1
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Roy S, Sengupta S. The RNA-DNA world and the emergence of DNA-encoded heritable traits. RNA Biol 2024; 21:1-9. [PMID: 38785360 PMCID: PMC11135857 DOI: 10.1080/15476286.2024.2355391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
The RNA world hypothesis confers a central role to RNA molecules in information encoding and catalysis. Even though evidence in support of this hypothesis has accumulated from both experiments and computational modelling, the transition from an RNA world to a world where heritable genetic information is encoded in DNA remains an open question. Recent experiments show that both RNA and DNA templates can extend complementary primers using free RNA/DNA nucleotides, either non-enzymatically or in the presence of a replicase ribozyme. Guided by these experiments, we analyse protocellular evolution with an expanded set of reaction pathways made possible through the presence of DNA nucleotides. By encapsulating these reactions inside three different types of protocellular compartments, each subject to distinct modes of selection, we show how protocells containing DNA-encoded replicases in low copy numbers and replicases in high copy numbers can dominate the population. This is facilitated by a reaction that leads to auto-catalytic synthesis of replicase ribozymes from DNA templates encoding the replicase after the chance emergence of a replicase through non-enzymatic reactions. Our work unveils a pathway for the transition from an RNA world to a mixed RNA-DNA world characterized by Darwinian evolution, where DNA sequences encode heritable phenotypes.
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Affiliation(s)
- Suvam Roy
- Department of Physical Sciences, Indian Institute of Science Education and ResearchKolkata, Mohanpur, West Bengal, India
| | - Supratim Sengupta
- Department of Physical Sciences, Indian Institute of Science Education and ResearchKolkata, Mohanpur, West Bengal, India
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2
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Chong LC, Lauber C. Viroid-like RNA-dependent RNA polymerase-encoding ambiviruses are abundant in complex fungi. Front Microbiol 2023; 14:1144003. [PMID: 37275138 PMCID: PMC10237039 DOI: 10.3389/fmicb.2023.1144003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/24/2023] [Indexed: 06/07/2023] Open
Abstract
Ambiviruses are hybrid infectious elements encoding the hallmark gene of RNA viruses, the RNA-dependent RNA polymerase, and self-cleaving RNA ribozymes found in many viroids. Ambiviruses are thought to be pathogens of fungi, although the majority of reported genomes have been identified in metatranscriptomes. Here, we present a comprehensive screen for ambiviruses in more than 46,500 fungal transcriptomes from the Sequence Read Archive (SRA). Our data-driven virus discovery approach identified more than 2,500 ambiviral sequences across the kingdom Fungi with a striking expansion in members of the phylum Basidiomycota representing the most complex fungal organisms. Our study unveils a large diversity of unknown ambiviruses with as little as 27% protein sequence identity to known members and sheds new light on the evolution of this distinct class of infectious agents with RNA genomes. No evidence for the presence of ambiviruses in human microbiomes was obtained from a comprehensive screen of respective metatranscriptomes available in the SRA.
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3
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Lee BD, Neri U, Roux S, Wolf YI, Camargo AP, Krupovic M, Simmonds P, Kyrpides N, Gophna U, Dolja VV, Koonin EV. Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs. Cell 2023; 186:646-661.e4. [PMID: 36696902 PMCID: PMC9911046 DOI: 10.1016/j.cell.2022.12.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/11/2022] [Accepted: 12/20/2022] [Indexed: 01/26/2023]
Abstract
Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters, a 5-fold increase compared to the previously identified viroid-like elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is far broader than currently known, and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes.
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Affiliation(s)
- Benjamin D Lee
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Uri Neri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Antonio Pedro Camargo
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015 Paris, France
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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4
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Ortolá B, Daròs JA. Viroids: Non-Coding Circular RNAs Able to Autonomously Replicate and Infect Higher Plants. BIOLOGY 2023; 12:biology12020172. [PMID: 36829451 PMCID: PMC9952643 DOI: 10.3390/biology12020172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
Viroids are a unique type of infectious agent, exclusively composed of a relatively small (246-430 nt), highly base-paired, circular, non-coding RNA. Despite the small size and non-coding nature, the more-than-thirty currently known viroid species infectious of higher plants are able to autonomously replicate and move systemically through the host, thereby inducing disease in some plants. After recalling viroid discovery back in the late 60s and early 70s of last century and discussing current hypotheses about their evolutionary origin, this article reviews our current knowledge about these peculiar infectious agents. We describe the highly base-paired viroid molecules that fold in rod-like or branched structures and viroid taxonomic classification in two families, Pospiviroidae and Avsunviroidae, likely gathering nuclear and chloroplastic viroids, respectively. We review current knowledge about viroid replication through RNA-to-RNA rolling-circle mechanisms in which host factors, notably RNA transporters, RNA polymerases, RNases, and RNA ligases, are involved. Systemic movement through the infected plant, plant-to-plant transmission and host range are also discussed. Finally, we focus on the mechanisms of viroid pathogenesis, in which RNA silencing has acquired remarkable importance, and also for the initiation of potential biotechnological applications of viroid molecules.
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5
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Roy S, Sengupta S. The Effect of Environment on the Evolution and Proliferation of Protocells of Increasing Complexity. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081227. [PMID: 36013406 PMCID: PMC9410160 DOI: 10.3390/life12081227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/01/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022]
Abstract
The formation, growth, division and proliferation of protocells containing RNA strands is an important step in ensuring the viability of a mixed RNA-lipid world. Experiments and computer simulations indicate that RNA encapsulated inside protocells can favor the protocell, promoting its growth while protecting the system from being over-run by selfish RNA sequences. Recent work has also shown that the rolling-circle replication mechanism can be harnessed to ensure the rapid growth of RNA strands and the probabilistic emergence and proliferation of protocells with functionally diverse ribozymes. Despite these advances in our understanding of a primordial RNA-lipid world, key questions remain about the ideal environment for the formation of protocells and its role in regulating the proliferation of functionally complex protocells. The hot spring hypothesis suggests that mineral-rich regions near hot springs, subject to dry-wet cycles, provide an ideal environment for the origin of primitive protocells. We develop a computational model to study protocellular evolution in such environments that are distinguished by the occurrence of three distinct phases, a wet phase, followed by a gel phase, and subsequently by a dry phase. We determine the conditions under which protocells containing multiple types of ribozymes can evolve and proliferate in such regions. We find that diffusion in the gel phase can inhibit the proliferation of complex protocells with the extent of inhibition being most significant when a small fraction of protocells is eliminated during environmental cycling. Our work clarifies how the environment can shape the evolution and proliferation of complex protocells.
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6
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Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators? LIFE (BASEL, SWITZERLAND) 2022; 12:life12010103. [PMID: 35054497 PMCID: PMC8781251 DOI: 10.3390/life12010103] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 01/09/2023]
Abstract
Viroids are a unique class of plant pathogens that consist of small circular RNA molecules, between 220 and 450 nucleotides in size. Viroids encode no proteins and are the smallest known infectious agents. Viroids replicate via the rolling circle mechanism, producing multimeric intermediates which are cleaved to unit length either by ribozymes formed from both polarities of the viroid genomic RNA or by coopted host RNAses. Many viroid-like small circular RNAs are satellites of plant RNA viruses. Ribozyviruses, represented by human hepatitis delta virus, are larger viroid-like circular RNAs that additionally encode the viral nucleocapsid protein. It has been proposed that viroids are direct descendants of primordial RNA replicons that were present in the hypothetical RNA world. We argue, however, that much later origin of viroids, possibly, from recently discovered mobile genetic elements known as retrozymes, is a far more parsimonious evolutionary scenario. Nevertheless, viroids and viroid-like circular RNAs are minimal replicators that are likely to be close to the theoretical lower limit of replicator size and arguably comprise the paradigm for replicator emergence. Thus, although viroid-like replicators are unlikely to be direct descendants of primordial RNA replicators, the study of the diversity and evolution of these ultimate genetic parasites can yield insights into the earliest stages of the evolution of life.
