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Hao J, Ma J, Wang Y. Understanding viroids, endogenous circular RNAs, and viroid-like RNAs in the context of biogenesis. PLoS Pathog 2024; 20:e1012299. [PMID: 38935625 PMCID: PMC11210808 DOI: 10.1371/journal.ppat.1012299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Affiliation(s)
- Jie Hao
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Junfei Ma
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Ying Wang
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
- Plant Molecular and Cell Biology Program, University of Florida, Gainesville, Florida, United States of America
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Wu J, Zhang Y, Li F, Zhang X, Ye J, Wei T, Li Z, Tao X, Cui F, Wang X, Zhang L, Yan F, Li S, Liu Y, Li D, Zhou X, Li Y. Plant virology in the 21st century in China: Recent advances and future directions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:579-622. [PMID: 37924266 DOI: 10.1111/jipb.13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/02/2023] [Indexed: 11/06/2023]
Abstract
Plant viruses are a group of intracellular pathogens that persistently threaten global food security. Significant advances in plant virology have been achieved by Chinese scientists over the last 20 years, including basic research and technologies for preventing and controlling plant viral diseases. Here, we review these milestones and advances, including the identification of new crop-infecting viruses, dissection of pathogenic mechanisms of multiple viruses, examination of multilayered interactions among viruses, their host plants, and virus-transmitting arthropod vectors, and in-depth interrogation of plant-encoded resistance and susceptibility determinants. Notably, various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in plants. We also recommend future plant virology studies in China.
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Affiliation(s)
- Jianguo Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Ye
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Taiyun Wei
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaorong Tao
- Department of Plant Pathology, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianbing Wang
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lili Zhang
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Dawei Li
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yi Li
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
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Ma J, Dissanayaka Mudiyanselage SD, Hao J, Wang Y. Cellular roadmaps of viroid infection. Trends Microbiol 2023; 31:1179-1191. [PMID: 37349206 PMCID: PMC10592528 DOI: 10.1016/j.tim.2023.05.014] [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: 03/16/2023] [Revised: 05/28/2023] [Accepted: 05/31/2023] [Indexed: 06/24/2023]
Abstract
Viroids are single-stranded circular noncoding RNAs that infect plants. According to the International Committee on Taxonomy of Viruses, there are 44 viroids known to date. Notably, more than 20 000 distinct viroid-like RNA sequences have recently been identified in existing sequencing datasets, suggesting an unprecedented complexity in biological roles of viroids and viroid-like RNAs. Interestingly, a human pathogen, hepatitis delta virus (HDV), also replicates via a rolling circle mechanism like viroids. Therefore, knowledge of viroid infection is informative for research on HDV and other viroid-like RNAs reported from various organisms. Here, we summarize recent advancements in understanding viroid shuttling among subcellular compartments for completing replication cycles, emphasizing regulatory roles of RNA motifs and structural dynamics in diverse biological processes. We also compare the knowledge of viroid intracellular trafficking with known pathways governing cellular RNA movement in cells. Future investigations on regulatory RNA structures and cognate factors in regulating viroid subcellular trafficking and replication will likely provide new insights into RNA structure-function relationships and facilitate the development of strategies controlling RNA localization and function in cells.
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Affiliation(s)
- Junfei Ma
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Current address: Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA
| | | | - Jie Hao
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Current address: Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Current address: Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA.
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Bragard C, Baptista P, Chatzivassiliou E, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas‐Cortes JA, Parnell S, Potting R, Stefani E, Thulke H, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Migheli Q, Vloutoglou I, Maiorano A, Pautasso M, Reignault PL. Pest categorisation of the avocado sunblotch viroid. EFSA J 2023; 21:e08116. [PMID: 37485255 PMCID: PMC10357502 DOI: 10.2903/j.efsa.2023.8116] [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] [Indexed: 07/25/2023] Open
Abstract
The EFSA Panel on Plant Health conducted a pest categorisation of the avocado sunblotch viroid (ASBVd) for the EU. The identity of ASBVd, a member of the genus Avsunviroid (family Avsunviroidae) is clearly defined and detection and identification methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. ASBVd has been reported in Australia, Ghana, Guatemala, Israel, Mexico, Peru, South Africa, USA (California, Florida) and Venezuela. In the EU, it has been reported in Greece (Crete Island) and Spain. The pathogen could establish in the EU wherever avocado (Persea americana) is grown. The only known natural host of ASBVd is avocado to which it causes the severe 'avocado sunblotch' disease, characterised by white, yellow, red or necrotic depressed areas or scars on the fruit surface, bleached veins and petioles of the leaf, and rectangular cracking patterns in the bark of the old branches. Fruit yield and quality are severely diminished. ASBVd infects under experimental conditions a few more species in the family Lauraceae. The viroid is naturally transmitted at an extremely high rate by seeds (up to 100% in asymptomatically infected trees), but with a low efficiency by pollen (only to the produced seeds), and possibly through root grafts. Plants for planting, including seeds, and fresh avocado fruits were identified as the most relevant pathways for further entry of ASBVd into the EU. Avocado crops are cultivated in southern EU countries. Should the pest further enter and establish in the EU, impact on the production of avocado is expected. Phytosanitary measures are available to prevent entry and spread of the viroid in the EU. ASBVd fulfils the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.
