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Pavon JAR, da Silva Neves NA, Pinho JB, de Souza VJ, Patroca da Silva S, Ribeiro Cruz AC, de Almeida Medeiros DB, Teixeira Nunes MR, Slhessarenko RD. Disclosing the virome of Aedes, Anopheles and Culex female mosquitoes, Alto Pantanal of Mato Grosso, Brazil, 2019. Virology 2024; 598:110182. [PMID: 39033587 DOI: 10.1016/j.virol.2024.110182] [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: 03/06/2024] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
Using Illumina NextSeq sequencing and bioinformatics, we identified and characterized thirty-three viral sequences of unsegmented and multipartite viral families in Aedes spp., Culex sp. and Anopheles darlingi female mosquito pools from Porto São Luiz and Pirizal, Alto Pantanal. Seventeen sequences belong to unsegmented viral families, twelve represent putative novel insect-specific viruses (ISVs) within families Chuviridae (3/33; partial genomes) and coding-complete sequences of Xinmoviridae (1/33), Rhabdoviridae (2/33) and Metaviridae (6/33); and five coding-complete sequences of already-known ISVs. Notably, two putative novel rhabdoviruses, Corixo rhabdovirus 1 and 2, were phylogenetically related to Coxipo dielmovirus, but separated from other Alpharhabdovirinae genera, sharing Anopheles spp. as host. Regarding multipartite families, sixteen segments of different putative novel viruses were identified (13 coding-complete segments) within Durnavirales (4/33), Elliovirales (1/33), Hareavirales (3/33) and Reovirales (8/33) orders. Overall, this study describes twenty-eight (28/33) putative novel ISVs and five (5/33) already described viruses using metagenomics approach.
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Affiliation(s)
- Janeth Aracely Ramirez Pavon
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, CEP 78060-900, Cuiabá, Mato Grosso, Brazil
| | - Nilvanei Aparecido da Silva Neves
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, CEP 78060-900, Cuiabá, Mato Grosso, Brazil
| | - João Batista Pinho
- Instituto de Biociências, Laboratório de Ecologia de Aves e Biodiversidade, Universidade Federal de Mato Grosso, Cuiabá, CEP 78060-900, Mato Grosso, Brazil
| | - Vilma Juscineide de Souza
- Coordenadoria de Vigilância Ambiental, Secretaria Estadual de Saúde, Centro Político Administrativo de Mato Grosso, Palácio Paiaguás, CEP 78049-902, Cuiabá, Mato Grosso, Brazil
| | | | | | | | - Márcio Roberto Teixeira Nunes
- Laboratório de Tecnologia Biomolecular, Centro de Ciências Biológicas, Universidade Federal Do Pará, CEP 66075-110, Belém, Pará, Brazil
| | - Renata Dezengrini Slhessarenko
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, CEP 78060-900, Cuiabá, Mato Grosso, Brazil.
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2
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Huang W, Zhang Y, Xiao N, Zhao W, Shi Y, Fang R. Trans-complementation of the viral movement protein mediates efficient expression of large target genes via a tobacco mosaic virus vector. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38923265 DOI: 10.1111/pbi.14418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/17/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024]
Abstract
The development of plant virus-based expression systems has expanded rapidly owing to their potential applications in gene functional and disease resistance research, and industrial production of pharmaceutical proteins. However, the low yield of certain proteins, especially high-molecular-mass proteins, restricts the production scale. In this study, we observed that the tobacco mosaic virus (TMV)-mediated expression of a foreign protein was correlated with the amount of the movement protein (MP) and developed a TMV-derived pAT-transMP vector system incorporating trans-complementation expression of MP. The system is capable of efficient expression of exogenous proteins, in particular those with a high molecular mass, and enables simultaneous expression of two target molecules. Furthermore, viral expression of competent CRISPR-Cas9 protein and construction of CRISPR-Cas9-mediated gene-editing system in a single pAT-transMP construct was achieved. The results demonstrated a novel role for TMV-MP in enhancing the accumulation of a foreign protein produced from the viral vector or a binary expression system. Further investigation of the mechanism underlying this role will be beneficial for optimization of plant viral vectors with broad applications.
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Affiliation(s)
- Weikuo Huang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, and National Plant Gene Research Center, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuman Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, and National Plant Gene Research Center, Beijing, China
| | - Na Xiao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, and National Plant Gene Research Center, Beijing, China
| | - Wenhui Zhao
- College of Veterinary Medicine, and College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Ying Shi
- College of Veterinary Medicine, and College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, and National Plant Gene Research Center, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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3
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Jiao G, Ye Z, Feng K, Zhang C, Chen J, Li J, He Y. Discovery of Two Novel Viruses of the Willow-Carrot Aphid, Cavariella aegopodii. Viruses 2024; 16:919. [PMID: 38932211 PMCID: PMC11209057 DOI: 10.3390/v16060919] [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: 04/11/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
The advancement of bioinformatics and sequencing technology has resulted in the identification of an increasing number of new RNA viruses. This study systematically identified the RNA virome of the willow-carrot aphid, Cavariella aegopodii (Hemiptera: Aphididae), using metagenomic sequencing and rapid amplification of cDNA ends (RACE) approaches. C. aegopodii is a sap-sucking insect widely distributed in Europe, Asia, North America, and Australia. The deleterious effects of C. aegopodii on crop growth primarily stem from its feeding activities and its role as a vector for transmitting plant viruses. The virome includes Cavariella aegopodii virga-like virus 1 (CAVLV1) and Cavariella aegopodii iflavirus 1 (CAIV1). Furthermore, the complete genome sequence of CAVLV1 was obtained. Phylogenetically, CAVLV1 is associated with an unclassified branch of the Virgaviridae family and is susceptible to host antiviral RNA interference (RNAi), resulting in the accumulation of a significant number of 22nt virus-derived small interfering RNAs (vsiRNAs). CAIV1, on the other hand, belongs to the Iflaviridae family, with vsiRNAs ranging from 18 to 22 nt. Our findings present a comprehensive analysis of the RNA virome of C. aegopodii for the first time, offering insights that could potentially aid in the future control of the willow-carrot aphid.
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Affiliation(s)
| | | | | | | | | | | | - Yujuan He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China (J.C.); (J.L.)
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Yue N, Jiang Z, Pi Q, Yang M, Gao Z, Wang X, Zhang H, Wu F, Jin X, Li M, Wang Y, Zhang Y, Li D. Zn2+-dependent association of cysteine-rich protein with virion orchestrates morphogenesis of rod-shaped viruses. PLoS Pathog 2024; 20:e1012311. [PMID: 38885273 PMCID: PMC11213338 DOI: 10.1371/journal.ppat.1012311] [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: 12/16/2023] [Revised: 06/28/2024] [Accepted: 05/31/2024] [Indexed: 06/20/2024] Open
Abstract
The majority of rod-shaped and some filamentous plant viruses encode a cysteine-rich protein (CRP) that functions in viral virulence; however, the roles of these CRPs in viral infection remain largely unknown. Here, we used barley stripe mosaic virus (BSMV) as a model to investigate the essential role of its CRP in virus morphogenesis. The CRP protein γb directly interacts with BSMV coat protein (CP), the mutations either on the His-85 site in γb predicted to generate a potential CCCH motif or on the His-13 site in CP exposed to the surface of the virions abolish the zinc-binding activity and their interaction. Immunogold-labeling assays show that γb binds to the surface of rod-shaped BSMV virions in a Zn2+-dependent manner, which enhances the RNA binding activity of CP and facilitates virion assembly and stability, suggesting that the Zn2+-dependent physical association of γb with the virion is crucial for BSMV morphogenesis. Intriguingly, the tightly binding of diverse CRPs to their rod-shaped virions is a general feature employed by the members in the families Virgaviridae (excluding the genus Tobamovirus) and Benyviridae. Together, these results reveal a hitherto unknown role of CRPs in the assembly and stability of virus particles, and expand our understanding of the molecular mechanism underlying virus morphogenesis.
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Affiliation(s)
- Ning Yue
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhihao Jiang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qinglin Pi
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Meng Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zongyu Gao
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xueting Wang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - He Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Fengtong Wu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xuejiao Jin
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Menglin Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Ying Wang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dawei Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 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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6
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Weiland JJ, Wyatt N, Camelo V, Spanner RE, Hladky LJ, Ramachandran V, Secor GA, Martin FN, Wintermantel WM, Bolton MD. Beet Soil-Borne Virus Is a Helper Virus for the Novel Beta vulgaris Satellite Virus 1A. PHYTOPATHOLOGY 2024; 114:1126-1136. [PMID: 38451582 DOI: 10.1094/phyto-08-23-0299-kc] [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: 03/08/2024]
Abstract
Sugar beet (Beta vulgaris) is grown in temperate regions around the world as a source of sucrose used for natural sweetening. Sugar beet is susceptible to a number of viral diseases, but identification of the causal agent(s) under field conditions is often difficult due to mixtures of viruses that may be responsible for disease symptoms. In this study, the application of RNAseq to RNA extracted from diseased sugar beet roots obtained from the field and from greenhouse-reared plants grown in soil infested with the virus disease rhizomania (causal agent beet necrotic yellow vein virus; BNYVV) yielded genome-length sequences from BNYVV, as well as beet soil-borne virus (BSBV). The nucleotide identities of the derived consensus sequence of BSBV RNAs ranged from 99.4 to 96.7% (RNA1), 99.3 to 95.3% (RNA2), and 98.3 to 95.9% (RNA3) compared with published BSBV sequences. Based on the BSBV genome consensus sequence, clones of the genomic RNAs 1, 2, and 3 were obtained to produce RNA copies of the genome through in vitro transcription. Capped RNA produced from the clones was infectious when inoculated into leaves of Chenopodium quinoa and B. vulgaris, and extracts from transcript-infected C. quinoa leaves could infect sugar beet seedling roots through a vortex inoculation method. Subsequent exposure of these infected sugar beet seedling roots to aviruliferous Polymyxa betae, the protist vector of both BNYVV and BSBV, confirmed that BSBV derived from the infectious clones could be transmitted by the vector. Co-inoculation of BSBV synthetic transcripts with transcripts of a cloned putative satellite virus designated Beta vulgaris satellite virus 1A (BvSat1A) resulted in the production of lesions on leaves of C. quinoa similar to those produced by inoculation with BSBV alone. Nevertheless, accumulation of genomic RNA and the encoded protein of the satellite virus in co-inoculated leaves was readily detected on Northern and Western blots, respectively, whereas no accumulation of satellite virus products occurred when satellite virus RNA was inoculated alone. The predicted sequence of the detected protein encoded by BvSat1A bears hallmarks of coat proteins of other satellite viruses, and virions of a size consistent with a satellite virus were observed in samples testing positive for the virus. The results demonstrate that BSBV is a helper virus for the novel satellite virus BvSat1A.
