The Experts below are selected from a list of 288 Experts worldwide ranked by ideXlab platform
Ricardo Flores - One of the best experts on this subject based on the ideXlab platform.
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Structure and Evolution of Viroids
Origin and Evolution of Viruses, 2020Co-Authors: Nuria Duran-vila, José-antonio Daròs, Santiago F. Elena, Ricardo FloresAbstract:ABSTRACT Viroids are minimal RNA replicons composed by a single-stranded and highly structured circular small RNA able to infect plants and induce diseases. Viroids lack protein-coding capacity and are therefore parasites of their host transcription machinery. The small size, circularity, high G+C content, and presence of hammerhead ribozymes in some Viroids, suggest their evolutionary origin in the RNA world. Phylogenetic reconstructions and structural and biological properties support a classification into two families—PospiViroidae and AvsunViroidae—whose members replicate in the nucleus and chloroplast, respectively. Viroids may have a common origin with a class of small satellite RNAs with which they share structural similarities and a rolling circle replication mechanism involving hammerhead ribozymes. Inoculation with infectious Viroid-cDNAs results in progenies readily accumulating genetic variation, with AvsunViroidae populations being more diverse than PospiViroidae populations. Moreover, assuming that the fitness of a haplotype is determined by its ability to fold into the secondary structure of minimum free energy, the estimated per site deleterious mutation rate in the AvsunViroidae is 10-fold higher than in the PospiViroidae. The dissimilar nuclear and chloroplastic RNA polymerases mediating replication in both families may influence their mutation rates, particularly when transcribing atypical RNA templates. Both families also differ in their structural robustness against mutation, with the PospiViroidae rod-like structures being more robust than the AvsunViroidae branched structures (and the redundant variants of a specific Viroid being more robust than their non-redundant counterparts). Chimeric Viroids might have emerged from recombination between co-infecting Viroids during transcription by a “jumping” RNA polymerase. Viroids polymorphic populations can be described by the quasispecies model of molecular evolution, and one of its main tenets (that a slow replicator outcompetes a faster one provided that the former is more robust against mutation) has been experimentally proven. Hosts play an important role in shaping the structure of Viroid populations. Specific domains of the Viroid secondary structure are responsible for symptom expression. Depending on their phylogenetic proximity, interactions between co-infecting Viroids may result in interference (cross-protection) or synergism, both of which may be governed by RNA silencing mechanisms that may have shaped Viroid structure and evolution as well. Wild plant species serve as symptomless reservoirs of certain Viroids, while their spread and persistence in cultivated species is associated with agricultural practices.
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Origin and Evolution of Viroids
Viroids and Satellites, 2020Co-Authors: Francesco Di Serio, Beatriz Navarro, Ricardo FloresAbstract:With their small, circular, nonprotein-coding RNA genome, which may be endowed with catalytic activity, Viroids have been proposed to be “fossils” of an RNA world preceding the cellular world based on DNA and proteins. This chapter summarizes the arguments sustaining this proposal and discusses the possible evolutionary scenarios for the adaptation of ancestor Viroids to a cellular environment. The implications of the quasispecies nature of Viroid populations and the constraints governing their evolution are also addressed, highlighting how a deeper understanding of Viroid evolution is closely linked to advances in the molecular mechanisms mediating plant–Viroid interactions.
