexed: 11/29/2024] Open
Abstract
This article reviews the literature concerning the largely forgotten tobamovirus gene products for which no functions have been ascribed. One of these gene products is the 54 kDa protein, representing the RNA-dependent RNA polymerase segment of the 183 kDa protein translated from the I1-subgenomic mRNA, but which has been found only by in vitro translation and not in plants. The other is a collection of small proteins, expressed from alternative reading frames (likely from internal ribosome entry sites) in either or both the movement protein gene or the capsid protein gene. Previously, two small proteins were referred to as the 4-6 kDa proteins, since only single proteins of such size had been characterized from tobacco mosaic virus and tomato mosaic virus genomes. Such putative proteins will be referred to here as P6 proteins, since many new proposed P6 open reading frames could be discerned, from an analysis of 45 of 47 tobamovirus genomes, with a coding capacity of >15 amino acids up to 94 amino acids, whereas other peptides with ≤15 amino acids were not considered here. The distribution of the putative P6 proteins among these tobamoviruses is described, as well as the various classes they fall into, based on their distribution with regard to the organization of other genes in the viral genomes. Models also are presented for possible functions of the 54 kDa protein and the P6 proteins, based on data in the literature.
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Affiliation(s)
- Peter Palukaitis
- Graduate School of Plant Protection and Quarantine, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Masoud Akbarimotlagh
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran 14115-111, Iran; (M.A.); (S.A.); (M.S.-B.)
| | - Sajad Astaraki
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran 14115-111, Iran; (M.A.); (S.A.); (M.S.-B.)
| | - Masoud Shams-Bakhsh
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran 14115-111, Iran; (M.A.); (S.A.); (M.S.-B.)
| | - Ju-Yeon Yoon
- Graduate School of Plant Protection and Quarantine, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Republic of Korea
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3
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Wang X, Bai Y, Shen Z, Zhang X, Cai C, Qiao C, Jiang C, Cheng L, Liu D, Yang A. Genome-wide analysis of tobacco NtTOM1/TOM3 gene family and identification of NtTOM1a/ NtTOM3a response to tobacco mosaic virus. BMC PLANT BIOLOGY 2024; 24:942. [PMID: 39385089 PMCID: PMC11465672 DOI: 10.1186/s12870-024-05632-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/24/2024] [Indexed: 10/11/2024]
Abstract
BACKGROUND TOBAMOVIRUS MULTIPLICATION 1 (TOM1) and its homolog TOBAMOVIRUS MULTIPLICATION 3 (TOM3) play a prominent role in the multiplication of tobacco mosaic virus (TMV) in higher plants. Although homologs of NtTOM1/TOM3 genes have been identified in several plant species, little is known about the characteristics and functions of NtTOM1/TOM3 at the genome-wide level in tobacco (Nicotiana tabacum L.). RESULTS In this study, we performed genome-wide identification and expression pattern analysis of the tobacco NtTOM1/TOM3 gene family. Twelve NtTOM1/TOM3 genes were identified and classified into four groups based on phylogenetic analysis. Sequence and conserved domain analyses showed that all these genes contained a specific DUF1084 domain. Expression pattern analysis showed that NtTOM1a, NtTOM1b, NtTOM1d, NtTOM3a, NtTOM3b, and NtTOM3d were induced by TMV at 1-, 3-, and 9 dpi, whereas the expression of other genes was not responsive to TMV at the early infection stage. TMV virion accumulation showed no obvious difference in either nttom1a or nttom3a mutants compared with the wild type. However, the virus propagation was significantly, but not completely, inhibited in the nttom1atom3a double mutant, indicating that other gene family members may function redundantly, such as NtTOM1b and NtTOM1d. In addition, overexpression of NtTOM1a or NtTOM3a also inhibited the TMV replication to some extent. CONCLUSIONS The present study performed genome-wide analysis of the NtTOM1/TOM3 gene family in tobacco, and identified NtTOM1a and NtTOM3a as important genes involved in TMV multiplication based on functional analysis. These results provide a theoretical basis for further improving TMV resistance in tobacco.
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Affiliation(s)
- Xuebo Wang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Tobacco Science Research Institute of Guangdong Province, Shaoguan, 512029, Guangdong, China
| | - Yalin Bai
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Zhan Shen
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Xinyao Zhang
- Technology Center, China Tobacco Hunan Industrial Co., Ltd, Changsha, 410007, China
| | - Changchun Cai
- Tobacco Research Institute of Hubei Province, Wuhan, 430030, China
| | - Chan Qiao
- Tobacco Research Institute of Mudanjiang, Harbin, 150076, China
| | - Caihong Jiang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Lirui Cheng
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Dan Liu
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| | - Aiguo Yang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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Wendlandt T, Britz B, Kleinow T, Hipp K, Eber FJ, Wege C. Getting Hold of the Tobamovirus Particle-Why and How? Purification Routes over Time and a New Customizable Approach. Viruses 2024; 16:884. [PMID: 38932176 PMCID: PMC11209083 DOI: 10.3390/v16060884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
This article develops a multi-perspective view on motivations and methods for tobamovirus purification through the ages and presents a novel, efficient, easy-to-use approach that can be well-adapted to different species of native and functionalized virions. We survey the various driving forces prompting researchers to enrich tobamoviruses, from the search for the causative agents of mosaic diseases in plants to their increasing recognition as versatile nanocarriers in biomedical and engineering applications. The best practices and rarely applied options for the serial processing steps required for successful isolation of tobamoviruses are then reviewed. Adaptations for distinct particle species, pitfalls, and 'forgotten' or underrepresented technologies are considered as well. The article is topped off with our own development of a method for virion preparation, rooted in historical protocols. It combines selective re-solubilization of polyethylene glycol (PEG) virion raw precipitates with density step gradient centrifugation in biocompatible iodixanol formulations, yielding ready-to-use particle suspensions. This newly established protocol and some considerations for perhaps worthwhile further developments could serve as putative stepping stones towards preparation procedures appropriate for routine practical uses of these multivalent soft-matter nanorods.
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Affiliation(s)
- Tim Wendlandt
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (B.B.); (T.K.)
| | - Beate Britz
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (B.B.); (T.K.)
| | - Tatjana Kleinow
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (B.B.); (T.K.)
| | - Katharina Hipp
- Electron Microscopy Facility, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany;
| | - Fabian J. Eber
- Department of Mechanical and Process Engineering, Offenburg University of Applied Sciences, Badstr. 24, 77652 Offenburg, Germany;
| | - Christina Wege
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (B.B.); (T.K.)
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5
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Zheng X, Li Y, Liu Y. Plant Immunity against Tobamoviruses. Viruses 2024; 16:530. [PMID: 38675873 PMCID: PMC11054417 DOI: 10.3390/v16040530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Tobamoviruses are a group of plant viruses that pose a significant threat to agricultural crops worldwide. In this review, we focus on plant immunity against tobamoviruses, including pattern-triggered immunity (PTI), effector-triggered immunity (ETI), the RNA-targeting pathway, phytohormones, reactive oxygen species (ROS), and autophagy. Further, we highlight the genetic resources for resistance against tobamoviruses in plant breeding and discuss future directions on plant protection against tobamoviruses.
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Affiliation(s)
- Xiyin Zheng
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yiqing Li
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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Grübel J, Wendlandt T, Urban D, Jauch CO, Wege C, Tovar GEM, Southan A. Soft Sub-Structured Multi-Material Biosensor Hydrogels with Enzymes Retained by Plant Viral Scaffolds. Macromol Biosci 2024; 24:e2300311. [PMID: 37922890 DOI: 10.1002/mabi.202300311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/13/2023] [Indexed: 11/07/2023]
Abstract
An all-soft multi-material combination consisting of a hydrogel based on poly(ethylene glycol) (PEG) coated with spatially defined spots of gelatin methacryloyl (GM) containing selectively addressable viral nanorods is presented, and its basic application as a qualitative biosensor with reporter enzymes displayed on the tobacco mosaic virus (TMV) bioscaffolds within the GM is demonstrated. Biologically inert PEG supports are equipped with GM spots serving as biological matrix for enzymes clustered on TMV particles preventing diffusion out of the gel. For this multi-material combination, i) the PEG-based hydrogel surface is modified to achieve a clear boundary between coated and non-coated regions by introducing either isothiouronium or thiol groups. ii) Cross-linking of the GM spots is studied to achieve anchoring to the hydrogel surface. iii) The enzymes horseradish peroxidase or penicillinase (Pen) are conjugated to TMV and integrated into the GM matrix. In contrast to free enzymes, enzyme-decorated TMVs persist in GM spots and show sustained enzyme activity as evidenced by specific color reaction after 7 days of washing, and for Pen after 22 months after dry storage. Therefore, the integration of enzyme-coupled TMV into hydrogel matrices is a promising and versatile approach to obtaining reusable and analyte-specific sensor components.
