Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state.

RNA
Shreyas S AthavaleLoren Dean Williams

Abstract

The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter- and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structural domain of the LSU. Domain III is primarily stabilized by intra-domain interactions, negligibly perturbed by inter-domain interactions, and is not penetrated by ribosomal proteins or other rRNA. We have probed the structure of Domain III rRNA alone and when contained within the intact 23S rRNA using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), in the absence and presence of magnesium. The combined results support the hypothesis that Domain III alone folds to a near-native state with secondary structure, intra-domain tertiary interactions, and inter-domain interactions that are independent of whether or not it is embedded in the intact 23S rRNA or within the LSU. The data presented support previous suggestions that Domain III was added relatively late in ribosomal evolution.

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Citations

Jun 16, 2012·PloS One·Shreyas S AthavaleLoren Dean Williams
Jan 26, 2013·PloS One·Shreyas S AthavaleStephen C Harvey
Jan 29, 2013·Nucleic Acids Research·Chiaolong HsiaoLoren Dean Williams
Feb 16, 2016·Scientific Reports·Burak GulenLoren Dean Williams
May 19, 2012·Current Opinion in Structural Biology·Jessica C BowmanLoren Dean Williams
Jan 19, 2016·Translation·Michael Gamalinda, John L Woolford
May 17, 2014·Nucleic Acids Research·Maud ContrantSébastien Pfeffer
Jul 19, 2016·Biochemistry·Kathryn A LanierLoren Dean Williams
Aug 16, 2016·Journal of Molecular Biology·Lizzette M Gómez RamosLoren Dean Williams
Jun 8, 2017·Nucleic Acids Research·Jamie L GilmoreKunio Takeyasu
Nov 11, 2018·Proceedings of the National Academy of Sciences of the United States of America·Marcus S BrayJennifer B Glass
Aug 14, 2020·Genome Biology and Evolution·Petar I PenevJennifer B Glass

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