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Ortolá B, Daròs JA. Viroids: Non-Coding Circular RNAs Able to Autonomously Replicate and Infect Higher Plants. BIOLOGY 2023; 12:biology12020172. [PMID: 36829451 PMCID: PMC9952643 DOI: 10.3390/biology12020172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
Viroids are a unique type of infectious agent, exclusively composed of a relatively small (246-430 nt), highly base-paired, circular, non-coding RNA. Despite the small size and non-coding nature, the more-than-thirty currently known viroid species infectious of higher plants are able to autonomously replicate and move systemically through the host, thereby inducing disease in some plants. After recalling viroid discovery back in the late 60s and early 70s of last century and discussing current hypotheses about their evolutionary origin, this article reviews our current knowledge about these peculiar infectious agents. We describe the highly base-paired viroid molecules that fold in rod-like or branched structures and viroid taxonomic classification in two families, Pospiviroidae and Avsunviroidae, likely gathering nuclear and chloroplastic viroids, respectively. We review current knowledge about viroid replication through RNA-to-RNA rolling-circle mechanisms in which host factors, notably RNA transporters, RNA polymerases, RNases, and RNA ligases, are involved. Systemic movement through the infected plant, plant-to-plant transmission and host range are also discussed. Finally, we focus on the mechanisms of viroid pathogenesis, in which RNA silencing has acquired remarkable importance, and also for the initiation of potential biotechnological applications of viroid molecules.
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Ayllón MA, Vainio EJ. Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle. Adv Virus Res 2023; 115:1-86. [PMID: 37173063 DOI: 10.1016/bs.aivir.2023.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.
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Affiliation(s)
- María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain; Departamento Biotecnología-Biología Vegetal, E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
| | - Eeva J Vainio
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Helsinki, Finland
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Dong K, Xu C, Kotta‐Loizou I, Jiang J, Lv R, Kong L, Li S, Hong N, Wang G, Coutts RHA, Xu W. Novel Viroid-Like RNAs Naturally Infect a Filamentous Fungus. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204308. [PMID: 36515275 PMCID: PMC9875651 DOI: 10.1002/advs.202204308] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/19/2022] [Indexed: 06/17/2023]
Abstract
To date, viroids have been found to naturally infect only plants, resulting in substantial losses for some crops. Whether viroids or viroid-like RNAs naturally infect non-plant hosts remains unknown. Here the existence of a set of exogenous, single-stranded circular RNAs, ranging in size from 157 to 450 nucleotides, isolated from the fungus Botryosphaeria dothidea and nominated B. dothidea RNAs (BdcRNAs) is reported. BdcRNAs replicate autonomously in the nucleus via a rolling-circle mechanism following a symmetric pathway. BdcRNA infection induces symptoms, because BdcRNAs can apparently modulate, to different degrees, specific biological traits (e.g., alter morphology, decrease growth rate, attenuate virulence, and increase or decrease tolerance to osmotic and oxidative stress) of the host fungus. Overall, BdcRNAs have genome characteristics similar to those of viroids and exhibit pathogenic effects on fungal hosts. It is proposed that these novel fungus infecting RNAs should be termed mycoviroids. BdcRNA(s) may be considered additional inhabitants at the frontier of life in terms of genomic complexity, and represent a new class of acellular entities endowed with regulatory functions, and novel epigenomic carriers of biological information.