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Affiliation(s)
- John J Weiland
- U.S. Department of Agriculture-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND
| | - Nathan Wyatt
- U.S. Department of Agriculture-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND
| | - Viviana Camelo
- U.S. Department of Agriculture-Agricultural Research Service, Sam Farr Crop Improvement and Protection Research Center, Salinas, CA
| | - Rebecca E Spanner
- U.S. Department of Agriculture-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND
- Department of Plant Pathology, North Dakota State University, Fargo, ND
| | - Laura Jenkins Hladky
- U.S. Department of Agriculture-Agricultural Research Service, Sam Farr Crop Improvement and Protection Research Center, Salinas, CA
| | - Vanitharani Ramachandran
- U.S. Department of Agriculture-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND
| | - Gary A Secor
- Department of Plant Pathology, North Dakota State University, Fargo, ND
| | - Frank N Martin
- U.S. Department of Agriculture-Agricultural Research Service, Sam Farr Crop Improvement and Protection Research Center, Salinas, CA
| | - William M Wintermantel
- U.S. Department of Agriculture-Agricultural Research Service, Sam Farr Crop Improvement and Protection Research Center, Salinas, CA
| | - Melvin D Bolton
- U.S. Department of Agriculture-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND
- Department of Plant Pathology, North Dakota State University, Fargo, ND
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7
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Kon T, Sato C, Fuji SI. Molecular characterization and host reaction to tomato mottle mosaic virus isolated from sweet pepper seeds in Japan. Arch Virol 2024; 169:113. [PMID: 38684570 DOI: 10.1007/s00705-024-06035-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/17/2024] [Indexed: 05/02/2024]
Abstract
Many countries have identified tomato mottle mosaic virus (ToMMV) as a serious threat to tomato production. Here, we constructed and characterized infectious clones of ToMMV isolated from Japanese sweet pepper seeds. The genome of the Japanese isolate is 6399 nucleotides in length and exhibits the highest identity with previously characterized isolates. For example, it is 99.7% identical to that of the Mauritius isolate, which occurs worldwide. Phylogenetic analysis based on complete genome sequences revealed that the Japanese isolates clustered in the same clade as those from other countries. When homozygous tomato cultivars with tobamovirus resistance genes were inoculated with an infectious cDNA clone of ToMMV, the virus systemically infected tomato plants with symptoms typical of Tm-1-carrying tomato cultivars. In contrast, tomato cultivars carrying Tm-2 or Tm-22 showed symptoms only on the inoculated leaves. Furthermore, when commercial cultivars of Tm-22 heterozygous tomato were inoculated with ToMMV, systemic infections were observed in all cultivars, with infection frequencies ranging from 25 to 100%. Inoculation of heterozygous sweet pepper cultivars with tobamovirus resistance genes (L1, L3, and L4) with ToMMV resulted in an infection frequency of about 70%, but most of the infected L1, L3, and L4 cultivars were symptomless, and 10-20% showed symptoms of necrosis and yellowing. Tomato mosaic virus strain L11A, an attenuated virus, did not provide cross-protection against ToMMV and led to systemic infection with typical symptoms. These results suggest that ToMMV might cause extensive damage to existing tomato and sweet pepper cultivars commonly grown in Japan.
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Affiliation(s)
- Tatsuya Kon
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195, Japan.
| | - Chinami Sato
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195, Japan
| | - Shin-Ichi Fuji
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195, Japan
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Wang D, Chen M, Peng J, Zheng H, Lu Y, Wu G, Wu J, Li J, Chen J, Yan F, Rao S. Transcriptome Analysis of Tomato Leaves Reveals Candidate Genes Responsive to Tomato Brown Rugose Fruit Virus Infection. Int J Mol Sci 2024; 25:4012. [PMID: 38612822 PMCID: PMC11012278 DOI: 10.3390/ijms25074012] [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: 03/03/2024] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
Tomato brown rugose fruit virus (ToBRFV) is a newly-emerging tobamovirus which was first reported on tomatoes in Israel and Jordan, and which has now spread rapidly in Asia, Europe, North America, and Africa. ToBRFV can overcome the resistance to other tobamoviruses conferred by tomato Tm-1, Tm-2, and Tm-22 genes, and it has seriously affected global crop production. The rapid and comprehensive transcription reprogramming of host plant cells is the key to resisting virus attack, but there have been no studies of the transcriptome changes induced by ToBRFV in tomatoes. Here, we made a comparative transcriptome analysis between tomato leaves infected with ToBRFV for 21 days and those mock-inoculated as controls. A total of 522 differentially expressed genes were identified after ToBRFV infection, of which 270 were up-regulated and 252 were down-regulated. Functional analysis showed that DEGs were involved in biological processes such as response to wounding, response to stress, protein folding, and defense response. Ten DEGs were selected and verified by qRT-PCR, confirming the reliability of the high-throughput sequencing data. These results provide candidate genes or signal pathways for the response of tomato leaves to ToBRFV infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (D.W.); (H.Z.); (J.L.)
| | - Shaofei Rao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (D.W.); (H.Z.); (J.L.)
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9
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Nash D, Ellmen I, Knapp JJ, Menon R, Overton AK, Cheng J, Lynch MDJ, Nissimov JI, Charles TC. A Novel Tiled Amplicon Sequencing Assay Targeting the Tomato Brown Rugose Fruit Virus (ToBRFV) Genome Reveals Widespread Distribution in Municipal Wastewater Treatment Systems in the Province of Ontario, Canada. Viruses 2024; 16:460. [PMID: 38543825 PMCID: PMC10974707 DOI: 10.3390/v16030460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 05/23/2024] Open
Abstract
Tomato Brown Rugose Fruit Virus (ToBRFV) is a plant pathogen that infects important Solanaceae crop species and can dramatically reduce tomato crop yields. The ToBRFV has rapidly spread around the globe due to its ability to escape detection by antiviral host genes which confer resistance to other tobamoviruses in tomato plants. The development of robust and reproducible methods for detecting viruses in the environment aids in the tracking and reduction of pathogen transmission. We detected ToBRFV in municipal wastewater influent (WWI) samples, likely due to its presence in human waste, demonstrating a widespread distribution of ToBRFV in WWI throughout Ontario, Canada. To aid in global ToBRFV surveillance efforts, we developed a tiled amplicon approach to sequence and track the evolution of ToBRFV genomes in municipal WWI. Our assay recovers 95.7% of the 6393 bp ToBRFV RefSeq genome, omitting the terminal 5' and 3' ends. We demonstrate that our sequencing assay is a robust, sensitive, and highly specific method for recovering ToBRFV genomes. Our ToBRFV assay was developed using existing ARTIC Network resources, including primer design, sequencing library prep, and read analysis. Additionally, we adapted our lineage abundance estimation tool, Alcov, to estimate the abundance of ToBRFV clades in samples.
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Affiliation(s)
- Delaney Nash
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
| | - Isaac Ellmen
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
| | - Jennifer J. Knapp
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
| | - Ria Menon
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
| | - Alyssa K. Overton
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
| | - Jiujun Cheng
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
| | - Michael D. J. Lynch
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
| | - Jozef I. Nissimov
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
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10
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Zhao YJ, Hosoya T, Urayama S, Hagiwara D. Seven new mycoviruses identified from isolated ascomycetous macrofungi. Virus Res 2024; 339:199290. [PMID: 38043725 PMCID: PMC10751708 DOI: 10.1016/j.virusres.2023.199290] [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: 10/13/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Mycoviruses have been described in all major fungal taxonomic groups. There has been much focus on commercially cultivated basidiomycetous macrofungi, while attention to viruses from ascomycetous macrofungi is lacking. Therefore, in this study, we conducted viral screening against fungal mycelia that were regenerated from ascomycetous macrofungi using agarose gel electrophoresis (AGE) and fragmented and primer-ligated dsRNA sequencing (FLDS). Among the 57 isolates, four isolates were detected with virus-like bands through screening with AGE, and subsequent FLDS analyses determined the viral sequences. Other isolates without virus-like bands in AGE were pooled to check for viral sequences. Using FLDS analysis, a total of seven new mycoviruses were identified, including two double-stranded RNA (dsRNA) viruses belonging to Quadriviridae and Partitiviridae, five positive-sense single-stranded RNA (ssRNA) viruses (three belonging to Mitoviridae, one belonging to Endornaviridae and one belonging to Virgaviridae). All viruses characterized in this study are novel species, and all the hosts are firstly reported to be infected by mycoviruses. These findings expand our knowledge of the diversity of mycoviruses from macrofungi in natural environments.
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Affiliation(s)
- Yan-Jie Zhao
- Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
| | - Tsuyoshi Hosoya
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan
| | - Syunichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Daisuke Hagiwara
- Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
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11
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Robinson CRP, Dolezal AG, Newton ILG. Host species and geography impact bee-associated RNA virus communities with evidence for isolation by distance in viral populations. ISME COMMUNICATIONS 2024; 4:ycad003. [PMID: 38304079 PMCID: PMC10833078 DOI: 10.1093/ismeco/ycad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 02/03/2024]
Abstract
Virus symbionts are important mediators of ecosystem function, yet we know little of their diversity and ecology in natural populations. The alarming decline of pollinating insects in many regions of the globe, especially the European honey bee, Apis mellifera, has been driven in part by worldwide transmission of virus pathogens. Previous work has examined the transmission of known honey bee virus pathogens to wild bee populations, but only a handful of studies have investigated the native viromes associated with wild bees, limiting epidemiological predictors associated with viral pathogenesis. Further, variation among different bee species might have important consequences in the acquisition and maintenance of bee-associated virome diversity. We utilized comparative metatranscriptomics to develop a baseline description of the RNA viromes associated with wild bee pollinators and to document viral diversity, community composition, and structure. Our sampling includes five wild-caught, native bee species that vary in social behavior as well as managed honey bees. We describe 26 putatively new RNA virus species based on RNA-dependent RNA polymerase phylogeny and show that each sampled bee species was associated with a specific virus community composition, even among sympatric populations of distinct host species. From 17 samples of a single host species, we recovered a single virus species despite over 600 km of distance between host populations and found strong evidence for isolation by distance in associated viral populations. Our work adds to the small number of studies examining viral prevalence and community composition in wild bees.
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Affiliation(s)
- Chris R P Robinson
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
| | - Adam G Dolezal
- Department of Entomology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Irene L G Newton
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
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12
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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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13
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Liu Y, Gao Y, Cheng X, Bai Y. Production of Double-Stranded RNA in Planta by a Potato Mop-Top Virus (PMTV)-Based Vector for Inducing Gene Silencing. Methods Mol Biol 2024; 2771:119-126. [PMID: 38285398 DOI: 10.1007/978-1-0716-3702-9_16] [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: 01/30/2024]
Abstract
RNA silencing (also known as gene silencing) is an evolutionary conserved mechanism that is involved in regulating gene expression, suppressing mobile elements, and defensing virus infection. RNA silencing is triggered by double-stranded RNA via Dicer or Dicer-like riboendonucleases. DsRNAs are also the replication intermediates of all RNA viruses; as a result, plant RNA viruses are ideal candidates to induce RNA silencing. A large body of plant viruses have been modified into vectors for RNA silencing in varied plant species. Here, we described a simple, time-saving, and operable system for gene function and genetic breeding study of potato and Nicotiana benthamiana using a potato mop-top (MPTV)-based vector.