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Affiliation(s)
- Jana Grübel
- Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Nobelstr. 12, 70569, Stuttgart, Germany
| | - Tim Wendlandt
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Daniela Urban
- Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Nobelstr. 12, 70569, Stuttgart, Germany
| | - Corinna O Jauch
- Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Nobelstr. 12, 70569, Stuttgart, Germany
| | - Christina Wege
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Günter E M Tovar
- Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Nobelstr. 12, 70569, Stuttgart, Germany
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Nobelstr. 12, 70569, Stuttgart, Germany
| | - Alexander Southan
- Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Nobelstr. 12, 70569, Stuttgart, Germany
- Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569, Stuttgart, Germany
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7
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Wang Y, Guo S, Sun W, Tu H, Tang Y, Xu Y, Guo R, Zhao Z, Yang Z, Wu J. Synthesis of 4 H-Pyrazolo[3,4- d]pyrimidin-4-one Hydrazine Derivatives as a Potential Inhibitor for the Self-Assembly of TMV Particles. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:2879-2887. [PMID: 38241724 DOI: 10.1021/acs.jafc.3c05334] [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: 01/21/2024]
Abstract
Tobacco mosaic virus coat protein (TMV-CP), as a potential target for the development of antiviral agents, can assist in the long-distance movement of viruses and plays an extremely important role in virus replication and propagation. This work focuses on the synthesis and the action mechanism of novel 4H-pyrazolo[3,4-d] pyrimidin-4-one hydrazine derivatives. The synthesized compounds exhibited promising antiviral activity on TMV. Specifically, compound G2 exhibited high inactivating activity (93%) toward TMV, slightly better than commercial reagent NNM (90%). The action of mechanism was further explored by employed molecular docking, molecular dynamics simulation, microscale thermophoresis, qRT-PCR, and transmission electron microscopy. Results indicated that G2 had the capability to interact with amino acid residues such as Trp352, Tyr139, and Asn73 in the active pocket of TMV-CP, creating strong hydrophobic interactions and thus obstructing the virus's self-assembly.
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Affiliation(s)
- Ya Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Shengxin Guo
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Wei Sun
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Hong Tu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Yao Tang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Ying Xu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Renjiang Guo
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Zhichao Zhao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Zhaokai Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Jian Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
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8
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Wu X, Zhang Y, Jiang X, Ma T, Guo Y, Wu X, Guo Y, Cheng X. Considerations in engineering viral vectors for genome editing in plants. Virology 2024; 589:109922. [PMID: 37924727 DOI: 10.1016/j.virol.2023.109922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
Plant viruses have been engineered to express proteins and induce gene silencing for decades. Recently, plant viruses have also been used to deliver components into plant cells for genome editing, a technique called virus-induced genome editing (VIGE). Although more than a dozen plant viruses have been engineered into VIGE vectors and VIGE has been successfully accomplished in some plant species, application of VIGE to crops that are difficult to tissue culture and/or have low regeneration efficiency is still tough. This paper discusses factors to consider for an ideal VIGE vector, including insertion capacity for foreign DNA, vertical transmission ability, expression level of the target gene, stability of foreign DNA insertion, and biosafety. We also proposed a step-by-step schedule for excavating the suitable viral vector for VIGE.
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Affiliation(s)
- Xiaoyun Wu
- College of Plant Protection, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China; Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, PR China
| | - Ying Zhang
- College of Plant Protection, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Xue Jiang
- College of Plant Protection, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Tingshuai Ma
- College of Plant Protection, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Yating Guo
- College of Plant Protection, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yushuang Guo
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, 550081, Guizhou, PR China.
| | - Xiaofei Cheng
- College of Plant Protection, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China; Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, PR China.
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9
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Zhang H, Hu Q. TOM1 family conservation within the plant kingdom for tobacco mosaic virus accumulation. MOLECULAR PLANT PATHOLOGY 2023; 24:1385-1399. [PMID: 37443447 PMCID: PMC10576174 DOI: 10.1111/mpp.13375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/03/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
The susceptibility factor TOBAMOVIRUS MULTIPLICATION 1 (TOM1) is required for efficient multiplication of tobacco mosaic virus (TMV). Although some phylogenetic and functional analyses of the TOM1 family members have been conducted, a comprehensive analysis of the TOM1 homologues based on phylogeny from the most ancient to the youngest representatives within the plant kingdom, analysis of support for tobamovirus accumulation and interaction with other host and viral proteins has not been reported. In this study, using Nicotiana benthamiana and TMV as a model system, we functionally characterized the TOM1 homologues from N. benthamiana and other plant species from different plant lineages. We modified a multiplex genome editing tool and generated a sextuple mutant in which TMV multiplication was dramatically inhibited. We showed that TOM1 homologues from N. benthamiana exhibited variable capacities to support TMV multiplication. Evolutionary analysis revealed that the TOM1 family is restricted to the plant kingdom and probably originated in the Chlorophyta division, suggesting an ancient origin of the TOM1 family. We found that the TOM1 family acquired the ability to promote TMV multiplication after the divergence of moss and spikemoss. Moreover, the capacity of TOM1 orthologues from different plant species to promote TMV multiplication and the interactions between TOM1 and TOM2A and between TOM1 and TMV-encoded replication proteins are highly conserved, suggesting a conserved nature of the TOM2A-TOM1-TMV Hel module in promoting TMV multiplication. Our study not only revealed a conserved nature of a gene module to promote tobamovirus multiplication, but also provides a valuable strategy for TMV-resistant crop development.
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Affiliation(s)
- Hui Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Qun Hu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
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10
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Spiegelman Z, Dinesh-Kumar SP. Breaking Boundaries: The Perpetual Interplay Between Tobamoviruses and Plant Immunity. Annu Rev Virol 2023; 10:455-476. [PMID: 37254097 DOI: 10.1146/annurev-virology-111821-122847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Plant viruses of the genus Tobamovirus cause significant economic losses in various crops. The emergence of new tobamoviruses such as the tomato brown rugose fruit virus (ToBRFV) poses a major threat to global agriculture. Upon infection, plants mount a complex immune response to restrict virus replication and spread, involving a multilayered defense system that includes defense hormones, RNA silencing, and immune receptors. To counter these defenses, tobamoviruses have evolved various strategies to evade or suppress the different immune pathways. Understanding the interactions between tobamoviruses and the plant immune pathways is crucial for the development of effective control measures and genetic resistance to these viruses. In this review, we discuss past and current knowledge of the intricate relationship between tobamoviruses and host immunity. We use this knowledge to understand the emergence of ToBRFV and discuss potential approaches for the development of new resistance strategies to cope with emerging tobamoviruses.
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Affiliation(s)
- Ziv Spiegelman
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Institute, Rishon LeZion, Israel;
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and Genome Center, College of Biological Sciences, University of California, Davis, California, USA
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11
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Wendlandt T, Koch C, Britz B, Liedek A, Schmidt N, Werner S, Gleba Y, Vahidpour F, Welden M, Poghossian A, Schöning MJ, Eber FJ, Jeske H, Wege C. Facile Purification and Use of Tobamoviral Nanocarriers for Antibody-Mediated Display of a Two-Enzyme System. Viruses 2023; 15:1951. [PMID: 37766357 PMCID: PMC10536799 DOI: 10.3390/v15091951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Immunosorbent turnip vein clearing virus (TVCV) particles displaying the IgG-binding domains D and E of Staphylococcus aureus protein A (PA) on every coat protein (CP) subunit (TVCVPA) were purified from plants via optimized and new protocols. The latter used polyethylene glycol (PEG) raw precipitates, from which virions were selectively re-solubilized in reverse PEG concentration gradients. This procedure improved the integrity of both TVCVPA and the wild-type subgroup 3 tobamovirus. TVCVPA could be loaded with more than 500 IgGs per virion, which mediated the immunocapture of fluorescent dyes, GFP, and active enzymes. Bi-enzyme ensembles of cooperating glucose oxidase and horseradish peroxidase were tethered together on the TVCVPA carriers via a single antibody type, with one enzyme conjugated chemically to its Fc region, and the other one bound as a target, yielding synthetic multi-enzyme complexes. In microtiter plates, the TVCVPA-displayed sugar-sensing system possessed a considerably increased reusability upon repeated testing, compared to the IgG-bound enzyme pair in the absence of the virus. A high coverage of the viral adapters was also achieved on Ta2O5 sensor chip surfaces coated with a polyelectrolyte interlayer, as a prerequisite for durable TVCVPA-assisted electrochemical biosensing via modularly IgG-assembled sensor enzymes.
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Affiliation(s)
- Tim Wendlandt
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Claudia Koch
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Beate Britz
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Anke Liedek
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Nora Schmidt
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Stefan Werner
- Nambawan Biotech GmbH/Now at Icon Genetics GmbH, Weinbergweg 22, 06120 Halle, Germany;
| | - Yuri Gleba
- Nomad Bioscience GmbH, Weinbergweg 22, 06120 Halle, Germany;
| | - Farnoosh Vahidpour
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany; (F.V.); (M.W.); (M.J.S.)
| | - Melanie Welden
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany; (F.V.); (M.W.); (M.J.S.)
| | | | - Michael J. Schöning
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany; (F.V.); (M.W.); (M.J.S.)
- Institute of Biological Information Processing (IBI-3), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Fabian J. Eber
- Department of Mechanical and Process Engineering, Offenburg University of Applied Sciences, 77652 Offenburg, Germany;
| | - Holger Jeske
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Christina Wege
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
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12
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Duran-Meza AL, Oster L, Sportsman R, Phillips M, Knobler CM, Gelbart WM. Long ssRNA undergoes continuous compaction in the presence of polyvalent cations. Biophys J 2023; 122:3469-3475. [PMID: 37501368 PMCID: PMC10502455 DOI: 10.1016/j.bpj.2023.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/12/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023] Open
Abstract
In the presence of polyvalent cations, long double-stranded DNA (dsDNA) in dilute solution undergoes a single-molecule, first-order, phase transition ("condensation"), a phenomenon that has been documented and analyzed by many years of experimental and theoretical studies. There has been no systematic effort, however, to determine whether long single-stranded RNA (ssRNA) shows an analogous behavior. In this study, using dynamic light scattering, analytical ultracentrifugation, and gel electrophoresis, we examine the effects of increasing polyvalent cation concentrations on the effective size of long ssRNAs ranging from 3000 to 12,000 nucleotides. Our results indicate that ssRNA does not undergo a discontinuous condensation as does dsDNA but rather a "continuous" decrease in size with increasing polyvalent cation concentration. And, instead of the 10-fold decrease in size shown by long dsDNA, we document a 50% decrease, as demonstrated for a range of lengths and sequences of ssRNA.
