The Experts below are selected from a list of 54 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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ICTV Virus Taxonomy Profile: Avsunviroidae.
The Journal of general virology, 2018Co-Authors: Francesco Di Serio, Georgios Vidalakis, Jacobus Th J Verhoeven, Jaroslav Matousek, Robert A. Owens, 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.
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Apple hammerhead viroid-like RNA is a bona fide viroid: Autonomous replication and structural features support its inclusion as a new member in the genus Pelamoviroid.
Virus research, 2018Co-Authors: P. Serra, Amber Messmer, Daniel Sanderson, Delano James, Ricardo FloresAbstract:Abstract Apple hammerhead viroid-like RNA (AHVd RNA) has been reported in different apple cultivars and geographic regions and, considering the presence of hammerhead ribozymes in both polarity strands, suspected to be either a viroid of the family Avsunviroidae or a viroid-like satellite RNA. Here we report that dimeric head-to-tail in vitro transcripts of a 433-nt reference variant of AHVd RNA from cultivar “Pacific Gala” are infectious when mechanically inoculated to apple, thus showing that this RNA is a bona fide viroid for which we have kept the name apple hammerhead viroid (AHVd) until its pathogenicity, if any, is better assessed. By combining thermodynamics-based predictions with co-variation analyses of the natural genetic diversity found in AHVd we have inferred the most likely conformations for both AHVd polarity strands in vivo, with that of the (+) polarity strand being stabilized by a kissing loop-interaction similar to those reported in peach latent mosaic viroid and chrysathemum chlorotic mottle viroid, the two known members of the genus Pelamoviroid (family Avsunviroidae). Therefore, AHVd RNA fulfills the biological and molecular criteria to be allocated to this genus, the members of which, intriguingly, display low global sequence identity but high structural conservation.
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Peach Latent Mosaic Viroid in Infected Peach
Viroids and Satellites, 2017Co-Authors: Ricardo Flores, Sonia Delgado, Wen-xing Xu, Marina Barba, Beatriz Navarro, Carmen Hernández, Ahmed HadidiAbstract:Abstract Within the family Avsunviroidae, encompassing viroids that replicate in plastids through a rolling-circle mechanism involving hammerhead ribozymes, peach latent mosaic viroid (PLMVd) is the type member of genus Pelamoviroid. With a size varying ranging from 335 to 351 nt, due to the presence of an insertion in some sequence variants, PLMVd adopts a branched conformation stabilized by a kissing-loop interaction in the plus strand. Most PLMVd infections in peach are symptomless, although certain PLMVd isolates induce leaf mosaics/blotches and albinism (peach calico, PC), fruit deformations and discolorations, delays in foliation, flowering, and ripening, and reduced longevity. Small (21 nt) viroid-derived RNAs containing the 12–14 nt insertion that characterizes PC-inducing isolates most likely cause PC by guiding cleavage of a host mRNA as predicted by RNA silencing. PLMVd, which has been detected in the major peach-growing areas worldwide, is transmitted by infected propagation material, pruning tools, aphids, and pollen, but not by seeds.
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Chrysanthemum Chlorotic Mottle Viroid
Viroids and Satellites, 2017Co-Authors: Ricardo Flores, Selma Gago-zachert, P. Serra, Marcos De La Peña, Beatriz NavarroAbstract:Abstract Chrysanthemum chlorotic mottle viroid (CChMVd) (398–401 nt) belongs to genus Pelamoviroid, family Avsunviroidae and, like other members of this family, replicates in plastids through a rolling-circle mechanism involving hammerhead ribozymes. CChMVd RNA adopts a branched conformation stabilized by a kissing-loop interaction, resembling peach latent mosaic viroid in this respect. Chrysanthemum is the only natural and experimental host for CChMVd, which in the most sensitive varieties induces leaf mottling and chlorosis, delay in flowering, and dwarfing. The viroid has been found in major chrysanthemum growing areas including Europe and Asia. There are natural variants in which the change (UUUC→GAAA) mapping at a tetraloop in the CChMVd branched conformation is sufficient to change the symptomatic phenotype into a nonsymptomatic one without altering the viroid titer. Preinfection with nonsymptomatic variants prevents challenge inoculation with symptomatic ones. Moreover, experimental coinoculation with symptomatic and nonsymptomatic CChMVd variants results in symptomless phenotypes only when the latter is in vast excess, thus indicating its lower fitness.
