title: Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state.
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.
authors.affiliation: School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
authors.forename: Shreyas S
authors.initials: SS
authors.lastname: Athavale
authors.forename: J Jared
authors.initials: JJ
authors.lastname: Gossett
authors.forename: Chiaolong
authors.initials: C
authors.lastname: Hsiao
authors.forename: Jessica C
authors.initials: JC
authors.lastname: Bowman
authors.forename: Eric
authors.initials: E
authors.lastname: O'Neill
authors.forename: Eli
authors.initials: E
authors.lastname: Hershkovitz
authors.forename: Thanawadee
authors.initials: T
authors.lastname: Preeprem
authors.forename: Nicholas V
authors.initials: NV
authors.lastname: Hud
authors.forename: Roger M
authors.initials: RM
authors.lastname: Wartell
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Harvey
authors.forename: Loren Dean
authors.initials: LD
authors.lastname: Williams
mesh_terms: D009690:Nucleic Acid Conformation; D012338:RNA, Ribosomal, 23S / Q000235:genetics*; D016963:Thermus thermophilus / Q000235:genetics*
chemical_list: D012338:RNA, Ribosomal, 23S