The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Ricardo Flores - One of the best experts on this subject based on the ideXlab platform.
-
ICTV Virus Taxonomy Profile: Pospiviroidae.
The Journal of general virology, 2021Co-Authors: Francesco Di Serio, Georgios Vidalakis, Jacobus Th J Verhoeven, Jaroslav Matousek, Robert A Owens, Teruo Sano, Vicente Pallás, John W. Randles, Ricardo FloresAbstract:Members of the family Pospiviroidae have single-stranded circular RNA genomes that adopt a rod-like or a quasi-rod-like conformation. These genomes contain a central conserved region that is involved in replication in the nucleus through an asymmetric RNA-RNA rolling-circle mechanism. Members of the family Pospiviroidae lack the hammerhead ribozymes that are typical of viroids classified in the family Avsunviroidae. The family Pospiviroidae includes the genera Apscaviroid, Cocadviroid, Coleviroid, Hostuviroid and Pospiviroid, with >25 species. This is a summary of the ICTV Report on the family Pospiviroidae, which is available at ictv.global/report/pospiviroidae.
-
symptomatic plant viroid infections in phytopathogenic fungi a request for a critical reassessment
Proceedings of the National Academy of Sciences of the United States of America, 2020Co-Authors: P Serra, Alberto Carbonell, Selma Gagozachert, Beatriz Navarro, Shifang Li, Francesco Di Serio, Ricardo FloresAbstract:Since their discovery (1), viroids—small (∼250 to 430 nt), non–protein-coding, circular RNAs—are thought to infect and cause disease only in plants (2); thus, the report that they infect and incite symptoms in filamentous phytopathogenic fungi (3) is surprising. Viroids are classified into two families (4). Members of the Pospiviroidae , including potato spindle tuber viroid (PSTVd) (1, 5), replicate in the nucleus through an RNA–RNA rolling-circle mechanism catalyzed by host enzymes (RNA polymerase, RNase, and RNA ligase). Members of the Avsunviroidae , like peach latent mosaic viroid (PLMVd) (6), form hammerhead ribozymes (HHRz) that functionally substitute the RNase during replication in chloroplasts (4). The host range of the second family is restricted to plant species (or relatives) in which the viroids were described. Unexpectedly, Wei et al. (3) report that seven viroids, including PLMVd and avocado sunblotch viroid (ASBVd) (both of the Avsunviroidae ), infect Nicotiana benthamiana , a known host for only some members of … [↵][1]1To whom correspondence may be addressed. Email: rflores{at}ibmcp.upv.es or francesco.diserio{at}ipsp.cnr.it. [1]: #xref-corresp-1-1
-
Viroid pathogenesis: a critical appraisal of the role of RNA silencing in triggering the initial molecular lesion.
FEMS microbiology reviews, 2020Co-Authors: Ricardo Flores, Sonia Delgado, Beatriz Navarro, Pedro Serra, Francesco Di SerioAbstract:The initial molecular lesions through which viroids, satellite RNAs and viruses trigger signal cascades resulting in plant diseases are hotly debated. Since viroids are circular non-protein-coding RNAs of ∼250-430 nucleotides, they appear very convenient to address this issue. Viroids are targeted by their host RNA silencing defense, generating viroid-derived small RNAs (vd-sRNAs) that are presumed to direct Argonaute (AGO) proteins to inactivate messenger RNAs, thus initiating disease. Here, we review the existing evidence. Viroid-induced symptoms reveal a distinction. Those attributed to vd-sRNAs from potato spindle tuber viroid and members of the family Pospiviroidae (replicating in the nucleus) are late, non-specific and systemic. In contrast, those attributed to vd-sRNAs from peach latent mosaic viroid (PLMVd) and other members of the family Avsunviroidae (replicating in plastids) are early, specific and local. Remarkably, leaf sectors expressing different PLMVd-induced chloroses accumulate viroid variants with specific pathogenic determinants. Some vd-sRNAs containing such determinant guide AGO1-mediated cleavage of mRNAs that code for proteins regulating chloroplast biogenesis/development. Therefore, the initial lesions and the expected phenotypes are connected by short signal cascades, hence supporting a cause-effect relationship. Intriguingly, one virus satellite RNA initiates disease through a similar mechanism, whereas in the Pospiviroidae and in plant viruses the situation remains uncertain.