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7
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Lee BD, Neri U, Oh CJ, Simmonds P, Koonin EV. ViroidDB: a database of viroids and viroid-like circular RNAs. Nucleic Acids Res 2022; 50:D432-D438. [PMID: 34751403 PMCID: PMC8728161 DOI: 10.1093/nar/gkab974] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 12/31/2022] Open
Abstract
We introduce ViroidDB, a value-added database that attempts to collect all known viroid and viroid-like circular RNA sequences into a single resource. Spanning about 10 000 unique sequences, ViroidDB includes viroids, retroviroid-like elements, small circular satellite RNAs, ribozyviruses, and retrozymes. Each sequence's secondary structure, ribozyme content, and cluster membership are predicted via a custom pipeline optimized for handling circular RNAs. The data can be explored via a purpose-built user interface that features visualizations, multiple sequence alignments, and a portal for downloading bulk data. Users can browse the data by sequence type, taxon, or typo-tolerant search of metadata fields. The database is freely accessible at https://viroids.org.
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MESH Headings
- Base Sequence
- Databases, Nucleic Acid
- Internet
- Metadata
- Nucleic Acid Conformation
- Plant Diseases/virology
- Plants/virology
- RNA, Catalytic/chemistry
- RNA, Catalytic/classification
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Circular/chemistry
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA, Viral/chemistry
- RNA, Viral/classification
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Sequence Alignment
- Software
- Viroids/classification
- Viroids/genetics
- Viroids/metabolism
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Affiliation(s)
- Benjamin D Lee
- National Center for Biotechnology Information, National Library of Medicine, National Institutes Health, Bethesda, MD 20894, USA
- Nuffield Department of Medicine, University of Oxford, Oxford OX1, UK
| | - Uri Neri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX1, UK
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes Health, Bethesda, MD 20894, USA
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8
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Roy S, Sengupta S. Evolution towards increasing complexity through functional diversification in a protocell model of the RNA world. Proc Biol Sci 2021; 288:20212098. [PMID: 34784760 PMCID: PMC8596018 DOI: 10.1098/rspb.2021.2098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/21/2021] [Indexed: 11/12/2022] Open
Abstract
The encapsulation of genetic material inside compartments together with the creation and sustenance of functionally diverse internal components are likely to have been key steps in the formation of 'live', replicating protocells in an RNA world. Several experiments have shown that RNA encapsulated inside lipid vesicles can lead to vesicular growth and division through physical processes alone. Replication of RNA inside such vesicles can produce a large number of RNA strands. Yet, the impact of such replication processes on the emergence of the first ribozymes inside such protocells and on the subsequent evolution of the protocell population remains an open question. In this paper, we present a model for the evolution of protocells with functionally diverse ribozymes. Distinct ribozymes can be created with small probabilities during the error-prone RNA replication process via the rolling circle mechanism. We identify the conditions that can synergistically enhance the number of different ribozymes inside a protocell and allow functionally diverse protocells containing multiple ribozymes to dominate the population. Our work demonstrates the existence of an effective pathway towards increasing complexity of protocells that might have eventually led to the origin of life in an RNA world.
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Affiliation(s)
- Suvam Roy
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India
| | - Supratim Sengupta
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India
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9
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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] [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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10
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Matoušek J, Steinbachová L, Drábková LZ, Kocábek T, Potěšil D, Mishra AK, Honys D, Steger G. Elimination of Viroids from Tobacco Pollen Involves a Decrease in Propagation Rate and an Increase of the Degradation Processes. Int J Mol Sci 2020; 21:E3029. [PMID: 32344786 PMCID: PMC7216239 DOI: 10.3390/ijms21083029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/19/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
Some viroids-single-stranded, non-coding, circular RNA parasites of plants-are not transmissible through pollen to seeds and to next generation. We analyzed the cause for the elimination of apple fruit crinkle viroid (AFCVd) and citrus bark cracking viroid (CBCVd) from male gametophyte cells of Nicotiana tabacum by RNA deep sequencing and molecular methods using infected and transformed tobacco pollen tissues at different developmental stages. AFCVd was not transferable from pollen to seeds in reciprocal pollinations, due to a complete viroid eradication during the last steps of pollen development and fertilization. In pollen, the viroid replication pathway proceeds with detectable replication intermediates, but is dramatically depressed in comparison to leaves. Specific and unspecific viroid degradation with some preference for (-) chains occurred in pollen, as detected by analysis of viroid-derived small RNAs, by quantification of viroid levels and by detection of viroid degradation products forming "comets" on Northern blots. The decrease of viroid levels during pollen development correlated with mRNA accumulation of several RNA-degrading factors, such as AGO5 nuclease, DICER-like and TUDOR S-like nuclease. In addition, the functional status of pollen, as a tissue with high ribosome content, could play a role during suppression of AFCVd replication involving transcription factors IIIA and ribosomal protein L5.
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Affiliation(s)
- Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (T.K.); (A.K.M.)
| | - Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Lenka Záveská Drábková
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Tomáš Kocábek
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (T.K.); (A.K.M.)
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic;
| | - Ajay Kumar Mishra
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (T.K.); (A.K.M.)
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, D-40204 Düsseldorf, Germany
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11
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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] [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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12
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Cong L, Zhao Y, Pogue AI, Lukiw WJ. Role of microRNA (miRNA) and Viroids in Lethal Diseases of Plants and Animals. Potential Contribution to Human Neurodegenerative Disorders. BIOCHEMISTRY (MOSCOW) 2018; 83:1018-1029. [PMID: 30472940 DOI: 10.1134/s0006297918090031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Both plants and animals have adopted a common strategy of using ~18-25-nucleotide small non-coding RNAs (sncRNAs), known as microRNAs (miRNAs), to transmit DNA-based epigenetic information. miRNAs (i) shape the total transcriptional output of individual cells; (ii) regulate and fine-tune gene expression profiles of cell clusters, and (iii) modulate cell phenotype in response to environmental stimuli and stressors. These miRNAs, the smallest known carriers of gene-encoded post-transcriptional regulatory information, not only regulate cellular function in healthy cells but also act as important mediators in the development of plant and animal diseases. Plants possess their own specific miRNAs; at least 32 plant species have been found to carry infectious sncRNAs called viroids, whose mechanisms of generation and functions are strikingly similar to those of miRNAs. This review highlights recent remarkable and sometimes controversial findings in miRNA signaling in plants and animals. Special attention is given to the intriguing possibility that dietary miRNAs and/or sncRNAs can function as mobile epigenetic and/or evolutionary linkers between different species and contribute to both intra- and interkingdom signaling. Wherever possible, emphasis has been placed on the relevance of these miRNAs to the development of human neurodegenerative diseases, such as Alzheimer's disease. Based on the current available data, we suggest that such xeno-miRNAs may (i) contribute to the beneficial properties of medicinal plants, (ii) contribute to the negative properties of disease-causing or poisonous plants, and (iii) provide cross-species communication between kingdoms of living organisms involving multiple epigenetic and/or potentially pathogenic mechanisms associated with the onset and pathogenesis of various diseases.
