1
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Wang Y, Shi Y, Li H, Chang J. Understanding Citrus Viroid Interactions: Experience and Prospects. Viruses 2024; 16:577. [PMID: 38675919 PMCID: PMC11053686 DOI: 10.3390/v16040577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Citrus is the natural host of at least eight viroid species, providing a natural platform for studying interactions among viroids. The latter manifests as antagonistic or synergistic phenomena. The antagonistic effect among citrus viroids intuitively leads to reduced symptoms caused by citrus viroids, while the synergistic effect leads to an increase in symptom severity. The interaction phenomenon is complex and interesting, and a deep understanding of the underlying mechanisms induced during this viroid interaction is of great significance for the prevention and control of viroid diseases. This paper summarizes the research progress of citrus viroids in recent years, focusing on the interaction phenomenon and analyzing their interaction mechanisms. It points out the core role of the host RNA silencing mechanism and viroid-derived siRNA (vd-siRNA), and provides suggestions for future research directions.
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Affiliation(s)
- Yafei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (Y.S.); (H.L.); (J.C.)
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2
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Dalakouras A, Koidou V, Papadopoulou K. DsRNA-based pesticides: Considerations for efficiency and risk assessment. Chemosphere 2024; 352:141530. [PMID: 38401868 DOI: 10.1016/j.chemosphere.2024.141530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/05/2024] [Accepted: 02/21/2024] [Indexed: 02/26/2024]
Abstract
In view of the ongoing climate change and the ever-growing world population, novel agricultural solutions are required to ensure sustainable food supply. Microbials, natural substances, semiochemicals and double stranded RNAs (dsRNAs) are all considered potential low risk pesticides. DsRNAs function at the molecular level, targeting specific regions of specific genes of specific organisms, provided that they share a minimal sequence complementarity of approximately 20 nucleotides. Thus, dsRNAs may offer a great alternative to conventional chemicals in environmentally friendly pest control strategies. Any low-risk pesticide needs to be efficient and exhibit low toxicological potential and low environmental persistence. Having said that, in the current review, the mode of dsRNA action is explored and the parameters that need to be taken into consideration for the development of efficient dsRNA-based pesticides are highlighted. Moreover, since dsRNAs mode of action differs from those of synthetic pesticides, custom-made risk assessment schemes may be required and thus, critical issues related to the risk assessment of dsRNA pesticides are discussed here.
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Affiliation(s)
| | - Venetia Koidou
- ELGO-DIMITRA, Institute of Industrial and Forage Crops, Larissa, Greece; University of Thessaly, Department of Biochemistry and Biotechnology, Larissa, Greece
| | - Kalliope Papadopoulou
- University of Thessaly, Department of Biochemistry and Biotechnology, Larissa, Greece
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3
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Qiu Y, Wang Y, Wu Y, Yang H, Yang M, Zhou C, Cao M. Effects of RNA silencing during antagonism between citrus exocortis viroid and citrus bark cracking viroid in Etrog citron (Citrus medica). Mol Plant Pathol 2024; 25:e13408. [PMID: 38041680 PMCID: PMC10788473 DOI: 10.1111/mpp.13408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 12/03/2023]
Abstract
Citrus exocortis viroid (CEVd) and citrus bark cracking viroid (CBCVd) are two important viroids that infect citrus plants and frequently occur as mixed infections in orchards. However, the mechanism of antagonism between the two viroids in mixed infections remains unclear. The CEVd/CBCVd-citron system and small RNA sequencing (sRNA-seq) were used to study the antagonism. When CBCVd was inoculated before CEVd, the CEVd titre was significantly reduced and the symptoms were attenuated. Viroid-derived sRNAs (vd-sRNAs) from CEVd and CBCVd were predominantly 21-nucleotide (nt) and 22-nt in length and had similar 5' base biases. Homologous sequences of the two viroids in the terminal right (TR) region are rich in vd-sRNAs, and the high frequency vd-sRNAs selected from the CBCVd TR region can be used to degrade the transcripts of CEVd in vivo directly. These results suggest that RNA silencing may play an important role in the antagonism of the two viroids, thus deepening our understanding of the molecular interaction of long noncoding RNAs in woody plants.
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Affiliation(s)
- Yuanjian Qiu
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Yafei Wang
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouChina
| | - Yujiao Wu
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Han Yang
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Mengxue Yang
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Changyong Zhou
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Mengji Cao
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
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4
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Márquez-Molins J, Villalba-Bermell P, Corell-Sierra J, Pallás V, Gomez G. Integrative time-scale and multi-omics analysis of host responses to viroid infection. Plant Cell Environ 2023. [PMID: 37378473 DOI: 10.1111/pce.14647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/18/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
Viroids are circular RNAs of minimal complexity compelled to subvert plant-regulatory networks to accomplish their infectious process. Studies focused on the response to viroid-infection have mostly addressed specific regulatory levels and considered specifics infection-times. Thus, much remains to be done to understand the temporal evolution and complex nature of viroid-host interactions. Here we present an integrative analysis of the temporal evolution of the genome-wide alterations in cucumber plants infected with hop stunt viroid (HSVd) by integrating differential host transcriptome, sRNAnome and methylome. Our results support that HSVd promotes the redesign of the cucumber regulatory-pathways predominantly affecting specific regulatory layers at different infection-phases. The initial response was characterised by a reconfiguration of the host-transcriptome by differential exon-usage, followed by a progressive transcriptional downregulation modulated by epigenetic changes. Regarding endogenous small RNAs, the alterations were limited and mainly occurred at the late stage. Significant host-alterations were predominantly related to the downregulation of transcripts involved in plant-defence mechanisms, the restriction of pathogen-movement and the systemic spreading of defence signals. We expect that these data constituting the first comprehensive temporal-map of the plant-regulatory alterations associated with HSVd infection could contribute to elucidate the molecular basis of the yet poorly known host-response to viroid-induced pathogenesis.
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Affiliation(s)
- Joan Márquez-Molins
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
- Department of Virologia Molecular y Evolutiva de Plantas, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Valencia, Spain
| | - Pascual Villalba-Bermell
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
| | - Julia Corell-Sierra
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
| | - Vicente Pallás
- Department of Virologia Molecular y Evolutiva de Plantas, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Valencia, Spain
| | - Gustavo Gomez
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
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5
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Ortolá B, Daròs JA. Viroids: Non-Coding Circular RNAs Able to Autonomously Replicate and Infect Higher Plants. Biology (Basel) 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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Di Serio F, Owens RA, Navarro B, Serra P, Martínez de Alba ÁE, Delgado S, Carbonell A, Gago-Zachert S. Role of RNA silencing in plant-viroid interactions and in viroid pathogenesis. Virus Res 2023; 323:198964. [PMID: 36223861 PMCID: PMC10194176 DOI: 10.1016/j.virusres.2022.198964] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Viroids are small, single-stranded, non-protein coding and circular RNAs able to infect host plants in the absence of any helper virus. They may elicit symptoms in their hosts, but the underlying molecular pathways are only partially known. Here we address the role of post-transcriptional RNA silencing in plant-viroid-interplay, with major emphasis on the involvement of this sequence-specific RNA degradation mechanism in both plant antiviroid defence and viroid pathogenesis. This review is a tribute to the memory of Dr. Ricardo Flores, who largely contributed to elucidate this and other molecular mechanisms involved in plant-viroid interactions.
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Affiliation(s)
- Francesco Di Serio
- Institute for Sustainable Plant Protection, National Research Council, Bari 70122, Italy.
| | - Robert A Owens
- Molecular Plant Pathology Laboratory, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Beatriz Navarro
- Institute for Sustainable Plant Protection, National Research Council, Bari 70122, Italy
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), Valencia 46022, Spain
| | - Ángel Emilio Martínez de Alba
- Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor 37185, Salamanca, Spain
| | - Sonia Delgado
- Instituto Agroforestal Mediterráneo (IAM-UPV), Camino de Vera, s/n 46022, Valencia, Spain
| | - Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), Valencia 46022, Spain
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
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7
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Marquez‐Molins J, Hernandez‐Azurdia AG, Urrutia‐Perez M, Pallas V, Gomez G. A circular RNA vector for targeted plant gene silencing based on an asymptomatic viroid. Plant J 2022; 112:284-293. [PMID: 35916236 PMCID: PMC9804161 DOI: 10.1111/tpj.15929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Gene silencing for functional studies in plants has been largely facilitated by manipulating viral genomes with inserts from host genes to trigger virus-induced gene silencing (VIGS) against the corresponding mRNAs. However, viral genomes encode multiple proteins and can disrupt plant homeostasis by interfering with endogenous cell mechanisms. To try to circumvent this functional limitation, we have developed a silencing method based on the minimal autonomously-infectious nucleic acids currently known: viroids, which lack proven coding capability. The genome of Eggplant latent viroid, an asymptomatic viroid, was manipulated with insertions ranging between 21 and 42 nucleotides. Our results show that, although larger insertions might be tolerated, the maintenance of the secondary structure appears to be critical for viroid genome stability. Remarkably, these modified ELVd molecules are able to induce systemic infection promoting the silencing of target genes in eggplant. Inspired by the design of artificial microRNAs, we have developed a simple and standardized procedure to generate stable insertions into the ELVd genome capable of silencing a specific target gene. Analogously to VIGS, we have termed our approach viroid-induced gene silencing, and demonstrate that it is a promising tool for dissecting gene functions in eggplant.