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Affiliation(s)
| | - Liya Oster
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California
| | - Richard Sportsman
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California
| | - Martin Phillips
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California.
| | - William M Gelbart
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California; Molecular Biology Institute, UCLA, Los Angeles, California; California NanoSystems Institute, UCLA, Los Angeles, California
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13
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Hak H, Raanan H, Schwarz S, Sherman Y, Dinesh‐Kumar SP, Spiegelman Z. Activation of Tm-2 2 resistance is mediated by a conserved cysteine essential for tobacco mosaic virus movement. MOLECULAR PLANT PATHOLOGY 2023; 24:838-848. [PMID: 37086003 PMCID: PMC10346382 DOI: 10.1111/mpp.13318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/08/2023] [Accepted: 02/12/2023] [Indexed: 05/03/2023]
Abstract
The tomato Tm-22 gene was considered to be one of the most durable resistance genes in agriculture, protecting against viruses of the Tobamovirus genus, such as tomato mosaic virus (ToMV) and tobacco mosaic virus (TMV). However, an emerging tobamovirus, tomato brown rugose fruit virus (ToBRFV), has overcome Tm-22 , damaging tomato production worldwide. Tm-22 encodes a nucleotide-binding leucine-rich repeat (NLR) class immune receptor that recognizes its effector, the tobamovirus movement protein (MP). Previously, we found that ToBRFV MP (MPToBRFV ) enabled the virus to overcome Tm-22 -mediated resistance. Yet, it was unknown how Tm-22 remained durable against other tobamoviruses, such as TMV and ToMV, for over 60 years. Here, we show that a conserved cysteine (C68) in the MP of TMV (MPTMV ) plays a dual role in Tm-22 activation and viral movement. Substitution of MPToBRFV amino acid H67 with the corresponding amino acid in MPTMV (C68) activated Tm-22 -mediated resistance. However, replacement of C68 in TMV and ToMV disabled the infectivity of both viruses. Phylogenetic and structural prediction analysis revealed that C68 is conserved among all Solanaceae-infecting tobamoviruses except ToBRFV and localizes to a predicted jelly-roll fold common to various MPs. Cell-to-cell and subcellular movement analysis showed that C68 is required for the movement of TMV by regulating the MP interaction with the endoplasmic reticulum and targeting it to plasmodesmata. The dual role of C68 in viral movement and Tm-22 immune activation could explain how TMV was unable to overcome this resistance for such a long period.
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Affiliation(s)
- Hagit Hak
- Department of Plant Pathology and Weed Research, Agricultural Research OrganizationThe Volcani InstituteRishon LeZionIsrael
| | - Hagai Raanan
- Department of Plant Pathology and Weed Research, Agricultural Research OrganizationThe Volcani InstituteRishon LeZionIsrael
- Gilat Research CenterAgricultural Research OrganizationNegevIsrael
| | - Shahar Schwarz
- Department of Plant Pathology and Weed Research, Agricultural Research OrganizationThe Volcani InstituteRishon LeZionIsrael
| | - Yifat Sherman
- Department of Plant Pathology and Weed Research, Agricultural Research OrganizationThe Volcani InstituteRishon LeZionIsrael
- The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Savithramma P. Dinesh‐Kumar
- Department of Plant Biology and Genome CenterCollege of Biological Sciences, University of CaliforniaDavisCaliforniaUSA
| | - Ziv Spiegelman
- Department of Plant Pathology and Weed Research, Agricultural Research OrganizationThe Volcani InstituteRishon LeZionIsrael
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14
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Shahgolzari M, Venkataraman S, Osano A, Akpa PA, Hefferon K. Plant Virus Nanoparticles Combat Cancer. Vaccines (Basel) 2023; 11:1278. [PMID: 37631846 PMCID: PMC10459942 DOI: 10.3390/vaccines11081278] [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: 05/19/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/27/2023] Open
Abstract
Plant virus nanoparticles (PVNPs) have garnered considerable interest as a promising nanotechnology approach to combat cancer. Owing to their biocompatibility, stability, and adjustable surface functionality, PVNPs hold tremendous potential for both therapeutic and imaging applications. The versatility of PVNPs is evident from their ability to be tailored to transport a range of therapeutic agents, including chemotherapy drugs, siRNA, and immunomodulators, thereby facilitating targeted delivery to the tumor microenvironment (TME). Furthermore, PVNPs may be customized with targeting ligands to selectively bind to cancer cell receptors, reducing off-target effects. Additionally, PVNPs possess immunogenic properties and can be engineered to exhibit tumor-associated antigens, thereby stimulating anti-tumor immune responses. In conclusion, the potential of PVNPs as a versatile platform for fighting cancer is immense, and further research is required to fully explore their potential and translate them into clinical applications.
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Affiliation(s)
- Mehdi Shahgolzari
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz 5166616471, Iran
| | - Srividhya Venkataraman
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Anne Osano
- Department of Natural Sciences, Bowie State University, Bowie, MD 20715, USA
| | - Paul Achile Akpa
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka 410001, Enugu State, Nigeria
| | - Kathleen Hefferon
- Department of Microbiology, Cornell University, Ithaca, NY 14850, USA
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15
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A Novel Platform for Root Protection Applies New Root-Coating Technologies to Mitigate Soil-Borne Tomato Brown Rugose Fruit Virus Disease. Viruses 2023; 15:v15030728. [PMID: 36992437 PMCID: PMC10051058 DOI: 10.3390/v15030728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/26/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
Tomato brown rugose fruit virus (ToBRFV) is a soil-borne virus showing a low percentage of ca. 3% soil-mediated infection when the soil contains root debris from a previous 30–50 day growth cycle of ToBRFV-infected tomato plants. We designed stringent conditions of soil-mediated ToBRFV infection by increasing the length of the pre-growth cycle to 90–120 days, adding a ToBRFV inoculum as well as truncating seedling roots, which increased seedling susceptibility to ToBRFV infection. These rigorous conditions were employed to challenge the efficiency of four innovative root-coating technologies in mitigating soil-mediated ToBRFV infection while avoiding any phytotoxic effect. We tested four different formulations, which were prepared with or without the addition of various virus disinfectants. We found that under conditions of 100% soil-mediated ToBRFV infection of uncoated positive control plants, root-coating with formulations based on methylcellulose (MC), polyvinyl alcohol (PVA), silica Pickering emulsion and super-absorbent polymer (SAP) that were prepared with the disinfectant chlorinated-trisodium phosphate (Cl-TSP) showed low percentages of soil-mediated ToBRFV infection of 0%, 4.3%, 5.5% and 0%, respectively. These formulations had no adverse effect on plant growth parameters when compared to negative control plants grown under non ToBRFV inoculation conditions.
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16
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Vaisman M, Hak H, Arazi T, Spiegelman Z. The Impact of Tobamovirus Infection on Root Development Involves Induction of Auxin Response Factor 10a in Tomato. PLANT & CELL PHYSIOLOGY 2023; 63:1980-1993. [PMID: 34977939 DOI: 10.1093/pcp/pcab179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/16/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Plant viruses cause systemic diseases that severely impair plant growth and development. While the accumulation of viruses in the root system has long been established, little is known as to how viruses affect root architecture. Here, we examined how the emerging tobamovirus, tomato brown rugose fruit virus (ToBRFV), alters root development in tomato. We found that ToBRFV and tobacco mosaic virus both invaded root systems during the first week of infection. ToBRFV infection of tomato plants resulted in a significant decrease in root biomass and elongation and root-to-shoot ratio and a marked suppression of root branching. Mutation in RNA-dependent RNA polymerase 6 increased the susceptibility of tomato plants to ToBRFV, resulting in severe reduction of various root growth parameters including root branching. Viral root symptoms were associated with the accumulation of auxin response factor 10a (SlARF10a) transcript, a homolog of Arabidopsis ARF10, a known suppressor of lateral root development. Interestingly, loss-of-function mutation in SlARF10a moderated the effect of ToBRFV on root branching. In contrast, downregulation of sly-miR160a, which targets SlARF10a, was associated with constitutive suppression root branching independent of viral infection. In addition, overexpression of a microRNA-insensitive mutant of SlARF10a mimicked the effect of ToBRFV on root development, suggesting a specific role for SlARF10a in ToBRFV-mediated suppression of root branching. Taken together, our results provide new insights into the impact of tobamoviruses on root development and the role of ARF10a in the suppression of root branching in tomato.
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Affiliation(s)
- Michael Vaisman
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Institute, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, PO Box 12, Rehovot 761001, Israel
| | - Hagit Hak
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Institute, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Tzahi Arazi
- Plant Sciences Institute, Agricultural Research Organization, The Volcani Institute, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Ziv Spiegelman
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Institute, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
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17
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Saunders K, Thuenemann EC, Peyret H, Lomonossoff GP. The Tobacco Mosaic Virus Origin of Assembly Sequence is Dispensable for Specific Viral RNA Encapsidation but Necessary for Initiating Assembly at a Single Site. J Mol Biol 2022; 434:167873. [PMID: 36328231 DOI: 10.1016/j.jmb.2022.167873] [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: 08/23/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
We have investigated whether the presence of the origin of assembly sequence (OAS) of tobacco mosaic virus (TMV) is necessary for the specific encapsidation of replicating viral RNA. To this end TMV coat protein was expressed from replicating RNA constructs with or without the OAS in planta. In both cases the replicating RNA was specifically encapsidated to give nucleoprotein nanorods, though the yield in the absence of the OAS was reduced to about 60% of that in its presence. Moreover, the nanorods generated in the absence of the OAS were more heterogeneous in length and contained frequent structural discontinuities. These results strongly suggest that the function of the OAS is to provide a unique site for the initiation of viral assembly, leading to a one-start helix, rather than the selection of virus RNA for packaging.