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Affiliation(s)
- L Cong
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112-2272, USA.,Department of Neurology, Shengjing Hospital, China Medical University, Heping District, Shenyang, Liaoning Province, China
| | - Y Zhao
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112-2272, USA.,Department of Anatomy and Cell Biology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112-2272, USA
| | - A I Pogue
- Alchem Biotech Research, Toronto, ON M5S 1A8, Canada
| | - W J Lukiw
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112-2272, USA. .,Department Neurology, Louisiana State University School of Medicine, New Orleans, LA 70112-2272, USA.,Department Ophthalmology, Louisiana State University School of Medicine, New Orleans, LA 70112-2272, USA
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13
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Zhao Y, Cong L, Lukiw WJ. Plant and Animal microRNAs (miRNAs) and Their Potential for Inter-kingdom Communication. Cell Mol Neurobiol 2017; 38:133-140. [DOI: 10.1007/s10571-017-0547-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/31/2017] [Indexed: 12/22/2022]
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14
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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] [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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15
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Daròs JA. Eggplant latent viroid: a friendly experimental system in the family Avsunviroidae. MOLECULAR PLANT PATHOLOGY 2016; 17:1170-7. [PMID: 26696449 PMCID: PMC6638527 DOI: 10.1111/mpp.12358] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/24/2015] [Accepted: 12/10/2015] [Indexed: 05/22/2023]
Abstract
TAXONOMY Eggplant latent viroid (ELVd) is the only species of the genus Elaviroid (family Avsunviroidae). All the viroids in the family Avsunviroidae contain hammerhead ribozymes in the strands of both polarities, and are considered to replicate in the chloroplasts of infected cells. This family includes two other genera: Avsunviroid and Pelamoviroid. PHYSICAL PROPERTIES ELVd consists of a single-stranded, circular, non-coding RNA of 332-335 nucleotides that folds in a branched quasi-rod-like minimum free-energy conformation. RNAs of complementary polarity exist in infected cells and are considered to be replication intermediates. Plus (+) polarity is assigned arbitrarily to the strand that accumulates at a higher concentration in infected tissues. HOST: To date, ELVd has only been shown to infect eggplant (Solanum melongena L.), the species in which it was discovered. A very narrow host range seems to be a common property in members of the family Avsunviroidae. SYMPTOMS ELVd infections of eggplants are apparently symptomless. TRANSMISSION ELVd is transmitted mechanically and by seed. USEFUL WEBSITE http://subviral.med.uottawa.ca.
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Affiliation(s)
- José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia), Avenida de los Naranjos s/n, 46022, Valencia, Spain.
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16
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Köse K, Erol K, Özgür E, Uzun L, Denizli A. PolyAdenine cryogels for fast and effective RNA purification. Colloids Surf B Biointerfaces 2016; 146:678-86. [PMID: 27434154 DOI: 10.1016/j.colsurfb.2016.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 06/24/2016] [Accepted: 07/02/2016] [Indexed: 11/26/2022]
Abstract
Cryogels are used effectively for many diverse applications in a variety of fields. The isolation or purification of RNA, one of the potential utilizations for cryogels, is crucial due to their vital roles such as encoding, decoding, transcription and translation, and gene expression. RNA principally exists within every living thing, but their tendency to denaturation easily is still the most challenging issue. Herein, we aimed to develop adenine incorporated polymeric cryogels as an alternative sorbent for cost-friendly and fast RNA purification with high capacity. For this goal, we synthesized the polymerizable derivative of adenine called as adenine methacrylate (AdeM) through the substitution reaction between adenine and methacryloyl chloride. Then, 2-hydroxyethyl methacrylate (HEMA)-based cryogels were prepared in a partially frozen aqueous medium by copolymerization of monomers, AdeM, and HEMA. The cryogels were characterized by using Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), surface area measurements, thermogravimetric analysis (TGA), and swelling tests. RNA adsorption experiments were performed via batch system while varying different conditions including pH, initial RNA concentration, temperature, and interaction time. We achieved high RNA adsorption capacity of cryogels, with the swelling ratio around 510%, as 11.86mg/g. The cryogels might be reused at least five times without significant decrease in adsorption capacity.
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Affiliation(s)
- Kazım Köse
- Hacettepe University, Department of Chemistry, Ankara, Turkey; Hitit University, Scientific Technical Research and Application Center, Çorum, Turkey
| | - Kadir Erol
- Hacettepe University, Department of Chemistry, Ankara, Turkey; Hitit University, Department of Chemistry, Çorum, Turkey
| | - Erdoğan Özgür
- Hacettepe University, Department of Chemistry, Ankara, Turkey
| | - Lokman Uzun
- Hacettepe University, Department of Chemistry, Ankara, Turkey.
| | - Adil Denizli
- Hacettepe University, Department of Chemistry, Ankara, Turkey
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17
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Campillo-Balderas JA, Lazcano A, Becerra A. Viral Genome Size Distribution Does not Correlate with the Antiquity of the Host Lineages. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00143] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Avina-Padilla K, Martinez de la Vega O, Rivera-Bustamante R, Martinez-Soriano JP, Owens RA, Hammond RW, Vielle-Calzada JP. In silico prediction and validation of potential gene targets for pospiviroid-derived small RNAs during tomato infection. Gene 2015; 564:197-205. [DOI: 10.1016/j.gene.2015.03.076] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/13/2015] [Accepted: 03/24/2015] [Indexed: 12/31/2022]
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19
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Balique F, Lecoq H, Raoult D, Colson P. Can plant viruses cross the kingdom border and be pathogenic to humans? Viruses 2015; 7:2074-98. [PMID: 25903834 PMCID: PMC4411691 DOI: 10.3390/v7042074] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/20/2015] [Accepted: 04/06/2015] [Indexed: 12/30/2022] Open
Abstract
Phytoviruses are highly prevalent in plants worldwide, including vegetables and fruits. Humans, and more generally animals, are exposed daily to these viruses, among which several are extremely stable. It is currently accepted that a strict separation exists between plant and vertebrate viruses regarding their host range and pathogenicity, and plant viruses are believed to infect only plants. Accordingly, plant viruses are not considered to present potential pathogenicity to humans and other vertebrates. Notwithstanding these beliefs, there are many examples where phytoviruses circulate and propagate in insect vectors. Several issues are raised here that question if plant viruses might further cross the kingdom barrier to cause diseases in humans. Indeed, there is close relatedness between some plant and animal viruses, and almost identical gene repertoires. Moreover, plant viruses can be detected in non-human mammals and humans samples, and there are evidence of immune responses to plant viruses in invertebrates, non-human vertebrates and humans, and of the entry of plant viruses or their genomes into non-human mammal cells and bodies after experimental exposure. Overall, the question raised here is unresolved, and several data prompt the additional extensive study of the interactions between phytoviruses and non-human mammals and humans, and the potential of these viruses to cause diseases in humans.
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Affiliation(s)
- Fanny Balique
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes (URMITE) UM 63 CNRS 7278 IRD 3R198 INSERM U1095, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, 13385 Marseille cedex 05, France.
- Institut National de la Recherche Agronomique (INRA), UR 407, Pathologie Végétale, 84140 Montfavet, France.
| | - Hervé Lecoq
- Institut National de la Recherche Agronomique (INRA), UR 407, Pathologie Végétale, 84140 Montfavet, France.
| | - Didier Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes (URMITE) UM 63 CNRS 7278 IRD 3R198 INSERM U1095, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, 13385 Marseille cedex 05, France.
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance publique - hôpitaux de Marseille, 264 rue Saint-Pierre, 13385 Marseille cedex 05, France.
| | - Philippe Colson
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes (URMITE) UM 63 CNRS 7278 IRD 3R198 INSERM U1095, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, 13385 Marseille cedex 05, France.
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance publique - hôpitaux de Marseille, 264 rue Saint-Pierre, 13385 Marseille cedex 05, France.