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Affiliation(s)
- Joan Marquez‐Molins
- Institute for Integrative Systems Biology (I2SysBio)Consejo Superior de Investigaciones Científicas (CSIC) ‐ Universitat de València (UV)Parc Científic, Cat. Agustín Escardino 946980PaternaSpain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones Científicas (CSIC) ‐ Universitat Politècnica de ValènciaCPI 8E, Av. de los Naranjos s/n46022ValenciaSpain
| | - Andrea Gabriela Hernandez‐Azurdia
- Institute for Integrative Systems Biology (I2SysBio)Consejo Superior de Investigaciones Científicas (CSIC) ‐ Universitat de València (UV)Parc Científic, Cat. Agustín Escardino 946980PaternaSpain
| | - María Urrutia‐Perez
- Institute for Integrative Systems Biology (I2SysBio)Consejo Superior de Investigaciones Científicas (CSIC) ‐ Universitat de València (UV)Parc Científic, Cat. Agustín Escardino 946980PaternaSpain
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones Científicas (CSIC) ‐ Universitat Politècnica de ValènciaCPI 8E, Av. de los Naranjos s/n46022ValenciaSpain
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio)Consejo Superior de Investigaciones Científicas (CSIC) ‐ Universitat de València (UV)Parc Científic, Cat. Agustín Escardino 946980PaternaSpain
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8
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Gómez G, Marquez-Molins J, Martinez G, Pallas V. Plant epigenome alterations: an emergent player in viroid-host interactions. Virus Res 2022; 318:198844. [DOI: 10.1016/j.virusres.2022.198844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/31/2022] [Accepted: 06/05/2022] [Indexed: 10/18/2022]
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9
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Carbonell A. RNAi tools for controlling viroid diseases. Virus Res 2022; 313:198729. [DOI: 10.1016/j.virusres.2022.198729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 12/01/2022]
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10
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Pallas V, Hernández C, Marcos JF, Daròs JA, Ambrós S, Navarro B, Navarro JA, Peña MDL, Gago-zachert S, Gas ME, Carbonell A, Lopez C, de Alba AE, Serio FD, Moreno P. In Memoriam of Ricardo Flores: The Career, Achievements, and Legacy of an inspirational plant virologist. Virus Res 2022. [DOI: 10.1016/j.virusres.2022.198718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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11
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Katsarou K, Kryovrysanaki N, Kalantidis K. Detection of Viroid RNA and vd-siRNA in N. benthamiana Plants: Northern Blot Analyses for Viroid and vd-siRNAs. Methods Mol Biol 2022; 2316:287-312. [PMID: 34845703 DOI: 10.1007/978-1-0716-1464-8_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Viroids are considered the most minimalistic group of pathogens. Despite their presumed inability to encode for proteins, viroids induce several diseases in plants of primary economic importance. The production of viroid derived siRNAs (vd-siRNAs) of 21-24 nt, accompanies viroid infections in plants and results from the activation of the RNA silencing mechanism and specifically the function of Dicer endonucleases. A comprehensive set of experiments for the study and thorough analysis of viroid-infected plants has been developed. Here we present a detailed experimental plan including optimized protocols for plant infection by agroinfiltration, RNA extraction, and northern blot hybridization for the detection of both viroid genomic RNA and vd-siRNAs.
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Affiliation(s)
- Konstantina Katsarou
- Biology Department, University of Crete, Heraklion, Greece
- IMBB/FoRTH, Heraklion, Greece
| | | | - Kriton Kalantidis
- Biology Department, University of Crete, Heraklion, Greece.
- IMBB/FoRTH, Heraklion, Greece.
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Vučurović A, Kutnjak D, Mehle N, Stanković I, Pecman A, Bulajić A, Krstić B, Ravnikar M. Detection of Four New Tomato Viruses in Serbia Using Post Hoc High-Throughput Sequencing Analysis of Samples From a Large-Scale Field Survey. Plant Dis 2021; 105:2325-2332. [PMID: 33761774 DOI: 10.1094/pdis-09-20-1915-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Tomato production worldwide is affected by numerous plant virus species. The early and accurate detection of viruses is a critical step for disease control. However, the simultaneous detection of the most known tomato viruses can be difficult because of the high number and diversity of tomato-infecting viruses. Here, we have identified four new viruses in Serbia by applying target-independent small RNA high-throughput sequencing (HTS). HTS was applied on pools of samples and separate samples, in total comprising 30 tomato samples that exhibited (severe) virus-like symptoms and were collected in Serbia during three annual surveys (2011 to 2013). These samples had previously tested negative for the presence of 16 tomato viruses using targeted detection methods. Three divergent complete genome sequences of Physostegia chlorotic mottled virus were obtained from different localities, indicating for the first time that this virus is widespread in Serbia and might represent an emergent viral pathogen of tomato. The tomato torrado virus was detected at one locality with devastating yield losses. The southern tomato virus was detected at two localities, and the spinach latent virus was detected at one locality. In addition, we detected the presence of one already-known virus in Serbia, the tomato spotted wilt orthotospovirus. All the HTS results were subsequently confirmed by targeted detection methods. In this study, the successful application of post hoc HTS testing of a limited number of pooled samples resulted in the discovery of new viruses. Thus, our results encourage the use of HTS in research and diagnostic laboratories, including laboratories that have limited resources to resolve disease etiology.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
- Institute of Phytomedicine, Department of Phytopathology, University of Belgrade-Faculty of Agriculture, 11080 Belgrade, Serbia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Ivana Stanković
- Institute of Phytomedicine, Department of Phytopathology, University of Belgrade-Faculty of Agriculture, 11080 Belgrade, Serbia
| | - Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Aleksandra Bulajić
- Institute of Phytomedicine, Department of Phytopathology, University of Belgrade-Faculty of Agriculture, 11080 Belgrade, Serbia
| | - Branka Krstić
- Institute of Phytomedicine, Department of Phytopathology, University of Belgrade-Faculty of Agriculture, 11080 Belgrade, Serbia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
- University of Nova Gorica, 5000 Nova Gorica, Slovenia
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Adkar-Purushothama CR, Iyer PS, Sano T, Perreault JP. sRNA Profiler: A User-Focused Interface for Small RNA Mapping and Profiling. Cells 2021; 10:cells10071771. [PMID: 34359940 PMCID: PMC8303536 DOI: 10.3390/cells10071771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022] Open
Abstract
Viroids are circular, highly structured, single-stranded, non-coding RNA pathogens known to infect and cause disease in several plant species. They are known to trigger the host plant’s RNA silencing machinery. The detection of viroid-derived small RNAs (vd-sRNA) in viroid-infected host plants opened a new avenue of study in host–viroid pathogenicity. Since then, several viroid research groups have studied the vd-sRNA retrieved from different host–viroid combinations. Such studies require the segregation of 21- to 24-nucleotide long small RNAs (sRNA) from a deep-sequencing databank, followed by separating the vd-sRNA from any sRNA within this group that showed sequence similarity with either the genomic or the antigenomic strands of the viroid. Such mapped vd-sRNAs are then profiled on both the viroid’s genomic and antigenomic strands for visualization. Although several commercial interfaces are currently available for this purpose, they are all programmed for linear RNA molecules. Hence, viroid researchers must develop a computer program that accommodates the sRNAs derived from the circular viroid genome. This is a laborious process, and consequently, it often creates a bottleneck for biologists. In order to overcome this constraint, and to help the research community in general, in this study, a python-based pattern matching interface was developed so as to be able to both profile and map sRNAs on a circular genome. A “matching tolerance” feature has been included in the program, thus permitting the mapping of the sRNAs derived from the quasi-species. Additionally, the “topology” feature allows the researcher to profile sRNA derived from both linear and circular RNA molecules. The efficiency of the program was tested using previously reported deep-sequencing data obtained from two independent studies. Clearly, this novel software should be a key tool with which to both evaluate the production of sRNA and to profile them on their target RNA species, irrespective of the topology of the target RNA molecule.
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Affiliation(s)
- Charith Raj Adkar-Purushothama
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 Rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada
- Correspondence: (C.R.A.-P.); (J.-P.P.)
| | - Pavithran Sridharan Iyer
- Département de Physique, Université de Sherbrooke, 2500 Boul. Université, Sherbrooke, QC J1K 2R1, Canada;
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan;
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 Rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada
- Correspondence: (C.R.A.-P.); (J.-P.P.)
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14
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Wassenegger M, Dalakouras A. Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants. Cells 2021; 10:1187. [PMID: 34067940 DOI: 10.3390/cells10051187] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
Viroids are plant pathogenic, circular, non-coding, single-stranded RNAs (ssRNAs). Members of the Pospiviroidae family replicate in the nucleus of plant cells through double-stranded RNA (dsRNA) intermediates, thus triggering the host’s RNA interference (RNAi) machinery. In plants, the two RNAi pillars are Post-Transcriptional Gene Silencing (PTGS) and RNA-directed DNA Methylation (RdDM), and the latter has the potential to trigger Transcriptional Gene Silencing (TGS). Over the last three decades, the employment of viroid-based systems has immensely contributed to our understanding of both of these RNAi facets. In this review, we highlight the role of Pospiviroidae in the discovery of RdDM, expound the gradual elucidation through the years of the diverse array of RdDM’s mechanistic details and propose a revised RdDM model based on the cumulative amount of evidence from viroid and non-viroid systems.