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Affiliation(s)
- Ye Liu
- College of Plant Protection, Northeast Agricultural University, Harbin, Heilongjiang, China
- Potato Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yanlin Gao
- Potato Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Xiaofei Cheng
- College of Plant Protection, Northeast Agricultural University, Harbin, Heilongjiang, China.
| | - Yanju Bai
- Potato Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
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14
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Dall'Ara M, Guo Y, Poli D, Gilmer D, Ratti C. Analysis of the relative frequencies of the multipartite BNYVV genomic RNAs in different plants and tissues. J Gen Virol 2024; 105. [PMID: 38197877 DOI: 10.1099/jgv.0.001950] [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: 01/11/2024] Open
Abstract
Multipartite virus genomes are composed of two or more segments, each packaged into an independent viral particle. A potential advantage of multipartitism is the regulation of gene expression through changes in the segment copy number. Soil-borne beet necrotic yellow vein virus (BNYVV) is a typical example of multipartism, given its high number of genomic positive-sense RNAs (up to five). Here we analyse the relative frequencies of the four genomic RNAs of BNYVV type B during infection of different host plants (Chenopodium quinoa, Beta macrocarpa and Spinacia oleracea) and organs (leaves and roots). By successfully validating a two-step reverse-transcriptase digital droplet PCR protocol, we show that RNA1 and -2 genomic segments always replicate at low and comparable relative frequencies. In contrast, RNA3 and -4 accumulate with variable relative frequencies, resulting in distinct RNA1 : RNA2 : RNA3 : RNA4 ratios, depending on the infected host species and organ.
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Affiliation(s)
- M Dall'Ara
- DISTAL-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy
| | - Y Guo
- DISTAL-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy
| | - D Poli
- DISTAL-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy
| | - D Gilmer
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, France
| | - C Ratti
- DISTAL-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy
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15
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Caldas-Garcia GB, Santos VC, Fonseca PLC, de Almeida JPP, Costa MA, Aguiar ERGR. The Viromes of Six Ecosystem Service Provider Parasitoid Wasps. Viruses 2023; 15:2448. [PMID: 38140687 PMCID: PMC10747428 DOI: 10.3390/v15122448] [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: 08/03/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 12/24/2023] Open
Abstract
Parasitoid wasps are fundamental insects for the biological control of agricultural pests. Despite the importance of wasps as natural enemies for more sustainable and healthy agriculture, the factors that could impact their species richness, abundance, and fitness, such as viral diseases, remain almost unexplored. Parasitoid wasps have been studied with regard to the endogenization of viral elements and the transmission of endogenous viral proteins that facilitate parasitism. However, circulating viruses are poorly characterized. Here, RNA viromes of six parasitoid wasp species are studied using public libraries of next-generation sequencing through an integrative bioinformatics pipeline. Our analyses led to the identification of 18 viruses classified into 10 families (Iflaviridae, Endornaviridae, Mitoviridae, Partitiviridae, Virgaviridae, Rhabdoviridae, Chuviridae, Orthomyxoviridae, Xinmoviridae, and Narnaviridae) and into the Bunyavirales order. Of these, 16 elements were described for the first time. We also found a known virus previously identified on a wasp prey which suggests viral transmission between the insects. Altogether, our results highlight the importance of virus surveillance in wasps as its service disruption can affect ecology, agriculture and pest management, impacting the economy and threatening human food security.
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Affiliation(s)
- Gabriela B. Caldas-Garcia
- Virus Bioinformatics Laboratory, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil; (G.B.C.-G.); (P.L.C.F.)
| | - Vinícius Castro Santos
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 30270-901, Brazil; (V.C.S.); (J.P.P.d.A.)
| | - Paula Luize Camargos Fonseca
- Virus Bioinformatics Laboratory, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil; (G.B.C.-G.); (P.L.C.F.)
- Department of Genetics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 30270-901, Brazil
| | - João Paulo Pereira de Almeida
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 30270-901, Brazil; (V.C.S.); (J.P.P.d.A.)
| | - Marco Antônio Costa
- Departament of Biological Sciences, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil;
| | - Eric Roberto Guimarães Rocha Aguiar
- Virus Bioinformatics Laboratory, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil; (G.B.C.-G.); (P.L.C.F.)
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16
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Zell R, Groth M, Selinka L, Selinka HC. Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany. Pathogens 2023; 12:1458. [PMID: 38133341 PMCID: PMC10745976 DOI: 10.3390/pathogens12121458] [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: 11/18/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Plant-infecting RNA viruses from 30 families and floating genera, as well as a great number of uncultured as yet-unclassified plant-associated viruses have been described. Even so, the plant RNA virosphere is still underexplored. RNA extracted from enriched virus particles of 50 L water samples from the Teltow Canal and the Havel River in Berlin, Germany, was sequenced using Illumina next-generation sequencing. Sequences were searched for plant viruses with BLAST and DIAMOND. Phylogenetic analyses were conducted with IQ-TREE 2. Altogether, 647 virus sequences greater than 1 kb were detected and further analyzed. These data revealed the presence of accepted and novel viruses related to Albetovirus, Alphaflexiviridae, Aspiviridae, Bromoviridae, Endornaviridae, Partitiviridae, Potyviridae, Solemoviridae, Tombusviridae and Virgaviridae. The vast majority of the sequences were novel and could not be taxonomically assigned. Several tombus- and endorna-like viruses make use of alternative translation tables that suggest unicellular green algae, ciliates, or diplomonades as their hosts. The identification of 27 albeto-like satellite viruses increases available sequence data five-fold. Sixteen new poty-like viruses align with other poty-like viruses in a link that combines the Astroviridae and Potyviridae families. Further, the identification of viruses with peptidase A6-like and peptidase A21-like capsid proteins suggests horizontal gene transfer in the evolution of these viruses.
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Affiliation(s)
- Roland Zell
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, 07745 Jena, Germany
| | - Marco Groth
- CF Next Generation Sequencing, Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Lukas Selinka
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, 07745 Jena, Germany
| | - Hans-Christoph Selinka
- Section II 1.4 Microbiological Risks, Department of Environmental Hygiene, German Environment Agency, 14195 Berlin, Germany
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17
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Zhao R, Su X, Yu F, Liu Z, Huang X. Identification and characterization of two closely related virga-like viruses latently infecting rubber trees ( Hevea brasiliensis). Front Microbiol 2023; 14:1286369. [PMID: 38156006 PMCID: PMC10752949 DOI: 10.3389/fmicb.2023.1286369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
A novel virga-like virus, provisionally named Rubber tree latent virus 2 (RTLV2), was identified from rubber tree (Hevea brasiliensis). It is a close relative of the previously reported Rubber tree latent virus 1 (RTLV1). The complete genomes of RTLV1 and RTLV2 were sequenced and comparatively analyzed in terms of genome organization, putative gene products and phylogenetic relationship. Both RTLV1 and RTLV2 have positive-sense single-stranded RNA genomes that encode seven open reading frames (ORFs), forming a similar genomic layout. In phylogenetic analyses based on replicase and coat protein amino acid sequences, RTLV1 and RTLV2 were clustered with unclassified virga-like viruses. They are distinct from currently recognized plant virus families. RTLV1 and RTLV2 can be distinguished from members of Virgaviridae by the presence of a putative coat protein duplex and a poly(A) tail at the 3'-terminus. The authenticity of RTLV1 and RTLV2 as infectious viruses was confirmed through field investigations and transmissibility assays. In conclusion, RTLV1 and RTLV2 represent a novel plant virus group that does not readily fit into current virus families.
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Affiliation(s)
- Ruibai Zhao
- College of Tropical Crops, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- School of Life Sciences, Hainan University, Haikou, China
| | - Xiaoqi Su
- College of Tropical Crops, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Fengjuan Yu
- College of Tropical Crops, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Zhu Liu
- School of Life Sciences, Hainan University, Haikou, China
| | - Xi Huang
- College of Tropical Crops, Sanya Nanfan Research Institute of Hainan University, Sanya, China
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18
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Shahriari Z, Su X, Zheng K, Zhang Z. Advances and Prospects of Virus-Resistant Breeding in Tomatoes. Int J Mol Sci 2023; 24:15448. [PMID: 37895127 PMCID: PMC10607384 DOI: 10.3390/ijms242015448] [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: 08/01/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Plant viruses are the main pathogens which cause significant quality and yield losses in tomato crops. The important viruses that infect tomatoes worldwide belong to five genera: Begomovirus, Orthotospovirus, Tobamovirus, Potyvirus, and Crinivirus. Tomato resistance genes against viruses, including Ty gene resistance against begomoviruses, Sw gene resistance against orthotospoviruses, Tm gene resistance against tobamoviruses, and Pot 1 gene resistance against potyviruses, have been identified from wild germplasm and introduced into cultivated cultivars via hybrid breeding. However, these resistance genes mainly exhibit qualitative resistance mediated by single genes, which cannot protect against virus mutations, recombination, mixed-infection, or emerging viruses, thus posing a great challenge to tomato antiviral breeding. Based on the epidemic characteristics of tomato viruses, we propose that future studies on tomato virus resistance breeding should focus on rapidly, safely, and efficiently creating broad-spectrum germplasm materials resistant to multiple viruses. Accordingly, we summarized and analyzed the advantages and characteristics of the three tomato antiviral breeding strategies, including marker-assisted selection (MAS)-based hybrid breeding, RNA interference (RNAi)-based transgenic breeding, and CRISPR/Cas-based gene editing. Finally, we highlighted the challenges and provided suggestions for improving tomato antiviral breeding in the future using the three breeding strategies.
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Affiliation(s)
- Zolfaghar Shahriari
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
- Crop and Horticultural Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz 617-71555, Iran
| | - Xiaoxia Su
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
| | - Kuanyu Zheng
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
| | - Zhongkai Zhang
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
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19
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Skelton A, Frew L, Ward R, Hodgson R, Forde S, McDonough S, Webster G, Chisnall K, Mynett M, Buxton-Kirk A, Fowkes AR, Weekes R, Fox A. Tomato Brown Rugose Fruit Virus: Survival and Disinfection Efficacy on Common Glasshouse Surfaces. Viruses 2023; 15:2076. [PMID: 37896853 PMCID: PMC10611295 DOI: 10.3390/v15102076] [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: 09/13/2023] [Revised: 10/06/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
Tomato brown rugose fruit virus (ToBRFV) is a contact-transmitted tobamovirus affecting many tomato growing regions of the world. This study investigated the effects of different glasshouse surfaces on the survival of the virus; the efficacy of different disinfectants; and heat treatment against ToBRFV (surfaces included steel, aluminium, hard plastic, polythene, glass and concrete). A bioassay followed by ELISA was used to check virus viability. ToBRFV survived for at least 7 days on all surfaces tested and on some for at least 6 months. The virus survived for over two hours on hands and gloves. Hand washing was shown to be unreliable for the removal of the virus. Glutaraldehyde and quaternary ammonium compound disinfectants were effective at one hour on all surfaces. Some other disinfectants were effective at one hour of contact time, on all surfaces except concrete. Sodium hypochlorite was partially effective against ToBRFV, even on concrete. A 5 min soak of plastic trays in water at 90 °C was effective at denaturing ToBRFV; however, 5 min at 70 °C was not. Heating infected sap showed the thermal inactivation point to be 90 °C, confirming the hot water treatment results and showing that deactivation was due to the heat treatment and not a washing effect of the water.
