ArticleProceedings of the National Academy of Sciences of the United States of America2018
A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 117 citations in OpenAlex.
- Article
- A key role for the exoribonuclease XRN1 in regulating the hepatitis B viral transcriptome.iScience · 2026Article
- A combined PIE-FRET and FCS assay to monitor RNA dynamics and cleavage by SARS-CoV-2 Nsp15.Scientific reports · 2026Article
- Rational design of mechanically active RNAs: de novo engineering of functional exoribonuclease-resistant RNAs.Nucleic acids research · 2026Article
- An A-rich linker between dengue virus tandem xrRNAs facilitates functional coordination.bioRxiv : the preprint server for biology · 2026Article
- Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers.Proteins · 2026Article
- A combined PIE-FRET and FCS assay to monitor RNA dynamics and cleavage by SARS-CoV-2 Nsp15.Research square · 2025Article
- A conserved viral RNA fold enables nuclease resistance across kingdoms of life.Nucleic acids research · 2025Article
- Tick-borne flavivirus exoribonuclease-resistant RNAs contain a double loop structure.Nature communications · 2025Article
- Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers.bioRxiv : the preprint server for biology · 2025Article
- The pseudoknot structure of a viral RNA reveals a conserved mechanism for programmed exoribonuclease resistance.bioRxiv : the preprint server for biology · 2024Article
- Assessing and engineering the IscB-ωRNA system for programmed genome editing.Nature chemical biology · 2024Article
- The role of structure in regulatory RNA elements.Bioscience reports · 2024Review
- The Dynamic Landscape of Capsid Proteins and Viral RNA Interactions in Flavivirus Genome Packaging and Virus Assembly.Pathogens (Basel, Switzerland) · 2024Review
- Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states.Cell chemical biology · 2024Review
- A Genetic Circuit Design for Targeted Viral RNA Degradation.Bioengineering (Basel, Switzerland) · 2023Article
- Xrn1-resistant RNA motifs are disseminated throughout the RNA virome and are able to block scanning ribosomes.Scientific reports · 2023Article
- Engineering circular RNA for enhanced protein production.Nature biotechnology · 2023Article
- Identification of consensus hairpin loop structure among the negative sense subgenomic RNAs of SARS-CoV-2.Bulletin of the National Research Centre · 2023Article
- Investigating the correlation between Xrn1-resistant RNAs and frameshifter pseudoknots.RNA biology · 2023Article
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
Abstract
Folded RNA elements that block processive 5' → 3' cellular exoribonucleases (xrRNAs) to produce biologically active viral noncoding RNAs have been discovered in flaviviruses, potentially revealing a new mode of RNA maturation. However, whether this RNA structure-dependent mechanism exists elsewhere and, if so, whether a singular RNA fold is required, have been unclear. Here we demonstrate the existence of authentic RNA structure-dependent xrRNAs in dianthoviruses, plant-infecting viruses unrelated to animal-infecting flaviviruses. These xrRNAs have no sequence similarity to known xrRNAs; thus, we used a combination of biochemistry and virology to characterize their sequence requirements and mechanism of stopping exoribonucleases. By solving the structure of a dianthovirus xrRNA by X-ray crystallography, we reveal a complex fold that is very different from that of the flavivirus xrRNAs. However, both versions of xrRNAs contain a unique topological feature, a pseudoknot that creates a protective ring around the 5' end of the RNA structure; this may be a defining structural feature of xrRNAs. Single-molecule FRET experiments reveal that the dianthovirus xrRNAs undergo conformational changes and can use "codegradational remodeling," exploiting the exoribonucleases' degradation-linked helicase activity to help form their resistant structure; such a mechanism has not previously been reported. Convergent evolution has created RNA structure-dependent exoribonuclease resistance in different contexts, which establishes it as a general RNA maturation mechanism and defines xrRNAs as an authentic functional class of RNAs.
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