-
Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy
RNA biology, 2019Co-Authors: Miguel Moreno, Ricardo Flores, Luis Vázquez, A. López-carrasco, J. A. Martín-gago, Carlos BrionesAbstract:Viroids are small infectious, non-protein-coding circular RNAs that replicate independently and, in some cases, incite diseases in plants. They are classified into two families: Pospiviroidae, composed of species that have a central conserved region (CCR) and replicate in the cell nucleus, and Avsunviroidae, containing species that lack a CCR and whose multimeric replicative intermediates of either polarity generated in plastids self-cleave through hammerhead ribozymes. The compact, rod-like or branched, secondary structures of viroid RNAs have been predicted by RNA folding algorithms and further examined using different in vitro and in vivo experimental techniques. However, direct data about their native tertiary structure remain scarce. Here we have applied atomic force microscopy (AFM) to image at single-molecule resolution different variant RNAs of three representative viroids: potato spindle tuber viroid (PSTVd, family Pospiviroidae), peach latent mosaic viroid and eggplant latent viroid (PLMVd and ELVd, family Avsunviroidae). Our results provide a direct visualization of their native, three-dimensional conformations at 0 and 4 mM Mg2+ and highlight the role that some elements of tertiary structure play in their stabilization. The AFM images show that addition of 4 mM Mg2+ to the folding buffer results in a size contraction in PSTVd and ELVd, as well as in PLMVd when the kissing-loop interaction that stabilizes its 3D structure is preserved.
-
ICTV Virus Taxonomy Profile: Avsunviroidae.
The Journal of general virology, 2018Co-Authors: Francesco Di Serio, Georgios Vidalakis, Jacobus Th J Verhoeven, Jaroslav Matousek, Vicente Pallás, John W. Randles, Ricardo FloresAbstract:Members of the family Avsunviroidae have a single-stranded circular RNA genome that adopts a rod-like or branched conformation and can form, in the strands of either polarity, hammerhead ribozymes involved in their replication in plastids through a symmetrical RNA–RNA rolling-circle mechanism. These viroids lack the central conserved region typical of members of the family Pospiviroidae. The family Avsunviroidae includes three genera, Avsunviroid, Pelamoviroid and Elaviroid, with a total of four species. This is a summary of the ICTV Report on the taxonomy of the family Avsunviroidae, which is available at http://www.ictv.global/report/Avsunviroidae.
José-antonio Daròs - One of the best experts on this subject based on the ideXlab platform.
-
Large-scale Production of Recombinant RNAs on a Circular Scaffold Using a Viroid-derived System in Escherichia coli.
Journal of visualized experiments : JoVE, 2018Co-Authors: Teresa Cordero, Veronica Aragones, José-antonio DaròsAbstract:With increasing interest in RNA biology and the use of RNA molecules in sophisticated biotechnological applications, the methods to produce large amounts of recombinant RNAs are limited. Here, we describe a protocol to produce large amounts of recombinant RNA in Escherichia coli based on co-expression of a chimeric molecule that contains the RNA of interest in a viroid scaffold and a plant tRNA ligase. Viroids are relatively small, non-coding, highly base-paired circular RNAs that are infectious to higher plants. The host plant tRNA ligase is an enzyme recruited by viroids that belong to the family Avsunviroidae, such as Eggplant latent viroid (ELVd), to mediate RNA circularization during viroid replication. Although ELVd does not replicate in E. coli, an ELVd precursor is efficiently transcribed by the E. coli RNA polymerase and processed by the embedded hammerhead ribozymes in bacterial cells, and the resulting monomers are circularized by the co-expressed tRNA ligase reaching a remarkable concentration. The insertion of an RNA of interest into the ELVd scaffold enables the production of tens of milligrams of the recombinant RNA per liter of bacterial culture in regular laboratory conditions. A main fraction of the RNA product is circular, a feature that facilitates the purification of the recombinant RNA to virtual homogeneity. In this protocol, a complementary DNA (cDNA) corresponding to the RNA of interest is inserted in a particular position of the ELVd cDNA in an expression plasmid that is used, along the plasmid to co-express eggplant tRNA ligase, to transform E. coli. Co-expression of both molecules under the control of strong constitutive promoters leads to production of large amounts of the recombinant RNA. The recombinant RNA can be extracted from the bacterial cells and separated from the bulk of bacterial RNAs taking advantage of its circularity.