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Affiliation(s)
- Keith Saunders
- Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Eva C Thuenemann
- Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hadrien Peyret
- Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - George P Lomonossoff
- Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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18
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Palukaitis P, Akbarimotlagh M, Baek E, Yoon JY. The Secret Life of the Inhibitor of Virus Replication. Viruses 2022; 14:2782. [PMID: 36560786 PMCID: PMC9787567 DOI: 10.3390/v14122782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
The inhibitor of virus replication (IVR) is an inducible protein that is not virus-target-specific and can be induced by several viruses. The GenBank was interrogated for sequences closely related to the tobacco IVR. Various RNA fragments from tobacco, tomato, and potato and their genomic DNA contained IVR-like sequences. However, IVRs were part of larger proteins encoded by these genomic DNA sequences, which were identified in Arabidopsis as being related to the cyclosome protein designated anaphase-promoting complex 7 (APC7). Sequence analysis of the putative APC7s of nine plant species showed proteins of 558-561 amino acids highly conserved in sequence containing at least six protein-binding elements of 34 amino acids called tetratricopeptide repeats (TPRs), which form helix-turn-helix structures. The structures of Arabidopsis APC7 and the tobacco IVR proteins were modeled using the AlphaFold program and superimposed, showing that IVR had the same structure as the C-terminal 34% of APC7, indicating that IVR was a product of the APC7 gene. Based on the presence of various transcription factor binding sites in the APC7 sequences upstream of the IVR coding sequences, we propose that IVR could be expressed by these APC7 gene sequences involving the transcription factor SHE1.
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Affiliation(s)
- Peter Palukaitis
- Department of Horticulture Sciences, Seoul Women’s University, Seoul 01797, Republic of Korea
| | - Masoud Akbarimotlagh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Eseul Baek
- Department of Horticulture Sciences, Seoul Women’s University, Seoul 01797, Republic of Korea
| | - Ju-Yeon Yoon
- Department of Plant Protection and Quarantine, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Republic of Korea
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19
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Shah SN, Saunders K, Thuenemann EC, Evans DJ, Lomonossoff GP. Designer-length palladium nanowires can be templated by the central channel of tobacco mosaic virus nanorods. Virology 2022; 577:155-162. [PMID: 36384077 DOI: 10.1016/j.virol.2022.10.014] [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: 09/23/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022]
Abstract
We have developed methods for the templated synthesis of palladium nanowires (Pd NWs) within the central channel of tobacco mosaic virus (TMV) nanorods of various lengths. We show that uniform 4 nm diameter Pd NWs can be produced by selective growth within these channels by including the capping reagent, poly(vinyl-pyrrolidone) (PVP30K) and reducing the metal precursor to metallic palladium with ascorbic acid. The length of the Pd NWs can be controlled either by varying the length of the nanorod templates and/or through alterations to the reaction conditions. We have also demonstrated bimetallic gold (Au)-palladium (Pd) in-situ metallization of TMV nanorods resulting in the production of Pd NWs 6 nm gold nanoparticles attached to their ends. The materials produced have many potential applications in the construction of nanoscale devices.
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Affiliation(s)
- Sachin N Shah
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK; Department of Chemistry, University of Hull, Hull, HU6 7RX, UK
| | - Keith Saunders
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Eva C Thuenemann
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - David J Evans
- Department of Chemistry, University of Hull, Hull, HU6 7RX, UK
| | - George P Lomonossoff
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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20
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Construction of electrochemiluminescence biosensor via click chemistry and ARGET-ATRP for detecting tobacco mosaic virus RNA. Anal Biochem 2022; 655:114834. [DOI: 10.1016/j.ab.2022.114834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/21/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022]
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21
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Creager ANH. Tobacco Mosaic Virus and the History of Molecular Biology. Annu Rev Virol 2022; 9:39-55. [PMID: 35704746 DOI: 10.1146/annurev-virology-100520-014520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The history of tobacco mosaic virus (TMV) includes many firsts in science, beginning with its being the first virus identified. This review offers an overview of a history of research on TMV, with an emphasis on its close connections to the emergence and development of molecular biology. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Angela N H Creager
- Department of History, Princeton University, Princeton, New Jersey; USA;
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22
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Saunders K, Thuenemann EC, Shah SN, Peyret H, Kristianingsih R, Lopez SG, Richardson J, Lomonossoff GP. The Use of a Replicating Virus Vector For in Planta Generation of Tobacco Mosaic Virus Nanorods Suitable For Metallization. Front Bioeng Biotechnol 2022; 10:877361. [PMID: 35557863 PMCID: PMC9086362 DOI: 10.3389/fbioe.2022.877361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
The production of designer-length tobacco mosaic virus (TMV) nanorods in plants has been problematic in terms of yields, particularly when modified coat protein subunits are incorporated. To address this, we have investigated the use of a replicating potato virus X-based vector (pEff) to express defined length nanorods containing either wild-type or modified versions of the TMV coat protein. This system has previously been shown to be an efficient method for producing virus-like particles of filamentous plant viruses. The length of the resulting TMV nanorods can be controlled by varying the length of the encapsidated RNA. Nanorod lengths were analyzed with a custom-written Python computer script coupled with the Nanorod UI user interface script, thereby generating histograms of particle length. In addition, nanorod variants were produced by incorporating coat protein subunits presenting metal-binding peptides at their C-termini. We demonstrate the utility of this approach by generating nanorods that bind colloidal gold nanoparticles.
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Affiliation(s)
- Keith Saunders
- Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Eva C. Thuenemann
- Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Sachin N. Shah
- Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Hadrien Peyret
- Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Ruth Kristianingsih
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Sergio G. Lopez
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Jake Richardson
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - George P. Lomonossoff
- Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- *Correspondence: George P. Lomonossoff,
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23
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Asad Z, Ashfaq M, Iqbal N, Muhammad Usman Aslam H, Riaz H, Hameed A, Parvaiz F, Sadiq N, Ali Khan K, Ahmad Z. Genetic Diversity of Cucumber Green Mottle Mosaic Virus (CGMMV) Infecting Cucurbits. Saudi J Biol Sci 2022; 29:3577-3585. [PMID: 35844387 PMCID: PMC9280310 DOI: 10.1016/j.sjbs.2022.02.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/07/2022] [Accepted: 02/15/2022] [Indexed: 11/25/2022] Open
Abstract
Cucumber green mottle mosaic virus (CGMMV), a well-known Tobamovirus, infects cucurbits across the globe. To determine its current status, molecular characterization, genetic recombination, gene flow and selection pressure, 10 districts from Punjab province of Pakistan were surveyed and a total of 2561 cucurbits samples were collected during 2019–2020. These samples were subjected to virus-specific double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA) for the detection of CGMMV. The results revealed that viral disease was prevalent in all surveyed districts of Punjab with an overall 25.69% disease incidence. ELISA positive samples were further confirmed through RT-PCR and sequencing of coat protein (CP) cistron. Sequence analysis showed that the present studied CGMMV isolates have 96–99.5% nucleotide and 94.40–99.50% amino acid identities with those already available in GenBank. Phylogenetic analysis also revealed that understudied isolates were closely related with South Korean (AB369274) and Japanese (V01551) isolates and clustered in a separate clad. Sequence polymorphisms were observed in 663 bp of sequence within 31 CGMMV isolates covering complete CP gene. Total number of sites were 662, of which 610 and 52 sites were monomorphic and polymorphic (segregating), respectively. Of these polymorphic, 24 were singleton variable and 28 were parsimony informative. Overall nucleotide diversity (π) in all the understudied 31 isolates was 0.00010 while a total of 1 InDel event was observed and InDel Diversity (k) was 0.065. Haplotype diversity analysis revealed that there was a total 29 haplotypes with haplotype diversity (Hd) of 0.993458 in all the 31 isolates which provide evidence of less diversity among Pakistani isolates. The statistical analysis revealed the values 2.568, 5.31304 and 4.86698 of Tajima's D, Fu, & Li’s F* and D*, respectively, which witnessed the population of CGMMV was under balanced selection pressure.
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24
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Peña EJ, Heinlein M. In Vivo Visualization of Mobile mRNA Particles in Plants Using BglG. Methods Mol Biol 2022; 2457:411-426. [PMID: 35349157 DOI: 10.1007/978-1-0716-2132-5_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cells have developed mechanisms for cytoplasmic RNA transport and localization that participate in the regulation and subcellular localization of protein synthesis. In addition, plants can exchange RNA molecules between cells through plasmodesmata and to distant tissues in the phloem. These mechanisms are hijacked by RNA viruses to establish their replication complexes and to disseminate their genomes throughout the plant organism with the help of virus-encoded movement proteins (MP). Live imaging of RNA molecules is a fundamental approach to understand the regulation and molecular basis of these processes. The most widely used experimental systems for the in vivo visualization of genetically encoded RNA molecules are based on fluorescently tagged RNA binding proteins that bind to specific motifs inserted into the RNA, thus allowing the tracking of the specific RNA molecule by fluorescent microscopy. Recently, we developed the use of the E. coli RNA binding protein BglG for the imaging of RNAs tagged with BglG-binding sites in planta. We describe here the detailed method by which we use this in vivo RNA tagging system for the real-time imaging of Tobacco mosaic virus (TMV) MP mRNA.
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Affiliation(s)
- Eduardo J Peña
- Instituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas-UNLP, CONICET, La Plata, Argentina
| | - Manfred Heinlein
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France.
