|Title||Secondary structures of rRNAs from all three domains of life.|
|Publication Type||Journal Article|
|Year of Publication||2014|
|Authors||Petrov, AS, Bernier, CR, Gulen, B, Waterbury, CC, Hershkovits, E, Hsiao, C, Harvey, SC, Hud, NV, Fox, GE, Wartell, RM, Williams, LDean|
|Keywords||Animals, Base Pairing, Drosophila melanogaster, Haloarcula marismortui, Humans, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Phylogeny, RNA, Archaeal, RNA, Bacterial, RNA, Fungal, RNA, Ribosomal, Saccharomyces cerevisiae, Thermus thermophilus|
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).
|Alternate Journal||PLoS ONE|
|PubMed Central ID||PMC3914948|