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Affiliation(s)
- Kaili Dong
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Chuan Xu
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Ioly Kotta‐Loizou
- Department of Life SciencesFaculty of Natural SciencesImperial College LondonLondonSW7 2AZUK
- Department of ClinicalPharmaceutical and Biological ScienceSchool of Life and Medical SciencesUniversity of HertfordshireHatfieldAL10 9ABUK
| | - Jingjing Jiang
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Ruiying Lv
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Linghong Kong
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Shifang Li
- Environment and Plant Protection InstituteChinese Academy of Tropical Agricultural SciencesXueyuan Road, Longhua DistrictHaikouHainan571101P. R. China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193P. R. China
| | - Ni Hong
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Guoping Wang
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Robert H. A. Coutts
- Department of ClinicalPharmaceutical and Biological ScienceSchool of Life and Medical SciencesUniversity of HertfordshireHatfieldAL10 9ABUK
| | - Wenxing Xu
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
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Afanasenko OS, Khiutti AV, Mironenko NV, Lashina NM. Transmission of potato spindle tuber viroid between <i>Phytophthora infestans</i> and host plants. Vavilovskii Zhurnal Genet Selektsii 2022; 26:272-280. [PMID: 35774366 PMCID: PMC9167824 DOI: 10.18699/vjgb-22-34] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/03/2022] [Accepted: 02/03/2021] [Indexed: 12/27/2022] Open
Abstract
Potato spindle tuber viroid (PSTVd) is a naked, circular, single-stranded RNA (356–363 nucleotides in length) which lacks any protein-coding sequences. It is an economically important pathogen and is classified as a high-risk plant quarantine disease. Moreover, it is known that PSTVd is mechanically transmitted by vegetative plant propagation through infected pollen, and by aphids. The aim of this study is to determine the possibility of viroid transmission by potato pathogen Phytophthora infestans (Mont.) de Bary. PSTVd-infected (strain VP87) potato cultivars Gala, Colomba, and Riviera were inoculated with P. infestans isolate PiVZR18, and in 7 days, after the appearance of symptoms, re-isolation of P. infestans on rye agar was conducted. RT-PCR diagnostics of PSTVd in a mixture of mycelia and sporangia were positive after 14 days of cultivation on rye agar. The PSTVd-infected P. infestans isolate PiVZR18v+ was used to inoculate the healthy, viroid-free plants of potato cv. Gala and tomato cv. Zagadka. After 60 days, an amplification fragment of PSTVd was detected in the tissues of one plant of tomato cv. Zagadka by RT-PCR with the primer set P3/P4, indicating successful transmission of PSTVd by P. infestans isolate PiVZR18v+. This result was confirmed by sequencing of the RT-PCR amplicon with primers P3/P4. The partial sequence of this amplicon was identical (99.5 %) to PSTVd strain VP87. RT-PCR showed the possibility of viroid stability in a pure culture of P. infestans isolate PiVZR18v+ after three consecutive passages on rye agar. PSTVd was not detected after the eighth passage on rye agar in P. infestans subculture. These results are initial evidence of potato viroid PSTVd being bidirectionally transferred between P. infestans and host plants
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de la Peña M, Gago-Zachert S. A life of research on circular RNAs and ribozymes: towards the origin of viroids, deltaviruses and life. Virus Res 2022; 314:198757. [PMID: 35346751 DOI: 10.1016/j.virusres.2022.198757] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/14/2022] [Accepted: 03/24/2022] [Indexed: 12/31/2022]
Abstract
The first examples of circular RNAs (circRNAs) were reported in the '70s as a family of minimal infectious agents of flowering plants; the viroids and viral satellites of circRNA. In some cases, these small circular genomes encode self-cleaving RNA motifs or ribozymes, including an exceptional circRNA infecting not plants but humans: the Hepatitis Delta Virus. Autocatalytic ribozymes not only allowed to propose a common rolling-circle replication mechanism for all these subviral agents, but also a tentative link with the origin of life as molecular fossils of the so-called RNA world. Despite the weak biologic connection between angiosperm plants and the human liver, diverse scientists, and most notably Ricardo Flores, firmly supported an evolutionary relationship between plant viroids and human deltavirus agents. The tireless and inspiring work done by Ricardo's lab in the field of infectious circRNAs fuelled multiple hypotheses for the origin of these entities, allowing advances in other fields, from eukaryotic circRNAs to small ribozymes in genomes from all life kingdoms. The recent discovery of a plethora of viral-like circRNAs with ribozymes in disparate biological samples may finally allow us to connect plant and animal subviral agents, confirming again that Ricardo's eye for science was always a keen eye.
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Affiliation(s)
- Marcos de la Peña
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). C/ Ingeniero Fausto Elio s/n, 46022, Valencia, Spain.
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Section Microbial Biotechnology, Halle/Saale D-06120, Germany
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Hadidi A, Sun L, Randles JW. Modes of Viroid Transmission. Cells 2022; 11:cells11040719. [PMID: 35203368 PMCID: PMC8870041 DOI: 10.3390/cells11040719] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 12/23/2022] Open
Abstract
Studies on the ways in which viroids are transmitted are important for understanding their epidemiology and for developing effective control measures for viroid diseases. Viroids may be spread via vegetative propagules, mechanical damage, seed, pollen, or biological vectors. Vegetative propagation is the most prevalent mode of spread at the global, national and local level while further dissemination can readily occur by mechanical transmission through crop handling with viroid-contaminated hands or pruning and harvesting tools. The current knowledge of seed and pollen transmission of viroids in different crops is described. Biological vectors shown to transmit viroids include certain insects, parasitic plants, and goats. Under laboratory conditions, viroids were also shown to replicate in and be transmitted by phytopathogenic ascomycete fungi; therefore, fungi possibly serve as biological vectors of viroids in nature. The term “mycoviroids or fungal viroids” has been introduced in order to denote these viroids. Experimentally, known sequence variants of viroids can be transmitted as recombinant infectious cDNA clones or transcripts. In this review, we endeavor to provide a comprehensive overview of the modes of viroid transmission under both natural and experimental situations. A special focus is the key findings which can be applied to the control of viroid diseases.