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Affiliation(s)
- Anna Skelton
- Fera Science Limited, York Biotech Campus, York YO41 1LZ, UK; (L.F.); (R.W.); (S.F.); (S.M.); (G.W.); (K.C.); (M.M.); (A.B.-K.); (A.R.F.); (R.W.); (A.F.)
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20
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Kong AT, Olmedo-Velarde A, Borth W, Wang KH, Hu JS, Melzer MJ. Molecular and Biological Characterization of a Novel Tobamovirus Infecting Sunn Hemp ( Crotalaria juncea) in Hawaii. PLANT DISEASE 2023; 107:3106-3112. [PMID: 37102725 DOI: 10.1094/pdis-09-22-2148-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Sunn hemp (Crotalaria juncea L.) cultivar Tropic Sun plants, stunted and displaying mottle and mosaic symptoms on foliage, were observed at a seed farm in Maui County, Hawaii. Lateral flow assays indicated the presence of either tobacco mosaic virus or a serologically related virus. High-throughput sequencing results coupled with real-time PCR experiments recovered the 6,455-nucleotide genome of a virus with an organization typical of tobamoviruses. Nucleotide and amino acid sequence comparisons and phylogenetic analyses indicated that this virus was most closely related to sunn-hemp mosaic virus but represents a distinct species. Sunn-hemp mottle virus (SHMoV) is being proposed as the common name of this virus. Transmission electron microscopy of virus extracts purified from symptomatic leaves revealed rod-shaped particles approximately 320 by 22 nm in size. In inoculation studies, the experimental host range of SHMoV appeared limited to members of the plant families Fabaceae and Solanaceae. Greenhouse experiments demonstrated plant-to-plant transmission of SHMoV that increased with ambient wind speed. Seeds from SHMoV-infected Tropic Sun were collected and were either surface disinfested or directly planted. A total of 924 seedlings germinated; 2 were positive for the virus, resulting in a seed transmission rate of 0.2%. Both infected plants came from the surface disinfestation treatment, suggesting that the virus might be unaffected by the treatment.
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Affiliation(s)
- Alexandra T Kong
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Alejandro Olmedo-Velarde
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853
| | - Wayne Borth
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Koon-Hui Wang
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - John S Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Michael J Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
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21
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Pan J, Ji L, Wu H, Wang X, Wang Y, Wu Y, Yang S, Shen Q, Liu Y, Zhang W, Zhang K, Shan T. Metagenomic analysis of herbivorous mammalian viral communities in the Northwest Plateau. BMC Genomics 2023; 24:568. [PMID: 37749507 PMCID: PMC10521573 DOI: 10.1186/s12864-023-09646-1] [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: 06/06/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Mammals are potential hosts for many infectious diseases. However, studies on the viral communities of herbivorous mammals in the Northwest Plateau are limited. Here, we studied the viral communities of herbivorous mammals in the Northwest Plateau using virus metagenomic analysis to analyze and compare the viral community composition of seven animal species. RESULTS By library construction and next-generation sequencing, contigs and singlets reads with similar viral sequences were classified into 24 viral families. Analyzed from the perspective of sampling areas, the virus community composition was relatively similar in two areas of Wuwei and Jinchang, Gansu Province. Analyzed from the perspective of seven animal species, the viral reads of seven animal species were mostly ssDNA and dominated by CRESS-DNA viruses. Phylogenetic analysis based on viral marker genes indicated that CRESS-DNA viruses and microviruses have high genetic diversity. In addition to DNA viruses, nodaviruses, pepper mild mottle viruses and picornaviruses were RNA viruses that we performed by phylogenetic analysis. The CRESS-DNA viruses and nodaviruses are believed to infect plants and insects, and microviruses can infect bacteria, identifying that they were likely from the diet of herbivorous mammals. Notably, two picornaviruses were identified from red deer and wild horse, showing that the picornavirus found in red deer had the relatively high similarity with human hepatitis A virus, and the picornavirus carried by wild horse could potentially form a new species within the Picornaviridae family. CONCLUSIONS This study explored the herbivorous mammalian virus community in the Northwest Plateau and the genetic characteristics of viruses that potentially threaten human health. It reveals the diversity and stability of herbivorous mammalian virus communities in the Northwest Plateau and helps to expand our knowledge of various herbivorous mammalian potentially pathogenic viruses.
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Grants
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
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Affiliation(s)
- Jiamin Pan
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Haisheng Wu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yan Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yan Wu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuwei Liu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
| | - Keshan Zhang
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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22
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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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23
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Park H, Denha S, Higgs PG. Evolution of Bipartite and Segmented Viruses from Monopartite Viruses. Viruses 2023; 15:v15051135. [PMID: 37243221 DOI: 10.3390/v15051135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/30/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
RNA viruses may be monopartite (all genes on one strand), multipartite (two or more strands packaged separately) or segmented (two or more strands packaged together). In this article, we consider competition between a complete monopartite virus, A, and two defective viruses, D and E, that have complementary genes. We use stochastic models that follow gene translation, RNA replication, virus assembly, and transmission between cells. D and E multiply faster than A when stored in the same host as A or when together in the same host, but they cannot multiply alone. D and E strands are packaged as separate particles unless a mechanism evolves that allows assembly of D + E segmented particles. We show that if defective viruses assemble rapidly into separate particles, the formation of segmented particles is selected against. In this case, D and E spread as parasites of A, and the bipartite D + E combination eliminates A if the transmissibility is high. Alternatively, if defective strands do not assemble rapidly into separate particles, then a mechanism for assembly of segmented particles is selected for. In this case, the segmented virus can eliminate A if transmissibility is high. Conditions of excess protein resources favor bipartite viruses, while conditions of excess RNA resources favor segmented viruses. We study the error threshold behavior that arises when deleterious mutations are introduced. Relative to bipartite and segmented viruses, deleterious mutations favor monopartite viruses. A monopartite virus can give rise to either a bipartite or a segmented virus, but it is unlikely that both will originate from the same virus.
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Affiliation(s)
- Hyunjin Park
- Department of Physics and Astronomy, McMaster University, 1280 Main St. West, Hamilton, ON L8M 4S1, Canada
| | - Saven Denha
- Department of Physics and Astronomy, McMaster University, 1280 Main St. West, Hamilton, ON L8M 4S1, Canada
| | - Paul G Higgs
- Department of Physics and Astronomy, McMaster University, 1280 Main St. West, Hamilton, ON L8M 4S1, Canada
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24
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Jogam P, Sandhya D, Alok A, Peddaboina V, Singh SP, Abbagani S, Zhang B, Allini VR. Editing of TOM1 gene in tobacco using CRISPR/Cas9 confers resistance to Tobacco mosaic virus. Mol Biol Rep 2023; 50:5165-5176. [PMID: 37119416 DOI: 10.1007/s11033-023-08440-2] [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: 10/13/2022] [Accepted: 04/06/2023] [Indexed: 05/01/2023]
Abstract
BACKGROUND Genome editing technology has become one of the excellent tools for precise plant breeding to develop novel plant germplasm. The Tobacco mosaic virus (TMV) is the most prominent pathogen that infects several Solanaceae plants, such as tobacco, tomato, and capsicum, which requires critical host factors for infection and replication of its genomic RNA in the host. The Tobamovirus multiplication (TOM) genes, such as TOM1, TOM2A, TOM2B, and TOM3, are involved in the multiplication of Tobamoviruses. TOM1 is a transmembrane protein necessary for efficient TMV multiplication in several plant species. The TOM genes are crucial recessive resistance genes that act against the tobamoviruses in various plant species. METHODS AND RESULTS The single guided RNA (sgRNA) was designed to target the first exon of the NtTOM1 gene and cloned into the pHSE401 vector. The pHSE401-NtTOM1 vector was introduced into Agrobacterium tumefaciens strain LBA4404 and then transformed into tobacco plants. The analysis on T0 transgenic plants showed the presence of the hptII and Cas9 transgenes. The sequence analysis of the NtTOM1 from T0 plants showed the indels. Genotypic evaluation of the NtTOM1 mutant lines displayed the stable inheritance of the mutations in the subsequent generations of tobacco plants. The NtTOM1 mutant lines successfully conferred resistance to TMV. CONCLUSIONS CRISPR/Cas genome editing is a reliable tool for investigating gene function and precision breeding across different plant species, especially the species in the Solanaceae family.
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Affiliation(s)
- Phanikanth Jogam
- Department of Biotechnology, Kakatiya University, Warangal, 506009, Telangana, India
| | - Dulam Sandhya
- Department of Biotechnology, Kakatiya University, Warangal, 506009, Telangana, India
| | - Anshu Alok
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | | | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, 140306, Punjab, India
| | - Sadanandam Abbagani
- Department of Biotechnology, Kakatiya University, Warangal, 506009, Telangana, India
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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25
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Genome Characterisation of the CGMMV Virus Population in Australia—Informing Plant Biosecurity Policy. Viruses 2023; 15:v15030743. [PMID: 36992452 PMCID: PMC10051534 DOI: 10.3390/v15030743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 03/15/2023] Open
Abstract
The detection of cucumber green mottle mosaic (CGMMV) in the Northern Territory (NT), Australia, in 2014 led to the introduction of strict quarantine measures for the importation of cucurbit seeds by the Australian federal government. Further detections in Queensland, Western Australia (WA), New South Wales and South Australia occurred in the period 2015–2020. To explore the diversity of the current Australian CGMMV population, 35 new coding sequence complete genomes for CGMMV isolates from Australian incursions and surveys were prepared for this study. In conjunction with published genomes from the NT and WA, sequence, phylogenetic, and genetic variation and variant analyses were performed, and the data were compared with those for international CGMMV isolates. Based on these analyses, it can be inferred that the Australian CGMMV population resulted from a single virus source via multiple introductions.
