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Host Selection-producing Variations in the Genome of Hop Stunt Viroid. Virus Res 2022; 311:198706. [PMID: 35143908 DOI: 10.1016/j.virusres.2022.198706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 11/21/2022]
Abstract
A random mutant pool of hop stunt viroid (HSVd) was created by shuffling cDNA fragments prepared from three natural HSVd variants obtained from grapevine, citrus, and plum. It was used to infect five host plant species: hop, cucumber, grapevine, peach, and citrus. After infection, progenies having variations characteristic for grapevine and citrus HSVd variants have been preferentially enriched in the homologous plant species, suggesting that strong but different selection pressures affected the genomic RNA when HSVd-infected either grapevine or citrus. In the progeny propagated in cucumber, hop, and peach, variations characteristic to grapevine, citrus, and plum HSVd variants were detected simultaneously as a blend. Accordingly, we showed that at least some of the host-specific variations found in HSVd variants isolated from host plant species, e.g., grapevine and citrus, seemed to have arisen from positive host selection pressures. The HSVd-grapevine variant was found to be ideally adaptable not only to grapevine but to various host plants as well.
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Chiumenti M, Navarro B, Candresse T, Flores R, Di Serio F. Reassessing species demarcation criteria in viroid taxonomy by pairwise identity matrices. Virus Evol 2021; 7:veab001. [PMID: 33623708 PMCID: PMC7887442 DOI: 10.1093/ve/veab001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
With a small, circular and non-protein coding RNA genome, viroids are the smallest infectious agents. They invade plants, which in turn may develop symptoms. Since their discovery about 50 years ago, more than thirty viroids have been reported and classified using as species demarcation less than 90 per cent sequence identity on the overall genome and evidence of biological divergence with respect to the closest related viroids. In the last few years, new viroids have been identified that infect latently their (frequently) woody hosts and have a narrow experimental hosts range, complicating and slowing down studies on their biology. As a consequence, several viroids are still waiting for classification. Moreover, the number of new viroids is expected to increase in the next years due to the use of high-throughput sequencing technologies with diagnostics purposes. Therefore, establishment of reliable species demarcation criteria mainly based on molecular features of viroids is needed. Here, viroid classification is reassessed and a scheme based on pairwise sequence identity matrices is developed. After identifying a threshold pairwise identity score (PWIS) for each viroid genus, to be used as a species demarcation criterion, we show that most of those yet unclassified viroids can be assigned to a known or to a new species, thus limiting the need for additional biological evidence to only a few more complex situations. The advantages of this PWIS-based method are that the proposed identity thresholds for species demarcations are not arbitrarily established and evidence for biological divergence is not mandatory. Importantly, the current classification is not essentially modified. A protocol for a tentative fast classification of new viroids according to the proposed approach is also provided.
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Affiliation(s)
- Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via Amendola 122/D, Bari 70126, Italy
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via Amendola 122/D, Bari 70126, Italy
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon Cedex, CS20032 33882, France
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia 46022, Spain
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via Amendola 122/D, Bari 70126, Italy
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SANO T. Progress in 50 years of viroid research-Molecular structure, pathogenicity, and host adaptation. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2021; 97:371-401. [PMID: 34380915 PMCID: PMC8403530 DOI: 10.2183/pjab.97.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/30/2021] [Indexed: 05/27/2023]
Abstract
Viroids are non-encapsidated, single-stranded, circular RNAs consisting of 246-434 nucleotides. Despite their non-protein-encoding RNA nature, viroids replicate autonomously in host cells. To date, more than 25 diseases in more than 15 crops, including vegetables, fruit trees, and flowers, have been reported. Some are pathogenic but others replicate without eliciting disease. Viroids were shown to have one of the fundamental attributes of life to adapt to environments according to Darwinian selection, and they are likely to be living fossils that have survived from the pre-cellular RNA world. In 50 years of research since their discovery, it was revealed that viroids invade host cells, replicate in nuclei or chloroplasts, and undergo nucleotide mutation in the process of adapting to new host environments. It was also demonstrated that structural motifs in viroid RNAs exert different levels of pathogenicity by interacting with various host factors. Despite their small size, the molecular mechanism of viroid pathogenicity turned out to be more complex than first thought.
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Affiliation(s)
- Teruo SANO
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
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Adkar-Purushothama CR, Perreault JP. Impact of Nucleic Acid Sequencing on Viroid Biology. Int J Mol Sci 2020; 21:ijms21155532. [PMID: 32752288 PMCID: PMC7432327 DOI: 10.3390/ijms21155532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/26/2022] Open
Abstract
The early 1970s marked two breakthroughs in the field of biology: (i) The development of nucleotide sequencing technology; and, (ii) the discovery of the viroids. The first DNA sequences were obtained by two-dimensional chromatography which was later replaced by sequencing using electrophoresis technique. The subsequent development of fluorescence-based sequencing method which made DNA sequencing not only easier, but many orders of magnitude faster. The knowledge of DNA sequences has become an indispensable tool for both basic and applied research. It has shed light biology of viroids, the highly structured, circular, single-stranded non-coding RNA molecules that infect numerous economically important plants. Our understanding of viroid molecular biology and biochemistry has been intimately associated with the evolution of nucleic acid sequencing technologies. With the development of the next-generation sequence method, viroid research exponentially progressed, notably in the areas of the molecular mechanisms of viroids and viroid diseases, viroid pathogenesis, viroid quasi-species, viroid adaptability, and viroid–host interactions, to name a few examples. In this review, the progress in the understanding of viroid biology in conjunction with the improvements in nucleotide sequencing technology is summarized. The future of viroid research with respect to the use of third-generation sequencing technology is also briefly envisaged.
