ArticleNucleic acids research2021
Formation of frameshift-stimulating RNA pseudoknots is facilitated by remodeling of their folding intermediates.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Coordinated translation initiation determines -1 programmed ribosomal frameshifting efficiency of chromosomal genes to impact on cell fitness.The FEBS journal · 2026Article
- Open questions on viral frameshifting: Exploiting the structural plasticity of the frameshifting element for therapeutic intervention.Biophysical journal · 2026Review
- Kinetic Traps in RNA Folding: Targeted Design of Frameshifting Element Mutants by Thermodynamic and Kinetic Analysis of the Chikungunya Virus.The journal of physical chemistry. B · 2026Article
- A DNA Scaffold Approach Facilitates 5' Labeling of the SARS-CoV-2 RNA Pseudoknot for Single-Molecule Förster Resonance Energy Transfer Investigation.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- Ribosome-induced mRNA pseudoknot interactions visualized by DMS MaP-Seq.bioRxiv : the preprint server for biology · 2025Article
- The Unpaved Road of Non-Coding RNA Structure-Function Relationships: Current Knowledge, Available Methodologies, and Future Trends.Non-coding RNA · 2025Review
- A Cascade of Conformational Switches in SARS-CoV-2 Frameshifting: Coregulation by Upstream and Downstream Elements.Biochemistry · 2025Article
- Heterogeneous and multiple conformational transition pathways between pseudoknots of the SARS-CoV-2 frameshift element.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Sarbecovirus programmed ribosome frameshift RNA element folding studied by NMR spectroscopy and comparative analyses.Nucleic acids research · 2024Article
- An intricate balancing act: Upstream and downstream frameshift co-regulatory elements.bioRxiv : the preprint server for biology · 2024Article
- -1 Programmed ribosomal frameshifting in Class 2 umbravirus-like RNAs uses multiple long-distance interactions to shift between active and inactive structures and destabilize the frameshift stimulating element.Nucleic acids research · 2023Article
- Structural and Functional Insights into Viral Programmed Ribosomal Frameshifting.Annual review of virology · 2023Review
- Translation initiation site of mRNA is selected through dynamic interaction with the ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Thoughts on how to think (and talk) about RNA structure.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Thinking Outside the Frame: Impacting Genomes Capacity by Programmed Ribosomal Frameshifting.Frontiers in molecular biosciences · 2022Review
- Programmed -1 ribosomal frameshifting from the perspective of the conformational dynamics of mRNA and ribosomes.Computational and structural biotechnology journal · 2021Review
- Unraveling the Role of Topoisomerase 3β (TOP3B) in mRNA Translation and Human Disease.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Programmed -1 ribosomal frameshifting is an essential regulation mechanism of translation in viruses and bacteria. It is stimulated by mRNA structures inside the coding region. As the structure is unfolded repeatedly by consecutive translating ribosomes, whether it can refold properly each time is important in performing its function. By using single-molecule approaches and molecular dynamics simulations, we found that a frameshift-stimulating RNA pseudoknot folds sequentially through its upstream stem S1 and downstream stem S2. In this pathway, S2 folds from the downstream side and tends to be trapped in intermediates. By masking the last few nucleotides to mimic their gradual emergence from translating ribosomes, S2 can be directed to fold from the upstream region. The results show that the intermediates are greatly suppressed, suggesting that mRNA refolding may be modulated by ribosomes. Moreover, masking the first few nucleotides of S1 favors the folding from S2 and yields native pseudoknots, which are stable enough to retrieve the masked nucleotides. We hypothesize that translating ribosomes can remodel an intermediate mRNA structure into a stable conformation, which may in turn stimulate backward slippage of the ribosome. This supports an interactive model of ribosomal frameshifting and gives an insightful account addressing previous experimental observations.
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