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25
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Translation of Plant RNA Viruses. Viruses 2021; 13:v13122499. [PMID: 34960768 PMCID: PMC8708638 DOI: 10.3390/v13122499] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/01/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022] Open
Abstract
Plant RNA viruses encode essential viral proteins that depend on the host translation machinery for their expression. However, genomic RNAs of most plant RNA viruses lack the classical characteristics of eukaryotic cellular mRNAs, such as mono-cistron, 5′ cap structure, and 3′ polyadenylation. To adapt and utilize the eukaryotic translation machinery, plant RNA viruses have evolved a variety of translation strategies such as cap-independent translation, translation recoding on initiation and termination sites, and post-translation processes. This review focuses on advances in cap-independent translation and translation recoding in plant viruses.
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Li P, Zhang Y, Gong P, Liu Y, Feng W, Yang H. Photoinduced atom transfer radical polymerization combined with click chemistry for highly sensitive detection of tobacco mosaic virus RNA. Talanta 2021; 235:122803. [PMID: 34517661 DOI: 10.1016/j.talanta.2021.122803] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/24/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
An electrochemical biosensor for highly sensitive detection of tobacco mosaic virus (TMV) RNA (tRNA) based on click chemistry and photoinduced atom transfer radical polymerization (photoATRP) is developed for the first time. Herein, tRNA is recognized and captured by hairpin DNA immobilized on the gold electrode surface by Au-S self-assembly. Propyl 2-bromoisobutyrate (PBIB), a photoATRP initiator containing an alkyne group, is conjugated to the azide group of hairpin DNA via a Cu(I)-catalyzed azidoalkyl cyclization reaction (CuAAC). Under the irradiation of 470 nm blue light, photoATRP is activated by the photoredox catalyst (eosin Y, EY), resulting in the formation of a large number of electroactive probes (ferrocenylmethyl methacrylate, FMMA), which significantly amplifies the signal. Under the optimal experimental parameters, the strategy has a wide linear detection (0.1 pM-10 nM) (R2 = 0.995) with a limit of detection (LOD) as low as 3.5 fM. In addition, the biosensor also exhibited good selectivity for mismatched bases, excellent stability and reproducibility. Moreover, satisfactory result was achieved when the biosensor was applied to the detection of tRNA from healthy rehmannia total RNA extracts, which demonstrates the great potential of the method in the practical detection of TMV.
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Affiliation(s)
- Peipei Li
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450046, PR China
| | - Yaping Zhang
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450046, PR China
| | - Pengfei Gong
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450046, PR China
| | - Yanju Liu
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450046, PR China.
| | - Weisheng Feng
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450046, PR China.
| | - Huaixia Yang
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450046, PR China.
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Dronina J, Samukaite-Bubniene U, Ramanavicius A. Advances and insights in the diagnosis of viral infections. J Nanobiotechnology 2021; 19:348. [PMID: 34717656 PMCID: PMC8556785 DOI: 10.1186/s12951-021-01081-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Viral infections are the most common among diseases that globally require around 60 percent of medical care. However, in the heat of the pandemic, there was a lack of medical equipment and inpatient facilities to provide all patients with viral infections. The detection of viral infections is possible in three general ways such as (i) direct virus detection, which is performed immediately 1-3 days after the infection, (ii) determination of antibodies against some virus proteins mainly observed during/after virus incubation period, (iii) detection of virus-induced disease when specific tissue changes in the organism. This review surveys some global pandemics from 1889 to 2020, virus types, which induced these pandemics, and symptoms of some viral diseases. Non-analytical methods such as radiology and microscopy also are overviewed. This review overlooks molecular analysis methods such as nucleic acid amplification, antibody-antigen complex determination, CRISPR-Cas system-based viral genome determination methods. Methods widely used in the certificated diagnostic laboratory for SARS-CoV-2, Influenza A, B, C, HIV, and other viruses during a viral pandemic are outlined. A comprehensive overview of molecular analytical methods has shown that the assay's sensitivity, accuracy, and suitability for virus detection depends on the choice of the number of regions in the viral open reading frame (ORF) genome sequence and the validity of the selected analytical method.
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Affiliation(s)
- Julija Dronina
- Laboratory of Nanotechnology, Department of Functional Materials and Electronics, Center for Physical Sciences and Technology, Sauletekio av. 3, Vilnius, Lithuania
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Urte Samukaite-Bubniene
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Arunas Ramanavicius
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania.
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Hak H, Spiegelman Z. The Tomato Brown Rugose Fruit Virus Movement Protein Overcomes Tm-22 Resistance in Tomato While Attenuating Viral Transport. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1024-1032. [PMID: 33970669 DOI: 10.1094/mpmi-01-21-0023-r] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Tomato brown rugose fruit virus is a new virus species in the Tobamovirus genus, causing substantial damage to tomato crops. Reports of recent tomato brown rugose fruit virus (ToBRFV) outbreaks from around the world indicate an emerging global epidemic. ToBRFV overcomes all tobamovirus resistances in tomato, including the durable Tm-22 resistance gene, which had been effective against multiple tobamoviruses. Here, we show that the ToBRFV movement protein (MPToBRFV) enables the virus to evade Tm-22 resistance. Transient expression of MPToBRFV failed to activate the Tm-22 resistance response. Replacement of the original MP sequence of tomato mosaic virus (ToMV) with MPToBRFV enabled this recombinant virus to infect Tm-22-resistant plants. Using hybrid protein analysis, we show that the elements required to evade Tm-22 are located between MPToBRFV amino acids 1 and 216 and not the C terminus, as previously assumed. Analysis of ToBRFV systemic infection in tomato revealed that ToBRFV spreads more slowly compared with ToMV. Interestingly, replacement of tobacco mosaic virus (TMV) and ToMV MPs with MPToBRFV caused an attenuation of systemic infection of both viruses. Cell-to-cell movement analysis showed that MPToBRFV moves less effectively compared with the TMV MP (MPTMV). These findings suggest that overcoming Tm-22 is associated with attenuated MP function. This may explain the high durability of Tm-22 resistance, which had remained unbroken for over 60 years.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Hagit Hak
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Ziv Spiegelman
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
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29
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Bartoschek MD, Ugur E, Nguyen TA, Rodschinka G, Wierer M, Lang K, Bultmann S. Identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells. Nucleic Acids Res 2021; 49:e62. [PMID: 33684219 PMCID: PMC8216290 DOI: 10.1093/nar/gkab132] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/20/2022] Open
Abstract
The genetic code of mammalian cells can be expanded to allow the incorporation of non-canonical amino acids (ncAAs) by suppressing in-frame amber stop codons (UAG) with an orthogonal pyrrolysyl-tRNA synthetase (PylRS)/tRNAPylCUA (PylT) pair. However, the feasibility of this approach is substantially hampered by unpredictable variations in incorporation efficiencies at different stop codon positions within target proteins. Here, we apply a proteomics-based approach to quantify ncAA incorporation rates at hundreds of endogenous amber stop codons in mammalian cells. With these data, we compute iPASS (Identification of Permissive Amber Sites for Suppression; available at www.bultmannlab.eu/tools/iPASS), a linear regression model to predict relative ncAA incorporation efficiencies depending on the surrounding sequence context. To verify iPASS, we develop a dual-fluorescence reporter for high-throughput flow-cytometry analysis that reproducibly yields context-specific ncAA incorporation efficiencies. We show that nucleotides up- and downstream of UAG synergistically influence ncAA incorporation efficiency independent of cell line and ncAA identity. Additionally, we demonstrate iPASS-guided optimization of ncAA incorporation rates by synonymous exchange of codons flanking the amber stop codon. This combination of in silico analysis followed by validation in living mammalian cells substantially simplifies identification as well as adaptation of sites within a target protein to confer high ncAA incorporation rates.
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Affiliation(s)
- Michael D Bartoschek
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Enes Ugur
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Tuan-Anh Nguyen
- Department of Chemistry, Synthetic Biochemistry, Technical University of Munich, Garching 85748, Germany
| | - Geraldine Rodschinka
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Kathrin Lang
- Department of Chemistry, Synthetic Biochemistry, Technical University of Munich, Garching 85748, Germany
| | - Sebastian Bultmann
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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30
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Alon DM, Hak H, Bornstein M, Pines G, Spiegelman Z. Differential Detection of the Tobamoviruses Tomato Mosaic Virus (ToMV) and Tomato Brown Rugose Fruit Virus (ToBRFV) Using CRISPR-Cas12a. PLANTS (BASEL, SWITZERLAND) 2021; 10:1256. [PMID: 34205558 PMCID: PMC8234260 DOI: 10.3390/plants10061256] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 12/22/2022]
Abstract
CRISPR/Cas12a-based detection is a novel approach for the efficient, sequence-specific identification of viruses. Here we adopt the use of CRISPR/Cas12a to identify the tomato brown rugose fruit virus (ToBRFV), a new and emerging tobamovirus which is causing substantial damage to the global tomato industry. Specific CRISPR RNAs (crRNAs) were designed to detect either ToBRFV or the closely related tomato mosaic virus (ToMV). This technology enabled the differential detection of ToBRFV and ToMV. Sensitivity assays revealed that viruses can be detected from 15-30 ng of RT-PCR product, and that specific detection could be achieved from a mix of ToMV and ToBRFV. In addition, we show that this method can enable the identification of ToBRFV in samples collected from commercial greenhouses. These results demonstrate a new method for species-specific detection of tobamoviruses. A future combination of this approach with isothermal amplification could provide a platform for efficient and user-friendly ways to distinguish between closely related strains and resistance-breaking pathogens.
