ArticleRNA (New York, N.Y.)2014
Distinct functional classes of ram mutations in 16S rRNA.
Article in RNA (New York, N.Y.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 16 citations in OpenAlex.
- RNAViruses · 2026Review
- Multiscale Modeling of the Bacterial Ribosome to Identify Potential Peptide Modulators and Their Allosteric Effects.Biochemistry · 2026Article
- Interplay of the ribosome A and CAR sites.NAR genomics and bioinformatics · 2026Article
- Role of the sarcin-ricin loop of 23S rRNA in biogenesis of the 50S ribosomal subunit.RNA (New York, N.Y.) · 2025Article
- Directed evolution of rRNA improves translation kinetics and recombinant protein yield.Nature communications · 2021Article
- A Ribosome Interaction Surface Sensitive to mRNA GCN Periodicity.Biomolecules · 2020Article
- Fail-safe genetic codes designed to intrinsically contain engineered organisms.Nucleic acids research · 2019Article
- Ribosomal ambiguity (ram) mutations promote the open (off) to closed (on) transition and thereby increase miscoding.Nucleic acids research · 2019Article
- Article
- Atomic mutagenesis at the ribosomal decoding site.RNA biology · 2017Article
- Intersubunit Bridges of the Bacterial Ribosome.Journal of molecular biology · 2016Review
- Epistasis analysis of 16S rRNA ram mutations helps define the conformational dynamics of the ribosome that influence decoding.RNA (New York, N.Y.) · 2016Article
- Roles of helix H69 of 23S rRNA in translation initiation.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Another look at mutations in ribosomal protein S4 lends strong support to the domain closure model.Journal of bacteriology · 2015Article
- Modulation of decoding fidelity by ribosomal proteins S4 and S5.Journal of bacteriology · 2015Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
During decoding, the ribosome selects the correct (cognate) aminoacyl-tRNA (aa-tRNA) from a large pool of incorrect aa-tRNAs through a two-stage mechanism. In the initial selection stage, aa-tRNA is delivered to the ribosome as part of a ternary complex with elongation factor EF-Tu and GTP. Interactions between codon and anticodon lead to activation of the GTPase domain of EF-Tu and GTP hydrolysis. Then, in the proofreading stage, aa-tRNA is released from EF-Tu and either moves fully into the A/A site (a step termed "accommodation") or dissociates from the ribosome. Cognate codon-anticodon pairing not only stabilizes aa-tRNA at both stages of decoding but also stimulates GTP hydrolysis and accommodation, allowing the process to be both accurate and fast. In previous work, we isolated a number of ribosomal ambiguity (ram) mutations in 16S rRNA, implicating particular regions of the ribosome in the mechanism of decoding. Here, we analyze a representative subset of these mutations with respect to initial selection, proofreading, RF2-dependent termination, and overall miscoding in various contexts. We find that mutations that disrupt inter-subunit bridge B8 increase miscoding in a general way, causing defects in both initial selection and proofreading. Mutations in or near the A site behave differently, increasing miscoding in a codon-anticodon-dependent manner. These latter mutations may create spurious favorable interactions in the A site for certain near-cognate aa-tRNAs, providing an explanation for their context-dependent phenotypes in the cell.
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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.