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20
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Ribozyme-independent replication of a defective hepatitis D virus RNA derived from hepatitis B/D patients receiving antiviral therapy. Biochem Biophys Res Commun 2014; 450:616-21. [PMID: 24931669 DOI: 10.1016/j.bbrc.2014.06.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/05/2014] [Indexed: 11/20/2022]
Abstract
Novel hepatitis D virus (HDV) RNA mutants carrying large fragment deletions were identified in the serum samples of two hepatitis B/D patients receiving antiviral therapy. Sequence analysis revealed that the deleted regions encompassed both ribozyme domains. The mutant persisted in the serum samples for at least 2 and 10 months, respectively in the two patients, raising the question of whether such mutants could replicate in the absence of ribozyme domains. Thirty anti-HDV antibody-positive serum samples derived from 17 patients receiving antiviral therapy were submitted for RT-PCR detection of HDV RNA deletion mutants. Large fragment HDV RNA deletions were found in 4 patients. Of them, two had liver biopsy samples available. Northern blot analysis revealed high molecular weight HDV RNA replication intermediates, genomic and anti-genomic senses, in the liver tissues. Transfection of an in vitro transcribed HDV RNA deletion mutant (1.28 kb) into Huh7 and HepG2 cells also resulted in generation of high molecular weight HDV RNA species in the hepatoma cells (>6.5 kb) with secretion of a 6.5 kb HDV RNA species into the medium. In conclusion, we discovered novel large fragment deletion mutants of HDV RNA in hepatitis B/D patients receiving antiviral therapy. Such mutants did not contain ribozyme domains but could replicate in the liver cells to generate high molecular weight but not unit-length HDV RNA.
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21
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Yoon JY, Cho IS, Choi GS, Choi SK. Construction of Infectious cDNA Clone of a Chrysanthemum stunt viroid Korean Isolate. THE PLANT PATHOLOGY JOURNAL 2014; 30:68-74. [PMID: 25288987 PMCID: PMC4174829 DOI: 10.5423/ppj.oa.08.2013.0076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/30/2013] [Accepted: 09/30/2013] [Indexed: 06/02/2023]
Abstract
Chrysanthemum stunt viroid (CSVd), a noncoding infectious RNA molecule, causes seriously economic losses of chrysanthemum for 3 or 4 years after its first infection. Monomeric cDNA clones of CSVd isolate SK1 (CSVd-SK1) were constructed in the plasmids pGEM-T easy vector and pUC19 vector. Linear positive-sense transcripts synthesized in vitro from the full-length monomeric cDNA clones of CSVd-SK1 could infect systemically tomato seedlings and chrysanthemum plants, suggesting that the linear CSVd RNA transcribed from the cDNA clones could be replicated as efficiently as circular CSVd in host species. However, direct inoculation of plasmid cDNA clones containing full-length monomeric cDNA of CSVd-SK1 failed to infect tomato and chrysanthemum and linear negative-sense transcripts from the plasmid DNAs were not infectious in the two plant species. The cDNA sequences of progeny viroid in systemically infected tomato and chrysanthemum showed a few substitutions at a specific nucleotide position, but there were no deletions and insertions in the sequences of the CSVd progeny from tomato and chrysanthemum plants.
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Affiliation(s)
- Ju-Yeon Yoon
- Department of Horticulture and Landscape, Seoul Women’s University, Seoul 139-774, Korea
| | - In-Sook Cho
- Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA 441-440, Korea
| | - Gug-Seoun Choi
- Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA 441-440, Korea
| | - Seung-Kook Choi
- Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA 441-440, Korea
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22
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Eamens AL, Smith NA, Dennis ES, Wassenegger M, Wang MB. In Nicotiana species, an artificial microRNA corresponding to the virulence modulating region of Potato spindle tuber viroid directs RNA silencing of a soluble inorganic pyrophosphatase gene and the development of abnormal phenotypes. Virology 2014; 450-451:266-77. [PMID: 24503090 DOI: 10.1016/j.virol.2013.12.019] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 12/08/2013] [Accepted: 12/15/2013] [Indexed: 11/26/2022]
Abstract
Potato spindle tuber viroid (PSTVd) is a small non-protein-coding RNA pathogen that can induce disease symptoms in a variety of plant species. How PSTVd induces disease symptoms is a long standing question. It has been suggested that PSTVd-derived small RNAs (sRNAs) could direct RNA silencing of a targeted host gene(s) resulting in symptom development. To test this, we expressed PSTVd sequences as artificial microRNAs (amiRNAs) in Nicotiana tabacum and Nicotiana benthamiana. One amiRNA, amiR46 that corresponds to sequences within the PSTVd virulence modulating region (VMR), induced abnormal phenotypes in both Nicotiana species that closely resemble those displayed by PSTVd infected plants. In N. tabacum amiR46 plants, phenotype severity correlated with amiR46 accumulation and expression down-regulation of the bioinformatically-identified target gene, a Nicotiana soluble inorganic pyrophosphatase (siPPase). Taken together, our phenotypic and molecular analyses suggest that disease symptom development in Nicotiana species following PSTVd infection results from sRNA-directed RNA silencing of the host gene, siPPase.
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Affiliation(s)
- Andrew L Eamens
- CSIRO Plant Industry, Clunies Ross Street, Canberra, ACT 2601, Australia
| | - Neil A Smith
- CSIRO Plant Industry, Clunies Ross Street, Canberra, ACT 2601, Australia
| | - Elizabeth S Dennis
- CSIRO Plant Industry, Clunies Ross Street, Canberra, ACT 2601, Australia
| | - Michael Wassenegger
- RLP AgroScience GmbH, AIPlanta-Institute for Plant Research, Neustadt, Germany; Centre for Organisational Studies (COS) Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Ming-Bo Wang
- CSIRO Plant Industry, Clunies Ross Street, Canberra, ACT 2601, Australia.
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23
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Ivica NA, Obermayer B, Campbell GW, Rajamani S, Gerland U, Chen IA. The Paradox of Dual Roles in the RNA World: Resolving the Conflict Between Stable Folding and Templating Ability. J Mol Evol 2013; 77:55-63. [DOI: 10.1007/s00239-013-9584-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 09/12/2013] [Indexed: 10/26/2022]
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24
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Moelling K. What contemporary viruses tell us about evolution: a personal view. Arch Virol 2013; 158:1833-48. [PMID: 23568292 PMCID: PMC3755228 DOI: 10.1007/s00705-013-1679-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 02/14/2013] [Indexed: 12/11/2022]
Abstract
Recent advances in information about viruses have revealed novel and surprising properties such as viral sequences in the genomes of various organisms, unexpected amounts of viruses and phages in the biosphere, and the existence of giant viruses mimicking bacteria. Viruses helped in building genomes and are driving evolution. Viruses and bacteria belong to the human body and our environment as a well-balanced ecosystem. Only in unbalanced situations do viruses cause infectious diseases or cancer. In this article, I speculate about the role of viruses during evolution based on knowledge of contemporary viruses. Are viruses our oldest ancestors?
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Affiliation(s)
- Karin Moelling
- Max Planck Institute for Molecular Genetics, Ihnestr 63-73, 14195, Berlin, Germany.
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25
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El-Murr N, Maurel MC, Rihova M, Vergne J, Hervé G, Kato M, Kawamura K. Behavior of a hammerhead ribozyme in aqueous solution at medium to high temperatures. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2012; 99:731-8. [PMID: 22915317 DOI: 10.1007/s00114-012-0954-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/17/2012] [Accepted: 07/19/2012] [Indexed: 11/28/2022]
Abstract
The "RNA world" hypothesis proposes that--early in the evolution of life--RNA molecules played important roles both in information storage and in enzymatic functions. However, this hypothesis seems to be inconsistent with the concept that life may have emerged under hydrothermal conditions since RNA molecules are considered to be labile under such extreme conditions. Presently, the possibility that the last common ancestor of the present organisms was a hyperthermophilic organism which is important to support the hypothesis of the hydrothermal origin of life has been subject of strong discussions. Consequently, it is of importance to study the behavior of RNA molecules under hydrothermal conditions from the viewpoints of stability, catalytic functions, and storage of genetic information of RNA molecules and determination of the upper limit of temperature where life could have emerged. In the present work, self-cleavage of a natural hammerhead ribozyme was examined at temperatures 10-200 °C. Self-cleavage was investigated in the presence of Mg(2+), which facilitates and accelerates this reaction. Self-cleavage of the hammerhead ribozyme was clearly observed at temperatures up to 60 °C, but at higher temperatures self-cleavage occurs together with hydrolysis and with increasing temperature hydrolysis becomes dominant. The influence of the amount of Mg(2+) on the reaction rate was also investigated. In addition, we discovered that the reaction proceeds in the presence of high concentrations of monovalent cations (Na(+) or K(+)), although very slowly. Furthermore, at high temperatures (above 60 °C), monovalent cations protect the ribozyme against degradation.
