Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells
Open Access
- 5 September 2019
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLoS Biology
- Vol. 17 (9), e3000393
- https://doi.org/10.1371/journal.pbio.3000393
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.Keywords
Funding Information
- National Science Foundation (MCB-1121024)
- National Institutes of Health (R35 GM122532)
This publication has 44 references indexed in Scilit:
- Coordinated conformational and compositional dynamics drive ribosome translocationNature Structural & Molecular Biology, 2013
- Rotation of the head of the 30S ribosomal subunit during mRNA translocationProceedings of the National Academy of Sciences of the United States of America, 2012
- Contribution of intersubunit bridges to the energy barrier of ribosomal translocationNucleic Acids Research, 2012
- Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA BindingScience, 2011
- Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sitesNature, 2010
- Crystal Structure of the Eukaryotic RibosomeScience, 2010
- Spontaneous Intersubunit Rotation in Single RibosomesMolecular Cell, 2008
- A Steric Block in Translation Caused by the Antibiotic SpectinomycinACS Chemical Biology, 2007
- Multiple Effects of S13 in Modulating the Strength of Intersubunit Interactions in the Ribosome During TranslationJournal of Molecular Biology, 2005
- Mutations of Non-canonical Base-pairs in the 3′ Major Domain ofEscherichia coli16 S Ribosomal RNA Affect the Initiation and Elongation of Protein SynthesisJournal of Molecular Biology, 1996