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Affiliation(s)
- Dan Mark Alon
- Department of Entomology, Agricultural Research Organization—the Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7505101, Israel;
- The Shmunis School of Molecular Cell Biology & Biotechnology, Faculty of Life Science, Tel Aviv University, Tel Aviv 69978, Israel;
| | - Hagit Hak
- Department of Plant Pathology and Weed Research, Agricultural Research Organization—the Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7505101, Israel;
| | - Menachem Bornstein
- The Shmunis School of Molecular Cell Biology & Biotechnology, Faculty of Life Science, Tel Aviv University, Tel Aviv 69978, Israel;
| | - Gur Pines
- Department of Entomology, Agricultural Research Organization—the Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7505101, Israel;
| | - Ziv Spiegelman
- The Shmunis School of Molecular Cell Biology & Biotechnology, Faculty of Life Science, Tel Aviv University, Tel Aviv 69978, Israel;
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31
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Nooraei S, Bahrulolum H, Hoseini ZS, Katalani C, Hajizade A, Easton AJ, Ahmadian G. Virus-like particles: preparation, immunogenicity and their roles as nanovaccines and drug nanocarriers. J Nanobiotechnology 2021; 19:59. [PMID: 33632278 PMCID: PMC7905985 DOI: 10.1186/s12951-021-00806-7] [Citation(s) in RCA: 376] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/15/2021] [Indexed: 12/24/2022] Open
Abstract
Virus-like particles (VLPs) are virus-derived structures made up of one or more different molecules with the ability to self-assemble, mimicking the form and size of a virus particle but lacking the genetic material so they are not capable of infecting the host cell. Expression and self-assembly of the viral structural proteins can take place in various living or cell-free expression systems after which the viral structures can be assembled and reconstructed. VLPs are gaining in popularity in the field of preventive medicine and to date, a wide range of VLP-based candidate vaccines have been developed for immunization against various infectious agents, the latest of which is the vaccine against SARS-CoV-2, the efficacy of which is being evaluated. VLPs are highly immunogenic and are able to elicit both the antibody- and cell-mediated immune responses by pathways different from those elicited by conventional inactivated viral vaccines. However, there are still many challenges to this surface display system that need to be addressed in the future. VLPs that are classified as subunit vaccines are subdivided into enveloped and non- enveloped subtypes both of which are discussed in this review article. VLPs have also recently received attention for their successful applications in targeted drug delivery and for use in gene therapy. The development of more effective and targeted forms of VLP by modification of the surface of the particles in such a way that they can be introduced into specific cells or tissues or increase their half-life in the host is likely to expand their use in the future. Recent advances in the production and fabrication of VLPs including the exploration of different types of expression systems for their development, as well as their applications as vaccines in the prevention of infectious diseases and cancers resulting from their interaction with, and mechanism of activation of, the humoral and cellular immune systems are discussed in this review.
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Affiliation(s)
- Saghi Nooraei
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P. O. BOX: 14155-6343, Tehran, 1497716316, Iran
| | - Howra Bahrulolum
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P. O. BOX: 14155-6343, Tehran, 1497716316, Iran
| | - Zakieh Sadat Hoseini
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P. O. BOX: 14155-6343, Tehran, 1497716316, Iran
| | - Camellia Katalani
- Sari Agriculture Science and Natural Resource University (SANRU), Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari, Iran
| | - Abbas Hajizade
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Andrew J Easton
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, UK.
| | - Gholamreza Ahmadian
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P. O. BOX: 14155-6343, Tehran, 1497716316, Iran.
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32
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Wang W, Li P, Zheng Z, Cheng D, Dong C, Yang H. Highly sensitive fluorescence detection of tobacco mosaic virus RNA based on disodium 4,4′-diazidostilbene-2,2′-disulfonate tetrahydrate in situ reaction. NEW J CHEM 2021. [DOI: 10.1039/d1nj02546e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel fluorescent turn-on method for TMV RNA via the reducing ability of an AA and DES in situ reaction was reported.
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Affiliation(s)
- Wenbin Wang
- Henan Key Laboratory of TCM Syndrome and Prescription in Signaling, Henan International Joint Laboratory of TCM Syndrome and Prescription in Signaling, Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, P. R. China
| | - Peipei Li
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, People's Republic of China
| | - Zhixian Zheng
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, People's Republic of China
| | - Di Cheng
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, People's Republic of China
| | - Chengming Dong
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, People's Republic of China
| | - Huaixia Yang
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, People's Republic of China
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33
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Peña EJ, Robles Luna G, Heinlein M. In vivo imaging of tagged mRNA in plant tissues using the bacterial transcriptional antiterminator BglG. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:271-282. [PMID: 33098198 DOI: 10.1111/tpj.15035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
RNA transport and localization represent important post-transcriptional mechanisms to determine the subcellular localization of protein synthesis. Plants have the capacity to transport messenger (m)RNA molecules beyond the cell boundaries through plasmodesmata and over long distances in the phloem. RNA viruses exploit these transport pathways to disseminate their infections and represent important model systems to investigate RNA transport in plants. Here, we present an in vivo plant RNA-labeling system based on the Escherichia coli RNA-binding protein BglG. Using the detection of RNA in mobile RNA particles formed by viral movement protein (MP) as a model, we demonstrate the efficiency and specificity of mRNA detection by the BglG system as compared with MS2 and λN systems. Our observations show that MP mRNA is specifically associated with MP in mobile MP particles but hardly with MP localized at plasmodesmata. MP mRNA is clearly absent from MP accumulating along microtubules. We show that the in vivo BglG labeling of the MP particles depends on the presence of the BglG-binding stem-loop aptamers within the MP mRNA and that the aptamers enhance the coprecipitation of BglG by MP, thus demonstrating the presence of an MP:MP mRNA complex. The BglG system also allowed us to monitor the cell-to-cell transport of the MP mRNA, thus linking the observation of mobile MP mRNA granules with intercellular MP mRNA transport. Given its specificity demonstrated here, the BglG system may be widely applicable for studying mRNA transport and localization in plants.
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Affiliation(s)
- Eduardo J Peña
- Université de Strasbourg, CNRS, IBMP UPR 2357, Strasbourg, F-67000, France
- Instituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, CONICET UNLP, La Plata, Argentina
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, CONICET UNLP, La Plata, Argentina
| | - Manfred Heinlein
- Université de Strasbourg, CNRS, IBMP UPR 2357, Strasbourg, F-67000, France
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Obeid R, Wehbe E, Rima M, Kabara M, Al Bersaoui R, Sabatier JM, Fajloun Z, Gereige D. First Detection of Tobacco Mosaic Virus in Tobacco Fields in Northern Lebanon. Infect Disord Drug Targets 2021; 21:534-540. [PMID: 32988357 DOI: 10.2174/1871526520666200928164057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/16/2020] [Accepted: 07/19/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Tobacco mosaic virus (TMV) is the most known virus in the plant mosaic virus family and is able to infect a wide range of crops, in particular, tobacco, causing a production loss. OBJECTIVES Herein, and for the first time in Lebanon, we investigated the presence of TMV infection in crops by analyzing 88 samples of tobacco, tomato, cucumber and pepper collected from different regions in North Lebanon. METHODS Double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA), revealed a potential TMV infection of four tobacco samples out of 88 crop samples collected. However, no tomato, cucumber and pepper samples were infected. The TMV+ tobacco samples were then extensively analyzed by RT-PCR to detect viral RNA using different primers covering all the viral genome. RESULTS AND DISCUSSION PCR results confirmed those of DAS-ELISA showing TMV infection of four tobacco samples collected from three crop fields of North Lebanon. In only one of four TMV+ samples, we were able to amplify almost all the regions of viral genome, suggesting possible mutations in the virus genome or an infection with a new, not yet identified, TMV strain. CONCLUSION Our study is the first in Lebanon, revealing TMV infection in crop fields and highlighting the danger that may affect the future of agriculture.
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Affiliation(s)
- Rami Obeid
- Faculty of Sciences 3, Lebanese University, Michel Slayman Tripoli Campus, Ras Maska 1352, Lebanon
| | - Elias Wehbe
- Faculty of Sciences 3, Lebanese University, Michel Slayman Tripoli Campus, Ras Maska 1352, Lebanon
| | - Mohamad Rima
- Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U964, CNRS U7104, Universite de Strasbourg, 67400 Illkirch, France
| | - Mohammad Kabara
- Water and Environment Science Laboratory, Public Health Faculty 3, Lebanese University, 1300 Tripoli, Lebanon
| | - Romeo Al Bersaoui
- Faculty of Sciences 3, Lebanese University, Michel Slayman Tripoli Campus, Ras Maska 1352, Lebanon
| | - Jean Marc Sabatier
- Institute of NeuroPhysiopathology, UMR 7051, Faculte de Medecine Secteur Nord, 51, Boulevard Pierre Dramard-CS80011, 13344-Marseille Cedex 15, France
| | - Ziad Fajloun
- Faculty of Sciences 3, Lebanese University, Michel Slayman Tripoli Campus, Ras Maska 1352, Lebanon
| | - Dalya Gereige
- Faculty of Sciences 3, Lebanese University, Michel Slayman Tripoli Campus, Ras Maska 1352, Lebanon
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35
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Thermodynamic analysis of proton- and urea-induced dissociation of tobacco mosaic virus: stoichiometry, common ion effect, cooperativity, heterogeneity of subunits and the effect of urea as a homogenizer. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-020-01125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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36
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Sheshukova EV, Ershova NM, Kamarova KA, Dorokhov YL, Komarova TV. The Tobamoviral Movement Protein: A "Conditioner" to Create a Favorable Environment for Intercellular Spread of Infection. FRONTIERS IN PLANT SCIENCE 2020; 11:959. [PMID: 32670343 PMCID: PMC7328123 DOI: 10.3389/fpls.2020.00959] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
During their evolution, viruses acquired genes encoding movement protein(s) (MPs) that mediate the intracellular transport of viral genetic material to plasmodesmata (Pd) and initiate the mechanisms leading to the increase in plasmodesmal permeability. Although the current view on the role of the viral MPs was primarily formed through studies on tobacco mosaic virus (TMV), the function of its MP has not been fully elucidated. Given the intercellular movement of MPs independent of genomic viral RNA (vRNA), this characteristic may induce favorable conditions ahead of the infection front for the accelerated movement of the vRNA (i.e. the MP plays a role as a "conditioner" of viral intercellular spread). This idea is supported by (a) the synthesis of MP from genomic vRNA early in infection, (b) the Pd opening and the MP transfer to neighboring cells without formation of the viral replication complex (VRC), and (c) the MP-mediated movement of VRCs beyond the primary infected cell. Here, we will consider findings that favor the TMV MP as a "conditioner" of enhanced intercellular virus movement. In addition, we will discuss the mechanism by which TMV MP opens Pd for extraordinary transport of macromolecules. Although there is no evidence showing direct effects of TMV MP on Pd leading to their dilatation, recent findings indicate that MPs exert their influence indirectly by modulating Pd external and structural macromolecules such as callose and Pd-associated proteins. In explaining this phenomenon, we will propose a mechanism for TMV MP functioning as a conditioner for virus movement.
