ArticleProceedings of the National Academy of Sciences of the United States of America2015
Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 77 citations in OpenAlex.
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- Structural and functional clues challenge the hypothesis that the yjdF riboswitch is natively regulated through broad recognition of azaaromatic compounds.Nucleic acids research · 2025Article
- RLDOCKScore: A Scoring Function for RNA-Ligand Docking and Small Molecule Virtual Screening.Journal of chemical theory and computation · 2025Article
- SMDesigner: a program to design sequence mutations to assess RNA structure.RNA (New York, N.Y.) · 2025Article
- Structurally distinct manganese-sensing riboswitch aptamers regulate different expression platform architectures.Nucleic acids research · 2025Article
- Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme.The Journal of chemical physics · 2024Article
- Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.Nucleic acids research · 2024Article
- Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression.Nature communications · 2024Article
- SPRank─A Knowledge-Based Scoring Function for RNA-Ligand Pose Prediction and Virtual Screening.Journal of chemical theory and computation · 2024Article
- Mechanistic Analysis of Riboswitch Ligand Interactions Provides Insights into Pharmacological Control over Gene Expression.bioRxiv : the preprint server for biology · 2024Article
- Full-Length NADBiochemistry · 2023Article
- A transient intermediate RNA structure underlies the regulatory function of theRNA (New York, N.Y.) · 2023Article
- Structure and function analysis of a type III preQThe Journal of biological chemistry · 2023Article
- Mechanism of Ligand Discrimination by theJournal of chemical information and modeling · 2023Article
- A riboswitch separated from its ribosome-binding site still regulates translation.Nucleic acids research · 2023Article
- Review
- Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets.Antibiotics (Basel, Switzerland) · 2022Article
- Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations.Cell reports. Physical science · 2022Article
- Affinity-Based Profiling of the Flavin Mononucleotide Riboswitch.Journal of the American Chemical Society · 2022Article
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
PreQ1-III riboswitches are newly identified RNA elements that control bacterial genes in response to preQ1 (7-aminomethyl-7-deazaguanine), a precursor to the essential hypermodified tRNA base queuosine. Although numerous riboswitches fold as H-type or HLout-type pseudoknots that integrate ligand-binding and regulatory sequences within a single folded domain, the preQ1-III riboswitch aptamer forms a HLout-type pseudoknot that does not appear to incorporate its ribosome-binding site (RBS). To understand how this unusual organization confers function, we determined the crystal structure of the class III preQ1 riboswitch from Faecalibacterium prausnitzii at 2.75 Å resolution. PreQ1 binds tightly (KD,app 6.5 ± 0.5 nM) between helices P1 and P2 of a three-way helical junction wherein the third helix, P4, projects orthogonally from the ligand-binding pocket, exposing its stem-loop to base pair with the 3' RBS. Biochemical analysis, computational modeling, and single-molecule FRET imaging demonstrated that preQ1 enhances P4 reorientation toward P1-P2, promoting a partially nested, H-type pseudoknot in which the RBS undergoes rapid docking (kdock ∼ 0.6 s(-1)) and undocking (kundock ∼ 1.1 s(-1)). Discovery of such dynamic conformational switching provides insight into how a riboswitch with bipartite architecture uses dynamics to modulate expression platform accessibility, thus expanding the known repertoire of gene control strategies used by regulatory RNAs.
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