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Affiliation(s)
- Nizar El-Murr
- ER12, ANBioPhy, Fonctions et Interactions des Acides Nucléiques, UPMC Univ Paris 6, 75005, Paris, France
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26
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Gómez G, Pallas V. Studies on subcellular compartmentalization of plant pathogenic noncoding RNAs give new insights into the intracellular RNA-traffic mechanisms. PLANT PHYSIOLOGY 2012; 159:558-64. [PMID: 22474218 PMCID: PMC3375924 DOI: 10.1104/pp.112.195214] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 04/02/2012] [Indexed: 05/22/2023]
MESH Headings
- 5' Untranslated Regions
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Chloroplasts/genetics
- Chloroplasts/metabolism
- Chromosomes, Plant/genetics
- Chromosomes, Plant/metabolism
- Cloning, Molecular
- Cytoplasm/genetics
- Cytoplasm/metabolism
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- Genes, Reporter
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- Physical Chromosome Mapping
- Plant Diseases/virology
- Plant Viruses/genetics
- Plant Viruses/metabolism
- Plant Viruses/pathogenicity
- RNA Stability
- RNA Transport
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Signal Transduction
- Nicotiana/genetics
- Nicotiana/metabolism
- Nicotiana/virology
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Affiliation(s)
- Gustavo Gómez
- Department of Molecular and Evolutionary Plant Virology, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Vicente Pallas
- Department of Molecular and Evolutionary Plant Virology, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain
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27
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Abstract
Viroids are the smallest autonomous infectious nucleic acids known today. They are non-coding, unencapsidated, circular RNAs with sizes ranging from 250 to 400 nucleotides and infect certain plants. These RNAs are transcribed by rolling-circle mechanisms in the plant host's nuclei (Pospiviroidae) or chloroplasts (Avsunviroidae). Since viroids lack any open reading frame, their pathogenicity has for a long time been a conundrum. Recent findings, however, show that viroid infection is associated with the appearance of viroid-specific small RNA (vsRNA). These have sizes similar to endogenous small interfering RNA and microRNA and thus might alter the normal gene expression in the host plant. In this review we will summarize the current knowledge on vsRNA and discuss the current hypotheses how they connect to the induced symptoms, which vary dramatically, depending on both the plant cultivar and the viroid strain.
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Affiliation(s)
- Christian Hammann
- Heisenberg Research Group Ribogenetics, Technical University of Darmstadt, Darmstadt, Germany.
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28
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Molina-Serrano D, Marqués J, Nohales MÁ, Flores R, Daròs JA. A chloroplastic RNA ligase activity analogous to the bacterial and archaeal 2´-5' RNA ligase. RNA Biol 2012; 9:326-33. [PMID: 22336712 DOI: 10.4161/rna.19218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Bacteria and archaea contain a 2'-5' RNA ligase that seals in vitro 2',3'-cyclic phosphodiester and 5'-hydroxyl RNA termini, generating a 2',5'-phosphodiester bond. In our search for an RNA ligase able to circularize the monomeric linear replication intermediates of viroids belonging to the family Avsunviroidae, which replicate in the chloroplast, we have identified in spinach (Spinacea oleracea L.) chloroplasts a new RNA ligase activity whose properties resemble those of the bacterial and archaeal 2'-5' RNA ligase. The spinach chloroplastic RNA ligase recognizes the 5'-hydroxyl and 2',3'-cyclic phosphodiester termini of Avocado sunblotch viroid and Eggplant latent viroid RNAs produced by hammerhead-mediated self-cleavage, yielding circular products linked through an atypical, most likely 2',5'-phosphodiester, bond. The enzyme neither requires divalent cations as cofactors, nor NTPs as substrate. The reaction apparently reaches equilibrium at a low ratio between the final circular product and the linear initial substrate. Even if its involvement in viroid replication seems unlikely, the identification of a 2'-5' RNA ligase activity in higher plant chloroplasts, with properties very similar to an analogous enzyme widely distributed in bacterial and archaeal proteomes, is intriguing and suggests an important biological role so far unknown.
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Affiliation(s)
- Diego Molina-Serrano
- Instituto de Biología Molecular y Celular de Plantas-Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Avenida de los Naranjos, Valencia, Spain
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29
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30
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Yazarlou A, Jafarpour B, Tarighi S, Habili N, Randles JW. New Iranian and Australian peach latent mosaic viroid variants and evidence for rapid sequence evolution. Arch Virol 2011; 157:343-7. [PMID: 22075917 DOI: 10.1007/s00705-011-1156-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 10/19/2011] [Indexed: 11/26/2022]
Abstract
Peach latent mosaic viroid isolates from peach and plum in Iran have been compared with an Australian isolate from nectarine. Thirteen sequence variants 336-338 nt in size were obtained. All variants clustered phylogenetically with variants reported from several hosts and countries. A total nucleic acid extract, a slightly longer than full-length RT-PCR amplicon, and a recombinant plasmid clone from the Australian isolate were all infectious to, and symptomatic in, mechanically inoculated peach seedlings. The infectious clone generated two progeny viroid molecules, which each showed 10 different mutations compared with the parent clone inoculated 30 days previously.
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Affiliation(s)
- Arezou Yazarlou
- Department of Plant Pathology, Ferdowsi University of Mashhad, Mashhad, Iran.
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31
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Acosta-Leal R, Duffy S, Xiong Z, Hammond RW, Elena SF. Advances in plant virus evolution: translating evolutionary insights into better disease management. PHYTOPATHOLOGY 2011; 101:1136-48. [PMID: 21554186 DOI: 10.1094/phyto-01-11-0017] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recent studies in plant virus evolution are revealing that genetic structure and behavior of virus and viroid populations can explain important pathogenic properties of these agents, such as host resistance breakdown, disease severity, and host shifting, among others. Genetic variation is essential for the survival of organisms. The exploration of how these subcellular parasites generate and maintain a certain frequency of mutations at the intra- and inter-host levels is revealing novel molecular virus-plant interactions. They emphasize the role of host environment in the dynamic genetic composition of virus populations. Functional genomics has identified host factors that are transcriptionally altered after virus infections. The analyses of these data by means of systems biology approaches are uncovering critical plant genes specifically targeted by viruses during host adaptation. Also, a next-generation resequencing approach of a whole virus genome is opening new avenues to study virus recombination and the relationships between intra-host virus composition and pathogenesis. Altogether, the analyzed data indicate that systematic disruption of some specific parameters of evolving virus populations could lead to more efficient ways of disease prevention, eradication, or tolerable virus-plant coexistence.
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32
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Wang Y, Shibuya M, Taneda A, Kurauchi T, Senda M, Owens RA, Sano T. Accumulation of Potato spindle tuber viroid-specific small RNAs is accompanied by specific changes in gene expression in two tomato cultivars. Virology 2011; 413:72-83. [PMID: 21353278 DOI: 10.1016/j.virol.2011.01.021] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 11/07/2010] [Accepted: 01/14/2011] [Indexed: 12/31/2022]
Abstract
To better understand the biogenesis of viroid-specific small RNAs and their possible role in disease induction, we have examined the accumulation of these small RNAs in potato spindle tuber viroid (PSTVd)-infected tomato plants. Large-scale sequence analysis of viroid-specific small RNAs revealed active production from the upper portion of the pathogenicity and central domains, two regions previously thought to be underrepresented. Profiles of small RNA populations derived from PSTVd antigenomic RNA were more variable, with differences between infected Rutgers (severe symptoms) and Moneymaker (mild symptoms) plants pointing to possible cultivar-specific differences in small RNA synthesis and/or stability. Using microarray analysis, we monitored the effects of PSTVd infection on the expression levels of >100 tomato genes containing potential binding sites for PSTVd small RNAs. Of 18 such genes down-regulated early in infection, two genes involved in gibberellin or jasmonic acid biosynthesis contain binding sites for PSTVd small RNAs in their respective ORFs.