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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, Shifang Li, Beatriz Navarro, Francesco Di Serio, Alberto Carbonell, Selma Gagozachert, 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
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specific argonautes selectively bind small rnas derived from potato spindle tuber Viroid and attenuate Viroid accumulation in vivo
Journal of Virology, 2014Co-Authors: Sofia Minoia, Beatriz Navarro, Francesco Di Serio, Alberto Carbonell, Andreas Gisel, James C Carrington, Ricardo FloresAbstract:ABSTRACT The identification of Viroid-derived small RNAs (vd-sRNAs) of 21 to 24 nucleotides (nt) in plants infected by Viroids (infectious non-protein-coding RNAs of just 250 to 400 nt) supports their targeting by Dicer-like enzymes, the first host RNA-silencing barrier. However, whether Viroids, like RNA viruses, are also targeted by the RNA-induced silencing complex (RISC) remains controversial. At the RISC core is one Argonaute (AGO) protein that, guided by endogenous or viral sRNAs, targets complementary RNAs. To examine whether AGO proteins also load vd-sRNAs, leaves of Nicotiana benthamiana infected by potato spindle tuber Viroid (PSTVd) were agroinfiltrated with plasmids expressing epitope-tagged versions of AGO1, AGO2, AGO3, AGO4, AGO5, AGO6, AGO7, AGO9, and AGO10 from Arabidopsis thaliana. Immunoprecipitation analyses of the agroinfiltrated halos revealed that all AGOs except AGO6, AGO7, and AGO10 associated with vd-sRNAs: AGO1, AGO2, and AGO3 preferentially with those of 21 and 22 nt, while AGO4, AGO5, and AGO9 additionally bound those of 24 nt. Deep-sequencing analyses showed that sorting of vd-sRNAs into AGO1, AGO2, AGO4, and AGO5 depended essentially on their 5′-terminal nucleotides, with the profiles of the corresponding AGO-loaded vd-sRNAs adopting specific hot spot distributions along the Viroid genome. Furthermore, agroexpression of AGO1, AGO2, AGO4, and AGO5 on PSTVd-infected tissue attenuated the level of the genomic RNAs, suggesting that they, or their precursors, are RISC targeted. In contrast to RNA viruses, PSTVd infection of N. benthamiana did not affect miR168-mediated regulation of the endogenous AGO1, which loaded vd-sRNAs with specificity similar to that of its A. thaliana counterpart. IMPORTANCE To contain invaders, particularly RNA viruses, plants have evolved an RNA-silencing mechanism relying on the generation by Dicer-like (DCL) enzymes of virus-derived small RNAs of 21 to 24 nucleotides (nt) that load and guide Argonaute (AGO) proteins to target and repress viral RNA. Viroids, despite their minimal genomes (non-protein-coding RNAs of only 250 to 400 nt), infect and incite disease in plants. The accumulation in these plants of 21- to 24-nt Viroid-derived small RNAs (vd-sRNAs) supports the notion that DCLs also target Viroids but does not clarify whether vd-sRNAs activate one or more AGOs. Here, we show that in leaves of Nicotiana benthamiana infected by potato spindle tuber Viroid, the endogenous AGO1 and distinct AGOs from Arabidopsis thaliana that were overexpressed were associated with vd-sRNAs displaying the same properties (5′-terminal nucleotide and size) previously established for endogenous and viral small RNAs. Overexpression of AGO1, AGO2, AGO4, and AGO5 attenuated Viroid accumulation, supporting their role in antiViroid defense.
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current status of Viroid taxonomy
Archives of Virology, 2014Co-Authors: F Di Serio, Ricardo Flores, Th J J Verhoeven, Shifang Li, Vicente Pallas, J W Randles, Teruo Sano, Georgios Vidalakis, Robert A OwensAbstract:Viroids are the smallest autonomous infectious nucleic acids known so far. With a small circular RNA genome of about 250-400 nt, which apparently does not code for any protein, Viroids replicate and move systemically in host plants. Since the discovery of the first Viroid almost forty-five years ago, many different Viroids have been isolated, characterized and, frequently, identified as the causal agents of plant diseases. The first Viroid classification scheme was proposed in the early 1990s and adopted by the International Committee on Taxonomy of Viruses (ICTV) a few years later. Here, the current Viroid taxonomy scheme and the criteria for Viroid species demarcation are discussed, highlighting the main taxonomic questions currently under consideration by the ICTV Viroid Study Group. The impact of correct taxonomic annotation of Viroid sequence variants is also addressed, taking into consideration the increasing application of next-generation sequencing and bioinformatics for known and previously unrecognized Viroids.
Beatriz Navarro - One of the best experts on this subject based on the ideXlab platform.