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15
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Navarro B, Gisel A, Serra P, Chiumenti M, Di Serio F, Flores R. Degradome Analysis of Tomato and Nicotiana benthamiana Plants Infected with Potato Spindle Tuber Viroid. Int J Mol Sci 2021; 22:3725. [PMID: 33918424 PMCID: PMC8038209 DOI: 10.3390/ijms22073725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022] Open
Abstract
Viroids are infectious non-coding RNAs that infect plants. During infection, viroid RNAs are targeted by Dicer-like proteins, generating viroid-derived small RNAs (vd-sRNAs) that can guide the sequence specific cleavage of cognate host mRNAs via an RNA silencing mechanism. To assess the involvement of these pathways in pathogenesis associated with nuclear-replicating viroids, high-throughput sequencing of sRNAs and degradome analysis were carried out on tomato and Nicotiana benthamiana plants infected by potato spindle tuber viroid (PSTVd). Both hosts develop similar stunting and leaf curling symptoms when infected by PSTVd, thus allowing comparative analyses. About one hundred tomato mRNAs potentially targeted for degradation by vd-sRNAs were initially identified. However, data from biological replicates and comparisons between mock and infected samples reduced the number of bona fide targets-i.e., those identified with high confidence in two infected biological replicates but not in the mock controls-to only eight mRNAs that encode proteins involved in development, transcription or defense. Somewhat surprisingly, results of RT-qPCR assays revealed that the accumulation of only four of these mRNAs was inhibited in the PSTVd-infected tomato. When these analyses were extended to mock inoculated and PSTVd-infected N. benthamiana plants, a completely different set of potential mRNA targets was identified. The failure to identify homologous mRNA(s) targeted by PSTVd-sRNA suggests that different pathways could be involved in the elicitation of similar symptoms in these two species. Moreover, no significant modifications in the accumulation of miRNAs and in the cleavage of their targeted mRNAs were detected in the infected tomato plants with respect to the mock controls. Taken together, these data suggest that stunting and leaf curling symptoms induced by PSTVd are elicited by a complex plant response involving multiple mechanisms, with RNA silencing being only one of the possible components.
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Affiliation(s)
- Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy; (B.N.); (M.C.)
| | - Andreas Gisel
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy;
- International Institute of Tropical Agriculture, Ibadan 200001, Nigeria
| | - Pedro Serra
- Istituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain; (P.S.); (R.F.)
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy; (B.N.); (M.C.)
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy; (B.N.); (M.C.)
| | - Ricardo Flores
- Istituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain; (P.S.); (R.F.)
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Venkataraman S, Badar U, Shoeb E, Hashim G, AbouHaidar M, Hefferon K. An Inside Look into Biological Miniatures: Molecular Mechanisms of Viroids. Int J Mol Sci 2021; 22:2795. [PMID: 33801996 PMCID: PMC8001946 DOI: 10.3390/ijms22062795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/17/2022] Open
Abstract
Viroids are tiny single-stranded circular RNA pathogens that infect plants. Viroids do not encode any proteins, yet cause an assortment of symptoms. The following review describes viroid classification, molecular biology and spread. The review also discusses viroid pathogenesis, host interactions and detection. The review concludes with a description of future prospects in viroid research.
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Affiliation(s)
| | | | | | | | | | - Kathleen Hefferon
- Cell and System Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; (S.V.); (U.B.); (E.S.); (G.H.); (M.A.)
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Flores R, Navarro B, Delgado S, Serra P, Di Serio F. Viroid pathogenesis: a critical appraisal of the role of RNA silencing in triggering the initial molecular lesion. FEMS Microbiol Rev 2021; 44:386-398. [PMID: 32379313 DOI: 10.1093/femsre/fuaa011] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 05/06/2020] [Indexed: 12/15/2022] Open
Abstract
The initial molecular lesions through which viroids, satellite RNAs and viruses trigger signal cascades resulting in plant diseases are hotly debated. Since viroids are circular non-protein-coding RNAs of ∼250-430 nucleotides, they appear very convenient to address this issue. Viroids are targeted by their host RNA silencing defense, generating viroid-derived small RNAs (vd-sRNAs) that are presumed to direct Argonaute (AGO) proteins to inactivate messenger RNAs, thus initiating disease. Here, we review the existing evidence. Viroid-induced symptoms reveal a distinction. Those attributed to vd-sRNAs from potato spindle tuber viroid and members of the family Pospiviroidae (replicating in the nucleus) are late, non-specific and systemic. In contrast, those attributed to vd-sRNAs from peach latent mosaic viroid (PLMVd) and other members of the family Avsunviroidae (replicating in plastids) are early, specific and local. Remarkably, leaf sectors expressing different PLMVd-induced chloroses accumulate viroid variants with specific pathogenic determinants. Some vd-sRNAs containing such determinant guide AGO1-mediated cleavage of mRNAs that code for proteins regulating chloroplast biogenesis/development. Therefore, the initial lesions and the expected phenotypes are connected by short signal cascades, hence supporting a cause-effect relationship. Intriguingly, one virus satellite RNA initiates disease through a similar mechanism, whereas in the Pospiviroidae and in plant viruses the situation remains uncertain.
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Affiliation(s)
- Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos s/n 46010, Valencia, Spain
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Via Amendola 122/D, 70126 Bari, Italy
| | - Sonia Delgado
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos s/n 46010, Valencia, Spain
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos s/n 46010, Valencia, Spain
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Via Amendola 122/D, 70126 Bari, Italy
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SANO T. Progress in 50 years of viroid research-Molecular structure, pathogenicity, and host adaptation. Proc Jpn Acad Ser B Phys Biol Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zhang Z, Xia C, Matsuda T, Taneda A, Murosaki F, Hou W, Owens RA, Li S, Sano T. Effects of Host-Adaptive Mutations on Hop Stunt Viroid Pathogenicity and Small RNA Biogenesis. Int J Mol Sci 2020; 21:ijms21197383. [PMID: 33036282 PMCID: PMC7582576 DOI: 10.3390/ijms21197383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/29/2020] [Accepted: 10/04/2020] [Indexed: 01/02/2023] Open
Abstract
Accidental transmission of hop stunt viroid (HSVd) from grapevine to hop has led to several epidemics of hop stunt disease with convergent evolution of HSVd-g(rape) into HSVd-h(op) containing five mutations. However, the biological function of these five mutations remains unknown. In this study, we compare the biological property of HSVd-g and HSVd-h by bioassay and analyze HSVd-specific small RNA (HSVd-sRNA) using high-throughput sequencing. The bioassay indicated an association of these five mutations with differences in infectivity, replication capacity, and pathogenicity between HSVd-g and HSVd-h, e.g., HSVd-g induced more severe symptoms than HSVd-h in cucumber. Site-directed mutagenesis of HSVd-g showed that the mutation at position 54 increased pathogenicity. HSVd-sRNA analysis of cucumber and hop plants infected with different HSVd variants showed that several sRNA species containing adaptive nucleotides were specifically down-regulated in plants infected with HSVd-h. Several HSVd-sRNAs containing adaptive mutations were predicted to target cucumber genes, but changes in the levels of these genes were not directly correlated with changes in symptom expression. Furthermore, expression levels of two other cucumber genes targeted by HSVd-RNAs, encoding ethylene-responsive transcription factor ERF011, and trihelix transcription factor GTL2, were altered by HSVd infection. The possible relationship between these two genes to HSVd pathogenicity is discussed.
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Affiliation(s)
- Zhixiang Zhang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (C.X.); (W.H.)
| | - Changjian Xia
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (C.X.); (W.H.)
| | - Takahiro Matsuda
- Plant Pathology Laboratory, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan; (T.M.); (F.M.)
| | - Akito Taneda
- Graduate School of Science and Technology, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan;
| | - Fumiko Murosaki
- Plant Pathology Laboratory, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan; (T.M.); (F.M.)
| | - Wanying Hou
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (C.X.); (W.H.)
| | - Robert A. Owens
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville, MD 20705, USA;
| | - Shifang Li
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (C.X.); (W.H.)
- Environment and Plant Protection Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (S.L.); (T.S.)
| | - Teruo Sano
- Plant Pathology Laboratory, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan; (T.M.); (F.M.)
- Correspondence: (S.L.); (T.S.)
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Kitabayashi S, Tsushima D, Adkar-Purushothama CR, Sano T. Identification and Molecular Mechanisms of Key Nucleotides Causing Attenuation in Pathogenicity of Dahlia Isolate of Potato Spindle Tuber Viroid. Int J Mol Sci 2020; 21:E7352. [PMID: 33027943 DOI: 10.3390/ijms21197352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/18/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022] Open
Abstract
While the potato spindle tuber viroid (PSTVd) variant, PSTVd-Dahlia (PSTVd-D or PSTVd-Dwt) induces very mild symptoms in tomato cultivar 'Rutgers', PSTVd-Intermediate (PSTVd-I or PSTVd-Iwt) induces severe symptoms. These two variants differ by nine nucleotides, of which six mutations are located in the terminal left (TL) to the pathogenicity (P) domains. To evaluate the importance of mutations located in the TL to the P domains, ten types of point mutants were created by swapping the nucleotides between the two viroid variants. Bioassay in tomato plants demonstrated that two mutants created on PSTVd-Iwt at positions 42 and 64 resulted in symptom attenuation. Phenotypic and RT-qPCR analysis revealed that mutation at position 42 of PSTVd-Iwt significantly reduced disease severity and accumulation of the viroid, whereas mutation at position 64 showed a significant reduction in stunting when compared to the PSTVd-Iwt infected plant. RT-qPCR analysis on pathogenesis-related protein 1b1 and chalcone synthase genes showed a direct correlation with symptom severity whereas the expansin genes were down-regulated irrespective of the symptom severity. These results indicate that the nucleotides at positions 42 and 64 are in concert with the ones at positions 43, 310, and 311/312, which determines the slower and stable accumulation of PSTVd-D without eliciting excessive host defense responses thus contributing in the attenuation of disease symptom.