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Affiliation(s)
- Ying Wang
- Plant Pathology Laboratory, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
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33
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Parisi O, Lepoivre P, Jijakli MH. Development of a Quick Quantitative Real-Time PCR for the In Vivo Detection and Quantification of Peach latent mosaic viroid. PLANT DISEASE 2011; 95:137-142. [PMID: 30743421 DOI: 10.1094/pdis-07-10-0512] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Viroids are plant pathogens infecting a broad range of herbaceous and tree crops. Among them, the Peach latent mosaic viroid (PLMVd) infects mainly peach trees, causing a loss of production with no curative options. Detecting this viroid is thus important for certification procedures aiming to avoid the release of infected material into orchards. Presented here is a complete detection method based on reverse transcription (RT) followed by a quantitative real-time polymerase chain reaction (PCR). New primers were selected and optimal reaction conditions determined for routine application of the method. The technique is 105 times more sensitive than the endpoint RT-PCR used for PLMVd detection, and permits earlier detection of PLMVd in infected plants. The quick, low-cost extraction procedure used and the quality of the results obtained make this method suitable for routine testing.
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Affiliation(s)
- Olivier Parisi
- Université de Liège, Gembloux Agro-Bio Tech, Plant Pathology Unit, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Philippe Lepoivre
- Université de Liège, Gembloux Agro-Bio Tech, Plant Pathology Unit, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - M Haissam Jijakli
- Université de Liège, Gembloux Agro-Bio Tech, Plant Pathology Unit, Passage des Déportés 2, 5030 Gembloux, Belgium
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Eiras M. VIROIDES, PEQUENOS RNAS PATOGÊNICOS CAPAZES DE REPLICAÇÃO AUTÔNOMA: MODELOS MOLECULARES PARA O ESTUDO DE INTERAÇÕES PATÓGENO-HOSPEDEIRO E EVOLUÇÃO. ARQUIVOS DO INSTITUTO BIOLÓGICO 2010. [DOI: 10.1590/1808-1657v77p7512010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
RESUMO Os viroides, apesar de serem constituídos por um pequeno RNA de fita simples, fortemente estruturado, circular, que não codifica proteínas, são capazes de se replicar de maneira autônoma em plantas superiores e causar doença interagindo diretamente com fatores do hospedeiro. Nesta revisão, serão apresentados e discutidos alguns dos mais recentes trabalhos envolvendo a interação de viroides com fatores do hospedeiro, incluindo aspectos relacionados à replicação, movimento e patogênese, além de suas características evolutivas. Nos últimos anos, alguns grupos de pesquisa têm se aventurado na busca por fatores do hospedeiro e mecanismos moleculares relacionados ao ciclo infeccioso dos viroides, tentando desvendar como esses pequenos RNAs interagem com o hospedeiro induzindo sintomas. Os viroides não codificam proteínas supressoras de silenciamento e, portanto, devem garantir sua existência utilizando estratégias baseadas em sua estrutura secundária, na compartimentalização em organelas, associação com fatores do hospedeiro e eficiência na replicação. A complexidade do ciclo infeccioso desses minúsculos RNAs indica que muitas interações desses patógenos com fatores do hospedeiro ainda devem ser identificadas.
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Affiliation(s)
- M. Eiras
- Instituto Biológico, Centro de Pesquisa e Desenvolvimento de Sanidade Vegetal, Brasil
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35
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Sano T. [Current progress in viroid research]. Uirusu 2010; 60:177-185. [PMID: 21488331 DOI: 10.2222/jsv.60.177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Viroids are autonomously replicating, small single-stranded circular RNA pathogens that cause diseases in infected, susceptible plants. They are non-coding RNA replicon which replicate depending on host transcriptional machinery and develop disease symptoms through interactions with cellular components of the host. The small size and unique molecular structure of viroid RNA makes them an attractive system to analyze molecular features responsible for pathogenesis, RNA transport, or molecular evolution and adaptation to specific host species. Here we show the latest progress in viroid research on new disease epidemics, molecular evolution and host adaptation, and pathogenesis in relation to viroid-induced RNA silencing.
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Affiliation(s)
- Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University.
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36
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Gómez G, Pallás V. Can the import of mRNA into chloroplasts be mediated by a secondary structure of a small non-coding RNA? PLANT SIGNALING & BEHAVIOR 2010; 5:1517-9. [PMID: 21057208 PMCID: PMC3115271 DOI: 10.1371/journal.pone.0012269] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 09/21/2010] [Indexed: 04/24/2023]
Abstract
The import of diverse nucleus-encoded proteins into chloroplasts is crucial for plant life. Although this crosstalk is mainly dependent on specific transit peptides, it has been recently reported that a non protein-coding RNA (ncRNA) based on a viroid-derived sequence (vdRNA) and acting as a 5´UTR-end mediates the functional import of GFP-mRNA into chloroplasts. This observation unearths a novel plant cell signaling pathway able to control the accumulation of the nuclear-encoded proteins in this organelle. The mechanisms regulating this chloroplast-specific localization remain yet unclear. To unravel the functional nature of this chloroplastic signal, here we dissect the 5´UTR-end responsible for the chloroplast targeting. A confocal microscopy analysis in Nicotiana benthamiana leaves of the transcripts expression carrying partial deletions of the 5`UTR-end indicate that an internal 110 nucleotides-length fragment is sufficient to mediate the traffic of functional GFP-mRNA into chloroplasts. However, the capability of this motif to act as a chloroplastic localization signal was enhanced when fused to either the 5` or the 3`region of the vd-5´UTR sequence. These findings suggest that the chloroplast-specific RNA targeting is dependent on a structural motif rather than on the RNA sequence.
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Affiliation(s)
- Gustavo Gómez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
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Teune JH, Steger G. NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome. J Nucleic Acids 2010; 2010. [PMID: 20871826 PMCID: PMC2943127 DOI: 10.4061/2010/495904] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 06/10/2010] [Accepted: 06/29/2010] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNA) are small regulatory, noncoding RNA molecules that are transcribed
as primary miRNAs (pri-miRNA) from eukaryotic genomes. At least in plants, their
regulatory activity is mediated through base-pairing with protein-coding messenger RNAs
(mRNA) followed by mRNA degradation or translation repression.
We describe NOVOMIR, a program for the identification of miRNA genes in plant
genomes. It uses a series of filter steps and a statistical model to discriminate a pre-miRNA
from other RNAs and does rely neither on prior knowledge of a miRNA target nor on
comparative genomics. The sensitivity and specificity of NOVOMIR for detection of premiRNAs
from Arabidopsis thaliana is ~0.83 and ~0.99, respectively. Plant pre-miRNAs
are more heterogeneous with respect to size and structure than animal pre-miRNAs. Despite
these difficulties, NOVOMIR is well suited to perform searches for pre-miRNAs on a
genomic scale. NOVOMIR is written in Perl and relies on two additional, free programs for prediction
of RNA secondary structure (RNALFOLD, RNASHAPES).