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Origin and Evolution of Viroids
Viroids and Satellites, 2020Co-Authors: Francesco Di Serio, Beatriz Navarro, Ricardo FloresAbstract:With their small, circular, nonprotein-coding RNA genome, which may be endowed with catalytic activity, Viroids have been proposed to be “fossils” of an RNA world preceding the cellular world based on DNA and proteins. This chapter summarizes the arguments sustaining this proposal and discusses the possible evolutionary scenarios for the adaptation of ancestor Viroids to a cellular environment. The implications of the quasispecies nature of Viroid populations and the constraints governing their evolution are also addressed, highlighting how a deeper understanding of Viroid evolution is closely linked to advances in the molecular mechanisms mediating plant–Viroid interactions.
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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, Shifang Li, Beatriz Navarro, Francesco Di Serio, Alberto Carbonell, Selma Gagozachert, 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
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Viroids Infecting the Grapevine
Grapevine Viruses: Molecular Biology Diagnostics and Management, 2017Co-Authors: F Di Serio, K. Izadpanah, M. Hajizadeh, Beatriz NavarroAbstract:Viroids are nonprotein-coding, small, circular RNAs infecting plants in which they may induce specific symptoms. Five different Viroids have been identified in the grapevine in the period elapsed from 1985 to 1990. Since then, no new Viroid has been reported from grapevines until the application of next-generation sequencing allowed the discovery of an additional Viroid and a new Viroid-like RNA. Possibly, new small, circular RNAs will be identified in the future by metagenomic approaches, but bioassays, which are time intensive and require phytopathological expertise, will always be needed for establishing conclusively their true identity as Viroids. Although Viroids generally do not elicit severe symptoms in grapevines, some of them are the agent of diseases in certain environmental conditions or in combination with certain viruses. Some of grapevine-infecting Viroids may cause severe diseases in other crops. This chapter reviews the molecular, biological, and epidemiological features of Viroids and Viroid-like RNAs infecting grapevines and the methods for their detection and control and discusses the future perspectives of research.
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specific argonautes selectively bind small rnas derived from potato spindle tuber Viroid and attenuate Viroid accumulation in vivo
Journal of Virology, 2014Co-Authors: Sofia Minoia, Beatriz Navarro, Francesco Di Serio, Alberto Carbonell, Andreas Gisel, James C Carrington, Ricardo FloresAbstract:ABSTRACT The identification of Viroid-derived small RNAs (vd-sRNAs) of 21 to 24 nucleotides (nt) in plants infected by Viroids (infectious non-protein-coding RNAs of just 250 to 400 nt) supports their targeting by Dicer-like enzymes, the first host RNA-silencing barrier. However, whether Viroids, like RNA viruses, are also targeted by the RNA-induced silencing complex (RISC) remains controversial. At the RISC core is one Argonaute (AGO) protein that, guided by endogenous or viral sRNAs, targets complementary RNAs. To examine whether AGO proteins also load vd-sRNAs, leaves of Nicotiana benthamiana infected by potato spindle tuber Viroid (PSTVd) were agroinfiltrated with plasmids expressing epitope-tagged versions of AGO1, AGO2, AGO3, AGO4, AGO5, AGO6, AGO7, AGO9, and AGO10 from Arabidopsis thaliana. Immunoprecipitation analyses of the agroinfiltrated halos revealed that all AGOs except AGO6, AGO7, and AGO10 associated with vd-sRNAs: AGO1, AGO2, and AGO3 preferentially with those of 21 and 22 nt, while AGO4, AGO5, and AGO9 additionally bound those of 24 nt. Deep-sequencing analyses showed that sorting of vd-sRNAs into AGO1, AGO2, AGO4, and AGO5 depended essentially on their 5′-terminal nucleotides, with the profiles of the corresponding AGO-loaded vd-sRNAs adopting specific hot spot distributions along the Viroid genome. Furthermore, agroexpression of AGO1, AGO2, AGO4, and AGO5 on PSTVd-infected tissue attenuated the level of the genomic RNAs, suggesting that they, or their precursors, are RISC targeted. In contrast to RNA viruses, PSTVd infection of N. benthamiana did not affect miR168-mediated regulation of the endogenous AGO1, which loaded vd-sRNAs with specificity similar to that of its A. thaliana counterpart. IMPORTANCE To contain invaders, particularly RNA viruses, plants have evolved an RNA-silencing mechanism relying on the generation by Dicer-like (DCL) enzymes of virus-derived small RNAs of 21 to 24 nucleotides (nt) that load and guide Argonaute (AGO) proteins to target and repress viral RNA. Viroids, despite their minimal genomes (non-protein-coding RNAs of only 250 to 400 nt), infect and incite disease in plants. The accumulation in these plants of 21- to 24-nt Viroid-derived small RNAs (vd-sRNAs) supports the notion that DCLs also target Viroids but does not clarify whether vd-sRNAs activate one or more AGOs. Here, we show that in leaves of Nicotiana benthamiana infected by potato spindle tuber Viroid, the endogenous AGO1 and distinct AGOs from Arabidopsis thaliana that were overexpressed were associated with vd-sRNAs displaying the same properties (5′-terminal nucleotide and size) previously established for endogenous and viral small RNAs. Overexpression of AGO1, AGO2, AGO4, and AGO5 attenuated Viroid accumulation, supporting their role in antiViroid defense.