-
Mutational Analysis of Eggplant Latent Viroid RNA Circularization by the Eggplant tRNA Ligase in Escherichia coli
Frontiers Media S.A., 2018Co-Authors: Teresa Cordero, Beltrán Ortolá, José-antonio DaròsAbstract:Eggplant latent viroid (ELVd) is a relatively small non-coding circular RNA that induces asymptomatic infections in eggplants (Solanum melongena L.). Like other viroid species that belong to the family Avsunviroidae, ELVd contains hammerhead ribozymes in the strands of both polarities that self-cleave RNAs producing terminal 5′-hydroxyl and 2′,3′-cyclic phosphodiester groups. Available experimental data indicate that ELVd replicates in the chloroplasts of infected cells through a symmetric rolling-circle mechanism, in which RNA circularization is catalyzed by the chloroplastic isoform of the tRNA ligase. In this work, a mutational analysis was performed to gain insight into the sequence and structural requirements of the tRNA ligase-mediated circularization of ELVd RNAs. In the predicted minimum free energy conformation of the monomeric linear ELVd RNA intermediate of plus (+) polarity, the ligation site is located in the lower part of an opened internal loop, which is present in a quasi-rod-like structure that occupies the center of the molecule. The mutations analyzed herein consisted of punctual nucleotide substitutions and deletions surrounding the ligation site on the upper and lower strands of the ELVd quasi-double-stranded structure. Computational predictions of the mutated ELVd conformations indicated different degrees of distortions compared to the minimum free energy conformation of the wild-type ELVd linear monomer of + polarity. When these mutant RNAs were expressed in Escherichia coli, they were all circularized by the eggplant tRNA ligase with approximately the same efficiency as the wild-type ELVd, except for those that directly affected the ribozyme domain. These results suggest that the viroid ribozyme domains, in addition to self-cleavage, are also involved in the tRNA ligase-mediated circularization of the monomeric linear replication intermediates
-
Eggplant Latent Viroid
Viroids and Satellites, 2017Co-Authors: José-antonio DaròsAbstract:Abstract Eggplant latent viroid (ELVd) is the only currently known member of the genus Elaviroid in the family Avsunviroidae. This viroid is able to infect eggplant (Solanum melongena L.) with no apparent symptom expression, and is transmitted both mechanically and by seed. The ELVd host range seems extremely narrow since it has not been able to be transmitted to other plant species. ELVd most probably replicates and accumulates in the chloroplasts of infected cells through a symmetric rolling-circle mechanism and its progeny shows a remarkable sequence and length variability.
-
Viroids: Small Noncoding Infectious RNAs with the Remarkable Ability of Autonomous Replication
Current Research Topics in Plant Virology, 2016Co-Authors: José-antonio DaròsAbstract:Viroids are infectious agents of plants, constituted exclusively by a noncoding small (246–401 nucleotides) circular RNA molecule. When this RNA manages to enter a cell of an appropriate host plant, it moves to the subcellular replication site and replicates through an RNA-to-RNA rolling circle mechanism. Viroid progeny is then able to move cell-to-cell through plamodesmata and long distances through the phloem to invade distal parts of host plants. Two types of viroids exist, classified into the families Pospiviroidae and Avsunviroidae. They replicate in the nucleus (Pospiviroidae) and chloroplast (Avsunviroidae), hijacking host enzymes. Members of the family Pospiviroidae recruit host DNA-dependent RNA polymerase II, RNase III and DNA ligase 1, while members of the Avsunviroidae (which contain embedded hammerhead ribozymes for self-cleavage) use host nuclear-encoded chloroplastic RNA polymerase and the chloroplastic isoform of tRNA ligase. Viroids are mainly transmitted mechanically from plant to plant, and frequently exert a pathogenic effect on infected plants. Some symptoms in viroid infections are induced by the viroid-derived small RNAs produced by the host defensive RNA silencing machinery. Interestingly, viroids are targets of the host Dicer-like and RNA-dependent RNA polymerase enzymes, but are particularly resistant to the action of the RNA-induced silencing complex.