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Affiliation(s)
| | - Natalia M. Ershova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Kamila A. Kamarova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri L. Dorokhov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana V. Komarova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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37
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Peña EJ, Heinlein M. Visualization of Transiently Expressed mRNA in Plants Using MS2. Methods Mol Biol 2020; 2166:103-120. [PMID: 32710405 DOI: 10.1007/978-1-0716-0712-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
RNA transport and localization are evolutionarily conserved processes that allow protein translation to occur at specific subcellular sites and thereby having fundamental roles in the determination of cell fates, embryonic patterning, asymmetric cell division, and cell polarity. In addition to localizing RNA molecules to specific subcellular sites, plants have the ability to exchange RNA molecules between cells through plasmodesmata (PD). Plant RNA viruses hijack the mechanisms of intracellular and intercellular RNA transport to establish localized replication centers within infected cells and then to disseminate their infectious genomes between cells and throughout the plant organism with the help of their movement proteins (MP). In this chapter, we describe the transient expression of the tobacco mosaic virus movement protein (TMV-MP) and the application of the MS2 system for the in vivo labeling of the MP-encoding mRNA. The MS2 method is based on the binding of the bacteriophage coat protein (CP) to its origin of assembly (OAS) in the phage RNA. Thus, to label a specific mRNA in vivo, a tandem repetition of a 19-nucleotide-long stem-loop (SL) sequence derived from the MS2 OAS sequence (MSL) is transcriptionally fused to the RNA under investigation. The RNA is detected by the co-expression of fluorescent protein-tagged MS2 CP (MCP), which binds to each of the MSL elements. In providing a detailed protocol for the in vivo visualization of TMV-MP mRNA tagged with the MS2 system in Nicotiana benthamiana epidermal cells, we describe (1) the specific DNA constructs, (2) Agrobacterium tumefaciens-mediated transfection for their transient expression in plants, and (3) imaging conditions required to obtain high-quality mRNA imaging data.
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Affiliation(s)
- Eduardo José Peña
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata CONICET, Fac. Cs. Exactas, U.N.L.P, La Plata, Argentina
| | - Manfred Heinlein
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France.
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Wege C, Koch C. From stars to stripes: RNA-directed shaping of plant viral protein templates-structural synthetic virology for smart biohybrid nanostructures. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 12:e1591. [PMID: 31631528 DOI: 10.1002/wnan.1591] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/04/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022]
Abstract
The self-assembly of viral building blocks bears exciting prospects for fabricating new types of bionanoparticles with multivalent protein shells. These enable a spatially controlled immobilization of functionalities at highest surface densities-an increasing demand worldwide for applications from vaccination to tissue engineering, biocatalysis, and sensing. Certain plant viruses hold particular promise because they are sustainably available, biodegradable, nonpathogenic for mammals, and amenable to in vitro self-organization of virus-like particles. This offers great opportunities for their redesign into novel "green" carrier systems by spatial and structural synthetic biology approaches, as worked out here for the robust nanotubular tobacco mosaic virus (TMV) as prime example. Natural TMV of 300 x 18 nm is built from more than 2,100 identical coat proteins (CPs) helically arranged around a 6,395 nucleotides ssRNA. In vitro, TMV-like particles (TLPs) may self-assemble also from modified CPs and RNAs if the latter contain an Origin of Assembly structure, which initiates a bidirectional encapsidation. By way of tailored RNA, the process can be reprogrammed to yield uncommon shapes such as branched nanoobjects. The nonsymmetric mechanism also proceeds on 3'-terminally immobilized RNA and can integrate distinct CP types in blends or serially. Other emerging plant virus-deduced systems include the usually isometric cowpea chlorotic mottle virus (CCMV) with further strikingly altered structures up to "cherrybombs" with protruding nucleic acids. Cartoon strips and pictorial descriptions of major RNA-based strategies induct the reader into a rare field of nanoconstruction that can give rise to utile soft-matter architectures for complex tasks. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.
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Affiliation(s)
- Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Claudia Koch
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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Arkhipenko MV, Nikitin NA, Baranov OA, Evtushenko EA, Atabekov JG, Karpova OV. Surface Charge Mapping on Virions and Virus-Like Particles of Helical Plant Viruses. Acta Naturae 2019; 11:73-78. [PMID: 31993237 PMCID: PMC6977955 DOI: 10.32607/20758251-2019-11-4-73-78] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022] Open
Abstract
Currently, the assembly of helical plant viruses is poorly understood. The viral assembly and infection may be affected by the charge distribution on the virion surface. However, only the total virion charge (isoelectric point) has been determined for most plant viruses. Here, we report on the first application of positively charged magnetic nanoparticles for mapping the surface charge distribution of helical plant viruses. The charge was demonstrated to be unevenly distributed on the surface of viruses belonging to different taxonomic groups, with the negative charge being predominantly located at one end of the virions. This charge distribution is mainly controlled by viral RNA.
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Affiliation(s)
- M. V. Arkhipenko
- Department of Virology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - N. A. Nikitin
- Department of Virology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - O. A. Baranov
- Department of Virology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - E. A. Evtushenko
- Department of Virology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - J. G. Atabekov
- Department of Virology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - O. V. Karpova
- Department of Virology, Lomonosov Moscow State University, Moscow, 119234 Russia
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40
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Cody WB, Scholthof HB. Plant Virus Vectors 3.0: Transitioning into Synthetic Genomics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:211-230. [PMID: 31185187 DOI: 10.1146/annurev-phyto-082718-100301] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant viruses were first implemented as heterologous gene expression vectors more than three decades ago. Since then, the methodology for their use has varied, but we propose it was the merging of technologies with virology tools, which occurred in three defined steps discussed here, that has driven viral vector applications to date. The first was the advent of molecular biology and reverse genetics, which enabled the cloning and manipulation of viral genomes to express genes of interest (vectors 1.0). The second stems from the discovery of RNA silencing and the development of high-throughput sequencing technologies that allowed the convenient and widespread use of virus-induced gene silencing (vectors 2.0). Here, we briefly review the events that led to these applications, but this treatise mainly concentrates on the emerging versatility of gene-editing tools, which has enabled the emergence of virus-delivered genetic queries for functional genomics and virology (vectors 3.0).
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Affiliation(s)
- Will B Cody
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA;
- Shriram Center for Biological and Chemical Engineering, Stanford University, Stanford, California 94305, USA
| | - Herman B Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA;
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41
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Balke I, Zeltins A. Use of plant viruses and virus-like particles for the creation of novel vaccines. Adv Drug Deliv Rev 2019; 145:119-129. [PMID: 30172923 DOI: 10.1016/j.addr.2018.08.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 07/24/2018] [Accepted: 08/27/2018] [Indexed: 12/15/2022]
Abstract
In recent decades, the development of plant virology and genetic engineering techniques has resulted in the construction of plant virus-based vaccines for protection against different infectious agents, cancers and autoimmune diseases in both humans and animals. Interaction studies between plant viruses and mammalian organisms have suggested that plant viruses and virus-like particles (VLPs) are safe and noninfectious to humans and animals. Plant viruses with introduced antigens are powerful vaccine components due to their strongly organized, repetitive spatial structure; they can elicit strong immune responses similar to those observed with infectious mammalian viruses. The analysis of published data demonstrated that at least 73 experimental vaccines, including 61 prophylactic and 12 therapeutic vaccines, have been constructed using plant viruses as a carrier structure for presentation of different antigens. This information clearly demonstrates that noninfectious viruses are also applicable as vaccine carriers. Moreover, several plant viruses have been used for platform development, and corresponding vaccines are currently being tested in human and veterinary clinical trials. This review therefore discusses the main principles of plant VLP vaccine construction, emphasizing the physical, chemical, genetic and immunological aspects. Results of the latest studies suggest that several plant virus-based vaccines will join the list of approved human and animal vaccines in the near future.
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Affiliation(s)
- Ina Balke
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga LV1067, Latvia
| | - Andris Zeltins
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga LV1067, Latvia.