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26
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Arboviruses and symbiotic viruses cooperatively hijack insect sperm-specific proteins for paternal transmission. Nat Commun 2023; 14:1289. [PMID: 36894574 PMCID: PMC9998617 DOI: 10.1038/s41467-023-36993-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/23/2023] [Indexed: 03/11/2023] Open
Abstract
Arboviruses and symbiotic viruses can be paternally transmitted by male insects to their offspring for long-term viral persistence in nature, but the mechanism remains largely unknown. Here, we identify the sperm-specific serpin protein HongrES1 of leafhopper Recilia dorsalis as a mediator of paternal transmission of the reovirus Rice gall dwarf virus (RGDV) and a previously undescribed symbiotic virus of the Virgaviridae family, Recilia dorsalis filamentous virus (RdFV). We show that HongrES1 mediates the direct binding of virions to leafhopper sperm surfaces and subsequent paternal transmission via interaction with both viral capsid proteins. Direct interaction of viral capsid proteins mediates simultaneously invasion of two viruses into male reproductive organs. Moreover, arbovirus activates HongrES1 expression to suppress the conversion of prophenoloxidase to active phenoloxidase, potentially producing a mild antiviral melanization defense. Paternal virus transmission scarcely affects offspring fitness. These findings provide insights into how different viruses cooperatively hijack insect sperm-specific proteins for paternal transmission without disturbing sperm functions.
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27
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Wang X, Larrea-Sarmiento A, Olmedo-Velarde A, Kong A, Borth W, Suzuki JY, Wall MM, Melzer M, Hu J. First detection and complete genome sequence of a new tobamovirus naturally infecting Hibiscus rosa-sinensis in Hawaii. Arch Virol 2023; 168:40. [PMID: 36609629 DOI: 10.1007/s00705-022-05634-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/11/2022] [Indexed: 01/09/2023]
Abstract
High-throughput sequencing was used to analyze Hibiscus rosa-sinensis (family Malvaceae) plants with virus-like symptoms in Hawaii. Bioinformatic and phylogenetic analysis revealed the presence of two tobamoviruses, hibiscus latent Fort Pierce virus (HLFPV) and a new tobamovirus with the proposed name "hibiscus latent Hawaii virus" (HLHV). This is the first report of the complete sequence, genome organization, and phylogenetic characterization of a tobamovirus infecting hibiscus in Hawaii. RT-PCR with virus-specific primers and Sanger sequencing further confirmed the presence of these viruses. Inoculation experiments showed that HLFPV could be mechanically transmitted to Nicotiana benthamiana and N. tabacum, while HLHV could only be mechanically transmitted to N. benthamiana.
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Affiliation(s)
- Xupeng Wang
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Adriana Larrea-Sarmiento
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Alejandro Olmedo-Velarde
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Alexandra Kong
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Wayne Borth
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Jon Y Suzuki
- United States Department of Agriculture, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
| | - Marisa M Wall
- United States Department of Agriculture, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
| | - Michael Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - John Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA.
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28
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He M, He CQ, Ding NZ. Evolution of cucurbit-infecting tobamoviruses: Recombination and codon usage bias. Virus Res 2023; 323:198970. [PMID: 36273733 PMCID: PMC10194277 DOI: 10.1016/j.virusres.2022.198970] [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: 08/16/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Currently, there are seven cucurbit-infecting tobamoviruses comprising cucumber green mottle mosaic virus (CGMMV), Kyuri green mottle mosaic virus (KGMMV), cucumber fruit mottle mosaic virus (CFMMV), zucchini green mottle mosaic virus (ZGMMV), cucumber mottle virus (CMoV), watermelon green mottle mosaic virus (WGMMV), and Trichosanthes mottle mosaic virus (TrMMV). To gain more insights into their evolution, recombination analyses were conducted. Four CGMMV isolates and one KGMMV isolate were suggested to be recombinants. And there was an interspecies recombination event between CGMMV and ZGMMV. Phylogenetic incongruence was also observed for CGMMV and KGMMV. A probable ancestral pattern was inferred for the gene junction region between RdRp and MP. Codon usage bias analysis revealed that the viral genes had additional influence independent of compositional constraint. In codon preference, the seven viruses were both similar to and different from the host cucumber (Cucumis sativus). Moreover, the viruses were not deficient in CpG and UpA dinucleotides.
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Affiliation(s)
- Mei He
- Dongying Institute, Shandong Normal University, Dongying 257000, China; College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Cheng-Qiang He
- Dongying Institute, Shandong Normal University, Dongying 257000, China; College of Life Science, Shandong Normal University, Jinan 250014, China.
| | - Nai-Zheng Ding
- Dongying Institute, Shandong Normal University, Dongying 257000, China; College of Life Science, Shandong Normal University, Jinan 250014, China.
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29
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Shakeri Sharaf Abad Sofla A, Taheri H, Ghodoum Parizipour MH, Soleymani F. Molecular and Phenotypic Responses of Rhizobacteria-Treated Tomato Plants to Tomato Mosaic Virus Under Greenhouse Conditions. IRANIAN JOURNAL OF BIOTECHNOLOGY 2023; 21:e3220. [PMID: 36811104 PMCID: PMC9938937 DOI: 10.30498/ijb.2022.319382.3220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 07/06/2022] [Indexed: 02/24/2023]
Abstract
Background Tomato mosaic disease, mainly caused by Tomato mosaic virus (ToMV), is one of the devastating viral diseases which adversely affects tomato yield, globally. Plant growth-promoting rhizobacteria (PGPR) have been recently used as bio-elicitors to induce resistance against plant viruses. Objectives The goal of this research was to apply PGPR in the tomato rhizosphere and to determine the response of plants challenged with ToMV infection, under greenhouse conditions. Materials and Methods Two different strains of PGPR, Pseudomonas fluorescens SM90 and Bacillus subtilis DR06, in single- and double-application methods applied to evaluate their effectiveness in inducing defense-related genes, viz., NPR1, COI1, and PR1-a before (induced systemic resistance [ISR]-prime) and after (ISR-boost) ToMV challenge. Additionally, to investigate the biocontrol potential of PGPR-treated plants against viral infection, plant growth indices, ToMV accumulation, and disease severity were compared in primed and non-primed plants. Results Analysis of expression patterns of putative defense-related genes before and after ToMV infection indicated that studied PGPR trigger defense priming through different signaling pathways acting at the transcriptional level and in a species-dependent manner. Moreover, the biocontrol efficacy of consortium treatment did not differ significantly from the single bacteria treatments, even though their mode of action differed in transcriptional changes of ISR-induced genes. Instead, simultaneous application of Pseudomonas fluorescens SM90 and Bacillus subtilis DR06 led to more significant growth indices than the single treatments suggesting that integrated application of the PGPR could additively reduce the disease severity and virus titer and promote the growth of the tomato plant. Conclusions These results suggested that enhanced defense priming via activation of the expression pattern of defense-related genes is responsible for biocontrol activity and growth promotion in PGPR-treated tomato plants challenged with ToMV compared to non-primed plants, under greenhouse conditions.
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Affiliation(s)
- Akram Shakeri Sharaf Abad Sofla
- Department of Plant Production and Genetics, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Iran
| | - Hengameh Taheri
- Department of Plant Production and Genetics, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Iran
| | - Mohamad Hamed Ghodoum Parizipour
- Department of Plant Protection, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Iran
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30
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Giesbers AKJ, Roenhorst A, Schenk MF, Westenberg M, Botermans M. African eggplant-associated virus: Characterization of a novel tobamovirus identified from Solanum macrocarpon and assessment of its potential impact on tomato and pepper crops. PLoS One 2023; 18:e0277840. [PMID: 37053240 PMCID: PMC10101479 DOI: 10.1371/journal.pone.0277840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/29/2023] [Indexed: 04/14/2023] Open
Abstract
A novel tobamovirus was identified in a fruit of Solanum macrocarpon imported into the Netherlands in 2018. This virus was further characterized in terms of host range, pathotype and genomic properties, because many tobamoviruses have the potential to cause severe damage in important crops. In the original fruit, two different genotypes of the novel virus were present. The virus was able to infect multiple plant species from the Solanaceae family after mechanical inoculation, as well as a member of the Apiaceae family. These species included economically important crops such as tomato and pepper, as well as eggplant and petunia. Both tomato and pepper germplasm were shown to harbor resistance against the novel virus. Since most commercial tomato and pepper varieties grown in European greenhouses harbor these relevant resistances, the risk of infection and subsequent impact on these crops is likely to be low in Europe. Assessment of the potential threat to eggplant, petunia, and other susceptible species needs further work. In conclusion, this study provides a first assessment of the potential phytosanitary risks of a newly discovered tobamovirus, which was tentatively named African eggplant-associated virus.
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Affiliation(s)
- Anne K J Giesbers
- Netherlands Institute for Vectors, Invasive plants and Plant health, Wageningen, The Netherlands
- National Plant Protection Organization (NPPO-NL), Netherlands Food and Consumer Product Safety Authority (NVWA), Wageningen, The Netherlands
| | - Annelien Roenhorst
- Netherlands Institute for Vectors, Invasive plants and Plant health, Wageningen, The Netherlands
- National Plant Protection Organization (NPPO-NL), Netherlands Food and Consumer Product Safety Authority (NVWA), Wageningen, The Netherlands
| | - Martijn F Schenk
- National Plant Protection Organization (NPPO-NL), Netherlands Food and Consumer Product Safety Authority (NVWA), Wageningen, The Netherlands
| | - Marcel Westenberg
- Netherlands Institute for Vectors, Invasive plants and Plant health, Wageningen, The Netherlands
- National Plant Protection Organization (NPPO-NL), Netherlands Food and Consumer Product Safety Authority (NVWA), Wageningen, The Netherlands
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive plants and Plant health, Wageningen, The Netherlands
- National Plant Protection Organization (NPPO-NL), Netherlands Food and Consumer Product Safety Authority (NVWA), Wageningen, The Netherlands
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31
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Betancourt WQ. Waterborne Plant Viruses of Importance in Agriculture. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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Identification of Three Viruses Infecting Mulberry Varieties. Viruses 2022; 14:v14112564. [PMID: 36423172 PMCID: PMC9696721 DOI: 10.3390/v14112564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Viruses-mediated genome editing in plants is a powerful strategy to develop plant cultivars with important and novel agricultural traits. Mulberry alba is an important economic tree species that has been cultivated in China for more than 5000 years. So far, only a few viruses have been identified from mulberry trees, and their application potential is largely unknown. Therefore, mining more virus resources from the mulberry tree can pave the way for the establishment of useful engineering tools. In this study, eight old mulberry plants were gathered in seven geographic areas for virome analysis. Based on transcriptome analysis, we discovered three viruses associated with mulberries: Citrus leaf blotch virus isolate mulberry alba 2 (CLBV-ML2), Mulberry-associated virga-like virus (MaVLV), and Mulberry-associated narna-like virus (MaNLV). The genome of CLBV-ML2 was completely sequenced and exhibited high homology with Citriviruses, considered to be members of the genus Citrivirus, while the genomes of MaVLV and MaNLV were nearly completed lacking the 5' and 3' termini sequences. We tentatively consider MaVLV to be members of the family Virgaviridae and MaNLV to be members of the genus Narnavirus based on the results of phylogenetic trees. The infection experiments showed that CLBV-ML2 could be detected in the inoculated seedlings of both N. benthamiana and Morus alba, while MaVLV could only be detected in N. benthamiana. All of the infected seedlings did not show obvious symptoms.