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survey on Viroids infecting grapevine in italy identification and characterization of australian grapevine Viroid and grapevine yellow speckle Viroid 2
European Journal of Plant Pathology, 2014Co-Authors: Giorgio Gambino, Beatriz Navarro, E M Torchetti, P La Notte, A Schneider, F Mannini, F Di SerioAbstract:Five Viroid species have been reported from grapevine. Hop stunt Viroid (HSVd) and Grapevine yellow speckle Viroid 1 (GYSVd-1) are distributed worldwide, whereas Grapevine yellow speckle Viroid 2 (GYSVd-2), Australian grapevine Viroid (AGVd) and Citrus exocortis Viroid (CEVd) are found only sporadically. However, the presence of AGVd and GYSVd-2 in several countries, including China, Turkey and Tunisia, suggests a wider dissemination, possibly also in Europe, where AGVd has never been found and GYSVd-2 has been occasionally identified in Italy. Taking advantage of a multiplex RT-PCR assay recently developed for detecting simultaneously these five Viroids, vines growing in Italy in commercial vineyards and germplasm collections were surveyed. Besides confirming the widespread presence of HSVd and GYSVd-1 in the field, GYSVd-2 and/or AGVd were identified in two grapevine table cultivars (Sultanina Bianca and Red Globe) from germplasm collections. Tests extended to vines cultivated in southern Italy confirmed the presence of both Viroids, which were further characterized. No major sequence divergences between the AGVd and GYSVd-2 variants from Italy and those previously described from other countries were observed. Phylogenetic analysis supported the close relationships among AGVd variants from Italy, Tunisia and Australia. To our knowledge this is the first report of AGVd in Europe and the first molecular characterization of GYSVd-2 isolates from a European country.
Biao Ding - One of the best experts on this subject based on the ideXlab platform.
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Intracellular and intercellular transport of Viroids.
Viral Transport in Plants, 2020Co-Authors: Biao Ding, Asuka ItayaAbstract:Viroids are small, noncoding and nonencapsidated RNAs that infect plants. To establish systemic infection, Viroid genomes or their derivatives must interact directly with cellular factors. There is increasing evidence that subcellular localization and systemic trafficking of Viroid RNAs are regulated, likely via interactions between Viroid RNA cis elements and specific cellular proteins. Here we summarize recent progress on the characterization of Viroid structures and host proteins that may play important roles in trafficking. We also discuss critical issues that need to be addressed in future investigations.
