ArticlePLoS biology2019
Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells.
Article in PLoS biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 32 citations in OpenAlex.
- Evidence for a Constrained Mutational Pathway to High-Level Spectinomycin Resistance inInternational journal of molecular sciences · 2026Article
- RNA functional modulation by Mitoxantrone via RNA structural ensemble repartitioning.Nature communications · 2026Article
- The role of ribosomal protein networks in ribosome dynamics.Nucleic acids research · 2025Article
- Article
- RNA tertiary structure and conformational dynamics revealed by BASH MaP.bioRxiv : the preprint server for biology · 2024Article
- Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS.Nucleic acids research · 2023Article
- Nano-DMS-MaP allows isoform-specific RNA structure determination.Nature methods · 2023Article
- Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS.bioRxiv : the preprint server for biology · 2023Article
- Single-Molecule Correlated Chemical Probing: A Revolution in RNA Structure Analysis.Accounts of chemical research · 2023Article
- Probing the dynamic RNA structurome and its functions.Nature reviews. Genetics · 2023Review
- CryoEM structures of pseudouridine-free ribosome suggest impacts of chemical modifications on ribosome conformations.Structure (London, England : 1993) · 2022Article
- Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP.Molecular cell · 2022Article
- Direct detection of RNA modifications and structure using single-molecule nanopore sequencing.Cell genomics · 2022Article
- Review
- Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP.Biochemistry · 2021Article
- SHAPE Directed Discovery of New Functions in Large RNAs.Accounts of chemical research · 2021Review
- Analysis of RNA-protein networks with RNP-MaP defines functional hubs on RNA.Nature biotechnology · 2021Article
- Time-Resolved, Single-Molecule, Correlated Chemical Probing of RNA.Journal of the American Chemical Society · 2020Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The ribosome moves between distinct structural states and is organized into multiple functional domains. Here, we examined hundreds of occurrences of pairwise through-space communication between nucleotides in the ribosome small subunit RNA using RNA interaction groups analyzed by mutational profiling (RING-MaP) single-molecule correlated chemical probing in bacterial cells. RING-MaP revealed four structural communities in the small subunit RNA, each distinct from the organization defined by the RNA secondary structure. The head domain contains 2 structural communities: the outer-head contains the pivot for head swiveling, and an inner-head community is structurally integrated with helix 44 and spans the entire ribosome intersubunit interface. In-cell binding by the antibiotic spectinomycin (Spc) barely perturbs its local binding pocket as revealed by the per-nucleotide chemical probing signal. In contrast, Spc binding overstabilizes long-range RNA-RNA contacts that extend 95 Å across the ribosome that connect the pivot for head swiveling with the axis of intersubunit rotation. The two major motions of the small subunit-head swiveling and intersubunit rotation-are thus coordinated via long-range RNA structural communication, which is specifically modulated by Spc. Single-molecule correlated chemical probing reveals trans-domain structural communication and rationalizes the profound functional effects of binding by a low-molecular-mass antibiotic to the megadalton ribosome.
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