ArticleBiochemistry2014
Ribosome RNA assembly intermediates visualized in living cells.
Article in Biochemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- In Vivo RNA Chemical Footprinting Analysis in Archaea.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Contribution of an alternative 16S rRNA helix to biogenesis of the 30S subunit of the ribosome.RNA (New York, N.Y.) · 2024Article
- Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS.Nucleic acids research · 2023Article
- Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS.bioRxiv : the preprint server for biology · 2023Article
- RNA secondary structure packages evaluated and improved by high-throughput experiments.Nature methods · 2022Article
- SHAPE Directed Discovery of New Functions in Large RNAs.Accounts of chemical research · 2021Review
- Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy.RNA (New York, N.Y.) · 2020Article
- Advances in RNA 3D Structure Modeling Using Experimental Data.Frontiers in genetics · 2020Review
- Probing RNA structure in vivo.Current opinion in structural biology · 2019Review
- Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells.PLoS biology · 2019Article
- Effects of Refolding on Large-Scale RNA Structure.Biochemistry · 2019Article
- Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions.ACS chemical biology · 2019Review
- Carbodiimide reagents for the chemical probing of RNA structure in cells.RNA (New York, N.Y.) · 2019Article
- In-cell RNA structure probing with SHAPE-MaP.Nature protocols · 2018Article
- Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility.The journal of physical chemistry letters · 2018Article
- Characterizing the Structure-Function Relationship of a Naturally Occurring RNA Thermometer.Biochemistry · 2017Article
- FoldAtlas: a repository for genome-wide RNA structure probing data.Bioinformatics (Oxford, England) · 2017Article
- An RNA Element That Facilitates Programmed Ribosomal Readthrough in Turnip Crinkle Virus Adopts Multiple Conformations.Journal of virology · 2016Article
- SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).Methods (San Diego, Calif.) · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
In cells, RNAs likely adopt numerous intermediate conformations prior to formation of functional RNA-protein complexes. We used single-nucleotide resolution selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to probe the structure of Escherichia coli 16S rRNA in healthy growing bacteria. SHAPE-directed modeling indicated that the predominant steady-state RNA conformational ensemble in dividing cells had a base-paired structure different from that expected on the basis of comparative sequence analysis and high-resolution studies of the 30S ribosomal subunit. We identified the major cause of these differences by stopping ongoing in-cell transcription (in essence, an in-cell RNA structure pulse-chase experiment) which caused the RNA to chase into a structure that closely resembled the expected one. Most helices that formed alternate RNA conformations under growth conditions interact directly with tertiary-binding ribosomal proteins and form a C-shape that surrounds the mRNA channel and decoding site. These in-cell experiments lead to a model in which ribosome assembly factors function as molecular struts to preorganize this intermediate and emphasize that the final stages of ribonucleoprotein assembly involve extensive protein-facilitated RNA conformational changes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.