ArticleRNA biology2017
Dissecting the secondary structure of the circular RNA of a nuclear viroid in vivo: A "naked" rod-like conformation similar but not identical to that observed in vitro.
Article in RNA biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 49 citations in OpenAlex.
- Analysis of Hop Stunt Viroid Diversity in Grapevine (Pathogens (Basel, Switzerland) · 2023Article
- Tobacco mosaic virus movement protein complements a Potato spindle tuber viroid RNA mutant impaired for mesophyll entry but not mutants unable to enter the phloem.PLoS pathogens · 2022Article
- A nuclear import pathway exploited by pathogenic noncoding RNAs.The Plant cell · 2022Article
- Conserved Motifs and Domains in Members ofCells · 2022Article
- Predicting the Structure of a Viroid : Structure, Structure Distribution, Consensus Structure, and Structure Drawing.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Studies on Viroid Shed Light on the Role of RNA Three-Dimensional Structural Motifs in RNA Trafficking in Plants.Frontiers in plant science · 2022Review
- A scenario for the emergence of protoviroids in the RNA world and for their further evolution into viroids and viroid-like RNAs by modular recombinations and mutations.Virus evolution · 2022Review
- Recent research progress on circular RNAs: Biogenesis, properties, functions, and therapeutic potential.Molecular therapy. Nucleic acids · 2021Review
- ICTV Virus Taxonomy Profile:The Journal of general virology · 2021Article
- Effect of VIRP1 Protein on Nuclear Import of Citrus Exocortis Viroid (CEVd).Biomolecules · 2021Article
- The role of circular RNAs in viral infection and related diseases.Virus research · 2021Review
- Impact of Nucleic Acid Sequencing on Viroid Biology.International journal of molecular sciences · 2020Review
- Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA.Nucleic acids research · 2020Article
- Perspectives on Circular RNAs as Prostate Cancer Biomarkers.Frontiers in cell and developmental biology · 2020Review
- A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana.PLoS pathogens · 2019Article
- In silico survey of the central conserved regions in viroids of theRNA (New York, N.Y.) · 2019Article
- Reassessment of Viroid RNA Cytosine Methylation Status at the Single Nucleotide Level.Viruses · 2019Article
- Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy.RNA biology · 2019Article
- Circular RNAs-The Road Less Traveled.Frontiers in molecular biosciences · 2019Review
- Viroid research and its significance for RNA technology and basic biochemistry.Nucleic acids research · 2018Review
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With a minimal (250-400 nt), non-protein-coding, circular RNA genome, viroids rely on sequence/structural motifs for replication and colonization of their host plants. These motifs are embedded in a compact secondary structure whose elucidation is crucial to understand how they function. Viroid RNA structure has been tackled in silico with algorithms searching for the conformation of minimal free energy, and in vitro by probing in solution with RNases, dimethyl sulphate and bisulphite, and with selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), which interrogates the RNA backbone at single-nucleotide resolution. However, in vivo approaches at that resolution have not been assayed. Here, after confirming by 3 termodynamics-based predictions and by in vitro SHAPE that the secondary structure adopted by the infectious monomeric circular (+) RNA of potato spindle tuber viroid (PSTVd) is a rod-like conformation with double-stranded segments flanked by loops, we have probed it in vivo with a SHAPE modification. We provide direct evidence that a similar, but not identical, rod-like conformation exists in PSTVd-infected leaves of Nicotiana benthamiana, verifying the long-standing view that this RNA accumulates in planta as a "naked" form rather than tightly associated with protecting host proteins. However, certain nucleotides of the central conserved region, including some of the loop E involved in key functions such as replication, are more SHAPE-reactive in vitro than in vivo. This difference is most likely due to interactions with proteins mediating some of these functions, or to structural changes promoted by other factors of the in vivo habitat.
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