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Chao S, Wang H, Zhang S, Chen G, Mao C, Hu Y, Yu F, Wang S, Lv L, Chen L, Feng G. Novel RNA Viruses Discovered in Weeds in Rice Fields. Viruses 2022; 14:2489. [PMID: 36366587 PMCID: PMC9717734 DOI: 10.3390/v14112489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/03/2022] [Accepted: 11/06/2022] [Indexed: 11/12/2022] Open
Abstract
Weeds often grow alongside crop plants. In addition to competing with crops for nutrients, water and space, weeds host insect vectors or act as reservoirs for viral diversity. However, little is known about viruses infecting rice weeds. In this work, we used metatranscriptomic deep sequencing to identify RNA viruses from 29 weed samples representing 23 weed species. A total of 224 RNA viruses were identified: 39 newly identified viruses are sufficiently divergent to comprise new families and genera. The newly identified RNA viruses clustered within 18 viral families. Of the identified viruses, 196 are positive-sense single-stranded RNA viruses, 24 are negative-sense single-stranded RNA viruses and 4 are double-stranded RNA viruses. We found that some novel RNA viruses clustered within the families or genera of several plant virus species and have the potential to infect plants. Collectively, these results expand our understanding of viral diversity in rice weeds. Our work will contribute to developing effective strategies with which to manage the spread and epidemiology of plant viruses.
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Affiliation(s)
- Shufen Chao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Haoran Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Shu Zhang
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430000, China
| | - Guoqing Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Chonghui Mao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Yang Hu
- Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550000, China
| | - Fengquan Yu
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110000, China
| | - Shuo Wang
- Sanya Agricultural Technology Extension and Service Centre, Sanya 572000, China
| | - Liang Lv
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430000, China
| | - Long Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
| | - Guozhong Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
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Kumar A, Solanki V, Katiyar A, Mandal B. Host biology and genomic properties of Plumeria mosaic virus, a tobamovirus discovered in a temple tree in India co-infecting with frangipani mosaic virus. Front Microbiol 2022; 13:1030042. [PMID: 36406428 PMCID: PMC9667028 DOI: 10.3389/fmicb.2022.1030042] [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: 08/28/2022] [Accepted: 10/11/2022] [Indexed: 01/25/2023] Open
Abstract
Temple tree (Plumeria rubra f. acutifolia), an important fragrant-flower tree extensively used in the urban landscaping is known to be infected with a tobamovirus, frangipani mosaic virus (FrMV). In this study, we describe another tobamovirus, Plumeria mosaic virus (PluMV) infecting temple tree in India. PluMV was isolated from an old temple tree co-infected with FrMV. The presence of another tobamovirus was initially realized based on the distinct symptoms on Gomphrena globosa (globe amaranth), a non-host of FrMV. PluMV was highly transmissible through simple rub-inoculation. In host-range study, brinjal (Solanum melongena), chilli (Capsicum annuum), datura (Datura stramonium), globe amaranth and tobacco (Nicotiana benthamiana, N. glutinosa, N. tabacum cv. Xanthi) could differentiate PluMV from FrMV. The complete genome sequence of PluMV was determined (6,688 nucleotides [nt], GenBank KJ395757), which showed the genome structure typical of tobamovirus encoding four proteins: small replicase (3,549 nt/130 kDa), large replicase (5,061 nt/188 kDa), movement protein (770 nt/29 kDa) and coat protein (527 nt/19 kDa). The 5' and 3' UTR of PluMV contained 91 and 284 nt, respectively. The PluMV genome was 45 nts longer than that of FrMV and shared only 71.4-71.6% sequence identity with FrMV and < 50% sequence identity with the rest of the other members of the genus Tobamovirus. PluMV shared a close but a divergent evolutionary relationship with FrMV. Based on the species demarcation guidelines of ICTV (<90% genome sequence identity), PluMV was considered as a new tobamovirus species. As PluMV was serologically related with FrMV, differential diagnostic assays such as simplex and duplex RT-PCR were developed, which revealed that PluMV naturally existed in both the species of temple tree, P. rubra f. acutifolia and P. rubra f. obtusa in India either alone or in mixed infection with FrMV.
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Affiliation(s)
- Alok Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India,School of Plant Sciences, College of Agriculture and Environmental Sciences, Haramaya University, Dire Dawa, Ethiopia,Alok Kumar, ;
| | - Vikas Solanki
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Akshay Katiyar
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Bikash Mandal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India,*Correspondence: Bikash Mandal, ;
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Kinsella CM, Deijs M, Gittelbauer HM, van der Hoek L, van Dijk K. Human Clinical Isolates of Pathogenic Fungi Are Host to Diverse Mycoviruses. Microbiol Spectr 2022; 10:e0161022. [PMID: 35993766 PMCID: PMC9603141 DOI: 10.1128/spectrum.01610-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/08/2022] [Indexed: 12/31/2022] Open
Abstract
Fungi host viruses from many families, and next-generation sequencing can be used to discover previously unknown genomes. Some fungus-infecting viruses (mycoviruses) confer hypovirulence on their pathogenic hosts, raising the possibility of therapeutic application in the treatment of fungal diseases. Though all fungi probably host mycoviruses, many human pathogens have none documented, implying the mycoviral catalogue remains at an early stage. Here, we carried out virus discovery on 61 cultures of pathogenic fungi covering 27 genera and at least 56 species. Using next-generation sequencing of total nucleic acids, we found no DNA viruses but did find a surprising RNA virus diversity of 11 genomes from six classified families and two unclassified lineages, including eight genomes likely representing new species. Among these was the first jivivirus detected in a fungal host (Aspergillus lentulus). We separately utilized rolling circle amplification and next-generation sequencing to identify ssDNA viruses specifically. We identified 13 new cressdnaviruses across all libraries, but unlike the RNA viruses, they could not be confirmed by PCR in either the original unamplified samples or freshly amplified nucleic acids. Their distributions among sequencing libraries and inconsistent detection suggest low-level contamination of reagents. This highlights both the importance of validation assays and the risks of viral host prediction on the basis of highly amplified sequencing libraries. Meanwhile, the detected RNA viruses provide a basis for experimentation to characterize possible hypovirulent effects, and hint at a wealth of uncharted viral diversity currently frozen in biobanks. IMPORTANCE Fungal pathogens of humans are a growing global health burden. Viruses of fungi may represent future therapeutic tools, but for many fungal pathogens there are no known viruses. Our study examined the viral content of diverse human-pathogenic fungi in a clinical biobank, identifying numerous viral genomes, including one lineage previously not known to infect fungi.
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Affiliation(s)
- Cormac M. Kinsella
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Martin Deijs
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - H. M. Gittelbauer
- Amsterdam UMC, Laboratory of Mycology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
| | - Lia van der Hoek
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Karin van Dijk
- Amsterdam UMC, Laboratory of Mycology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
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Inhibition of Cell-Free Translation and Replication of Tobacco Mosaic Virus RNA by Exogenously Added 5'-Proximal Fragments of the Genomic RNA. Viruses 2022; 14:v14091962. [PMID: 36146772 PMCID: PMC9502800 DOI: 10.3390/v14091962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Replication proteins of tobacco mosaic virus (TMV), a positive-sense RNA virus, co-translationally bind to a 5′-proximal ~70-nucleotide (nt) region of the genomic RNA, referred to as the nuclease-resistant (NR) region for replication template selection. Therefore, disruption of the interaction between the viral replication proteins and viral genomic RNA is expected to inhibit the replication of TMV. In this study, we demonstrate that the addition of small RNA fragments (18–33 nts in length) derived from different regions within the NR region inhibit the binding of TMV replication proteins to viral RNA and TMV RNA replication in a cell-free system. Intriguingly, some of the small RNA fragments also inhibited the translation of mRNA in a sequence-nonspecific manner. These results highlight the pleiotropic roles of the 5′-proximal region of the TMV genome.
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37
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Kondo H, Botella L, Suzuki N. Mycovirus Diversity and Evolution Revealed/Inferred from Recent Studies. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:307-336. [PMID: 35609970 DOI: 10.1146/annurev-phyto-021621-122122] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
High-throughput virome analyses with various fungi, from cultured or uncultured sources, have led to the discovery of diverse viruses with unique genome structures and even neo-lifestyles. Examples in the former category include splipalmiviruses and ambiviruses. Splipalmiviruses, related to yeast narnaviruses, have multiple positive-sense (+) single-stranded (ss) RNA genomic segments that separately encode the RNA-dependent RNA polymerase motifs, the hallmark of RNA viruses (members of the kingdom Orthornavirae). Ambiviruses appear to have an undivided ssRNA genome of 3∼5 kb with two large open reading frames (ORFs) separated by intergenic regions. Another narna-like virus group has two fully overlapping ORFs on both strands of a genomic segment that span more than 90% of the genome size. New virus lifestyles exhibited by mycoviruses include the yado-kari/yado-nushi nature characterized by the partnership between the (+)ssRNA yadokarivirus and an unrelated dsRNA virus (donor of the capsid for the former) and the hadaka nature of capsidless 10-11 segmented (+)ssRNA accessible by RNase in infected mycelial homogenates. Furthermore, dsRNA polymycoviruses with phylogenetic affinity to (+)ssRNA animal caliciviruses have been shown to be infectious as dsRNA-protein complexes or deproteinized naked dsRNA. Many previous phylogenetic gaps have been filled by recently discovered fungal and other viruses, which haveprovided interesting evolutionary insights. Phylogenetic analyses and the discovery of natural and experimental cross-kingdom infections suggest that horizontal virus transfer may have occurred and continue to occur between fungi and other kingdoms.
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Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
| | - Leticia Botella
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University, Brno, Czech Republic
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
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To Be Seen or Not to Be Seen: Latent Infection by Tobamoviruses. PLANTS 2022; 11:plants11162166. [PMID: 36015469 PMCID: PMC9415976 DOI: 10.3390/plants11162166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Tobamoviruses are among the most well-studied plant viruses and yet there is still a lot to uncover about them. On one side of the spectrum, there are damage-causing members of this genus: such as the tobacco mosaic virus (TMV), tomato brown rugose fruit virus (ToBRFV) and cucumber green mottle mosaic virus (CGMMV), on the other side, there are members which cause latent infection in host plants. New technologies, such as high-throughput sequencing (HTS), have enabled us to discover viruses from asymptomatic plants, viruses in mixed infections where the disease etiology cannot be attributed to a single entity and more and more researchers a looking at non-crop plants to identify alternative virus reservoirs, leading to new virus discoveries. However, the diversity of these interactions in the virosphere and the involvement of multiple viruses in a single host is still relatively unclear. For such host–virus interactions in wild plants, symptoms are not always linked with the virus titer. In this review, we refer to latent infection as asymptomatic infection where plants do not suffer despite systemic infection. Molecular mechanisms related to latent behavior of tobamoviruses are unknown. We will review different studies which support different theories behind latency.