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Naoi T, Kitabayashi S, Kasai A, Sugawara K, Adkar-Purushothama CR, Senda M, Hataya T, Sano T. Suppression of RNA-dependent RNA polymerase 6 in tomatoes allows potato spindle tuber viroid to invade basal part but not apical part including pluripotent stem cells of shoot apical meristem. PLoS One 2020; 15:e0236481. [PMID: 32716919 PMCID: PMC7384629 DOI: 10.1371/journal.pone.0236481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/06/2020] [Indexed: 01/29/2023] Open
Abstract
RNA-dependent RNA polymerase 6 (RDR6) is one of the key factors in plant defense responses and suppresses virus or viroid invasion into shoot apical meristem (SAM) in Nicotiana benthamiana. To evaluate the role of Solanum lycopersicum (Sl) RDR6 upon viroid infection, SlRDR6-suppressed (SlRDR6i) ‘Moneymaker’ tomatoes were generated by RNA interference and inoculated with intermediate or lethal strain of potato spindle tuber viroid (PSTVd). Suppression of SlRDR6 did not change disease symptoms of both PSTVd strains in ‘Moneymaker’ tomatoes. Analysis of PSTVd distribution in shoot apices by in situ hybridization revealed that both PSTVd strains similarly invade the basal part but not apical part including pluripotent stem cells of SAM in SlRDR6i plants at a low rate unlike a previous report in N. benthamiana. In addition, unexpectedly, amount of PSTVd accumulation was apparently lower in SlRDR6i plants than in control tomatoes transformed with empty cassette in early infection especially in the lethal strain. Meanwhile, SlRDR6 suppression did not affect the seed transmission rates of PSTVd. These results indicate that RDR6 generally suppresses PSTVd invasion into SAM in plants, while suppression of RDR6 does not necessarily elevate amount of PSTVd accumulation. Additionally, our results suggest that host factors such as RDR1 other than RDR6 may also be involved in the protection of SAM including pluripotent stem cells from PSTVd invasion and effective RNA silencing causing the decrease of PSTVd accumulation during early infection in tomato plants.
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Affiliation(s)
- Takashi Naoi
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Syoya Kitabayashi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Atsushi Kasai
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Kohei Sugawara
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Charith Raj Adkar-Purushothama
- Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Mineo Senda
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Tatsuji Hataya
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
- * E-mail: (TH); (TS)
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
- * E-mail: (TH); (TS)
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Adkar-Purushothama CR, Bolduc F, Bru P, Perreault JP. Insights Into Potato Spindle Tuber Viroid Quasi-Species From Infection to Disease. Front Microbiol 2020; 11:1235. [PMID: 32719659 PMCID: PMC7349936 DOI: 10.3389/fmicb.2020.01235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/14/2020] [Indexed: 12/31/2022] Open
Abstract
Viroids are non-coding RNA plant pathogens that are characterized by their possession of a high mutation level. Although the sequence heterogeneity in viroid infected plants is well understood, shifts in viroid population dynamics due to mutations over the course of infection remain poorly understood. In this study, the ten most abundant sequence variants of potato spindle tuber viroid RG1 (PSTVd) expressed at different time intervals in PSTVd infected tomato plants were identified by high-throughput sequencing. The sequence variants, forming a quasi-species, were subjected to both the identification of the regions favoring mutations and the effect of the mutations on viroid secondary structure and viroid derived small RNAs (vd-sRNA). At week 1 of PSTVd infection, 25% of the sequence variants were similar to the "master" sequence (i.e., the sequence used for inoculation). The frequency of the master sequence within the population increased to 70% at week 2 after PSTVd infection, and then stabilized for the rest of the disease cycle (i.e., weeks 3 and 4). While some sequence variants were abundant at week 1 after PSTVd infection, they tended to decrease in frequency over time. For example, the variants with insertions at positions 253 or 254, positions that could affect the Loop E as well as the metastable hairpin I structure that has been shown important during replication and viroid infectivity, resulted in decreased frequency. Data obtained by in silico analysis of the viroid derived small RNAs (vd-sRNA) was also analyzed. A few mutants had the potential of positively affecting the viroid's accumulation by inducing the RNA silencing of the host's defense related genes. Variants with mutations that could negatively affect viroid abundance were also identified because their derived vd-sRNA were no longer capable of targeting any host mRNA or of changing its target sequence from a host defense gene to some other non-important host gene. Together, these findings open avenues into understanding the biological role of sequence variants, this viroid's interaction with host components, stable and metastable structures generated by mutants during the course of infection, and the influence of sequence variants on stabilizing viroid population dynamics.
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Affiliation(s)
- Charith Raj Adkar-Purushothama
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - François Bolduc
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierrick Bru
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, QC, Canada
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Cottilli P, Belda-Palazón B, Adkar-Purushothama CR, Perreault JP, Schleiff E, Rodrigo I, Ferrando A, Lisón P. Citrus exocortis viroid causes ribosomal stress in tomato plants. Nucleic Acids Res 2019; 47:8649-8661. [PMID: 31392997 PMCID: PMC6895259 DOI: 10.1093/nar/gkz679] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/23/2019] [Accepted: 07/30/2019] [Indexed: 12/26/2022] Open
Abstract
Viroids are naked RNAs that do not code for any known protein and yet are able to infect plants causing severe diseases. Because of their RNA nature, many studies have focused on the involvement of viroids in RNA-mediated gene silencing as being their pathogenesis mechanism. Here, the alterations caused by the Citrus exocortis viroid (CEVd) on the tomato translation machinery were studied as a new aspect of viroid pathogenesis. The presence of viroids in the ribosomal fractions of infected tomato plants was detected. More precisely, CEVd and its derived viroid small RNAs were found to co-sediment with tomato ribosomes in vivo, and to provoke changes in the global polysome profiles, particularly in the 40S ribosomal subunit accumulation. Additionally, the viroid caused alterations in ribosome biogenesis in the infected tomato plants, affecting the 18S rRNA maturation process. A higher expression level of the ribosomal stress mediator NAC082 was also detected in the CEVd-infected tomato leaves. Both the alterations in the rRNA processing and the induction of NAC082 correlate with the degree of viroid symptomatology. Taken together, these results suggest that CEVd is responsible for defective ribosome biogenesis in tomato, thereby interfering with the translation machinery and, therefore, causing ribosomal stress.
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Affiliation(s)
- Patrick Cottilli
- Instituto de Biología Molecular y Celular de Plantas. Universitat Politècnica de València (UPV) - Consejo Superior de Investigaciones Científicas (CSIC). Ciudad Politécnica de la Innovación (CPI), Valencia 46022, Spain
| | - Borja Belda-Palazón
- Instituto de Biología Molecular y Celular de Plantas. Universitat Politècnica de València (UPV) - Consejo Superior de Investigaciones Científicas (CSIC). Ciudad Politécnica de la Innovación (CPI), Valencia 46022, Spain
| | - Charith Raj Adkar-Purushothama
- RNA Group, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Jean-Pierre Perreault
- RNA Group, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants & Buchmann Institute for Molecular Life Science, Goethe University; Frankfurt Institute for Advanced Studies; Frankfurt/Main 60438, Germany
| | - Ismael Rodrigo
- Instituto de Biología Molecular y Celular de Plantas. Universitat Politècnica de València (UPV) - Consejo Superior de Investigaciones Científicas (CSIC). Ciudad Politécnica de la Innovación (CPI), Valencia 46022, Spain
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas. Universitat Politècnica de València (UPV) - Consejo Superior de Investigaciones Científicas (CSIC). Ciudad Politécnica de la Innovación (CPI), Valencia 46022, Spain
| | - Purificación Lisón
- Instituto de Biología Molecular y Celular de Plantas. Universitat Politècnica de València (UPV) - Consejo Superior de Investigaciones Científicas (CSIC). Ciudad Politécnica de la Innovación (CPI), Valencia 46022, Spain
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Adkar-Purushothama CR, Perreault JP. Current overview on viroid-host interactions. Wiley Interdiscip Rev RNA 2019; 11:e1570. [PMID: 31642206 DOI: 10.1002/wrna.1570] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 01/03/2023]
Abstract
Viroids are one of the most enigmatic highly structured, circular, single-stranded RNA phytopathogens. Although they are not known to code for any peptide, viroids induce visible symptoms in susceptible host plants that resemble those associated with many plant viruses. It is known that viroids induce disease symptoms by direct interaction with host factors; however, the precise mechanism by which this occurs remains poorly understood. Studies on the host's responses to viroid infection, host susceptibility and nonhost resistance have been underway for several years, but much remains to be done in order to fully understand the complex nature of viroid-host interactions. Recent progress using molecular biology techniques combined with computational algorithms, in particular evidence of the role of viroid-derived small RNAs in the RNA silencing pathways of a disease network, has widened the knowledge of viroid pathogenicity. The complexity of viroid-host interactions has been revealed in the past decades to include, but not be limited to, the involvement of host factors, viroid structural complexity, and viroid-induced ribosomal stress, which is further boosted by the discovery of long noncoding RNAs (lncRNAs). In this review, the current understanding of the viroid-host interaction has been summarized with the goal of simplifying the complexity of viroid biology for future research. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Charith Raj Adkar-Purushothama
- MYM Nutraceuticals Inc, Vancouver, British Columbia, Canada.,RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada
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Takino H, Kitajima S, Hirano S, Oka M, Matsuura T, Ikeda Y, Kojima M, Takebayashi Y, Sakakibara H, Mino M. Global transcriptome analyses reveal that infection with chrysanthemum stunt viroid (CSVd) affects gene expression profile of chrysanthemum plants, but the genes involved in plant hormone metabolism and signaling may not be silencing target of CSVd-siRNAs. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.plgene.2019.100181] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Wang Y, Wu J, Qiu Y, Atta S, Zhou C, Cao M. Global Transcriptomic Analysis Reveals Insights into the Response of 'Etrog' Citron ( Citrus medica L.) to Citrus Exocortis Viroid Infection. Viruses 2019; 11:E453. [PMID: 31109003 DOI: 10.3390/v11050453] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/11/2019] [Accepted: 05/15/2019] [Indexed: 12/11/2022] Open
Abstract
Citrus exocortis viroid (CEVd) is the causal agent of citrus exocortis disease. We employed CEVd-infected ‘Etrog’ citron as a system to study the feedback regulation mechanism using transcriptome analysis in this study. Three months after CEVd infection, the transcriptome of fresh leaves was analyzed, and 1530 differentially expressed genes were detected. The replication of CEVd in citron induced upregulation of genes encoding key proteins that were involved in the RNA silencing pathway such as Dicer-like 2, RNA-dependent RNA polymerase 1, argonaute 2, argonaute 7, and silencing defective 3, as well as those genes encoding proteins that are related to basic defense responses. Many genes involved in secondary metabolite biosynthesis and chitinase activity were upregulated, whereas other genes related to cell wall and phytohormone signal transduction were downregulated. Moreover, genes encoding disease resistance proteins, pathogenicity-related proteins, and heat shock cognate 70 kDa proteins were also upregulated in response to CEVd infection. These results suggest that basic defense and RNA silencing mechanisms are activated by CEVd infection, and this information improves our understanding of the pathogenesis of viroids in woody plants.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Kryovrysanaki N, Alexiadis A, Grigoriadou AM, Katsarou K, Kalantidis K. SERRATE, a miRNA biogenesis factor, affects viroid infection in Nicotiana benthamiana and Nicotiana tabacum. Virology 2019; 528:164-175. [PMID: 30599275 DOI: 10.1016/j.virol.2018.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 12/15/2018] [Indexed: 12/14/2022]
Abstract
Viroids are plant infecting, non - coding RNA molecules of economic importance. Potato spindle tuber viroid (PSTVd), the type species of Pospiviroidae family, has been shown to be affected by specific RNA silencing pathways. Dicer like 1 (DCL1), a key player in micro RNA (miRNA) pathway has been previously linked with PSTVd infectivity. In this report we aim to further dissect the interaction between the miRNA pathway and Pospiviroid virulence. We mainly focused on the Zinc-finger protein SERRATE (SE) a co-factor of DCL1 and core component of miRNA pathway. We generated Nicotiana tabacum and Nicotiana benthamiana SE knock-down plants exhibiting considerable miRNA reduction and strong phenotypic abnormalities. PSTVd infection of SE suppressed plants resulted in a significant viroid reduction, especially at the initial infection stages. This positive correlation between SE levels and viroid infectivity underlines its role in PSTVd life cycle and reveals the importance of the miRNA pathway upon viroid infection.
