Secondary structures of rRNAs from all three domains of life

• Published in: PloS one Vol. 9; no. 2; p. e88222
• Main Authors: Petrov, Anton S, Bernier, Chad R, Gulen, Burak, Waterbury, Chris C, Hershkovits, Eli, Hsiao, Chiaolong, Harvey, Stephen C, Hud, Nicholas V, Fox, George E, Wartell, Roger M, Williams, Loren Dean
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 05.02.2014; Public Library of Science (PLoS)
• Subjects: Acids; Animals; Base Pairing; Base pairs; Biochemistry; Bioinformatics; Biology; Chemistry; Drosophila melanogaster; Drosophila melanogaster - chemistry; Drosophila melanogaster - genetics; E coli; Escherichia coli; Evolution; Fungi; Haloarcula marismortui - chemistry; Haloarcula marismortui - genetics; Helices; Humans; Models, Molecular; Molecular interactions; Molecular Sequence Data; Nucleic Acid Conformation; Phylogenetics; Phylogeny; Ribosomes; RNA; RNA, Archaeal - chemistry; RNA, Archaeal - genetics; RNA, Bacterial - chemistry; RNA, Bacterial - genetics; RNA, Fungal - chemistry; RNA, Fungal - genetics; RNA, Ribosomal - chemistry; RNA, Ribosomal - genetics; rRNA; Saccharomyces cerevisiae; Saccharomyces cerevisiae - chemistry; Saccharomyces cerevisiae - genetics; Thermus thermophilus - chemistry; Thermus thermophilus - genetics
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0088222

Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU) 23S/28S and small subunit (SSU) 16S/18S rRNAs of Escherichia coli, Thermus thermophilus, Haloarcula marismortui (LSU rRNA only), Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available (http://apollo.chemistry.gatech.edu/RibosomeGallery). Mapping of data onto 2° structures was performed on the RiboVision server (http://apollo.chemistry.gatech.edu/RiboVision).