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rna 3 dimensional structural motifs as a critical constraint of Viroid rna evolution
PLOS Pathogens, 2018Co-Authors: Ying Wang, Craig L Zirbel, Neocles B Leontis, Biao DingAbstract:Viroids are circular noncoding RNAs infecting plants [1, 2]. During infection, Viroids, like RNA viruses, generate swarms of sequence variants called quasispecies [3, 4]. Viroids in AvsunViroidae family replicate in chloroplasts and display the highest mutation rates among all living entities [5]. Viroids in PospiViroidae family replicate in the nucleus with a relatively lower mutation rate resembling some RNA viruses [6]. Those sequence variants generated during replication are described by the concept of sequence space, which harnesses a geometric representation to illustrate genetic similarities via physical distances. Given the high mutation rate and fast propagation, Viroid RNAs have a potentially large sequence space for the evolution of new variants. However, in reality, they use only a small fraction of this space. Constraints of viral sequence space may include genome size, replication fidelity, error thresholds, host or tissue tropism, etc. These factors have been nicely reviewed elsewhere [3, 7, 8] and are not the focus of this Pearl. In addition, RNA secondary structures have been considered, though not adequately, as a constraint factor [8]. Viroids, in contrast to viruses, entirely rely on their RNA structural motifs for function due to their noncoding nature, which offers insights into their capacity to explore regions of sequence space influenced by RNA structures. Here, we describe that 3-dimensional (3D) structural motifs formed by non–Watson-Crick (non-WC) base pairs in Viroid RNAs act as a critical constraint for the sequence space of Viroid genome evolution. This constraint operates because RNA 3D motifs can play crucial roles by mediating (1) RNA–RNA interactions for the folding of a part or a whole of RNA into a distinct tertiary conformation and (2) RNA–protein interactions. Therefore, mutations in a 3D motif that do not disrupt the structure and function will be retained in the population, whereas mutations that disrupt the 3D structures of motifs, and consequently the function, will be lost.
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comprehensive transcriptome analyses reveal that potato spindle tuber Viroid triggers genome wide changes in alternative splicing inducible trans acting activity of phased secondary small interfering rnas and immune responses
Journal of Virology, 2017Co-Authors: Yi Zheng, Ying Wang, Biao DingAbstract:ABSTRACT Many pathogens express noncoding RNAs (ncRNAs) during infection processes. In the most extreme case, pathogenic ncRNAs alone (such as Viroids) can infect eukaryotic organisms, leading to diseases. While a few pathogenic ncRNAs have been implicated in regulating gene expression, the functions of most pathogenic ncRNAs in host-pathogen interactions remain unclear. Here, we employ potato spindle tuber Viroid (PSTVd) infecting tomato as a system to dissect host interactions with pathogenic ncRNAs, using comprehensive transcriptome analyses. We uncover various new activities in regulating gene expression during PSTVd infection, such as genome-wide alteration in alternative splicing of host protein-coding genes, enhanced guided-cleavage activities of a host microRNA, and induction of the trans -acting function of phased secondary small interfering RNAs. Furthermore, we reveal that PSTVd infection massively activates genes involved in plant immune responses, mainly those in the calcium-dependent protein kinase and mitogen-activated protein kinase cascades, as well as prominent genes involved in hypersensitive responses, cell wall fortification, and hormone signaling. Intriguingly, our data support a notion that plant immune systems can respond to pathogenic ncRNAs, which has broad implications for providing new opportunities for understanding the complexity of immune systems in differentiating “self” and “nonself,” as well as lay the foundation for resolving the long-standing question regarding the pathogenesis mechanisms of Viroids and perhaps other infectious RNAs. IMPORTANCE Numerous pathogens, including viruses, express pathogenic noncoding transcripts during infection. In the most extreme case, pathogenic noncoding RNAs alone (i.e., Viroids) can cause disease in plants. While some work has demonstrated that pathogenic noncoding RNAs interact with host factors for function, the biological significance of pathogenic noncoding RNAs in host-pathogen interactions remains largely unclear. Here, we apply comprehensive genome-wide analyses of plant-Viroid interactions and discover several novel molecular activities underlying nuclear-replicating Viroid infection processes in plants, including effects on the expression and function of host noncoding transcripts, as well as the alternative splicing of host protein-coding genes. Importantly, we show that plant immunity is activated upon infection of a nuclear-replicating Viroid, which is a new concept that helps to understand Viroid-based pathogenesis. Our finding has broad implications for understanding the complexity of host immune systems and the diverse functions of noncoding RNAs.