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42
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Ibrahim A, Odon V, Kormelink R. Plant Viruses in Plant Molecular Pharming: Toward the Use of Enveloped Viruses. FRONTIERS IN PLANT SCIENCE 2019; 10:803. [PMID: 31275344 PMCID: PMC6594412 DOI: 10.3389/fpls.2019.00803] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/04/2019] [Indexed: 05/03/2023]
Abstract
Plant molecular pharming has emerged as a reliable platform for recombinant protein expression providing a safe and low-cost alternative to bacterial and mammalian cells-based systems. Simultaneously, plant viruses have evolved from pathogens to molecular tools for recombinant protein expression, chimaeric viral vaccine production, and lately, as nanoagents for drug delivery. This review summarizes the genesis of viral vectors and agroinfection, the development of non-enveloped viruses for various biotechnological applications, and the on-going research on enveloped plant viruses.
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Mickoleit F, Altintoprak K, Wenz NL, Richter R, Wege C, Schüler D. Precise Assembly of Genetically Functionalized Magnetosomes and Tobacco Mosaic Virus Particles Generates a Magnetic Biocomposite. ACS APPLIED MATERIALS & INTERFACES 2018; 10:37898-37910. [PMID: 30360046 DOI: 10.1021/acsami.8b16355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Magnetosomes represent magnetic nanoparticles with unprecedented characteristics. Both their crystal morphology and the composition of the enveloping membrane can be manipulated by genetic means, allowing the display of functional moieties on the particle surface. In this study, we explore the generation of a new biomaterial assembly by coupling magnetosomes with tobacco mosaic virus (TMV) particles, both functionalized with complementary recognition sites. TMV consists of single-stranded RNA encapsidated by more than 2100 coat proteins, which enable chemical modification via functional groups. Incubation of EmGFP- or biotin-decorated TMV particles with magnetosomes genetically functionalized with GFP-binding nanobodies or streptavidin, respectively, results in the formation of magnetic, mesoscopic, strand-like biocomposites. TMV facilitates the agglomeration of magnetosomes by providing a scaffold. The size of the TMV-magnetosome mesostrands can be adjusted by varying the TMV-magnetosome particle ratios. The versatility of this novel material combination is furthermore demonstrated by coupling magnetosomes and terminal, 5'-functionalized TMV particles with high molecular precision, which results in "drumstick"-like TMV-magnetosome complexes. In summary, our approaches provide promising strategies for the generation of new biomaterial assemblies that could be used as scaffold for the introduction of further functionalities, and we foresee a broad application potential in the biomedical and biotechnological field.
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Affiliation(s)
| | - Klara Altintoprak
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems , University of Stuttgart , D-70569 Stuttgart , Germany
| | - Nana L Wenz
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems , University of Stuttgart , D-70569 Stuttgart , Germany
| | | | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems , University of Stuttgart , D-70569 Stuttgart , Germany
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44
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Lomonossoff GP, Wege C. TMV Particles: The Journey From Fundamental Studies to Bionanotechnology Applications. Adv Virus Res 2018; 102:149-176. [PMID: 30266172 PMCID: PMC7112118 DOI: 10.1016/bs.aivir.2018.06.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ever since its initial characterization in the 19th century, tobacco mosaic virus (TMV) has played a prominent role in the development of modern virology and molecular biology. In particular, research on the three-dimensional structure of the virus particles and the mechanism by which these assemble from their constituent protein and RNA components has made TMV a paradigm for our current view of the morphogenesis of self-assembling structures, including viral particles. More recently, this knowledge has been applied to the development of novel reagents and structures for applications in biomedicine and bionanotechnology. In this article, we review how fundamental science has led to TMV being at the vanguard of these new technologies.
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Affiliation(s)
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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45
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Poghossian A, Jablonski M, Koch C, Bronder TS, Rolka D, Wege C, Schöning MJ. Field-effect biosensor using virus particles as scaffolds for enzyme immobilization. Biosens Bioelectron 2018; 110:168-174. [DOI: 10.1016/j.bios.2018.03.036] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 03/01/2018] [Accepted: 03/16/2018] [Indexed: 11/27/2022]
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46
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Schwenger A, Jurkowski TP, Richert C. Capturing and Stabilizing Folded Proteins in Lattices Formed with Branched Oligonucleotide Hybrids. Chembiochem 2018; 19:1523-1530. [DOI: 10.1002/cbic.201800145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Alexander Schwenger
- Institut für Organische ChemieUniversität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Tomasz P. Jurkowski
- Institut für Biochemie und Technische BiochemieUniversität Stuttgart Allmandring 31 70569 Stuttgart Germany
| | - Clemens Richert
- Institut für Organische ChemieUniversität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
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47
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Electrochemically-Driven Insertion of Biological Nanodiscs into Solid State Membrane Pores as a Basis for "Pore-In-Pore" Membranes. NANOMATERIALS 2018; 8:nano8040237. [PMID: 29652841 PMCID: PMC5923567 DOI: 10.3390/nano8040237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/09/2018] [Accepted: 04/11/2018] [Indexed: 11/17/2022]
Abstract
Nanoporous membranes are of increasing interest for many applications, such as molecular filters, biosensors, nanofluidic logic and energy conversion devices. To meet high-quality standards, e.g., in molecular separation processes, membranes with well-defined pores in terms of pore diameter and chemical properties are required. However, the preparation of membranes with narrow pore diameter distributions is still challenging. In the work presented here, we demonstrate a strategy, a "pore-in-pore" approach, where the conical pores of a solid state membrane produced by a multi-step top-down lithography procedure are used as a template to insert precisely-formed biomolecular nanodiscs with exactly defined inner and outer diameters. These nanodiscs, which are the building blocks of tobacco mosaic virus-deduced particles, consist of coat proteins, which self-assemble under defined experimental conditions with a stabilizing short RNA. We demonstrate that the insertion of the nanodiscs can be driven either by diffusion due to a concentration gradient or by applying an electric field along the cross-section of the solid state membrane. It is found that the electrophoresis-driven insertion is significantly more effective than the insertion via the concentration gradient.
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48
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Wenz NL, Piasecka S, Kalinowski M, Schneider A, Richert C, Wege C. Building expanded structures from tetrahedral DNA branching elements, RNA and TMV protein. NANOSCALE 2018; 10:6496-6510. [PMID: 29569670 DOI: 10.1039/c7nr07743b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
By combining both chemical and enzymatic ligation with procedures guiding the self-assembly of nanotubular tobacco mosaic virus (TMV)-like particles (TLPs), novel nucleoprotein structures based on DNA-terminated branching elements, RNA scaffolds and TMV coat protein (CP) are made accessible. Tetrahedral tetrakis(hydroxybiphenyl)adamantane cores with four 5'-phosphorylated dinucleotide arms were coupled to DNA linkers by chemical ligation. The resulting three-dimensional (3D) branching elements were enzymatically ligated to the 3' termini of RNA scaffolds either prior to or after the RNAs' incorporation into TLPs. Thus, architectures with interconnected nanotube domains in two different length classes were generated, each containing 70 CP subunits per 10 nm length. Short TMV origin-of-assembly-containing RNA scaffolds ligated to the DNA allowed the growth of protein-coated 34 nm tubes on the terminal RNA strands in situ. Alternatively, 290 nm pre-fabricated tubes with accessible RNA 3' termini, attained by DNA blocking elements hybridized to the RNAs, were ligated with the branched cores. Both approaches resulted in four-armed nanoobjects, demonstrating a so far unique combination of organic synthesis of branching elements, enzymatic modifications, nucleic acid-based scaffolding and RNA-guided and DNA-controlled assembly of tubular RNA-encapsidating protein domains, yielding a novel class of 3D nucleoprotein architectures with polyvalent protein elements. In the long term, the production route might give rise to supramolecular systems with complex functionalities, installed via the orthogonal coupling of effector molecules to TLP domains.
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Affiliation(s)
- Nana L Wenz
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Sylwia Piasecka
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Matthäus Kalinowski
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Angela Schneider
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
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Abstract
The discovery of a new class of pathogen, viruses, in the late 19th century, ushered in a period of study of the biochemical and structural properties of these entities in which plant viruses played a prominent role. This was, in large part, due to the relative ease with which sufficient quantities of material could be produced for such analyses. As analytical techniques became increasingly sensitive, similar studies could be performed on the viruses from other organisms. However, plant viruses continued to play an important role in the development of molecular biology, including the demonstration that RNA can be infectious, the determination of the genetic code, the mechanism by which viral RNAs are translated, and some of the early studies on gene silencing. Thus, the study of plant viruses should not be considered a "niche" subject but rather part of the mainstream of virology and molecular biology.
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50
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Dickmeis C, Altintoprak K, van Rijn P, Wege C, Commandeur U. Bioinspired Silica Mineralization on Viral Templates. Methods Mol Biol 2018; 1776:337-362. [PMID: 29869253 DOI: 10.1007/978-1-4939-7808-3_23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant virus capsids are attractive entities for nanotechnological applications because of their variation in shape and natural assembly ability. This chapter describes the production and modification of three differently shaped plant virus capsids for silica mineralization purposes. The chosen plant viruses exhibit either an icosahedral (cowpea mosaic virus, CPMV), or a flexuous rod-like structure (potato virus X, PVX), or a rigid rod-like shape (tobacco mosaic virus, TMV), and are well-known and frequently used plant viruses for biotechnological applications. We describe the production (including genetic or chemical modification) and purification of the plant viruses or of empty virus-like particles in the case of CPMV, as well as the characterization of these harvested templates. The mineralization procedures and differences in the protocols specific to the distinct viruses are described, and the analyses of the mineralization results are explained.
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Affiliation(s)
- Christina Dickmeis
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Klara Altintoprak
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Patrick van Rijn
- Faculty of Medical Sciences, University of Groningen, AV, Groningen, The Netherlands
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Ulrich Commandeur
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany.
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