-
Eggplant latent viroid: a friendly experimental system in the family Avsunviroidae
Molecular plant pathology, 2016Co-Authors: José-antonio DaròsAbstract: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.
Gerhard Steger - One of the best experts on this subject based on the ideXlab platform.
-
Viroid quasispecies revealed by deep sequencing.
RNA biology, 2016Co-Authors: Joseph R. J. Brass, Jaroslav Matousek, Gerhard StegerAbstract:Viroids are non-coding single-stranded circular RNA molecules that replicate autonomously in infected host plants causing mild to lethal symptoms. Their genomes contain about 250-400 nucleotides, depending on viroid species. Members of the family Pospiviroidae, like the Potato spindle tuber viroid (PSTVd), replicate via an asymmetric rolling-circle mechanism using the host DNA-dependent RNA-Polymerase II in the nucleus, while members of Avsunviroidae are replicated in a symmetric rolling-circle mechanism probably by the nuclear-encoded polymerase in chloroplasts. Viroids induce the production of viroid-specific small RNAs (vsRNA) that can direct (post-)transcriptional gene silencing against host transcripts or genomic sequences. Here, we used deep-sequencing to analyze vsRNAs from plants infected with different PSTVd variants to elucidate the PSTVd quasipecies evolved during infection. We recovered several novel as well as previously known PSTVd variants that were obviously competent in replication and identified common strand-specific mutations. The calculated mean error rate per nucleotide position was less than [Formula: see text], quite comparable to the value of [Formula: see text] reported for a member of Avsunviroidae. The resulting error threshold allows the synthesis of longer-than-unit-length replication intermediates as required by the asymmetric rolling-circle mechanism of members of Pospiviroidae.
-
Viroid quasispecies revealed by deep sequencing.
RNA biology, 2016Co-Authors: Joseph R. J. Brass, Jaroslav Matousek, Robert A Owens, Gerhard StegerAbstract:ABSTRACTViroids are non-coding single-stranded circular RNA molecules that replicate autonomously in infected host plants causing mild to lethal symptoms. Their genomes contain about 250–400 nucleotides, depending on viroid species. Members of the family Pospiviroidae, like the Potato spindle tuber viroid (PSTVd), replicate via an asymmetric rolling-circle mechanism using the host DNA-dependent RNA-Polymerase II in the nucleus, while members of Avsunviroidae are replicated in a symmetric rolling-circle mechanism probably by the nuclear-encoded polymerase in chloroplasts. Viroids induce the production of viroid-specific small RNAs (vsRNA) that can direct (post-)transcriptional gene silencing against host transcripts or genomic sequences. Here, we used deep-sequencing to analyze vsRNAs from plants infected with different PSTVd variants to elucidate the PSTVd quasipecies evolved during infection. We recovered several novel as well as previously known PSTVd variants that were obviously competent in replicatio...
-
Viroid quasispecies revealed by deep sequencing
2016Co-Authors: Joseph R. J. Brass, Jaroslav Matousek, Gerhard StegerAbstract:Viroids are non-coding single-stranded circular RNA molecules that replicate autonomously in infected host plants causing mild to lethal symptoms. Their genomes contain about 250–400 nucleotides, depending on viroid species. Members of the family Pospiviroidae, like the Potato spindle tuber viroid (PSTVd), replicate via an asymmetric rolling-circle mechanism using the host DNA-dependent RNA-Polymerase II in the nucleus, while members of Avsunviroidae are replicated in a symmetric rolling-circle mechanism probably by the nuclear-encoded polymerase in chloroplasts. Viroids induce the production of viroid-specific small RNAs (vsRNA) that can direct (post-)transcriptional gene silencing against host transcripts or genomic sequences. Here, we used deep-sequencing to analyze vsRNAs from plants infected with different PSTVd variants to elucidate the PSTVd quasipecies evolved during infection. We recovered several novel as well as previously known PSTVd variants that were obviously competent in replication and identified common strand-specific mutations. The calculated mean error rate per nucleotide position was less than 5 × 10−3, quite comparable to the value of 2.5 × 10−3 reported for a member of Avsunviroidae. The resulting error threshold allows the synthesis of longer-than-unit-length replication intermediates as required by the asymmetric rolling-circle mechanism of members of Pospiviroidae.
