The Long-Range P3 Helix of the Tetrahymena Ribozyme Is Disrupted during Folding between the Native and Misfolded Conformations

• Published in: Journal of molecular biology Vol. 425; no. 15; pp. 2670 - 2686
• Main Authors: Mitchell, David, Jarmoskaite, Inga, Seval, Nikhil, Seifert, Soenke, Russell, Rick
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 09.08.2013
• Subjects: catalytic activity; catalytic RNA; Cations, Divalent - metabolism; group I intron; introns; magnesium; Magnesium - metabolism; Models, Biological; Models, Molecular; mutants; Mutation; Nucleic Acid Conformation; RNA; RNA Folding; RNA topology; RNA, Catalytic - chemistry; RNA, Catalytic - genetics; RNA, Catalytic - metabolism; Scattering, Small Angle; structured RNA; Tetrahymena; Tetrahymena - enzymology; topology; X-radiation; structured RNA; catalytic RNA; group I intron; RNA folding; RNA topology; DMS; EDTA; SAXS; ethylenediaminetetraacetic acid; dimethyl sulfate; small-angle X-ray scattering
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2013.05.008

RNAs are prone to misfolding, but how misfolded structures are formed and resolved remains incompletely understood. The Tetrahymena group I intron ribozyme folds in vitro to a long-lived misfolded conformation (M) that includes extensive native structure but is proposed to differ in topology from the native state (N). A leading model predicts that exchange of the topologies requires unwinding of the long-range, core helix P3, despite the presence of P3 in both conformations. To test this model, we constructed 16 mutations to strengthen or weaken P3. Catalytic activity and in-line probing showed that nearly all of the mutants form the M state before folding to N. The P3-weakening mutations accelerated refolding from M (3- to 30-fold) and the P3-strengthening mutations slowed refolding (6- to 1400-fold), suggesting that P3 indeed unwinds transiently. Upon depletion of Mg2+, the mutations had analogous effects on unfolding from N to intermediates that subsequently fold to M. The magnitudes for the P3-weakening mutations were larger than in refolding from M, and small-angle X-ray scattering showed that the ribozyme expands rapidly to intermediates from which P3 is disrupted subsequently. These results are consistent with previous results indicating unfolding of native peripheral structure during refolding from M, which probably permits rearrangement of the core. Together, our results demonstrate that exchange of the native and misfolded conformations requires loss of a core helix in addition to peripheral structure. Further, the results strongly suggest that misfolding arises from a topological error within the ribozyme core, and a specific topology is proposed. [Display omitted] •Structure and properties of misfolded Tetrahymena ribozyme (M) are probed.•Weakening P3 accelerates refolding of M and strengthening P3 slows refolding.•Small-angle X-ray scattering shows that loss of tertiary contacts can precede P3 disruption.•Unfolding requirements support a specific model of alternative topology in the M state.