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

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 hypothesiz...

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Bibliographic Details
Published in:RNA (Cambridge) 2012-04, Vol.18 (4), p.752-758
Main Authors: Athavale, Shreyas S, Gossett, J Jared, Hsiao, Chiaolong, Bowman, Jessica C, O'Neill, Eric, Hershkovitz, Eli, Preeprem, Thanawadee, Hud, Nicholas V, Wartell, Roger M, Harvey, Stephen C, Williams, Loren Dean
Format: Article
Language:English
Subjects:
Nucleic Acid Conformation
RNA, Ribosomal, 23S - genetics
Thermus thermophilus - genetics
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Summary: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.
ISSN:1355-8382
1469-9001
DOI:10.1261/rna.030692.111