-
viroid specific small rna in plant disease
RNA Biology, 2012Co-Authors: Christian Hammann, Gerhard StegerAbstract: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.
-
Viroids: The Smallest Known Infectious Agents Cause Accumulation of Viroid-Specific Small RNAs
From Nucleic Acids Sequences to Molecular Medicine, 2012Co-Authors: Jaroslav Matousek, Detlev Riesner, Gerhard StegerAbstract:Viroids are plant-infectious, noncoding, unencapsidated, circular RNAs ranging in size from 250 to 400 nucleotides that are transcribed in a rolling-circle mechanism either in nuclei (Pospiviroidae) or in chloroplasts (Avsunviroidae) of plant hosts. The pathogenic effect caused by viroids is still an enigma: Potato spindle tuber viroid (PSTVd), the type strain of Pospiviroidae, causes typical symptoms in tomato plants, but the severity of symptoms depends on the tomato cultivar; different strains of PSTVd, which vary in sequence by a few mutations from each other, induce symptoms from very mild up to necrosis upon infection of a cultivar. According to recent findings, viroids cause the accumulation of viroid-specific small RNAs (vsRNA) similar in size to small interfering (siRNA) and miRNAs, but they do escape the cytoplasmic silencing mechanism. In this chapter, we will discuss these findings and hypotheses on the biogenesis of viroid-specific small RNAs and connections to symptom induction.
Robert A Owens - One of the best experts on this subject based on the ideXlab platform.
-
ICTV Virus Taxonomy Profile: Pospiviroidae.
The Journal of general virology, 2021Co-Authors: Francesco Di Serio, Georgios Vidalakis, Jacobus Th J Verhoeven, Jaroslav Matousek, Robert A Owens, Teruo Sano, Vicente Pallás, John W. Randles, Ricardo FloresAbstract:Members of the family Pospiviroidae have single-stranded circular RNA genomes that adopt a rod-like or a quasi-rod-like conformation. These genomes contain a central conserved region that is involved in replication in the nucleus through an asymmetric RNA-RNA rolling-circle mechanism. Members of the family Pospiviroidae lack the hammerhead ribozymes that are typical of viroids classified in the family Avsunviroidae. The family Pospiviroidae includes the genera Apscaviroid, Cocadviroid, Coleviroid, Hostuviroid and Pospiviroid, with >25 species. This is a summary of the ICTV Report on the family Pospiviroidae, which is available at ictv.global/report/pospiviroidae.
-
Viroid quasispecies revealed by deep sequencing.
RNA biology, 2016Co-Authors: Joseph R. J. Brass, Jaroslav Matousek, Robert A Owens, Gerhard StegerAbstract:ABSTRACTViroids are non-coding single-stranded circular RNA molecules that replicate autonomously in infected host plants causing mild to lethal symptoms. Their genomes contain about 250–400 nucleotides, depending on viroid species. Members of the family Pospiviroidae, like the Potato spindle tuber viroid (PSTVd), replicate via an asymmetric rolling-circle mechanism using the host DNA-dependent RNA-Polymerase II in the nucleus, while members of Avsunviroidae are replicated in a symmetric rolling-circle mechanism probably by the nuclear-encoded polymerase in chloroplasts. Viroids induce the production of viroid-specific small RNAs (vsRNA) that can direct (post-)transcriptional gene silencing against host transcripts or genomic sequences. Here, we used deep-sequencing to analyze vsRNAs from plants infected with different PSTVd variants to elucidate the PSTVd quasipecies evolved during infection. We recovered several novel as well as previously known PSTVd variants that were obviously competent in replicatio...
-
Potato spindle tuber viroid: the simplicity paradox resolved?