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Affiliation(s)
- Ahmed Hadidi
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
- Correspondence:
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, China;
| | - John W. Randles
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA 5005, Australia;
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11
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Flores R, Navarro B, Serra P, Di Serio F. A Scenario for the Emergence of Protoviroids in the RNA World and for Their Further Evolution into Viroids and Viroid-Like RNAs by Modular Recombinations and Mutations. Virus Evol 2022; 8:veab107. [PMID: 35223083 PMCID: PMC8865084 DOI: 10.1093/ve/veab107] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/10/2021] [Accepted: 01/14/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Viroids are tiny, circular and non-coding RNAs that are able to replicate and systemically infect plants. The smallest known pathogens, they have been proposed to represent survivors from the RNA world that likely preceded the cellular world currently dominating life on the earth. Although the small, circular and compact nature of viroid genomes, some of which are also endowed with catalytic activity mediated by hammerhead ribozymes, support this proposal, the lack of feasible evolutionary routes and the identification of hammerhead ribozymes in a large number of DNA genomes of organisms along the tree of life has led some to question such a proposal. Here, we reassess the origin and subsequent evolution of viroids by complementing phylogenetic reconstructions with molecular data, including the primary and higher-order structure of the genomic RNAs, their replication and recombination mechanisms and selected biological information. Features of some viroid-like RNAs found in plants, animal, and possibly fungi are also considered. The resulting evolutionary scenario supports the emergence of protoviroids in the RNA world, mainly as replicative modules, followed by further increase in genome complexity based on module/domain shuffling and combination, and mutation. Such a modular evolutionary scenario would have facilitated the inclusion in the protoviroid genomes of complex RNA structures (or coding sequences, as in the case of hepatitis ∂ virus and delta-like agents), likely needed for their adaptation from the RNA world to a life based on cells, thus generating the ancestors of current infectious viroids and viroid-like RNAs. Other non-infectious viroid-like RNAs, such as retroviroid-like RNA elements and retrozymes, could also be derived from protoviroids if their reverse transcription and integration into viral or eukaryotic DNA, respectively, are considered as a possible key step in their evolution. Comparison of evidence supporting a general and modular evolutionary model for viroids and viroid-like RNAs with that favoring alternative scenarios provides reasonable reasons to keep alive the hypothesis that these small RNA pathogens may be relics of a precellular world.
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Affiliation(s)
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via Amendola 122/D, Bari 70126, Italy
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, Valencia 46022, Spain
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Abstract
Viroids are small, single-stranded, circular RNAs infecting plants. Composed of only a few hundred nucleotides and being unable to code for proteins, viroids represent the lowest level of complexity for an infectious agent, even below that of the smallest known viruses. Despite the relatively small size, viroids contain RNA structural elements embracing all the information needed to interact with host factors involved in their infectious cycle, thus providing models for studying structure-function relationships of RNA. Viroids are specifically targeted to nuclei (family Pospiviroidae) or chloroplasts (family Avsunviroidae), where replication based on rolling-circle mechanisms takes place. They move locally and systemically through plasmodesmata and phloem, respectively, and may elicit symptoms in the infected host, with pathogenic pathways linked to RNA silencing and other plant defense responses. In this review, recent advances in the dissection of the complex interplay between viroids and plants are presented, highlighting knowledge gaps and perspectives for future research. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Beatriz Navarro
- Institute for Sustainable Plant Protection, National Research Council of Italy; I-70126 Bari, Italy;
| | - Ricardo Flores
- Institute of Molecular and Cellular Biology of Plants (UPV-CSIC), Polytechnic University of Valencia, 46022 Valencia, Spain
| | - Francesco Di Serio
- Institute for Sustainable Plant Protection, National Research Council of Italy; I-70126 Bari, Italy;
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Reply to Serra et al.: Nucleotide substitutions in plant viroid genomes that multiply in phytopathogenic fungi. Proc Natl Acad Sci U S A 2020; 117:10129-10130. [PMID: 32317376 DOI: 10.1073/pnas.2001670117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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