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the biology of Viroid host interactions
Annual Review of Phytopathology, 2009Co-Authors: Biao DingAbstract:Viroids are single-stranded, circular, and noncoding RNAs that infect plants. They replicate in the nucleus or chloroplast and then traffic cell-to-cell through plasmodesmata and long distance through the phloem to establish systemic infection. They also cause diseases in certain hosts. All functions are mediated directly by the Viroid RNA genome or genome-derived RNAs. I summarize recent advances in the understanding of Viroid structures and cellular factors enabling these functions, emphasizing conceptual developments, major knowledge gaps, and future directions. Newly emerging experimental systems and research tools are discussed that are expected to enable significant progress in a number of key areas. I highlight examples of groundbreaking contributions of Viroid research to the development of new biological principles and offer perspectives on using Viroid models to continue advancing some frontiers of life science.
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rnai mediated resistance to potato spindle tuber Viroid in transgenic tomato expressing a Viroid hairpin rna construct
Molecular Plant Pathology, 2009Co-Authors: Nora Schwind, Biao Ding, Asuka Itaya, Michele Zwiebel, Mingbo Wang, Gabi Krczal, Michael WasseneggerAbstract:SUMMARY Because of their highly ordered structure, mature Viroid RNA molecules are assumed to be resistant to degradation by RNA interference (RNAi). In this article, we report that transgenic tomato plants expressing a hairpin RNA (hpRNA) construct derived from Potato spindle tuber Viroid (PSTVd) sequences exhibit resistance to PSTVd infection. Resistance seems to be correlated with high-level accumulation of hpRNA-derived short interfering RNAs (siRNAs) in the plant. Thus, although small RNAs produced by infecting Viroids [small RNAs of PSTVd (srPSTVds)] do not silence Viroid RNAs efficiently to prevent their replication, hpRNA-derived siRNAs (hp-siRNAs) appear to effectively target the mature Viroid RNA. Genomic mapping of the hp-siRNAs revealed an unequal distribution of 21- and 24-nucleotide siRNAs of both (+)- and (–)-strand polarities along the PSTVd genome. These data suggest that RNAi can be employed to engineer plants for Viroid resistance, as has been well established for viruses.
Gerhard Steger - One of the best experts on this subject based on the ideXlab platform.
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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.
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Viroids: The Smallest Known Infectious Agents Cause Accumulation of Viroid-Specific Small RNAs
From Nucleic Acids Sequences to Molecular Medicine, 2012Co-Authors: Jaroslav Matoušek, 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.
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characterization of plant mirnas and small rnas derived from potato spindle tuber Viroid pstvd in infected tomato
Biological Chemistry, 2010Co-Authors: Natalie Diermann, Detlev Riesner, Jaroslav Matoušek, Markus Junge, Gerhard StegerAbstract:: To defend against invading pathogens, plants possess RNA silencing mechanisms involving small RNAs (miRNAs, siRNAs). Also Viroids - plant infectious, non-coding, unencapsidated RNA - cause the production of Viroid-specific small RNAs (vsRNA), but Viroids do escape the cytoplasmic silencing mechanism. Viroids with minor sequence variations can produce different symptoms in infected plants, suggesting an involvement of vsRNAs in symptom production. We analyzed by deep sequencing the spectrum of vsRNAs induced by the PSTVd strain AS1, which causes strong symptoms such as dwarfing and necrosis upon infection of tomato plants cv Rutgers. Indeed, vsRNAs found with highest frequency mapped to the pathogenicity-modulating domain of PSTVd, supporting an involvement of vsRNAs in symptom production. Furthermore, in PSTVd AS1-infected plants the accumulation of some endogenous miRNAs, which are involved in leaf development via regulation of transcription factors, is suppressed. The latter finding supports the hypothesis that a miRNA-dependent (mis)regulation of transcription factors causes the Viroid symptoms.
Francesco Di Serio - One of the best experts on this subject based on the ideXlab platform.