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Niu E, Ye C, Zhao W, Kondo H, Wu Y, Chen J, Andika IB, Sun L. Coat protein of Chinese wheat mosaic virus upregulates and interacts with cytosolic glyceraldehyde-3-phosphate dehydrogenase, a negative regulator of plant autophagy, to promote virus infection. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1631-1645. [PMID: 35713231 DOI: 10.1111/jipb.13313] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Autophagy is an intracellular degradation mechanism involved in antiviral defense, but the strategies employed by plant viruses to counteract autophagy-related defense remain unknown for the majority of the viruses. Herein, we describe how the Chinese wheat mosaic virus (CWMV, genus Furovirus) interferes with autophagy and enhances its infection in Nicotiana benthamiana. Yeast two-hybrid screening and in vivo/in vitro assays revealed that the 19 kDa coat protein (CP19K) of CWMV interacts with cytosolic glyceraldehyde-3-phosphate dehydrogenases (GAPCs), negative regulators of autophagy, which bind autophagy-related protein 3 (ATG3), a key factor in autophagy. CP19K also directly interacts with ATG3, possibly leading to the formation of a CP19K-GAPC-ATG3 complex. CP19K-GAPC interaction appeared to intensify CP19K-ATG3 binding. Moreover, CP19K expression upregulated GAPC gene transcripts and reduced autophagic activities. Accordingly, the silencing of GAPC genes in transgenic N. benthamiana reduced CWMV accumulation, whereas CP19K overexpression enhanced it. Overall, our results suggest that CWMV CP19K interferes with autophagy through the promotion and utilization of the GAPC role as a negative regulator of autophagy.
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Affiliation(s)
- Erbo Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Xi'an, 712100, China
| | - Chaozheng Ye
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Xi'an, 712100, China
| | - Wanying Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Xi'an, 712100, China
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Xi'an, 712100, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Xi'an, 712100, China
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
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Kondo H, Maejima H, Maruyama K, Fujita M, Ohki T. First Report of Chinese Wheat Mosaic Virus that Infects Barley in Japan. PLANT DISEASE 2022; 106:PDIS12212803PDN. [PMID: 35084947 DOI: 10.1094/pdis-12-21-2803-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- H Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan
| | - H Maejima
- Nagano Prefecture Agricultural Experiment Station, Suzaka, Nagano, 382-0051, Japan
| | - K Maruyama
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan
| | - M Fujita
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan
| | - T Ohki
- NARO Hokkaido Agricultural Research Center, Sapporo, Hokkaido, 062-8555, Japan
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Truong Nguyen PT, Culverwell CL, Suvanto MT, Korhonen EM, Uusitalo R, Vapalahti O, Smura T, Huhtamo E. Characterisation of the RNA Virome of Nine Ochlerotatus Species in Finland. Viruses 2022; 14:1489. [PMID: 35891469 PMCID: PMC9324324 DOI: 10.3390/v14071489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 02/01/2023] Open
Abstract
RNA viromes of nine commonly encountered Ochlerotatus mosquito species collected around Finland in 2015 and 2017 were studied using next-generation sequencing. Mosquito homogenates were sequenced from 91 pools comprising 16-60 morphologically identified adult females of Oc. cantans, Oc. caspius, Oc. communis, Oc. diantaeus, Oc. excrucians, Oc. hexodontus, Oc. intrudens, Oc. pullatus and Oc. punctor/punctodes. In total 514 viral Reverse dependent RNA polymerase (RdRp) sequences of 159 virus species were recovered, belonging to 25 families or equivalent rank, as follows: Aliusviridae, Aspiviridae, Botybirnavirus, Chrysoviridae, Chuviridae, Endornaviridae, Flaviviridae, Iflaviridae, Negevirus, Partitiviridae, Permutotetraviridae, Phasmaviridae, Phenuiviridae, Picornaviridae, Qinviridae, Quenyavirus, Rhabdoviridae, Sedoreoviridae, Solemoviridae, Spinareoviridae, Togaviridae, Totiviridae, Virgaviridae, Xinmoviridae and Yueviridae. Of these, 147 are tentatively novel viruses. One sequence of Sindbis virus, which causes Pogosta disease in humans, was detected from Oc. communis from Pohjois-Karjala. This study greatly increases the number of mosquito-associated viruses known from Finland and presents the northern-most mosquito-associated viruses in Europe to date.
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Affiliation(s)
- Phuoc T. Truong Nguyen
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
| | - C. Lorna Culverwell
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- The Natural History Museum, Cromwell Road, South Kensington, London SW5 7BD, UK
| | - Maija T. Suvanto
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
| | - Essi M. Korhonen
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
| | - Ruut Uusitalo
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
- Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Gustaf Hällströmin Katu 2, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
- Virology and Immunology, Diagnostic Center, HUSLAB, Helsinki University Hospital, FI-00029 Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
| | - Eili Huhtamo
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
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Yue N, Jiang Z, Zhang X, Li Z, Wang X, Wen Z, Gao Z, Pi Q, Zhang Y, Wang X, Han C, Yu J, Li D. Palmitoylation of γb protein directs a dynamic switch between Barley stripe mosaic virus replication and movement. EMBO J 2022; 41:e110060. [PMID: 35642376 PMCID: PMC9251889 DOI: 10.15252/embj.2021110060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Viral replication and movement are intimately linked; however, the molecular mechanisms regulating the transition between replication and subsequent movement remain largely unknown. We previously demonstrated that the Barley stripe mosaic virus (BSMV) γb protein promotes viral replication and movement by interacting with the αa replicase and TGB1 movement proteins. Here, we found that γb is palmitoylated at Cys-10, Cys-19, and Cys-60 in Nicotiana benthamiana, which supports BSMV infection. Intriguingly, non-palmitoylated γb is anchored to chloroplast replication sites and enhances BSMV replication, whereas palmitoylated γb protein recruits TGB1 to the chloroplasts and forms viral replication-movement intermediate complexes. At the late stages of replication, γb interacts with NbPAT15 and NbPAT21 and is palmitoylated at the chloroplast periphery, thereby shifting viral replication to intracellular and intercellular movement. We also show that palmitoylated γb promotes virus cell-to-cell movement by interacting with NbREM1 to inhibit callose deposition at the plasmodesmata. Altogether, our experiments reveal a model whereby palmitoylation of γb directs a dynamic switch between BSMV replication and movement events during infection.
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Affiliation(s)
- Ning Yue
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zhihao Jiang
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xuan Zhang
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zhenggang Li
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xueting Wang
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zhiyan Wen
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zongyu Gao
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Qinglin Pi
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yongliang Zhang
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xian‐Bing Wang
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Chenggui Han
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Jialin Yu
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Dawei Li
- State Key Laboratory of Agro‐Biotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
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Molecular characterization of a novel virga-like virus associated with wheat. Arch Virol 2022; 167:1909-1913. [PMID: 35752685 DOI: 10.1007/s00705-022-05473-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/31/2022] [Indexed: 11/27/2022]
Abstract
In this work, we report the detection of a novel single-strand RNA virus from wheat, tentatively named "Triticum aestivum-associated virga-like virus 1" (TaAVLV1). Further characterization revealed that the complete genome of TaAVLV1 is divided into two segments, RNA1 and RNA2, which are 3530 and 3466 nt in length, excluding their respective polyA tails, and each contains only one open reading frame (ORF). The ORF of RNA1 encodes an RNA-dependent RNA polymerase (RdRp), while the ORF of RNA2 encodes a putative protein with methyltransferase and helicase domains. Phylogenetic analysis showed that the RdRp of TaAVLV1 is closely related to those of members of the unclassified virga-like virus group in the family Virgaviridae. Thus, we have identified TaAVLV1 as a putative novel virga-like virus belonging to the family Virgaviridae.
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In Silico Pesticide Discovery for New Anti-Tobacco Mosaic Virus Agents: Reactivity, Molecular Docking, and Molecular Dynamics Simulations. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12062818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Considerable data are available regarding the molecular genetics of the tobacco mosaic virus. The disease caused by the tobacco mosaic virus is still out of control due to the lack of an efficient functional antagonist chemical molecule. Extensive research was carried out to try to find effective new anti-tobacco mosaic virus agents, however no study could find an effective agent which could completely inhibit the disease caused by the virus. In recent years, molecular docking, combined with molecular dynamics, which is considered to be one of the most important methods of drug discovery and design, were used to evaluate the type of binding between the ligand and its protein enzyme. The aim of the current work was to assess the in silico anti-tobacco mosaic virus activity for a selection of 41 new and 2 reference standard compounds. These compounds were chosen to examine their reactivity and binding efficiency with the tobacco mosaic virus coat protein (PDB ID: 2OM3). A comparison was made between the activity of the selected compounds and that for ningnanmycin and ribavirin, which are common inhibitors of plant viruses. The simulation results obtained from the molecular docking and molecular dynamics showed that two compounds of the antofine analogues could bind with the tobacco mosaic virus coat protein receptor better than ningnanmycin and ribavirin.
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45
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Complete genome sequence of a novel virga-like virus infecting Hevea brasiliensis. Arch Virol 2022; 167:965-968. [PMID: 35112201 DOI: 10.1007/s00705-021-05306-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/08/2021] [Indexed: 11/02/2022]
Abstract
Here, we report the complete genome sequence and organization of a novel virus detected in rubber trees (Hevea brasiliensis). Because the infected plants were asymptomatic, this virus was tentatively named "rubber tree latent virus 1" (RTLV1). The full genome of RTLV1 is 9,422 nt in length and contains three open reading frames with a 157-nt 5' untranslated region (UTR) and a 316-nt 3' UTR. The replicase shares the highest amino acid (aa) sequence identity (32.62%), with only 31% query coverage, with the replicase of Hubei virga-like virus 11. Phylogenetic analysis based on the aa sequence of ORF1 showed that RTLV1 clustered with unclassified members of the family Virgaviridae in a clade that was not closely related to any genus in this family.
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46
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Moyo L, Raikhy G, Hamid A, Mallik I, Gudmestad NC, Gray S, Pappu HR. Phylogenetics of tobacco rattle virus isolates from potato (Solanum tuberosum L.) in the USA: a multi-gene approach to evolutionary lineage. Virus Genes 2022; 58:42-52. [PMID: 34671909 DOI: 10.1007/s11262-021-01875-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/05/2021] [Indexed: 01/22/2023]
Abstract
Tobacco rattle virus (TRV) is an important soil-borne virus of potato that is transmitted by stubby-root nematodes. TRV causes corky ringspot, a tuber disease of economic importance to potato production. Utilizing protein-coding regions of the whole genome and a range of computational tools, the genetic diversity, and population structure of TRV isolates from several potato-growing regions (Colorado, Idaho, Indiana, Minnesota, Nebraska, North Dakota, and Washington State) in the USA were determined. Phylogenetic analyses based on RNA2 nucleotide sequences, the coat protein (CP) and nematode transmission (2b) genes, showed geographical clustering of USA isolates with previously known American isolates, while European isolates grouped in a distinct cluster. This was corroborated by the observed genetic differentiation and infrequent gene flow between American and European isolates. Low genetic diversity was revealed among American isolates compared to European isolates. Phylogenetic clustering based on RNA1 genes (RdRp, RdRp-RT, and 1a) were all largely incongruent to that of 1b gene (virus suppressor of RNA silencing). This genetic incongruence suggested the influence of recombination. Furthermore, the RdRp, RdRp-RT, and 1a genes were predicted to be more conserved and under negative selection, while the 1b gene was less constrained. Different evolutionary lineages between TRV RNA1 and RNA2 genomic segments were revealed.