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Affiliation(s)
- Nikoleta Kryovrysanaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, GR-7110 Heraklion, Crete, Greece; Department of Biology, University of Crete, Vassilika Vouton, GR-71409 Heraklion, Crete, Greece.
| | - Anastasios Alexiadis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, GR-7110 Heraklion, Crete, Greece; Department of Biology, University of Crete, Vassilika Vouton, GR-71409 Heraklion, Crete, Greece
| | - Alexandra M Grigoriadou
- Department of Biology, University of Crete, Vassilika Vouton, GR-71409 Heraklion, Crete, Greece
| | - Konstantina Katsarou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, GR-7110 Heraklion, Crete, Greece
| | - Kriton Kalantidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, GR-7110 Heraklion, Crete, Greece; Department of Biology, University of Crete, Vassilika Vouton, GR-71409 Heraklion, Crete, Greece.
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Matsushita Y, Yanagisawa H, Sano T. Vertical and Horizontal Transmission of Pospiviroids. Viruses 2018; 10:E706. [PMID: 30545048 DOI: 10.3390/v10120706] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 12/14/2022] Open
Abstract
Viroids are highly structured, single-stranded, non-protein-coding circular RNA pathogens. Some viroids are vertically transmitted through both viroid-infected ovule and pollen. For example, potato spindle tuber viroid, a species that belongs to Pospiviroidae family, is delivered to the embryo through the ovule or pollen during the development of reproductive tissues before embryogenesis. In addition, some of Pospiviroidae are also horizontally transmitted by pollen. Tomato planta macho viroid in pollen infects to the ovary from pollen tube during pollen tube elongation and eventually causes systemic infection, resulting in the establishment of horizontal transmission. Furthermore, fertilization is not required to accomplish the horizontal transmission. In this review, we will overview the recent research progress in vertical and horizontal transmission of viroids, mainly by focusing on histopathological studies, and also discuss the impact of seed transmission on viroid dissemination and seed health.
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Thibaut O, Claude B. Innate Immunity Activation and RNAi Interplay in Citrus Exocortis Viroid-Tomato Pathosystem. Viruses 2018; 10:E587. [PMID: 30373191 PMCID: PMC6266551 DOI: 10.3390/v10110587] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/18/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022] Open
Abstract
Although viroids are the smallest and simplest plant pathogens known, the molecular mechanisms underlying their pathogenesis remain unclear. To unravel these mechanisms, a dual approach was implemented consisting of in silico identification of potential tomato silencing targets of pospiviroids, and the experimental validation of these targets through the sequencing of small RNAs and RNA ends extracted from tomatoes infected with a severe isolate of Citrus exocortis viroid (CEVd). The generated RNA ends were also used to monitor the differentially-expressed genes. These analyses showed that when CEVd symptoms are well established: (i) CEVd are degraded by at least three Dicer-like (DCL) proteins and possibly by RNA-induced silencing complex (RISC), (ii) five different mRNAs are partially degraded through post-transcriptional gene silencing (PTGS), including argonaute 2a, which is further degraded in phasiRNAs, (iii) Dicer-like 2b and 2d are both upregulated and degraded in phasiRNAs, and (iv) CEVd infection induced a significant shift in gene expression allowing to explain the usual symptoms of pospiviroids on tomato and to demonstrate the constant activation of host innate immunity and systemic acquired resistance (SAR) by these pathogenic RNAs. Finally, based on in silico analysis, potential immunity receptor candidates of viroid-derived RNAs are suggested.
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Affiliation(s)
- Olivier Thibaut
- Life Sciences Department, Walloon agricultural research Centre, Rue de Liroux 4, 5030 Gembloux, Belgium.
- UCLouvain, Earth&Life Institute, Croix du Sud 2bte L7.05.03, 1348 Louvain-la-Neuve, Belgium.
| | - Bragard Claude
- UCLouvain, Earth&Life Institute, Croix du Sud 2bte L7.05.03, 1348 Louvain-la-Neuve, Belgium.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
Small RNAs (sRNA) are a significant group of gene expression regulators for multiple biological processes in eukaryotes. In plants, many sRNA silencing pathways produce extensive array of sRNAs with specialized roles. The evidence on record advocates for the functions of sRNAs during plant microbe interactions. Host sRNAs are reckoned as mandatory elements of plant defense. sRNAs involved in plant defense processes via different pathways include both short interfering RNA (siRNA) and microRNA (miRNA) that actively regulate immunity in response to pathogenic attack via tackling pathogen-associated molecular patterns (PAMPs) and other effectors. In response to pathogen attack, plants protect themselves with the help of sRNA-dependent immune systems. That sRNA-mediated plant defense responses play a role during infections is an established fact. However, the regulations of several sRNAs still need extensive research. In this review, we discussed the topical advancements and findings relevant to pathogen attack and plant defense mediated by sRNAs. We attempted to point out diverse sRNAs as key defenders in plant systems. It is hoped that sRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases.
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Affiliation(s)
- Waqar Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad 38040, Pakistan.
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Muhammad Qasim
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Liande Wang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Nabeshima T, Doi M, Hosokawa M. Comparative Analysis of Chrysanthemum Stunt Viroid Accumulation and Movement in Two Chrysanthemum ( Chrysanthemum morifolium) Cultivars with Differential Susceptibility to the Viroid Infection. Front Plant Sci 2017; 8:1940. [PMID: 29250083 PMCID: PMC5715398 DOI: 10.3389/fpls.2017.01940] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
Chrysanthemum stunt viroid (CSVd) was inoculated into two chrysanthemum (Chrysanthemum morifolium) cultivars, the CSVd-susceptible cultivar Piato and the CSVd-resistant cultivar Mari Kazaguruma. For CSVd inoculation, grafting and Agrobacterium-mediated inoculation were used. In grafting experiments, CSVd was detectable in Mari Kazaguruma after grafting onto infected Piato, but after removal of infected rootstocks, CSVd could not be detected in the uppermost leaves. In agroinfection experiments, CSVd systemic infection was observed in Piato but not in Mari Kazaguruma. However, agro-inoculated leaves of Mari Kazaguruma accumulated circular CSVd RNA to levels equivalent to those in Piato at 7 days post-inoculation. In situ detection of CSVd in inoculated leaves revealed that CSVd was absent in phloem of Mari Kazaguruma, while CSVd strongly localized to this site in Piato. We hypothesize that CSVd resistance in Mari Kazaguruma relates not to CSVd replication but to CSVd movement in leaves.
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Pecman A, Kutnjak D, Gutiérrez-Aguirre I, Adams I, Fox A, Boonham N, Ravnikar M. Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches. Front Microbiol 2017; 8:1998. [PMID: 29081770 PMCID: PMC5645528 DOI: 10.3389/fmicb.2017.01998] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/28/2017] [Indexed: 01/19/2023] Open
Abstract
Next generation sequencing (NGS) technologies are becoming routinely employed in different fields of virus research. Different sequencing platforms and sample preparation approaches, in the laboratories worldwide, contributed to a revolution in detection and discovery of plant viruses and viroids. In this work, we are presenting the comparison of two RNA sequence inputs (small RNAs vs. ribosomal RNA depleted total RNA) for the detection of plant viruses by Illumina sequencing. This comparison includes several viruses, which differ in genome organization and viroids from both known families. The results demonstrate the ability for detection and identification of a wide array of known plant viruses/viroids in the tested samples by both approaches. In general, yield of viral sequences was dependent on viral genome organization and the amount of viral reads in the data. A putative novel Cytorhabdovirus, discovered in this study, was only detected by analysing the data generated from ribosomal RNA depleted total RNA and not from the small RNA dataset, due to the low number of short reads in the latter. On the other hand, for the viruses/viroids under study, the results showed higher yields of viral sequences in small RNA pool for viroids and viruses with no RNA replicative intermediates (single stranded DNA viruses).
