Search results for "viroid"
showing 10 items of 22 documents
Highly efficient construction of infectious viroid-derived clones
2019
[Background] Viroid research generally relies on infectious cDNA clones that consist of dimers of the entire viroid sequence. At present, those dimers are generated by self-ligation of monomeric cDNA, a strategy that presents several disadvantages: (i) low efficiency, (ii) it is a non-oriented reaction requiring tedious screenings and (iii) additional steps are required for cloning into a binary vector for agroinfiltration or for in vitro RNA production.
Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology
2020
In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview r…
The effect of RNA substitution models on viroid and RNA virus phylogenies.
2018
Abstract Many viroids and RNA viruses have genomes that exhibit secondary structure, with paired nucleotides forming stems and loops. Such structures violate a key assumption of most methods of phylogenetic reconstruction, that sequence change is independent among sites. However, phylogenetic analyses of these transmissible agents rarely use evolutionary models that account for RNA secondary structure. Here, we assess the effect of using RNA-specific nucleotide substitution models on the phylogenetic inference of viroids and RNA viruses. We obtained data sets comprising full-genome nucleotide sequences from six viroid and ten single-stranded RNA virus species. For each alignment, we inferre…
Symptom severity, infection progression and plant responses in solanum plants caused by three pospiviroids vary with the inoculation procedure
2021
This article belongs to the Section Molecular Plant Sciences.
Hop stunt viroid: A polyphagous pathogenic RNA that has shed light on viroid–host interactions
2021
[Taxonomy]: Hop stunt viroid (HSVd) is the type species of the genus Hostuviroid (family Pospiviroidae). The other species of this genus is Dahlia latent viroid, which presents an identical central conserved region (CCR) but lacks other structural hallmarks present in Hop stunt viroid. HSVd replication occurs in the nucleus through an asymmetric rolling-circle model as in the other members of the family Pospiviroidae, which also includes the genera Pospiviroid, Cocadviroid, Apscaviroid, and Coleoviroid.
Different rates of spontaneous mutation of chloroplastic and nuclear viroids as determined by high-fidelity ultra-deep sequencing
2017
[EN] Mutation rates vary by orders of magnitude across biological systems, being higher for simpler genomes. The simplest known genomes correspond to viroids, subviral plant replicons constituted by circular non-coding RNAs of few hundred bases. Previous work has revealed an extremely high mutation rate for chrysanthemum chlorotic mottle viroid, a chloroplastreplicating viroid. However, whether this is a general feature of viroids remains unclear. Here, we have used high-fidelity ultra-deep sequencing to determine the mutation rate in a common host (eggplant) of two viroids, each representative of one family: the chloroplastic eggplant latent viroid (ELVd, Avsunviroidae) and the nuclear pot…
Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo
2019
This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs. Viroids are small, non-coding, circular RNA molecules that infect plants. Different hypotheses for their evolutionary origin have been put forward, such as an early emergence in a precellular RNA World or several de novo independent evolutionary origins in plants. Here, we discuss the plausibility of de novo emergence of viroid-like replicons by giving theoretical support to the likelihood of different steps along a parsimonious evolutionary pathway. While Avsunviroidae-like structures are relatively easy to obtain through evolution of a population of random RNA sequences of fixe…
Processing of RNAs of the Family Avsunviroidae in Chlamydomonas reinhardtii Chloroplasts
2007
ABSTRACT The family Avsunviroidae comprises four viroid species with the ability to form hammerhead ribozymes that mediate self-cleavage of the multimeric plus and minus strands resulting from replication in the chloroplast through a symmetric rolling-circle mechanism. Research on these RNAs is restricted by their host range, which is limited to the plants wherein they were initially identified and some closely related species. Here we report cleavage and ligation in transplastomic Chlamydomonas reinhardtii expressing plus- and minus-strand dimeric transcripts of representative members of the family Avsunviroidae . Despite the absence of viroid RNA-RNA transcription, the C. reinhardtii -bas…
C7(P32) and C6(P34) PR proteins induced in tomato leaves by citrus exocortis viroid infection are chitinases
1990
[EN] Two chitinases induced in tomato leaves (Lycopersicon esculentum Mill cv. Rutgers) by citrus exocortis viroid (CEV) infection were purified. Their molecular masses determined by sodium dodecyl sulfate-gel electrophoresis were 32 kDa and 34 kDa and by filtration through Sephadex G-100 were 23 kDa and 25 kDa, respectively. These chitinases (P32 and P34) have been shown to be identical to the tomato pathogenesis-related proteins C7 and C6. They were purified in three stages: ammonium sulphate fractionation, chitin affinity chromatography and CM-Sepharose chromatography. The characterization of P32, the major component of the CEV-induced chitinase activity, revealed a basic protein (pI, 8·…
Mutational analysis of eggplant latent viroid RNA processing in Chlamydomonas reinhardtii chloroplast.
2009
Viroids of the family Avsunviroidae, such as eggplant latent viroid (ELVd), contain hammerhead ribozymes and replicate in the chloroplasts of the host plant through an RNA-based symmetrical rolling-circle mechanism in which oligomeric RNAs of both polarity are processed to monomeric linear RNAs (by cleavage) and to monomeric circular RNAs (by ligation). Using an experimental system consisting of transplastomic lines of the alga Chlamydomonas reinhardtii, a mutational analysis of sequence and structural elements in the ELVd molecule that are involved in transcript processing in vivo in a chloroplastic context was carried out. A collection of six insertion and three deletion ELVd mutants was …