title: Ribosomal small subunit domains radiate from a central core.
abstract: The domain architecture of a large RNA can help explain and/or predict folding, function, biogenesis and evolution. We offer a formal and general definition of an RNA domain and use that definition to experimentally characterize the rRNA of the ribosomal small subunit. Here the rRNA comprising a domain is compact, with a self-contained system of molecular interactions. A given rRNA helix or stem-loop must be allocated uniquely to a single domain. Local changes such as mutations can give domain-wide effects. Helices within a domain have interdependent orientations, stabilities and interactions. With these criteria we identify a core domain (domain A) of small subunit rRNA. Domain A acts as a hub, linking the four peripheral domains and imposing orientational and positional restraints on the other domains. Experimental characterization of isolated domain A, and mutations and truncations of it, by methods including selective 2'OH acylation analyzed by primer extension and circular dichroism spectroscopy are consistent with our architectural model. The results support the utility of the concept of an RNA domain. Domain A, which exhibits structural similarity to tRNA, appears to be an essential core of the small ribosomal subunit.
authors.affiliation: School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America.
authors.forename: Burak
authors.initials: B
authors.lastname: Gulen
authors.affiliation: School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America.
authors.forename: Anton S
authors.initials: AS
authors.lastname: Petrov
authors.affiliation: School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America.
authors.forename: C Denise
authors.initials: CD
authors.lastname: Okafor
authors.affiliation: School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America.
authors.forename: Drew
authors.initials: D
authors.lastname: Vander Wood
authors.affiliation: School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America.
authors.forename: Eric B
authors.initials: EB
authors.lastname: O'Neill
authors.affiliation: School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America.
authors.forename: Nicholas V
authors.initials: NV
authors.lastname: Hud
authors.affiliation: School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America.
authors.forename: Loren Dean
authors.initials: LD
authors.lastname: Williams
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D008958:Models, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation; D012336:RNA, Ribosomal, 16S / Q000737:chemistry* / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry* / Q000378:metabolism; D012269:Ribosomal Proteins / Q000737:chemistry* / Q000378:metabolism; D054680:Ribosome Subunits, Small, Bacterial / Q000737:chemistry* / Q000378:metabolism; D016963:Thermus thermophilus / Q000737:chemistry* / Q000378:metabolism
chemical_list: D012336:RNA, Ribosomal, 16S; D012269:Ribosomal Proteins; D012343:RNA, Transfer