Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA

Hori, Naoto; Denesyuk, Natalia A.; Thirumalai, D.

Abstract

Both the small and large subunits of the ribosome, the molecular machine that synthesizes proteins, are complexes of ribosomal RNAs (rRNAs) and a number of proteins. In bacteria, the small subunit has a single 16S rRNA whose folding is the first step in its assembly. The central domain of the 16S rRNA folds independently, driven either by Mg2+ ions or by interaction with ribosomal proteins. In order to provide a quantitative description of ion-induced folding of the ∼350 nucleotide rRNA, we carried out extensive coarse-grained molecular simulations spanning Mg2+ concentration between 0–30 mM. The Mg2+ dependence of the radius of gyration shows that globally the rRNA folds cooperatively. Surprisingly, various structural elements order at different Mg2+ concentrations, indicative of the heterogeneous assembly even within a single domain of the rRNA. Binding of Mg2+ ions is highly specific, with successive ion condensation resulting in nucleation of tertiary structures. We also predict the Mg2+-dependent protection factors, measurable in hydroxyl radical footprinting experiments, which corroborate the specificity of Mg2+- induced folding. The simulations, which agree quantitatively with several experiments on the folding of a three-way junction, show that its folding is preceded by formation of other tertiary contacts in the central junction. Our work provides a starting point in simulating the early events in the assembly of the small subunit of the ribosome.

Citation

Hori, N., Denesyuk, N. A., & Thirumalai, D. (2021). Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA. Proceedings of the National Academy of Sciences, 118(10), Article e2020837118. https://doi.org/10.1073/pnas.2020837118

• Journal Article Type: Article
• Acceptance Date: Dec 21, 2020
• Online Publication Date: Mar 9, 2021
• Publication Date: Mar 9, 2021
• Deposit Date: Dec 23, 2020
• Publicly Available Date: Sep 10, 2021
• Journal: Proceedings of the National Academy of Sciences
• Print ISSN: 0027-8424
• Electronic ISSN: 1091-6490
• Publisher: National Academy of Sciences
• Peer Reviewed: Peer Reviewed
• Volume: 118
• Issue: 10
• Article Number: e2020837118
• DOI: https://doi.org/10.1073/pnas.2020837118
• Keywords: RNA folding, Divalent ions, Ribosome assembly, Coarse-grained simulation
• Public URL: https://nottingham-repository.worktribe.com/output/5172565
• Publisher URL: https://www.pnas.org/content/118/10/e2020837118