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Chrysanthemum Chlorotic Mottle Viroid: a System for Reverse Genetics in the Family Avsunviroidae (Hammerhead Viroids)
2007Co-Authors: Ricardo FloresAbstract:Viroids are small single-stranded circular RNAs able to infect plants. Chrysanthemum chlorotic mottle was one of the first viroid diseases reported, but identification and characterization of the causing RNA was delayed by its low accumulation in vivo. Chrysanthemum chlorotic mottle viroid (CChMVd) (398-401 nt) adopts a branched conformation instead of the rod-like secondary structure characteristic of most viroids. The natural sequence variability and the effects of artificial mutants support that the branched conformation is physiologically relevant and additionally stabilized by a kissing-loop interaction critical for RNA in vitro folding and in vivo viability. CChMVd shares structural similarities with peach latent mosaic viroid, with which forms the genus Pelamoviroid within the family Avsunviroidae. CChMVd adopts hammerhead structures that catalyze self-cleavage of the oligomeric strands of both polarities resulting from replication through a symmetric rolling-circle mechanism. The two CChMVd hammerheads display peculiarities: the plus has an extra A close to the central conserved core, and the minus an unsually long helix II. There are non-symptomatic strains (CChMVd-NS) that protect against challenge inoculation with severe strains (CChMVd-S). Introduction by site-directed mutagenesis of one of the CChMVd-NS specific mutations (UUUCGAAA) is sufficient to change the symptomatic phenotype into non-symptomatic without altering the viroid titer. This pathogenicity determinant maps at a tetraloop of the CChMVd branched conformation. Co-inoculations with typical CChMVd-S and -NS variants showed that the infected plants remain symptomless only when the latter was in more than a 100fold excess, indicating the higher fitness of the S variant. RNA silencing could mediate the observed cross-protection.
Francesco Di Serio - One of the best experts on this subject based on the ideXlab platform.
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ICTV Virus Taxonomy Profile: Avsunviroidae.
The Journal of general virology, 2018Co-Authors: Francesco Di Serio, Georgios Vidalakis, Jacobus Th J Verhoeven, Jaroslav Matousek, Robert A. Owens, 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.
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Peach latent mosaic viroid: not so latent.
Molecular plant pathology, 2006Co-Authors: Ricardo Flores, Sonia Delgado, Carmen Hernández, Maria-elena Rodio, Silvia Ambrós, Francesco Di SerioAbstract:SUMMARY Taxonomy: Peach latent mosaic viroid (PLMVd) is the type species of the genus Pelamoviroid within the family Avsunviroidae of chloroplastic viroids with hammerhead ribozymes. Physical properties: A small circular RNA of 336–351 nt (differences in size result from the absence or presence of certain insertions) adopting a branched conformation stabilized by a pseudoknot between two kissing loops. This particular conformation is most likely responsible for the insolubility of PLMVd in highly saline conditions (in which other viroids adopting a rod-like conformation are soluble). Both polarity strands are able to form hammerhead structures and to self-cleave during replication as predicted by these ribozymes. Biological properties: Although most infections occur without conspicuous symptoms, certain PLMVd isolates induce leaf mosaics, blotches and in the most extreme cases albinism (peach calico, PC), flower streaking, delays in foliation, flowering and ripening, deformations and decolorations of fruits, which usually present cracked sutures and enlarged roundish stones, bud necrosis, stem pitting and premature ageing of the trees, which also adopt a characteristic growing pattern (open habit). The molecular determinant for PC has been mapped at a 12–14-nt insertion that folds into a hairpin capped by a U-rich loop present only in certain variants. PLMVd is horizontally transmitted by the propagation of infected buds and to a lesser extent by pruning tools and aphids, but not by pollen; the viroid is not vertically transmitted through seed. Interesting features: This provides a suitable system for studying how a minimal non-protein-coding catalytic RNA replicates (subverting a DNA-dependent RNA polymerase to transcribe an RNA template), moves, interferes with the metabolism of its host (inciting specific symptoms and a defensive RNA silencing response) and evolves following a quasi-species model characterized by a complex spectrum of variants.
José-antonio Daròs - One of the best experts on this subject based on the ideXlab platform.
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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.
P. Serra - One of the best experts on this subject based on the ideXlab platform.
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Apple hammerhead viroid-like RNA is a bona fide viroid: Autonomous replication and structural features support its inclusion as a new member in the genus Pelamoviroid.
Virus research, 2018Co-Authors: P. Serra, Amber Messmer, Daniel Sanderson, Delano James, Ricardo FloresAbstract:Abstract Apple hammerhead viroid-like RNA (AHVd RNA) has been reported in different apple cultivars and geographic regions and, considering the presence of hammerhead ribozymes in both polarity strands, suspected to be either a viroid of the family Avsunviroidae or a viroid-like satellite RNA. Here we report that dimeric head-to-tail in vitro transcripts of a 433-nt reference variant of AHVd RNA from cultivar “Pacific Gala” are infectious when mechanically inoculated to apple, thus showing that this RNA is a bona fide viroid for which we have kept the name apple hammerhead viroid (AHVd) until its pathogenicity, if any, is better assessed. By combining thermodynamics-based predictions with co-variation analyses of the natural genetic diversity found in AHVd we have inferred the most likely conformations for both AHVd polarity strands in vivo, with that of the (+) polarity strand being stabilized by a kissing loop-interaction similar to those reported in peach latent mosaic viroid and chrysathemum chlorotic mottle viroid, the two known members of the genus Pelamoviroid (family Avsunviroidae). Therefore, AHVd RNA fulfills the biological and molecular criteria to be allocated to this genus, the members of which, intriguingly, display low global sequence identity but high structural conservation.