Molecular plant pathology, 2007Co-Authors: Robert A OwensAbstract:Potato spindle tuber viroid (PSTVd) is the type species of the genus Posipiviroid, family Pospiviroidae. An absence of hammerhead ribozymes and the presence of a 'central conserved region' distinguish PSTVd and related viroids from members of a second viroid family, the Avsunviroidae. Viroids are small, unencapsidated, circular, single-stranded RNA molecules which replicate autonomously when inoculated into host plants. Because viroids are non-protein-coding RNAs, designation of the more abundant, highly infectious polarity strand as the positive strand is arbitrary. PSTVd assumes a rod-like, highly structured conformation that is resistant to nuclease degradation in vitro. Naturally occurring sequence variants of PSTVd range in size from 356 to 361 nt. HOSTS AND SYMPTOMS: The natural host range of PSTVd-cultivated potato, certain other Solanum spp., and avocado-appears to be quite limited. Foliar symptoms in potato are often obscure, and the severity of tuber symptoms (elongation with the appearance of prominent bud scales/eyebrows and growth cracks) depends on both temperature and length of infection. PSTVd has a broad experimental host range, especially among solanaceous species, and strains are classified as mild, intermediate or severe based upon the symptoms observed in sensitive tomato cultivars. These symptoms include shortening of internodes, petioles and mid-ribs, severe epinasty and wrinkling of the leaves, and necrosis of mid-ribs, petioles and stems.
-
Potato spindle tuber viroid: the simplicity paradox resolved?
Molecular plant pathology, 2007Co-Authors: Robert A OwensAbstract:SUMMARY Taxonomy: Potato spindle tuber viroid (PSTVd) is the type species of the genus Posipiviroid , family Pospiviroidae . An absence of hammerhead ribozymes and the presence of a ‘central conserved region’ distinguish PSTVd and related viroids from members of a second viroid family, the Avsunviroidae . Physical properties: Viroids are small, unencapsidated, circular, single-stranded RNA molecules which replicate autonomously when inoculated into host plants. Because viroids are non-proteincoding RNAs, designation of the more abundant, highly infectious polarity strand as the positive strand is arbitrary. PSTVd assumes a rod-like, highly structured conformation that is resistant to nuclease degradation in vitro . Naturally occurring sequence variants of PSTVd range in size from 356 to 361 nt. Hosts and symptoms: The natural host range of PSTVd— cultivated potato, certain other Solanum spp., and avocado— appears to be quite limited. Foliar symptoms in potato are often obscure, and the severity of tuber symptoms (elongation with the appearance of prominent bud scales/eyebrows and growth cracks) depends on both temperature and length of infection. PSTVd has a broad experimental host range, especially among solanaceous species, and strains are classified as mild, intermediate or severe based upon the symptoms observed in sensitive tomato cultivars. These symptoms include shortening of internodes, petioles and mid-ribs, severe epinasty and wrinkling of the leaves, and necrosis of mid-ribs, petioles and stems.
Francesco Di Serio - One of the best experts on this subject based on the ideXlab platform.
-
ICTV Virus Taxonomy Profile: Pospiviroidae.
The Journal of general virology, 2021Co-Authors: Francesco Di Serio, Georgios Vidalakis, Jacobus Th J Verhoeven, Jaroslav Matousek, Robert A Owens, Teruo Sano, Vicente Pallás, John W. Randles, Ricardo FloresAbstract:Members of the family Pospiviroidae have single-stranded circular RNA genomes that adopt a rod-like or a quasi-rod-like conformation. These genomes contain a central conserved region that is involved in replication in the nucleus through an asymmetric RNA-RNA rolling-circle mechanism. Members of the family Pospiviroidae lack the hammerhead ribozymes that are typical of viroids classified in the family Avsunviroidae. The family Pospiviroidae includes the genera Apscaviroid, Cocadviroid, Coleviroid, Hostuviroid and Pospiviroid, with >25 species. This is a summary of the ICTV Report on the family Pospiviroidae, which is available at ictv.global/report/pospiviroidae.