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Affiliation(s)
- Jan-Hendrik Teune
- Institut für Physikalische Biologie, Universitätsstr. 1, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
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38
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Rodrigo G, Carrera J, Jaramillo A, Elena SF. Optimal viral strategies for bypassing RNA silencing. J R Soc Interface 2010; 8:257-68. [PMID: 20573628 DOI: 10.1098/rsif.2010.0264] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The RNA silencing pathway constitutes a defence mechanism highly conserved in eukaryotes, especially in plants, where the underlying working principle relies on the repressive action triggered by the intracellular presence of double-stranded RNAs. This immune system performs a post-transcriptional suppression of aberrant mRNAs or viral RNAs by small interfering RNAs (siRNAs) that are directed towards their target in a sequence-specific manner. However, viruses have evolved strategies to escape from silencing surveillance while promoting their own replication. Several viruses encode suppressor proteins that interact with different elements of the RNA silencing pathway and block it. The different suppressors are not phylogenetically nor structurally related and also differ in their mechanism of action. Here, we adopt a model-driven forward-engineering approach to understand the evolution of suppressor proteins and, in particular, why viral suppressors preferentially target some components of the silencing pathway. We analysed three strategies characterized by different design principles: replication in the absence of a suppressor, suppressors targeting the first protein component of the pathway and suppressors targeting the siRNAs. Our results shed light on the question of whether a virus must opt for devoting more time into transcription or into translation and on which would be the optimal step of the silencing pathway to be targeted by suppressors. In addition, we discussed the evolutionary implications of such designing principles.
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Affiliation(s)
- Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
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Martinez G, Donaire L, Llave C, Pallas V, Gomez G. High-throughput sequencing of Hop stunt viroid-derived small RNAs from cucumber leaves and phloem. MOLECULAR PLANT PATHOLOGY 2010; 11:347-59. [PMID: 20447283 PMCID: PMC6640512 DOI: 10.1111/j.1364-3703.2009.00608.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Small RNA (sRNA)-guided processes, referred to as RNA silencing, regulate endogenous and exogenous gene expression. In plants and some animals, these processes are noncell autonomous and can operate beyond the site of initiation. Viroids, the smallest self-replicating plant pathogens known, are inducers, targets and evaders of this regulatory mechanism and, consequently, the presence of viroid-derived sRNAs (vd-sRNAs) is usually associated with viroid infection. However, the pathways involved in the biogenesis of vd-sRNAs are largely unknown. Here, we analyse, by high-throughput pyrosequencing, the profiling of the Hop stunt viroid (HSVd) vd-sRNAs recovered from the leaves and phloem of infected cucumber (Cucumis sativus) plants. HSVd vd-sRNAs are mostly 21 and 22 nucleotides in length and derived equally from plus and minus HSVd RNA strands. The widespread distribution of vd-sRNAs across the genome reveals that the totality of the HSVd RNA genome contributes to the formation of vd-sRNAs. Our sequence data suggest that viroid-derived double-stranded RNA functions as one of the main precursors of vd-sRNAs. Remarkably, phloem vd-sRNAs accumulated preferentially as 22-nucleotide species with a consensus sequence over-represented. This bias in size and sequence in the HSVd vd-sRNA population recovered from phloem exudate suggests the existence of a selective trafficking of vd-sRNAs to the phloem tissue of infected cucumber plants.
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Affiliation(s)
- German Martinez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
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40
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Abstract
This article addresses some of the questions relating to how hepatitis delta virus (HDV), an agent so far unique in the animal world, might have arisen. HDV was discovered in patients infected with hepatitis B virus (HBV). It generally makes HBV infections more damaging to the liver. It is a subviral satellite agent that depends upon HBV envelope proteins for its assembly and ability to infect new cells. In other aspects of replication, HDV is both independent of and very different from HBV. In addition, the small single-stranded circular RNA genome of HDV, and its mechanism of replication, demonstrate an increasing number of similarities to the viroids - a large family of helper-independent subviral agents that cause pathogenesis in plants.
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Affiliation(s)
- John Taylor
- Chase Cancer Center, PA 19111, USA, Tel.: +1 215 728 2436, Fax: +1 215 728 2412,
| | - Martin Pelchat
- Department of Biochemistry, Microbiology & Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada, Tel.: +1 613 562 5800 ext. 8846, Fax: +1 613 562 5452,
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Ivanova D, Vachev T, Baev V, Minkov I, Gozmanova M. Identification of Potato Spindle Tuber Viroid Small RNA in Orobanche Ramosaby Microarray. BIOTECHNOL BIOTEC EQ 2010. [DOI: 10.1080/13102818.2010.10817829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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42
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Navarro B, Pantaleo V, Gisel A, Moxon S, Dalmay T, Bisztray G, Di Serio F, Burgyán J. Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PLoS One 2009; 4:e7686. [PMID: 19890399 PMCID: PMC2767511 DOI: 10.1371/journal.pone.0007686] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 10/07/2009] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Viroids are circular, highly structured, non-protein-coding RNAs that, usurping cellular enzymes and escaping host defense mechanisms, are able to replicate and move through infected plants. Similarly to viruses, viroid infections are associated with the accumulation of viroid-derived 21-24 nt small RNAs (vd-sRNAs) with the typical features of the small interfering RNAs characteristic of RNA silencing, a sequence-specific mechanism involved in defense against invading nucleic acids and in regulation of gene expression in most eukaryotic organisms. METHODOLOGY/PRINCIPAL FINDINGS To gain further insights on the genesis and possible role of vd-sRNAs in plant-viroid interaction, sRNAs isolated from Vitis vinifera infected by Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1) were sequenced by the high-throughput platform Solexa-Illumina, and the vd-sRNAs were analyzed. The large majority of HSVd- and GYSVd1-sRNAs derived from a few specific regions (hotspots) of the genomic (+) and (-) viroid RNAs, with a prevalence of those from the (-) strands of both viroids. When grouped according to their sizes, vd-sRNAs always assumed a distribution with prominent 21-, 22- and 24-nt peaks, which, interestingly, mapped at the same hotspots. CONCLUSIONS/SIGNIFICANCE These findings show that different Dicer-like enzymes (DCLs) target viroid RNAs, preferentially accessing to the same viroid domains. Interestingly, our results also suggest that viroid RNAs may interact with host enzymes involved in the RNA-directed DNA methylation pathway, indicating more complex scenarios than previously thought for both vd-sRNAs genesis and possible interference with host gene expression.
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Affiliation(s)
- Beatriz Navarro
- Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Torino and Bari, Italy
| | - Vitantonio Pantaleo
- Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Torino and Bari, Italy
| | - Andreas Gisel
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Simon Moxon
- School of Computing Sciences, University of East Anglia, Norwich, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - Francesco Di Serio
- Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Torino and Bari, Italy
| | - József Burgyán
- Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Torino and Bari, Italy
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43
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Abstract
Hepatitis delta virus (HDV) is a subviral agent dependent upon hepatitis B virus (HBV). HDV uses the envelope proteins of HBV to achieve assembly and infection of target cells. Otherwise, the replication of the RNA genome of HDV is totally different from that of its helper virus, and involves redirection of host polymerase activity. This chapter is concerned with recent developments in our understanding of the genome replication process.
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Affiliation(s)
- John M Taylor
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
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44
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Viroid replication: rolling-circles, enzymes and ribozymes. Viruses 2009; 1:317-34. [PMID: 21994552 PMCID: PMC3185496 DOI: 10.3390/v1020317] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Revised: 09/09/2009] [Accepted: 09/09/2009] [Indexed: 12/05/2022] Open
Abstract
Viroids, due to their small size and lack of protein-coding capacity, must rely essentially on their hosts for replication. Intriguingly, viroids have evolved the ability to replicate in two cellular organella, the nucleus (family Pospiviroidae) and the chloroplast (family Avsunviroidae). Viroid replication proceeds through an RNA-based rolling-circle mechanism with three steps that, with some variations, operate in both polarity strands: i) synthesis of longer-than-unit strands catalyzed by either the nuclear RNA polymerase II or a nuclear-encoded chloroplastic RNA polymerase, in both instances redirected to transcribe RNA templates, ii) cleavage to unit-length, which in the family Avsunviroidae is mediated by hammerhead ribozymes embedded in both polarity strands, while in the family Pospiviroidae the oligomeric RNAs provide the proper conformation but not the catalytic activity, and iii) circularization. The host RNA polymerases, most likely assisted by additional host proteins, start transcription from specific sites, thus implying the existence of viroid promoters. Cleavage and ligation in the family Pospiviroidae is probably catalyzed by an RNase III-like enzyme and an RNA ligase able to circularize the resulting 5′ and 3′ termini. Whether a chloroplastic RNA ligase mediates circularization in the family Avsunviroidae, or this reaction is autocatalytic, remains an open issue.
