886 research outputs found
Revisiting the non-coding nature of pospiviroids
Abstract : Viroids are small, circular, highly structured pathogens that infect a broad range of plants, causing economic losses. Since their discovery in the 1970s, they have been considered as non-coding pathogens. In the last few years, the discovery of other RNA entities, similar in terms of size and structure, that were shown to be translated (e.g., cirRNAs, precursors of miRNA, RNA satellites) as well as studies showing that some viroids are located in ribosomes, have reignited the idea that viroids may be translated. In this study, we used advanced bioinformatic analysis, in vitro experiments and LC-MS/MS to search for small viroid peptides of the PSTVd. Our results suggest that in our experimental conditions, even though the circular form of PSTVd is found in ribosomes, no produced peptides were identified. This indicates that the presence of PSTVd in ribosomes is most probably not related to peptide production but rather to another unknown function that requires further study
Elucidation of the structures of all members of the Avsunviroidae family
Abstract: Viroids are small single-stranded RNA pathogens which cause
significant damage to plants. As their nucleic acids do not encode
for any proteins, they are dependant solely on their structure for
their propagation. The elucidation of the secondary structures of
viroids has been limited because of the exhaustive and timeconsuming
nature of classic approaches. Here, the method of
high-throughput selective 2'-hydroxyl acylation analysed by
primer extension (hSHAPE) has been adapted to probe the
viroid structure. The data obtained using this method were then
used as input for computer-assisted structure prediction using
RNAstructure software in order to determine the secondary structures
of the RNA strands of both (+) and (–) polarities of all
Avsunviroidae members, one of the two families of viroids. The
resolution of the structures of all of the members of the family
provides a global view of the complexity of these RNAs. The
structural differences between the two polarities, and any plausible
tertiary interactions, were also analysed. Interestingly, the
structures of the (+) and (–) strands were found to be different for
each viroid species. The structures of the recently isolated grapevine
hammerhead viroid-like RNA strands were also solved. This
species shares several structural features with the Avsunviroidae
family, although its infectious potential remains to be determined.
To our knowledge, this article represents the first report of the
structural elucidation of a complete family of viroids
Cultivated Grapevines Represent a Symptomless Reservoir for the Transmission of Hop Stunt Viroid to Hop Crops: 15 Years of Evolutionary Analysis
Hop stunt was a mysterious disorder that first emerged in the 1940s in commercial hops in Japan. To investigate the origin of this disorder, we infected hops with natural Hop stunt viroid (HpSVd) isolates derived from four host species (hop, grapevine, plum and citrus), which except for hop represent possible sources of the ancestral viroid. These plants were maintained for 15 years, then analyzed the HpSVd variants present. Here we show that the variant originally found in cultivated grapevines gave rise to various combinations of mutations at positions 25, 26, 54, 193, and 281. However, upon prolonged infection, these variants underwent convergent evolution resulting in a limited number of adapted mutants. Some of them showed nucleotide sequences identical to those currently responsible for hop stunt epidemics in commercial hops in Japan, China, and the United States. Therefore, these results indicate that we have successfully reproduced the original process by which a natural HpSVd variant naturally introduced into cultivated hops was able to mutate into the HpSVd variants that are currently present in commercial hops. Furthermore, and importantly, we have identified cultivated grapevines as a symptomless reservoir in which HSVd can evolve and be transmitted to hop crops to cause epidemics
Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNA`s
The analysis of small circular sequences requires specialized tools. While
the differences between linear and circular sequences can be neglected in the case of long molecules such as bacterial genomes since in practice all analysis is performed in sequence windows, this is not true for viroids and related sequences which are usually only a few hundred basepairs long. In this contribution we present basic algorithms and corresponding software for circular RNAs. In particular, we discuss the problem of pairwise and multiple cyclic sequence alignments with affine gap costs, and an extension of a recent approach to circular RNA folding to the computation of consensus structures
Viroid Intercellular Trafficking: RNA Motifs, Cellular Factors and Broad Impacts
Viroids are noncoding RNAs that infect plants. In order to establish systemic infection, these RNAs must traffic from an initially infected host cell into neighboring cells and ultimately throughout a whole plant. Recent studies have identified structural motifs in a viroid that are required for trafficking, enabling further studies on the mechanisms of their function. Some cellular proteins interact with viroids in vivo and may play a role in viroid trafficking, which can now be directly tested by using a virus-induced gene silencing system that functions efficiently in plant species from which these factors were identified. This review discusses these recent advances, unanswered questions and the use of viroid infection as an highly productive model to elucidate mechanisms of RNA trafficking that is of broad biological significance
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