title: Secondary structure and domain architecture of the 23S and 5S rRNAs.
abstract: We present a de novo re-determination of the secondary (2°) structure and domain architecture of the 23S and 5S rRNAs, using 3D structures, determined by X-ray diffraction, as input. In the traditional 2° structure, the center of the 23S rRNA is an extended single strand, which in 3D is seen to be compact and double helical. Accurately assigning nucleotides to helices compels a revision of the 23S rRNA 2° structure. Unlike the traditional 2° structure, the revised 2° structure of the 23S rRNA shows architectural similarity with the 16S rRNA. The revised 2° structure also reveals a clear relationship with the 3D structure and is generalizable to rRNAs of other species from all three domains of life. The 2° structure revision required us to reconsider the domain architecture. We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness. The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed. Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted. Editable 2° structures mapped with various data are provided (http://apollo.chemistry.gatech.edu/RibosomeGallery).
authors.affiliation: School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
authors.forename: Anton S
authors.initials: AS
authors.lastname: Petrov
authors.forename: Chad R
authors.initials: CR
authors.lastname: Bernier
authors.forename: Eli
authors.initials: E
authors.lastname: Hershkovits
authors.forename: Yuzhen
authors.initials: Y
authors.lastname: Xue
authors.forename: Chris C
authors.initials: CC
authors.lastname: Waterbury
authors.forename: Chiaolong
authors.initials: C
authors.lastname: Hsiao
authors.forename: Victor G
authors.initials: VG
authors.lastname: Stepanov
authors.forename: Eric A
authors.initials: EA
authors.lastname: Gaucher
authors.forename: Martha A
authors.initials: MA
authors.lastname: Grover
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Harvey
authors.forename: Nicholas V
authors.initials: NV
authors.lastname: Hud
authors.forename: Roger M
authors.initials: RM
authors.lastname: Wartell
authors.forename: George E
authors.initials: GE
authors.lastname: Fox
authors.forename: Loren Dean
authors.initials: LD
authors.lastname: Williams
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D059370:RNA Folding; D020871:RNA Stability; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000737:chemistry*; D012341:RNA, Ribosomal, 5S / Q000737:chemistry*; D012270:Ribosomes / Q000737:chemistry / Q000235:genetics; D013329:Structure-Activity Relationship
chemical_list: D012329:RNA, Bacterial; D012338:RNA, Ribosomal, 23S; D012341:RNA, Ribosomal, 5S