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Origin and Evolution of Viroids
Viroids and Satellites, 2020Co-Authors: Francesco Di Serio, Beatriz Navarro, Ricardo FloresAbstract:With their small, circular, nonprotein-coding RNA genome, which may be endowed with catalytic activity, Viroids have been proposed to be “fossils” of an RNA world preceding the cellular world based on DNA and proteins. This chapter summarizes the arguments sustaining this proposal and discusses the possible evolutionary scenarios for the adaptation of ancestor Viroids to a cellular environment. The implications of the quasispecies nature of Viroid populations and the constraints governing their evolution are also addressed, highlighting how a deeper understanding of Viroid evolution is closely linked to advances in the molecular mechanisms mediating plant–Viroid interactions.
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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, Shifang Li, Beatriz Navarro, Francesco Di Serio, Alberto Carbonell, Selma Gagozachert, 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
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specific argonautes selectively bind small rnas derived from potato spindle tuber Viroid and attenuate Viroid accumulation in vivo
Journal of Virology, 2014Co-Authors: Sofia Minoia, Beatriz Navarro, Francesco Di Serio, Alberto Carbonell, Andreas Gisel, James C Carrington, Ricardo FloresAbstract:ABSTRACT The identification of Viroid-derived small RNAs (vd-sRNAs) of 21 to 24 nucleotides (nt) in plants infected by Viroids (infectious non-protein-coding RNAs of just 250 to 400 nt) supports their targeting by Dicer-like enzymes, the first host RNA-silencing barrier. However, whether Viroids, like RNA viruses, are also targeted by the RNA-induced silencing complex (RISC) remains controversial. At the RISC core is one Argonaute (AGO) protein that, guided by endogenous or viral sRNAs, targets complementary RNAs. To examine whether AGO proteins also load vd-sRNAs, leaves of Nicotiana benthamiana infected by potato spindle tuber Viroid (PSTVd) were agroinfiltrated with plasmids expressing epitope-tagged versions of AGO1, AGO2, AGO3, AGO4, AGO5, AGO6, AGO7, AGO9, and AGO10 from Arabidopsis thaliana. Immunoprecipitation analyses of the agroinfiltrated halos revealed that all AGOs except AGO6, AGO7, and AGO10 associated with vd-sRNAs: AGO1, AGO2, and AGO3 preferentially with those of 21 and 22 nt, while AGO4, AGO5, and AGO9 additionally bound those of 24 nt. Deep-sequencing analyses showed that sorting of vd-sRNAs into AGO1, AGO2, AGO4, and AGO5 depended essentially on their 5′-terminal nucleotides, with the profiles of the corresponding AGO-loaded vd-sRNAs adopting specific hot spot distributions along the Viroid genome. Furthermore, agroexpression of AGO1, AGO2, AGO4, and AGO5 on PSTVd-infected tissue attenuated the level of the genomic RNAs, suggesting that they, or their precursors, are RISC targeted. In contrast to RNA viruses, PSTVd infection of N. benthamiana did not affect miR168-mediated regulation of the endogenous AGO1, which loaded vd-sRNAs with specificity similar to that of its A. thaliana counterpart. IMPORTANCE To contain invaders, particularly RNA viruses, plants have evolved an RNA-silencing mechanism relying on the generation by Dicer-like (DCL) enzymes of virus-derived small RNAs of 21 to 24 nucleotides (nt) that load and guide Argonaute (AGO) proteins to target and repress viral RNA. Viroids, despite their minimal genomes (non-protein-coding RNAs of only 250 to 400 nt), infect and incite disease in plants. The accumulation in these plants of 21- to 24-nt Viroid-derived small RNAs (vd-sRNAs) supports the notion that DCLs also target Viroids but does not clarify whether vd-sRNAs activate one or more AGOs. Here, we show that in leaves of Nicotiana benthamiana infected by potato spindle tuber Viroid, the endogenous AGO1 and distinct AGOs from Arabidopsis thaliana that were overexpressed were associated with vd-sRNAs displaying the same properties (5′-terminal nucleotide and size) previously established for endogenous and viral small RNAs. Overexpression of AGO1, AGO2, AGO4, and AGO5 attenuated Viroid accumulation, supporting their role in antiViroid defense.