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Chrysanthemum Chlorotic Mottle Viroid
Viroids and Satellites, 2017Co-Authors: Ricardo Flores, Selma Gago-zachert, P. Serra, Marcos De La Peña, Beatriz NavarroAbstract:Abstract Chrysanthemum chlorotic mottle viroid (CChMVd) (398–401 nt) belongs to genus Pelamoviroid, family Avsunviroidae and, like other members of this family, replicates in plastids through a rolling-circle mechanism involving hammerhead ribozymes. CChMVd RNA adopts a branched conformation stabilized by a kissing-loop interaction, resembling peach latent mosaic viroid in this respect. Chrysanthemum is the only natural and experimental host for CChMVd, which in the most sensitive varieties induces leaf mottling and chlorosis, delay in flowering, and dwarfing. The viroid has been found in major chrysanthemum growing areas including Europe and Asia. There are natural variants in which the change (UUUC→GAAA) mapping at a tetraloop in the CChMVd branched conformation is sufficient to change the symptomatic phenotype into a nonsymptomatic one without altering the viroid titer. Preinfection with nonsymptomatic variants prevents challenge inoculation with symptomatic ones. Moreover, experimental coinoculation with symptomatic and nonsymptomatic CChMVd variants results in symptomless phenotypes only when the latter is in vast excess, thus indicating its lower fitness.
Ahmed Hadidi - One of the best experts on this subject based on the ideXlab platform.
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Peach Latent Mosaic Viroid in Infected Peach
Viroids and Satellites, 2017Co-Authors: Ricardo Flores, Sonia Delgado, Wen-xing Xu, Marina Barba, Beatriz Navarro, Carmen Hernández, Ahmed HadidiAbstract:Abstract Within the family Avsunviroidae, encompassing viroids that replicate in plastids through a rolling-circle mechanism involving hammerhead ribozymes, peach latent mosaic viroid (PLMVd) is the type member of genus Pelamoviroid. With a size varying ranging from 335 to 351 nt, due to the presence of an insertion in some sequence variants, PLMVd adopts a branched conformation stabilized by a kissing-loop interaction in the plus strand. Most PLMVd infections in peach are symptomless, although certain PLMVd isolates induce leaf mosaics/blotches and albinism (peach calico, PC), fruit deformations and discolorations, delays in foliation, flowering, and ripening, and reduced longevity. Small (21 nt) viroid-derived RNAs containing the 12–14 nt insertion that characterizes PC-inducing isolates most likely cause PC by guiding cleavage of a host mRNA as predicted by RNA silencing. PLMVd, which has been detected in the major peach-growing areas worldwide, is transmitted by infected propagation material, pruning tools, aphids, and pollen, but not by seeds.
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a novel multiplex rt pcr probe capture hybridization rt pcr elisa for simultaneous detection of six viroids in four genera apscaviroid hostuviroid Pelamoviroid and pospiviroid
Journal of Virological Methods, 2002Co-Authors: A M Shamloul, F Faggioli, J M Keith, Ahmed HadidiAbstract:A rapid and sensitive assay was developed for the detection and identification of viroids by standard or multiplex reverse transcription-polymerase chain reaction (RT-PCR)-probe capture hybridization (RT-PCR-ELISA). The assay was applied successfully for the detection and identification of the following six viroid species from infected tissues: Potato spindle tuber viroid (Pospiviroid), Peach latent mosaic viroid (Pelamoviroid), Apple scar skin viroid (Apscaviroid), Apple dimple fruit viroid (Apscaviroid), Pear blister canker viroid (Apscaviroid), and Hop stunt viroid (Hostuviroid). Total RNA was obtained from infected tissue by the Qiagen RNeasy kit and, then viroid cDNA was synthesized using viroid specific complementary DNA primer. To identify and differentiate the amplicons of the six viroids, each amplicon was digoxigenin (DIG)-labelled during the amplification process, and then detected by a colorimetric system using a biotinylated cDNA capture probe specific for each viroid. The results revealed that each capture probe hybridized only to its complementary DIG-labelled amplicon. Thus the six viroids can be detected and differentiated in a multiplex RT-PCR-ELISA assay. In the multiplex assay, cDNAs of six viroids were synthesized simultaneously in one tube, DIG-labelled during amplification, then a portion of the DIG-labelled amplified products was hybridized with selected capture probe. All the six viroid capture probes hybridized to their respective complementary DIG-labelled RT-PCR-amplified product. These findings are important for viroid detection and identification for studying host-viroid interactions and for management and control viroid diseases.