-
symptomatic plant viroid infections in phytopathogenic fungi a request for a critical reassessment
Proceedings of the National Academy of Sciences of the United States of America, 2020Co-Authors: P Serra, Alberto Carbonell, Selma Gagozachert, Beatriz Navarro, Shifang Li, Francesco Di Serio, Ricardo FloresAbstract:Since their discovery (1), viroids—small (∼250 to 430 nt), non–protein-coding, circular RNAs—are thought to infect and cause disease only in plants (2); thus, the report that they infect and incite symptoms in filamentous phytopathogenic fungi (3) is surprising. Viroids are classified into two families (4). Members of the Pospiviroidae , including potato spindle tuber viroid (PSTVd) (1, 5), replicate in the nucleus through an RNA–RNA rolling-circle mechanism catalyzed by host enzymes (RNA polymerase, RNase, and RNA ligase). Members of the Avsunviroidae , like peach latent mosaic viroid (PLMVd) (6), form hammerhead ribozymes (HHRz) that functionally substitute the RNase during replication in chloroplasts (4). The host range of the second family is restricted to plant species (or relatives) in which the viroids were described. Unexpectedly, Wei et al. (3) report that seven viroids, including PLMVd and avocado sunblotch viroid (ASBVd) (both of the Avsunviroidae ), infect Nicotiana benthamiana , a known host for only some members of … [↵][1]1To whom correspondence may be addressed. Email: rflores{at}ibmcp.upv.es or francesco.diserio{at}ipsp.cnr.it. [1]: #xref-corresp-1-1
-
Viroid pathogenesis: a critical appraisal of the role of RNA silencing in triggering the initial molecular lesion.
FEMS microbiology reviews, 2020Co-Authors: Ricardo Flores, Sonia Delgado, Beatriz Navarro, Pedro Serra, Francesco Di SerioAbstract:The initial molecular lesions through which viroids, satellite RNAs and viruses trigger signal cascades resulting in plant diseases are hotly debated. Since viroids are circular non-protein-coding RNAs of ∼250-430 nucleotides, they appear very convenient to address this issue. Viroids are targeted by their host RNA silencing defense, generating viroid-derived small RNAs (vd-sRNAs) that are presumed to direct Argonaute (AGO) proteins to inactivate messenger RNAs, thus initiating disease. Here, we review the existing evidence. Viroid-induced symptoms reveal a distinction. Those attributed to vd-sRNAs from potato spindle tuber viroid and members of the family Pospiviroidae (replicating in the nucleus) are late, non-specific and systemic. In contrast, those attributed to vd-sRNAs from peach latent mosaic viroid (PLMVd) and other members of the family Avsunviroidae (replicating in plastids) are early, specific and local. Remarkably, leaf sectors expressing different PLMVd-induced chloroses accumulate viroid variants with specific pathogenic determinants. Some vd-sRNAs containing such determinant guide AGO1-mediated cleavage of mRNAs that code for proteins regulating chloroplast biogenesis/development. Therefore, the initial lesions and the expected phenotypes are connected by short signal cascades, hence supporting a cause-effect relationship. Intriguingly, one virus satellite RNA initiates disease through a similar mechanism, whereas in the Pospiviroidae and in plant viruses the situation remains uncertain.
-
ICTV Virus Taxonomy Profile: Avsunviroidae.
The Journal of general virology, 2018Co-Authors: Francesco Di Serio, Georgios Vidalakis, Jacobus Th J Verhoeven, Jaroslav Matousek, Vicente Pallás, John W. Randles, Ricardo FloresAbstract:Members of the family Avsunviroidae have a single-stranded circular RNA genome that adopts a rod-like or branched conformation and can form, in the strands of either polarity, hammerhead ribozymes involved in their replication in plastids through a symmetrical RNA–RNA rolling-circle mechanism. These viroids lack the central conserved region typical of members of the family Pospiviroidae. The family Avsunviroidae includes three genera, Avsunviroid, Pelamoviroid and Elaviroid, with a total of four species. This is a summary of the ICTV Report on the taxonomy of the family Avsunviroidae, which is available at http://www.ictv.global/report/Avsunviroidae.
-
Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs.
Frontiers in microbiology, 2012Co-Authors: Ricardo Flores, Francesco Di Serio, P Serra, Sofia Minoia, Beatriz NavarroAbstract:As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson-Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non-canonical pairs and that specific loops in the rod-like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunviroidae adopt multibranched conformations occasionally stabilized by kissing-loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures - either global or local - determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.