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small rnas containing the pathogenic determinant of a chloroplast replicating Viroid guide the degradation of a host mrna as predicted by rna silencing
Plant Journal, 2012Co-Authors: Beatriz Navarro, Ricardo Flores, Sonia Delgado, Andreas Gisel, Maria Elena Rodio, Francesco Di SerioAbstract:SUMMARYHow Viroids, tiny non-protein-coding RNAs ( 250–400 nt), incite disease is unclear. One hypothesis is thatViroid-derived small RNAs (vd-sRNAs; 21–24 nt) resulting from the host defensive response, via RNA silencing,may target for cleavagecell mRNAs andtrigger a signal cascade, eventuallyleading tosymptoms.Peachlatentmosaic Viroid (PLMVd), a chloroplast-replicating Viroid, is particularly appropriate to tackle this questionbecauseit inducesanalbinism(peachcalico,PC)strictlyassociatedwithvariantscontainingaspecific12–14-nthairpin insertion. By dissecting albino and green leaf sectors of Prunus persica (peach) seedlings inoculatedwith PLMVd natural and artificial variants, and cloning their progeny, we have established that the hairpininsertion sequence is involved in PC. Furthermore, using deep sequencing, semi-quantitative RT-PCR and RNAligase-mediated rapid amplification of cDNA ends (RACE), we have determined that two PLMVd-sRNAscontaining the PC-associated insertion (PC-sRNA8a and PC-sRNA8b) target for cleavage the mRNA encodingthe chloroplastic heat-shock protein 90 (cHSP90), thus implicating RNA silencing in the modulation of hostgene expression by a Viroid. Chloroplast malformations previously reported in PC-expressing tissues areconsistent with the downregulation of cHSP90, which participates in chloroplast biogenesis and plastid-to-nucleus signal transduction in Arabidopsis. Besides PC-sRNA8a and PC-sRNA8b, both deriving from the less-abundant PLMVd ()) strand, we have identified other PLMVd-sRNAs potentially targeting peach mRNAs.These results also suggest that sRNAs derived from other PLMVd regions may downregulate additional peachgenes, ultimately resulting in other symptoms or in a more favorable host environment for Viroid infection.Keywords: chloroplast development, heat-shock protein 90, non-coding RNAs, PLMVd, RNA silencing, Viroidpathogenesis.INTRODUCTIONViroids are minimal RNAs that infect and often cause severediseases in plants (Flores et al., 2005; Tsagris et al., 2008;Ding, 2009). Based on their properties, among which theability to replicate through specific pathways of a rolling-circle mechanism in certain subcellular compartments iskey,Viroidspeciesareclassifiedintotwofamilies.ThefamilyPospiViroidae, type species Potato spindle tuber Viroid(PSTVd) (Diener, 1972; Gross et al., 1978), clusters Viroidsreplicating and accumulating in the nucleus, whereas thefamily AvsunViroidae, type species Avocado sunblotchViroid(ASBVd)(Symons,1981;Hutchinset al.,1986),includesViroidswithhammerheadribozymesinbothpolaritystrandsthat mediate self-cleavage of their replicative intermediatesgenerated in plastids (mostly chloroplasts) (Flores et al.,2000). Despite being composed of just a small (246–401 nt),circular, non-protein-coding RNA, Viroids can usurp andredirect the host machinery for completing their infectiouscycle. Therefore, Viroids largely differ from viruses, thereplication, movement and pathogenesis of which partlyrely on proteins encoded in their own genome. However,similarly to changes incited by viruses, Viroid infectionscause profound changes in their host homeostasis (Itaya
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deep sequencing of Viroid derived small rnas from grapevine provides new insights on the role of rna silencing in plant Viroid interaction
PLOS ONE, 2009Co-Authors: Beatriz Navarro, Francesco Di Serio, Vitantonio Pantaleo, Andreas Gisel, Simon Moxon, Tamas Dalmay, Gyorgy Denes Bisztray, Jozsef BurgyanAbstract: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.