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Affiliation(s)
- Lindani Moyo
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA
- Department of Environmental Science and Health, National University of Science and Technology, PO Box AC939, Ascot, Bulawayo, Zimbabwe
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7600, South Africa
| | - Gaurav Raikhy
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | - Aflaq Hamid
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | - Ipsita Mallik
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Neil C Gudmestad
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Stewart Gray
- Section of Plant Pathology and Plant-Microbe Biology, School of Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA.
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA.
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47
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Reynard JS, Turco S, Brodard J, Kellenberger I, Maclot F, Schumpp O, Gugerli P, Pooggin MM. Identification and Molecular Characterization of a Novel Hordeivirus Associated With Yellow Mosaic Disease of Privet ( Ligustrum vulgare) in Europe. Front Microbiol 2021; 12:723350. [PMID: 34646247 PMCID: PMC8503643 DOI: 10.3389/fmicb.2021.723350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Wild plants serve as a large reservoir of known and yet-unknown viruses and as a source of viral pathogens of cultivated plants. Yellow mosaic disease of forest shrub Ligustrum vulgare (privet) was recurrently observed in Europe for more than 100 years. Using a universal virus identification approach based on deep sequencing and de novo assembly of viral small interfering (si)RNAs we identified a causative agent of this disease in Switzerland and reconstructed its complete 3-segmented RNA genome. Notably, a short 3'-terminal common region (CR) attached to each segment via a ∼53-71 nucleotide poly(A) tract, as determined by RT-PCR sequencing, was initially identified as an orphan siRNA contig with conserved tRNA-like secondary structure. Phylogenomic analysis classified this virus as a novel member in the genus Hordeivirus of family Virgaviridae, which we named ligustrum mosaic virus (LigMV). Similar to other hordeiviruses, LigMV formed rod-shape virions (visualized by electron microscopy), was transmitted through seeds and could also be mechanically transmitted to herbaceous hosts Chenopodium quinoa and Nicotiana benthamiana. Blot hybridization analysis identified genomic and subgenomic RNAs, sharing the 3'-CR and likely serving as monocistronic mRNAs for seven evolutionarily-conserved viral proteins including two subunits of viral RNA-dependent RNA polymerase, coat protein, triple gene block proteins mediating viral movement and cysteine-rich suppressor of RNA silencing. Analysis of size, polarity, and hotspot profiles of viral siRNAs suggested that they are produced by the plant antiviral Dicer-like (DCL) proteins DCL2 and DCL4 processing double-stranded intermediates of genomic RNA replication. Whole genome sequencing of French and Austrian isolates of LigMV revealed its genetic stability over a wide geographic range (>99% nucleotide identity to Swiss isolates and each other), suggesting its persistence and spread in Europe via seed dispersal.
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Affiliation(s)
| | - Silvia Turco
- Department of Environmental Sciences, Botany, University of Basel, Basel, Switzerland
| | - Justine Brodard
- Virology-Phytoplasmology Laboratory, Agroscope, Nyon, Switzerland
| | | | - François Maclot
- Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Olivier Schumpp
- Virology-Phytoplasmology Laboratory, Agroscope, Nyon, Switzerland
| | - Paul Gugerli
- Virology-Phytoplasmology Laboratory, Agroscope, Nyon, Switzerland
| | - Mikhail M Pooggin
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, IRD, Institute Agro, Montpellier, France
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48
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Quintanilha-Peixoto G, Fonseca PLC, Raya FT, Marone MP, Bortolini DE, Mieczkowski P, Olmo RP, Carazzolle MF, Voigt CA, Soares ACF, Pereira GAG, Góes-Neto A, Aguiar ERGR. The Sisal Virome: Uncovering the Viral Diversity of Agave Varieties Reveals New and Organ-Specific Viruses. Microorganisms 2021; 9:microorganisms9081704. [PMID: 34442783 PMCID: PMC8400513 DOI: 10.3390/microorganisms9081704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 12/29/2022] Open
Abstract
Sisal is a common name for different plant varieties in the genus Agave (especially Agave sisalana) used for high-quality natural leaf fiber extraction. Despite the economic value of these plants, we still lack information about the diversity of viruses (virome) in non-tequilana species from the genus Agave. In this work, by associating RNA and DNA deep sequencing we were able to identify 25 putative viral species infecting A. sisalana, A. fourcroydes, and Agave hybrid 11648, including one strain of Cowpea Mild Mottle Virus (CPMMV) and 24 elements likely representing new viruses. Phylogenetic analysis indicated they belong to at least six viral families: Alphaflexiviridae, Betaflexiviridae, Botourmiaviridae, Closteroviridae, Partitiviridae, Virgaviridae, and three distinct unclassified groups. We observed higher viral taxa richness in roots when compared to leaves and stems. Furthermore, leaves and stems are very similar diversity-wise, with a lower number of taxa and dominance of a single viral species. Finally, approximately 50% of the identified viruses were found in all Agave organs investigated, which suggests that they likely produce a systemic infection. This is the first metatranscriptomics study focused on viral identification in species from the genus Agave. Despite having analyzed symptomless individuals, we identified several viruses supposedly infecting Agave species, including organ-specific and systemic species. Surprisingly, some of these putative viruses are probably infecting microorganisms composing the plant microbiota. Altogether, our results reinforce the importance of unbiased strategies for the identification and monitoring of viruses in plant species, including those with asymptomatic phenotypes.
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Affiliation(s)
- Gabriel Quintanilha-Peixoto
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
| | - Paula Luize Camargos Fonseca
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
| | - Fábio Trigo Raya
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | - Marina Pupke Marone
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | - Dener Eduardo Bortolini
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
| | - Piotr Mieczkowski
- High-Throughput Sequencing Facility, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA;
| | - Roenick Proveti Olmo
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
- CNRS UPR9022, INSERM U1257, Université de Strasbourg, 67084 Strasbourg, France
| | - Marcelo Falsarella Carazzolle
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | | | - Ana Cristina Fermino Soares
- Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas 44380-000, Brazil;
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
- Correspondence: (A.G.-N.); (E.R.G.R.A.)
| | - Eric Roberto Guimarães Rocha Aguiar
- Center of Biotechnology and Genetics, Department of Biological Science, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Correspondence: (A.G.-N.); (E.R.G.R.A.)
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Parry R, James ME, Asgari S. Uncovering the Worldwide Diversity and Evolution of the Virome of the Mosquitoes Aedes aegypti and Aedes albopictus. Microorganisms 2021; 9:microorganisms9081653. [PMID: 34442732 PMCID: PMC8398489 DOI: 10.3390/microorganisms9081653] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/13/2021] [Accepted: 07/27/2021] [Indexed: 12/16/2022] Open
Abstract
Aedes aegypti, the yellow fever mosquito, and Aedes albopictus, the Asian tiger mosquito, are the most significant vectors of dengue, Zika, and Chikungunya viruses globally. Studies examining host factors that control arbovirus transmission demonstrate that insect-specific viruses (ISVs) can modulate mosquitoes’ susceptibility to arbovirus infection in both in vivo and in vitro co-infection models. While research is ongoing to implicate individual ISVs as proviral or antiviral factors, we have a limited understanding of the composition and diversity of the Aedes virome. To address this gap, we used a meta-analysis approach to uncover virome diversity by analysing ~3000 available RNA sequencing libraries representing a worldwide geographic range for both mosquitoes. We identified ten novel viruses and previously characterised viruses, including mononegaviruses, orthomyxoviruses, negeviruses, and a novel bi-segmented negev-like group. Phylogenetic analysis suggests close relatedness to mosquito viruses implying likely insect host range except for one arbovirus, the multi-segmented Jingmen tick virus (Flaviviridae) in an Italian colony of Ae. albopictus. Individual mosquito transcriptomes revealed remarkable inter-host variation of ISVs within individuals from the same colony and heterogeneity between different laboratory strains. Additionally, we identified striking virus diversity in Wolbachia infected Aedes cell lines. This study expands our understanding of the virome of these important vectors. It provides a resource for further assessing the ecology, evolution, and interaction of ISVs with their mosquito hosts and the arboviruses they transmit.
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Affiliation(s)
- Rhys Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence:
| | - Maddie E James
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (M.E.J.); (S.A.)
| | - Sassan Asgari
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (M.E.J.); (S.A.)
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50
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Vélez-Olmedo JB, Fribourg CE, Melo FL, Nagata T, de Oliveira AS, Resende RO. Tobamoviruses of two new species trigger resistance in pepper plants harbouring functional L alleles. J Gen Virol 2021; 102. [PMID: 33210991 DOI: 10.1099/jgv.0.001524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Tobamoviruses are often referred to as the most notorious viral pathogens of pepper crops. These viruses are not transmitted by invertebrate vectors, but rather by physical contact and seeds. In this study, pepper plants displaying mild mottle and mosaic symptoms were sampled in four different regions of Peru. Upon double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) tests, seven samples cross-reacted weakly with antibodies against pepper mild mottle virus (PMMoV), suggesting the presence of tobamoviruses. When employing RT-PCR, conserved primers amplified cDNA fragments of viruses from two putative new tobamovirus species in the samples. The complete genome of two representative isolates were, therefore, sequenced and analysed in silico. These viruses, which were tentatively named yellow pepper mild mottle virus (YPMMoV) and chilli pepper mild mottle virus (CPMMoV), shared highest nucleotide genome sequence identities of 83 and 85 % with bell pepper mottle virus (BpeMV), respectively. Mechanical inoculation of indicator plants with YPMMoV and CPMMoV isolates did not show any obvious differences in host ranges. These viruses were also inoculated mechanically on pepper plants harbouring different resistance L alleles to determine their pathotypes. Pepper plants carrying unfunctional L alleles (L 0) to tobamoviruses were infected by all isolates and presented differential symptomatology for YPMMoV and CPMMoV. On the other hand, pepper plants carrying L 1, L 2, L 3 and L 4 alleles were resistant to all isolates, indicating that these viruses belong to pathotype P0.
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Affiliation(s)
- Jefferson B Vélez-Olmedo
- Departamento de Fitopatologia, Universidade de Brasília, Brasília, Brazil.,Departamento de Ciéncias Agronómicas, Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Portoviejo, 130105 Ecuador
| | - Cesar E Fribourg
- Departamento de Fitopatología, Universidad Nacional Agraria, Lima, Peru
| | - Fernando L Melo
- Departamento de Fitopatologia, Universidade de Brasília, Brasília, Brazil
| | - Tatsuya Nagata
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Athos S de Oliveira
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
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