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Suzuki T, Ikeda S, Kasai A, Taneda A, Fujibayashi M, Sugawara K, Okuta M, Maeda H, Sano T. RNAi-Mediated Down-Regulation of Dicer-Like 2 and 4 Changes the Response of 'Moneymaker' Tomato to Potato Spindle Tuber Viroid Infection from Tolerance to Lethal Systemic Necrosis, Accompanied by Up-Regulation of miR398, 398a-3p and Production of Excessive Amount of Reactive Oxygen Species. Viruses 2019; 11:v11040344. [PMID: 31013904 PMCID: PMC6521110 DOI: 10.3390/v11040344] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/08/2019] [Accepted: 04/10/2019] [Indexed: 12/14/2022] Open
Abstract
To examine the role of RNA silencing in plant defenses against viroids, a Dicer-like 2 and 4 (DCL2&4)–double knockdown transgenic tomato plant line, 72E, was created. The expression of endogenous SlDCL2s and SlDCL4 in line 72E decreased to about a half that of the empty cassette line, EC. When challenged with potato spindle tuber viroid (PSTVd), line 72E showed significantly higher levels of PSTVd accumulation early in the course of the infection and lethal systemic necrosis late in the infection. The size distribution of PSTVd-derived small RNAs was significantly different with the number of RNAs of 21 and 22 nucleotides (nt) in line 72E, at approximately 66.7% and 5% of those in line EC, respectively. Conversely, the numbers of 24 nt species increased by 1100%. Furthermore, expression of the stress-responsive microRNA species miR398 and miR398a-3p increased 770% and 868% in the PSTVd-infected line 72E compared with the PSTVd-infected EC. At the same time, the expression of cytosolic and chloroplast-localized Cu/Zn-superoxide dismutase 1 and 2 (SOD1 and SOD2) and the copper chaperon for SOD (CCS1) mRNAs, potential targets of miR398 or 398a-3p, decreased significantly in the PSTVd-infected line 72E leaves, showing necrosis. In concert with miR398 and 398a-3p, SODs control the detoxification of reactive oxygen species (ROS) generated in cells. Since high levels of ROS production were observed in PSTVd-infected line 72E plants, it is likely that the lack of full dicer-likes (DCL) activity in these plants made them unable to control excessive ROS production after PSTVd infection, as disruption in the ability of miR398 and miR398a-3p to regulate SODs resulted in the development of lethal systemic necrosis.
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Affiliation(s)
- Takahiro Suzuki
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
- Union Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
| | - Sho Ikeda
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Atsushi Kasai
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Akito Taneda
- Graduate School of Science and Technology, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Misato Fujibayashi
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Kohei Sugawara
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Maki Okuta
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Hayato Maeda
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
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Hadidi A. Next-Generation Sequencing and CRISPR/Cas13 Editing in Viroid Research and Molecular Diagnostics. Viruses 2019; 11:E120. [PMID: 30699972 PMCID: PMC6409718 DOI: 10.3390/v11020120] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 12/12/2022] Open
Abstract
Viroid discovery as well as the economic significance of viroids and biological properties are presented. Next-generation sequencing (NGS) technologies combined with informatics have been applied to viroid research and diagnostics for almost a decade. NGS provides highly efficient, rapid, low-cost high-throughput sequencing of viroid genomes and of the 21⁻24 nt vd-sRNAs generated by the RNA silencing defense of the host. NGS has been utilized in various viroid studies which are presented. The discovery during the last few years that prokaryotes have heritable adaptive immunity mediated through clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated Cas proteins, have led to transformative advances in molecular biology, notably genome engineering and most recently molecular diagnostics. The potential application of the CRISPR-Cas13a system for engineering viroid interference in plants is suggested by targeting specific motifs of three economically important viroids. The CRISPR-Cas13 system has been utilized recently for the accurate detection of human RNA viruses by visual read out in 90 min or less and by paper-based assay. Multitarget RNA tests by this technology have a good potential for application as a rapid and accurate diagnostic assay for known viroids. The CRISPR/Cas system will work only for known viroids in contrast to NGS, but it should be much faster.
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Affiliation(s)
- Ahmed Hadidi
- United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA.
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Yanagisawa H, Matsushita Y. Differences in dynamics of horizontal transmission of Tomato planta macho viroid and Potato spindle tuber viroid after pollination with viroid-infected pollen. Virology 2018; 516:258-264. [PMID: 29425768 DOI: 10.1016/j.virol.2018.01.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/26/2018] [Accepted: 01/27/2018] [Indexed: 11/17/2022]
Abstract
For viroids, pollen transmission is an important transmission pathway to progeny seeds and new hosts. In the current study, we found that Tomato planta macho viroid (TPMVd)-but not Potato spindle tuber viroid (PSTVd)-was horizontally transmitted by pollen from petunia plants. Using tissue-printing hybridization to track the changes in viroid distribution after pollination, we noted that TPMVd was present in petunia stigma, styles, and eventually ovaries, whereas PSTVd was detected in the stigma and upper style but not the ovary. These findings suggest that horizontal transmission of viroids depends on the infection of the lower style and ovary during the elongation of pollen tubes after pollination. Additionally, TPMVd was transmitted horizontally, leading to systematic infection, when we used TPMVd-infected petunia pollen to pollinate the flowers of healthy tomato plants. Fertilization typically does not occur after heterologous pollination and thus likely is not required to accomplish horizontal transmission of viroids.
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Affiliation(s)
- Hironobu Yanagisawa
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8666, Japan; The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan.
| | - Yosuke Matsushita
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8519, Japan.
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