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Affiliation(s)
- Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ian Adams
- Fera Science Ltd., York, United Kingdom
| | | | - Neil Boonham
- Fera Science Ltd., York, United Kingdom
- Institute for Agri-Food Research and Innovation, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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Pokorn T, Radišek S, Javornik B, Štajner N, Jakše J. Development of hop transcriptome to support research into host-viroid interactions. PLoS One 2017; 12:e0184528. [PMID: 28886174 PMCID: PMC5590963 DOI: 10.1371/journal.pone.0184528] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/25/2017] [Indexed: 01/08/2023] Open
Abstract
Viroids, the smallest known pathogens, unable to encode any proteins, can cause severe diseases in their host plants. One of the proposed mechanisms of their pathogenicity includes silencing the host's genes via viroid-derived small RNAs, which are products of the host's immune response to the viroid's double stranded RNA. Humulus lupulus (hop) plants are hosts to several viroids; two of them, HLVd and CBCVd, are interesting models for studying host-viroid interactions, due to the symptomless infection of the former and severe stunting disease caused by the latter. To study these interactions, we constructed a deep hop NGS transcriptome based on 35 Gb paired-end sequencing data assembled into over 74 Mb of contigs. These transcripts were used for in-silico prediction of target transcripts of vd-sRNA of the two aforementioned viroids, using two different software tools. Prediction models revealed that 1062 and 1387 hop transcripts share nucleotide similarities with HLVd- and CBCVd-derived small RNAs, respectively, so they could be silenced in an RNA interference process. Furthermore, we selected 17 transcripts from 4 groups of targets involved in the metabolism of plant hormones, small RNA biogenesis, transcripts with high complementarity with viroid-derived small RNAs and transcripts targeted by CBCVd-derived small RNAs with high cellular concentrations. Their expression was monitored by reverse transcription quantitative PCR performed using leaf, flower and cone samples. Additionally, the expression of 5 pathogenesis related genes was monitored. Expression analysis confirmed high expression levels of four pathogenesis related genes in leaves of HLVd and CBCVd infected hop plants. Expression fluctuations were observed for the majority of targets, with possible evidence of downregulation of GATA transcription factor by CBCVd- and of linoleate 13S-lipoxygenase by HLVd-derived small RNAs. These results provide a deep transcriptome of hop and the first insights into complex viroid-hop plant interactions.
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Affiliation(s)
- Tine Pokorn
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sebastjan Radišek
- Department of Plant Protection, Slovenian Institute of Hop Research and Brewing, Žalec, Slovenia
| | - Branka Javornik
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nataša Štajner
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Jakše
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Flores R, Navarro B, Kovalskaya N, Hammond RW, Di Serio F. Engineering resistance against viroids. Curr Opin Virol 2017; 26:1-7. [PMID: 28738223 DOI: 10.1016/j.coviro.2017.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/28/2017] [Accepted: 07/05/2017] [Indexed: 01/19/2023]
Abstract
Viroids, the smallest infectious agents endowed with autonomous replication, are tiny single-stranded circular RNAs (∼250 to 400nt) without protein-coding ability that, despite their simplicity, infect and often cause disease in herbaceous and woody plants of economic relevance. To mitigate the resulting losses, several strategies have been developed, the most effective of which include: firstly, search for naturally resistant cultivars and breeding for resistance, secondly, induced resistance by pre-infection with mild strains, thirdly, ribonucleases targeting double-stranded RNAs and catalytic antibodies endowed with intrinsic ribonuclease activity, fourthly, antisense, and sense, RNAs, fifthly, catalytic antisense RNAs derived from hammerhead ribozymes, and sixthly, hairpin RNAs and artificial small RNAs for RNA interference. The mechanisms underpinning these strategies, most of which have been implemented via genetic transformation, together with their present results and future potential, are the subject of this review.
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Affiliation(s)
- Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia 46022, Spain.
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Natalia Kovalskaya
- Molecular Plant Pathology Laboratory, USDA-ARS-BARC, Beltsville, MD 20705, USA
| | - Rosemarie W Hammond
- Molecular Plant Pathology Laboratory, USDA-ARS-BARC, Beltsville, MD 20705, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
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Carbonell A, Daròs J. Artificial microRNAs and synthetic trans-acting small interfering RNAs interfere with viroid infection. Mol Plant Pathol 2017; 18:746-753. [PMID: 28026103 PMCID: PMC6638287 DOI: 10.1111/mpp.12529] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/14/2016] [Accepted: 12/17/2016] [Indexed: 05/18/2023]
Abstract
Artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) are two classes of artificial small RNAs (sRNAs) engineered to silence endogenous transcripts as well as viral RNAs in plants. Here, we explore the possibility of using amiRNAs and syn-tasiRNAs to specifically interfere with infections by viroids, small (250-400-nucleotide) non-coding circular RNAs with compact secondary structure infecting a wide range of plant species. The combined use of recent high-throughput methods for artificial sRNA construct generation and the Potato spindle tuber viroid (PSTVd)-Nicotiana benthamiana pathosystem allowed for the simple and time-effective screening of multiple artificial sRNAs targeting sites distributed along PSTVd RNAs of (+) or (-) polarity. The majority of amiRNAs were highly active in agroinfiltrated leaves when co-expressed with an infectious PSTVd transcript, as were syn-tasiRNAs derived from a construct including the five most effective amiRNA sequences. A comparative analysis showed that the effects of the most effective amiRNA and of the syn-tasiRNAs were similar in agroinfiltrated leaves, as well as in upper non-agroinfiltrated leaves in which PSTVd accumulation was significantly delayed. These results suggest that amiRNAs and syn-tasiRNAs can be used effectively to control viroid infections in plants.
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Affiliation(s)
- Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas‐Universidad Politécnica de Valencia)Valencia46022Spain
| | - José‐Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas‐Universidad Politécnica de Valencia)Valencia46022Spain
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Abstract
Biological processes such as defense mechanisms and microbial offense strategies are regulated through RNA induced interference in eukaryotes. Genetic mutations are modulated through biogenesis of small RNAs which directly impacts upon host development. Plant defense mechanisms are regulated and supported by a diversified group of small RNAs which are involved in streamlining several RNA interference pathways leading toward the initiation of pathogen gene silencing mechanisms. In the similar context, pathogens also utilize the support of small RNAs to launch their offensive attacks. Also there are strong evidences about the active involvement of these RNAs in symbiotic associations. Interestingly, small RNAs are not limited to the individuals in whom they are produced; they also show cross kingdom influences through variable interactions with other species thus leading toward the inter-organismic gene silencing. The phenomenon is understandable in the microbes which utilize these mechanisms to overcome host defense line. Understanding the mechanism of triggering host defense strategies can be a valuable step toward the generation of disease resistant host plants. We think that the cross kingdom trafficking of small RNA is an interesting insight that is needed to be explored for its vitality.
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Affiliation(s)
- Waqar Islam
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Saif Ul Islam
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Muhammad Qasim
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Liande Wang
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
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40
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Lv DQ, Liu SW, Zhao JH, Zhou BJ, Wang SP, Guo HS, Fang YY. Replication of a pathogenic non-coding RNA increases DNA methylation in plants associated with a bromodomain-containing viroid-binding protein. Sci Rep 2016; 6:35751. [PMID: 27767195 PMCID: PMC5073342 DOI: 10.1038/srep35751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/30/2016] [Indexed: 12/23/2022] Open
Abstract
Viroids are plant-pathogenic molecules made up of single-stranded circular non-coding RNAs. How replicating viroids interfere with host silencing remains largely unknown. In this study, we investigated the effects of a nuclear-replicating Potato spindle tuber viroid (PSTVd) on interference with plant RNA silencing. Using transient induction of silencing in GFP transgenic Nicotiana benthamiana plants (line 16c), we found that PSTVd replication accelerated GFP silencing and increased Virp1 mRNA, which encodes bromodomain-containing viroid-binding protein 1 and is required for PSTVd replication. DNA methylation was increased in the GFP transgene promoter of PSTVd-replicating plants, indicating involvement of transcriptional gene silencing. Consistently, accelerated GFP silencing and increased DNA methylation in the of GFP transgene promoter were detected in plants transiently expressing Virp1. Virp1 mRNA was also increased upon PSTVd infection in natural host potato plants. Reduced transcript levels of certain endogenous genes were also consistent with increases in DNA methylation in related gene promoters in PSTVd-infected potato plants. Together, our data demonstrate that PSTVd replication interferes with the nuclear silencing pathway in that host plant, and this is at least partially attributable to Virp1. This study provides new insights into the plant-viroid interaction on viroid pathogenicity by subverting the plant cell silencing machinery.
