Viroids: An Ariadne’s thread into the RNA labyrinth

Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Universidad Politécnica de Valencia, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
EMBO Reports (Impact Factor: 9.06). 07/2006; 7(6):593-8. DOI: 10.1038/sj.embor.7400706
Source: PubMed


Viroids are structurally, functionally and evolutionarily different from viruses. Despite their small, non-protein-encoding, single-stranded circular RNA genome, viroids can infect higher plants and cause certain diseases. Members of the two viroid families, Pospiviroidae and Avsunviroidae, have evolved to usurp the transcriptional machinery of their host nuclei and chloroplasts, respectively, in which replication proceeds through a rolling-circle mechanism involving RNA polymerization, cleavage and ligation. Remarkably, viroids subvert certain DNA-dependent RNA polymerases to transcribe RNA templates, and, in the family Avsunviroidae, post-transcriptional cleavage is catalysed by hammerhead ribozymes. Viroids are models for studying RNA evolution and for analysing RNA transport in plants, because they can move intracellularly, intercellularly through plasmodesmata and to distal parts of the plant through the vascular system. Viroids elicit RNA-silencing phenomena, which might mediate some of their biological properties, including pathogenesis. As some viroids behave as catalytic RNAs, they are regarded as remnants of the RNA world.

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Available from: José-Antonio Daròs
    • "In fact, our own observations of eggplant ELVd-infected tissues by in situ hybridization with digoxigeninlabeled RNA probes support the chloroplastic accumulation of this viroid (Marqués andDaròs, unpublished results). Exactly how members of the family Avsunviroidae reach plastids has been an intriguing question for a long time (Daròs et al., 2006), but in 2010Gómez andPallás published the fascinating observation that a green fluorescent protein (GFP), transitorily expressed in N. benthamiana tissues by Agrobacterium tumefaciens infiltration, was translated in the chloroplast when ELVd sequences were fused at the 5' untranslated region (UTR) of messenger RNA (mRNA). More specifically, these authors inserted a chimeric ELVd sequence that consisted of a fragment of the minus strand of ELVd-AJ536613 (position 54 to 267, note that the numbering of the minus strand goes backward), followed by a fragment of the plus strand of ELVd-AJ536613 (position 54 to 261, including two mutations) immediately upstream of the initiation codon of a fluorescent protein mRNA (see GenBank accession number HM136583). "
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    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 nt that folds in a branched quasi-rod-like minimum free-energy conformation. RNAs of complementary polarity exist in infected cells and are considered 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 where it was discovered. A very narrow host range seems 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: This article is protected by copyright. All rights reserved.
    No preview · Article · Dec 2015 · Molecular Plant Pathology
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    • "In some viroids, replication is achieved through an asymmetric replication pathway with only one rolling circle, where linear oligomeric antigenomic strands are formed and used as templates for synthesis of the genomic strands. The genomic strands are then processed by an RNase III-like enzyme (but not ribozyme), resulting in monomeric sequences [12]. In this model, the ribozyme sites may not be needed. "
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    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.
    Full-text · Article · Jun 2014 · Biochemical and Biophysical Research Communications
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    • "It remains unclear how viroids cause diseases in plants, although it is most commonly accepted that it happens via an RNA-silencing mechanism. Viroid-specific siRNAs that can act as endogenous miRNAs may base-pair with host mRNAs, blocking normal gene expression and inducing disease (Wang et al., 2004; Daros et al., 2006; Owens, 2007; Navarro et al., 2009). Apart from vegetative propagation, the most common mechanism of PSTVd transmission is mechanical, by direct contact of non-infected with infected plants or with agricultural machinery, although other mechanisms of transmission have been suggested. "
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    ABSTRACT: This paper reports the development of a single tube, real-time, reverse transcription loop-mediated isothermal amplifi-cation (RT-LAMP) assay for detecting Potato spindle tuber viroid (PSTVd), one of the quarantine pathogens of potato in Europe and North America. The method enables detection of a broad range of PSTVd isolates, and is about 10 times more sensitive than the conventional reverse transcription polymerase chain reaction (RT-PCR) assay. Its benefits are not only its speed (15–25 min to obtain results) and cost effectiveness (resulting from time saved as well as cheaper consumables), but also its demonstrated ability to be performed in the field, using portable instruments.
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