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45
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Owens RA, Hammond RW. Viroid pathogenicity: one process, many faces. Viruses 2009; 1:298-316. [PMID: 21994551 PMCID: PMC3185495 DOI: 10.3390/v1020298] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 08/31/2009] [Accepted: 09/01/2009] [Indexed: 12/28/2022] Open
Abstract
Despite the non-coding nature of their small RNA genomes, the visible symptoms of viroid infection resemble those associated with many plant virus diseases. Recent evidence indicates that viroid-derived small RNAs acting through host RNA silencing pathways play a key role in viroid pathogenicity. Host responses to viroid infection are complex, involving signaling cascades containing host-encoded protein kinases and crosstalk between hormonal and defense-signaling pathways. Studies of viroid-host interaction in the context of entire biochemical or developmental pathways are just beginning, and many working hypotheses have yet to be critically tested.
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Affiliation(s)
- Robert A. Owens
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville, MD 20705, USA; E-mail:
| | - Rosemarie W. Hammond
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville, MD 20705, USA; E-mail:
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46
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Martínez F, Marqués J, Salvador ML, Daròs JA. Mutational analysis of eggplant latent viroid RNA processing in Chlamydomonas reinhardtii chloroplast. J Gen Virol 2009; 90:3057-3065. [PMID: 19675190 DOI: 10.1099/vir.0.013425-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viroids of the family Avsunviroidae, such as eggplant latent viroid (ELVd), contain hammerhead ribozymes and replicate in the chloroplasts of the host plant through an RNA-based symmetrical rolling-circle mechanism in which oligomeric RNAs of both polarity are processed to monomeric linear RNAs (by cleavage) and to monomeric circular RNAs (by ligation). Using an experimental system consisting of transplastomic lines of the alga Chlamydomonas reinhardtii, a mutational analysis of sequence and structural elements in the ELVd molecule that are involved in transcript processing in vivo in a chloroplastic context was carried out. A collection of six insertion and three deletion ELVd mutants was created and expressed in C. reinhardtii chloroplast. All mutants cleaved efficiently except for the control with an insertion inside the hammerhead ribozyme domain, supporting the prediction that this domain is necessary and sufficient to mediate transcript cleavage in vivo. However, two deletion mutants that cleaved efficiently showed ligation defects, indicating that during RNA circularization, other parts of the molecule are involved in addition to the hammerhead ribozyme domain. This is probably a quasi double-stranded structure present in the central part of the molecule which contains the ligation site in an internal loop. However, the mutations prevented the viroid from infecting its natural host, eggplant, indicating that they affected other essential functions in ELVd infectious cycle. The insertion in the terminal loop of the right upper hairpin of ELVd did not have this effect; it was tolerated and partially maintained in the progeny.
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Affiliation(s)
- Fernando Martínez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos, 46022 Valencia, Spain
| | - Jorge Marqués
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos, 46022 Valencia, Spain
| | - María L Salvador
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Avenida Dr Moliner, 46100 Burjassot, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos, 46022 Valencia, Spain
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47
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Coleus blumei viroid 6: a new tentative member of the genus Coleviroid derived from natural genome shuffling. Arch Virol 2009; 154:993-7. [PMID: 19434474 DOI: 10.1007/s00705-009-0388-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 04/20/2009] [Indexed: 10/20/2022]
Abstract
Coleus blumei can be infected by several viroids of the genus Coleviroid. One year after detecting a mixed infection of coleus blumei viroid 1 (CbVd-1) and 5 (CbVd-5) in coleus seedlings inoculated with these two viroids, we found an additional viroid-like RNA. Sequence analysis revealed a viroid of 342 nucleotides that contains the central conserved region of coleviroids and is a chimera of the left half of CbVd-3 and the right half of CbVd-5. This new viroid, tentatively referred to as coleus blumei viroid 6 (CbVd-6), appears to have arisen from a natural recombination event or genome shuffling.
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48
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Gómez G, Martínez G, Pallás V. Interplay between viroid-induced pathogenesis and RNA silencing pathways. TRENDS IN PLANT SCIENCE 2009; 14:264-9. [PMID: 19375972 DOI: 10.1016/j.tplants.2009.03.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 02/20/2009] [Accepted: 03/02/2009] [Indexed: 05/22/2023]
Abstract
Of all known plant pathogens, viroids have the lowest biological complexity. Their genome consists of a naked RNA without protein-encoding capacity. However, viroids contain sufficient genetic information to establish infection in susceptible hosts. The process by which this tiny RNA subverts the plant cell machinery by coercing the host to express symptoms of viroid infection is the 'Holy Grail' that has been searched for since the first viroid-induced disease was described. Recently, a large body of evidence has led to the emergent view that RNA silencing has a crucial role in viroid pathogenesis and evolution. Here, we chronologically analyse the relevant findings supporting this idea and propose a model to explain the possible interrelation between the trans-acting small interfering RNA (ta-siRNA) biogenesis pathway and viroid replication and pathogenesis.
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Affiliation(s)
- Gustavo Gómez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
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49
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Bernad L, Duran-Vila N, Elena SF. Effect of citrus hosts on the generation, maintenance and evolutionary fate of genetic variability of citrus exocortis viroid. J Gen Virol 2009; 90:2040-2049. [PMID: 19403756 DOI: 10.1099/vir.0.010769-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Citrus exocortis viroid (CEVd) populations are composed of closely related haplotypes whose frequencies in the population result from the equilibrium between mutation, selection and genetic drift. The genetic diversity of CEVd populations infecting different citrus hosts was studied by comparing populations recovered from infected trifoliate orange and sour orange seedling trees after 10 years of evolution, with the ancestral population maintained for the same period in the original host, Etrog citron. Furthermore, populations isolated from these trifoliate orange and sour orange trees were transmitted back to Etrog citron plants and the evolution of their mutant spectra was studied. The results indicate that (i) the amount and composition of the within-plant genetic diversity generated varies between these two hosts and is markedly different from that which is characteristic of the original Etrog citron host and (ii) the genetic diversity found after transmitting back to Etrog citron is indistinguishable from that which is characteristic of the ancestral Etrog citron population, regardless of the citrus plant from which the evolved populations were isolated. The relationship between the CEVd populations from Etrog citron and trifoliate orange, both sensitive hosts, and those from sour orange, which is a tolerant host, is discussed.
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Affiliation(s)
- Lucía Bernad
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Moncada, 46113 València, Spain
| | - Núria Duran-Vila
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Moncada, 46113 València, Spain
| | - Santiago F Elena
- The Santa Fe Institute, Santa Fe, NM 87501, USA
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, 46022 València, Spain
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Hou WY, Sano T, Li F, Wu ZJ, Li L, Li SF. Identification and characterization of a new coleviroid (CbVd-5). Arch Virol 2008; 154:315-20. [PMID: 19112552 DOI: 10.1007/s00705-008-0276-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Accepted: 11/11/2008] [Indexed: 11/28/2022]
Abstract
A viroid-like RNA was detected from coleus (Coleus blumei) in China. It consisted of 274 nucleotides and had 66% sequence identity with a member of the closest known viroid species. The predicted secondary structure is rod-shaped with extensive base pairing, and it has the conserved region characteristic of the genus Coleviroid. Two terminal sequences that are highly conserved among some members of the genus were also identified. The viroid-like RNA was successfully transmitted to coleus by slash-inoculation. This viroid was identified as a new member of the genus Coleviroid, and we tentatively propose the name Coleus blumei viroid 5 (CbVd-5).
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Affiliation(s)
- Wan-Ying Hou
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West No. 2, Beijing 100193, People's Republic of China
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