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MESH Headings
- DNA Methylation
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Green Fluorescent Proteins/genetics
- Plant Diseases/genetics
- Plant Diseases/virology
- Plant Proteins/metabolism
- Plants, Genetically Modified
- Promoter Regions, Genetic
- RNA Interference
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Untranslated/biosynthesis
- RNA, Viral/biosynthesis
- RNA-Binding Proteins/metabolism
- Solanum tuberosum/metabolism
- Solanum tuberosum/virology
- Nicotiana/genetics
- Nicotiana/metabolism
- Nicotiana/virology
- Viroids/genetics
- Viroids/pathogenicity
- Viroids/physiology
- Virus Replication/genetics
- Virus Replication/physiology
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Affiliation(s)
- Dian-Qiu Lv
- Virus-free Seedling Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, China
| | - Shang-Wu Liu
- Virus-free Seedling Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bang-Jun Zhou
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shao-Peng Wang
- Virus-free Seedling Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuan-Yuan Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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41
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Katsarou K, Mavrothalassiti E, Dermauw W, Van Leeuwen T, Kalantidis K. Combined Activity of DCL2 and DCL3 Is Crucial in the Defense against Potato Spindle Tuber Viroid. PLoS Pathog 2016; 12:e1005936. [PMID: 27732664 PMCID: PMC5061435 DOI: 10.1371/journal.ppat.1005936] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 09/14/2016] [Indexed: 12/22/2022] Open
Abstract
Viroids are self replicating non-coding RNAs capable of infecting a wide range of plant hosts. They do not encode any proteins, thus the mechanism by which they escape plant defenses remains unclear. RNAi silencing is a major defense mechanism against virus infections, with the four DCL proteins being principal components of the pathway. We have used Nicotiana benthamiana as a model to study Potato spindle tuber viroid infection. This viroid is a member of the Pospiviroidae family and replicates in the nucleus via an asymmetric rolling circle mechanism. We have created knock-down plants for all four DCL genes and their combinations. Previously, we showed that DCL4 has a positive effect on PSTVd infectivity since viroid levels drop when DCL4 is suppressed. Here, we show that PSTVd levels remain decreased throughout infection in DCL4 knockdown plants, and that simultaneous knockdown of DCL1, DCL2 or DCL3 together with DCL4 cannot reverse this effect. Through infection of plants suppressed for multiple DCLs we further show that a combined suppression of DCL2 and DCL3 has a major effect in succumbing plant antiviral defense. Based on our results, we further suggest that Pospoviroids may have evolved to be primarily processed by DCL4 as it seems to be a DCL protein with less detrimental effects on viroid infectivity. These findings pave the way to delineate the complexity of the relationship between viroids and plant RNA silencing response.
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Affiliation(s)
- Konstantina Katsarou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | | | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Belgium
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, The Netherlands
| | - Kriton Kalantidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
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42
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Palma-Martínez I, Guerrero-Mandujano A, Ruiz-Ruiz MJ, Hernández-Cortez C, Molina-López J, Bocanegra-García V, Castro-Escarpulli G. Active Shiga-Like Toxin Produced by Some Aeromonas spp., Isolated in Mexico City. Front Microbiol 2016; 7:1552. [PMID: 27757103 PMCID: PMC5048074 DOI: 10.3389/fmicb.2016.01552] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/16/2016] [Indexed: 12/29/2022] Open
Abstract
RNA silencing is a conserved mechanism that utilizes small RNAs (sRNAs) to direct the regulation of gene expression at the transcriptional or post-transcriptional level. Plants utilizing RNA silencing machinery to defend pathogen infection was first identified in plant–virus interaction and later was observed in distinct plant–pathogen interactions. RNA silencing is not only responsible for suppressing RNA accumulation and movement of virus and viroid, but also facilitates plant immune responses against bacterial, oomycete, and fungal infection. Interestingly, even the same plant sRNA can perform different roles when encounters with different pathogens. On the other side, pathogens counteract by generating sRNAs that directly regulate pathogen gene expression to increase virulence or target host genes to facilitate pathogen infection. Here, we summarize the current knowledge of the characterization and biogenesis of host- and pathogen-derived sRNAs, as well as the different RNA silencing machineries that plants utilize to defend against different pathogens. The functions of these sRNAs in defense and counter-defense and their mechanisms for regulation during different plant–pathogen interactions are also discussed.
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Affiliation(s)
- Ingrid Palma-Martínez
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Mexico City, Mexico
| | - Andrea Guerrero-Mandujano
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Mexico City, Mexico
| | - Manuel J Ruiz-Ruiz
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico NacionalMexico City, Mexico; Laboratorio Central de Análisis Clínicos Unidad Médica de Alta Especialidad Hospital de Pediatría "Silvestre Frenk Freund," Centro Médico Nacional Siglo XXIMexico City, Mexico
| | - Cecilia Hernández-Cortez
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico NacionalMexico City, Mexico; Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico NacionalMexico City, Mexico
| | - José Molina-López
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México Mexico City, Mexico
| | | | - Graciela Castro-Escarpulli
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Mexico City, Mexico
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Bagherian SAA, Hamzehzarghani H, Izadpanah K, Djavaheri M. Effects of potato spindle tuber viroid infection on tomato metabolic profile. J Plant Physiol 2016; 201:42-53. [PMID: 27393919 DOI: 10.1016/j.jplph.2016.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 05/25/2016] [Accepted: 06/21/2016] [Indexed: 06/06/2023]
Abstract
Viroids are the smallest plant pathogens consisting of a single stranded circular RNA molecule with a strong secondary structure, lacking a coat protein or any other proteins. The mechanism of viroid pathogenicity has remained unclear. Recent advances in instrumentation and data mining have made it possible to study the effects of various stresses on primary and secondary metabolisms. Here, we have utilized metabolic profiling approach to show how PSTVd infection alters tomato metabolic profile and the related pathways. Three terminal leaflets of third true leaf of 20-day-old tolerant tomato cultivar 'Moneymaker' were mechanically inoculated by PSTVd intermediate variant cDNAs and samples were taken from eighth leaf, 19days post-inoculation. Metabolites were extracted and analyzed by gas chromatography/mass spectrometry (GC/MS) and subjected to statistical data analysis. Affected pathways were identified by Pathway Tools program and were compared with microarray data previously reported. The study showed that 79 metabolites changed significantly and 23 pathways were identified in relation to these metabolites. Fourteen of these pathways were similar to those reported in other works. The altered pathways in PSTVd infected tomato leaves included, eight cutin and wax biosynthesis, seven pathways that produce defense related compounds, two energy generator pathways, three hormone biosynthesis pathways, two signal transduction pathways, and one nucleotide biosynthesis pathway. Our data on up/down-regulation of pathways supported the data produced on their corresponding gene(s) up/down-regulation.
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Affiliation(s)
| | | | | | - Mohammad Djavaheri
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz, Iran
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44
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Dalakouras A, Dadami E, Wassenegger M, Krczal G, Wassenegger M. RNA-directed DNA methylation efficiency depends on trigger and target sequence identity. Plant J 2016; 87:202-14. [PMID: 27121647 DOI: 10.1111/tpj.13193] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/06/2016] [Accepted: 04/06/2016] [Indexed: 06/05/2023]
Abstract
RNA-directed DNA methylation (RdDM) in plants has been extensively studied, but the RNA molecules guiding the RdDM machinery to their targets are still to be characterized. It is unclear whether these molecules require full complementarity with their target. In this study, we have generated Nicotiana tabacum (Nt) plants carrying an infectious tomato apical stunt viroid (TASVd) transgene (Nt-TASVd) and a non-infectious potato spindle tuber viroid (PSTVd) transgene (Nt-SB2). The two viroid sequences exhibit 81% sequence identity. Nt-TASVd and Nt-SB2 plants were genetically crossed. In the progeny plants (Nt-SB2/TASVd), deep sequencing of small RNAs (sRNAs) showed that TASVd infection was associated with the accumulation of abundant small interfering RNAs (siRNAs) that mapped along the entire TASVd but only partially matched the SB2 transgene. TASVd siRNAs efficiently targeted SB2 RNA for degradation, but no transitivity was detectable. Bisulfite sequencing in the Nt-SB2/TASVd plants revealed that the TASVd transgene was targeted for dense cis-RdDM along its entire sequence. In the same plants, the SB2 transgene was targeted for trans-RdDM. The SB2 methylation pattern, however, was weak and heterogeneous, pointing to a positive correlation between trigger-target sequence identity and RdDM efficiency. Importantly, trans-RdDM on SB2 was also detected at sites where no homologous siRNAs were detected. Our data indicate that RdDM efficiency depends on the trigger-target sequence identity, and is not restricted to siRNA occupancy. These findings support recent data suggesting that RNAs with sizes longer than 24 nt (>24-nt RNAs) trigger RdDM.
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Affiliation(s)
- Athanasios Dalakouras
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Neustadt, 67435, Germany
| | - Elena Dadami
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Neustadt, 67435, Germany
| | - Michèle Wassenegger
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Neustadt, 67435, Germany
| | - Gabi Krczal
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Neustadt, 67435, Germany
| | - Michael Wassenegger
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Neustadt, 67435, Germany
- Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, Heidelberg, 69120, Germany
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45
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Flores R, Owens RA, Taylor J. Pathogenesis by subviral agents: viroids and hepatitis delta virus. Curr Opin Virol 2016; 17:87-94. [PMID: 26897654 DOI: 10.1016/j.coviro.2016.01.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 01/21/2016] [Accepted: 01/29/2016] [Indexed: 12/18/2022]
Abstract
The viroids of plants are the simplest known infectious genetic elements. They have RNA genomes of up to 400 nucleotides in length and no protein encoding capacity. Hepatitis delta virus (HDV), an infectious agent found only in humans co-infected with hepatitis B virus (HBV), is just slightly more complex, with an RNA genome of about 1700 nucleotides, and the ability to express just one small protein. Viroid and HDV RNAs share several features that include circular structure, compact folding, and replication via a rolling-circle mechanism. Both agents were detected because of their obvious pathogenic effects. Their simplicity demands a greater need than conventional RNA or DNA viruses to redirect host components for facilitating their infectious cycle, a need that directly and indirectly incites pathogenic effects. The mechanisms by which these pathogenic effects are produced are the topic of this review. In this context, RNA silencing mediates certain aspects of viroid pathogenesis.
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Affiliation(s)
- Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia 46022, Spain.
| | - Robert A Owens
- Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD 20705, USA.
| | - John Taylor
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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46
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Tsushima D, Tsushima T, Sano T. Molecular dissection of a dahlia isolate of potato spindle tuber viroid inciting a mild symptoms in tomato. Virus Res 2015; 214:11-8. [PMID: 26732488 DOI: 10.1016/j.virusres.2015.12.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 12/19/2015] [Accepted: 12/21/2015] [Indexed: 12/30/2022]
Abstract
The dahlia isolate of potato spindle tuber viroid (PSTVd) accumulates slowly and induces mild disease symptoms in tomato (Solanum lycopersicum, cv. Rutgers) plants in contrast to the intermediate isolate (PSTVd-I). The dahlia isolate (PSTVd-D) differs from PSTVd-I in eight locations: 42 and 43 in the terminal left (TL); 64/65, 311, and 312/313 in the pathogenicity (P); 118 and 126 in the variable (V); and 201 in the terminal right (TR) domains. To investigate the molecular determinants in the PSTVd-D genome responsible for the attenuation of symptom severity and lower replication/accumulation in tomato plants, a series of mutants between PSTVd-D and PSTVd-I were constructed by focusing first on the mutations in the TL and P domains in the left-hand half of the molecule. Then, more detailed analysis was performed on the three mutations at positions 118, 126, and 201 in the V and TR domains. One of these mutations is located around the boundary of the right border of the RY-motif, a predicted recognition site of Virp1, a viroid-binding protein. Of 14 mutants (seven based on PSTVd-D and the other seven based on PSTVd-I) examined, 11 propagated stably and three lost infectivity. Mutations in the TL and P domains (42U, 43C, 310U/C, and U or UU insertion to 311/312 in PSTVd mild types) majorly influenced the expression of mild-like symptoms. In contrast, when each of the mutations at 118, 126, and 201 in the V and TR domains were exchanged independently, they minimally influenced systemic accumulation and symptom expression. Mutants based on PSTVd-D with PSTVd-I-type mutations at nucleotide positions 118, 126, and/or 201 showed mild symptoms similar to PSTVd-D, but their systemic accumulation was a little faster than PSTVd-D. In contrast, mutants based on PSTVd-I with PSTVd-D-type mutations at 118, 126, and/or 201 nucleotide positions showed severe symptoms similar to PSTVd-I, and the systemic accumulation was similar to or a little slower than PSTVd-I. The nucleotide at position 201 could be changed to U, G, or A, but C was not acceptable for replication. Because introduction of C at the position 201 can change the loop structure at the right boundary of the RY-motif's consensus sequence, the loop structure may influence recognition by Virp1.
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Affiliation(s)
- Daiki Tsushima
- Department of Bio-resources, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan; Union Graduate school of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Taro Tsushima
- Department of Bio-resources, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Teruo Sano
- Department of Bio-resources, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan.
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47
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Adkar-Purushothama CR, Kasai A, Sugawara K, Yamamoto H, Yamazaki Y, He YH, Takada N, Goto H, Shindo S, Harada T, Sano T. RNAi mediated inhibition of viroid infection in transgenic plants expressing viroid-specific small RNAs derived from various functional domains. Sci Rep 2015; 5:17949. [PMID: 26656294 DOI: 10.1038/srep17949] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 11/09/2015] [Indexed: 12/25/2022] Open
Abstract
Previous attempts to develop RNAi-mediated viroid-resistant transgenic plants using nearly full-length Potato spindle tuber viroid (PSTVd) hairpin RNA (hpRNA) were successful; however unusual phenotypes resembling viroid infection occurred. Therefore, in the present work, transgenic Nicotiana benthamiana lines expressing both partial and truncated versions of PSTVd hpRNA were developed. Specifically, seven partial or truncated versions of PSTVd sequences were selected according to the hotspots of both PSTVd-sRNAs and functional domains of the PSTVd. A total of 21 transgenic lines Nicotiana benthamiana were developed under the control of either the CaMV-35S or the CoYMV promoters. All of the transgenic lines established here were monitored for the induction of phenotypic changes, for PSTVd-sRNA expression and for the resistance against PSTVd infection. Additionally, this study demonstrates the use of inverted repeat construct sequences as short as 26- to -49 nucleotides for both the efficient expression of the PSTVd-sRNA and the inhibition of PSTVd infection.
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48
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Spanò R, Mascia T, Kormelink R, Gallitelli D. Grafting on a Non-Transgenic Tolerant Tomato Variety Confers Resistance to the Infection of a Sw5-Breaking Strain of Tomato spotted wilt virus via RNA Silencing. PLoS One 2015; 10:e0141319. [PMID: 26496695 DOI: 10.1371/journal.pone.0141319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA silencing controls endogenous gene expression and drives defensive reactions against invasive nucleic acids like viruses. In plants, it has been demonstrated that RNA silencing can be transmitted through grafting between scions and silenced rootstocks to attenuate virus and viroid accumulation in the scions. This has been obtained mostly using transgenic plants, which may be a drawback in current agriculture. In the present study, we examined the dynamics of infection of a resistance-breaking strain of Tomato spotted wilt virus (RB-TSWV) through the graft between an old Apulian (southern Italy) tomato variety, denoted Sl-Ma, used as a rootstock and commercial tomato varieties used as scions. In tests with non-grafted plants, Sl-Ma showed resistance to the RB-TSWV infection as viral RNA accumulated at low levels and plants recovered from disease symptoms by 21 days post inoculation. The resistance trait was transmitted to the otherwise highly susceptible tomato genotypes grafted onto Sl-Ma. The results from the analysis of small RNAs hallmark genes involved in RNA silencing and virus-induced gene silencing suggest that RNA silencing is involved in the resistance showed by Sl-Ma against RB-TSWV and in scions grafted on this rootstock. The results from self-grafted susceptible tomato varieties suggest also that RNA silencing is enhanced by the graft itself. We can foresee interesting practical implications of the approach described in this paper.
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49
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Spanò R, Mascia T, Kormelink R, Gallitelli D. Grafting on a Non-Transgenic Tolerant Tomato Variety Confers Resistance to the Infection of a Sw5-Breaking Strain of Tomato spotted wilt virus via RNA Silencing. PLoS One 2015; 10:e0141319. [PMID: 26496695 PMCID: PMC4619829 DOI: 10.1371/journal.pone.0141319] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 10/07/2015] [Indexed: 02/03/2023] Open
Abstract
RNA silencing controls endogenous gene expression and drives defensive reactions against invasive nucleic acids like viruses. In plants, it has been demonstrated that RNA silencing can be transmitted through grafting between scions and silenced rootstocks to attenuate virus and viroid accumulation in the scions. This has been obtained mostly using transgenic plants, which may be a drawback in current agriculture. In the present study, we examined the dynamics of infection of a resistance-breaking strain of Tomato spotted wilt virus (RB-TSWV) through the graft between an old Apulian (southern Italy) tomato variety, denoted Sl-Ma, used as a rootstock and commercial tomato varieties used as scions. In tests with non-grafted plants, Sl-Ma showed resistance to the RB-TSWV infection as viral RNA accumulated at low levels and plants recovered from disease symptoms by 21 days post inoculation. The resistance trait was transmitted to the otherwise highly susceptible tomato genotypes grafted onto Sl-Ma. The results from the analysis of small RNAs hallmark genes involved in RNA silencing and virus-induced gene silencing suggest that RNA silencing is involved in the resistance showed by Sl-Ma against RB-TSWV and in scions grafted on this rootstock. The results from self-grafted susceptible tomato varieties suggest also that RNA silencing is enhanced by the graft itself. We can foresee interesting practical implications of the approach described in this paper.
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Affiliation(s)
- Roberta Spanò
- Dipartimento di Scienze del Suolo della Pianta e Degli Alimenti, Università degli Studi di Bari Aldo Moro, Via Amendola 165/A, Bari, Italy
- Istituto di Virologia vegetale del CNR, Unità Operativa di Supporto di Bari, Via Amendola 165/A, Bari, Italy
| | - Tiziana Mascia
- Dipartimento di Scienze del Suolo della Pianta e Degli Alimenti, Università degli Studi di Bari Aldo Moro, Via Amendola 165/A, Bari, Italy
- Istituto di Virologia vegetale del CNR, Unità Operativa di Supporto di Bari, Via Amendola 165/A, Bari, Italy
- * E-mail:
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Donato Gallitelli
- Dipartimento di Scienze del Suolo della Pianta e Degli Alimenti, Università degli Studi di Bari Aldo Moro, Via Amendola 165/A, Bari, Italy
- Istituto di Virologia vegetale del CNR, Unità Operativa di Supporto di Bari, Via Amendola 165/A, Bari, Italy
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Gago-Zachert S. Viroids, infectious long non-coding RNAs with autonomous replication. Virus Res 2015; 212:12-24. [PMID: 26319312 DOI: 10.1016/j.virusres.2015.08.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/20/2015] [Accepted: 08/22/2015] [Indexed: 10/23/2022]
Abstract
Transcriptome deep-sequencing studies performed during the last years confirmed that the vast majority of the RNAs transcribed in higher organisms correspond to several types of non-coding RNAs including long non-coding RNAs (lncRNAs). The study of lncRNAs and the identification of their functions, is still an emerging field in plants but the characterization of some of them indicate that they play an important role in crucial regulatory processes like flowering regulation, and responses to abiotic stress and plant hormones. A second group of lncRNAs present in plants is formed by viroids, exogenous infectious subviral plant pathogens well known since many years. Viroids are composed of circular RNA genomes without protein-coding capacity and subvert enzymatic activities of their hosts to complete its own biological cycle. Different aspects of viroid biology and viroid-host interactions have been elucidated in the last years and some of them are the main topic of this review together with the analysis of the state-of-the-art about the growing field of endogenous lncRNAs in plants.
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Affiliation(s)
- Selma Gago-Zachert
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany.
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