Data mapping onto rRNA Secondary and Three-Dimensional Structures

Anton S. Petrov, Chad R. Bernier, & Loren Dean Williams Ribo Evo Center: Georgia Tech, Atlanta, GA, US
revised: August 20, 2013

This site contains LSU and SSU rRNA secondary structures for six species: E. coli, H. marismortui, T. thermophilus, S. cerevisiae, D. melanogaster and H. sapiens. These secondary structures are derived from 3D structures and accurately portray all base pairs and helices as far as possible. The secondary structures are mapped with a variety of data.
For each species there is an LSU directory (with 23S-25S-28S/5.8S/5S rRNAs) and an SSU directory (with 16S/18S rRNAs). Each directory contains representations of the relevant rRNA secondary structure mapped with various structural and phylogenetic data. In addition there is a utility directory with generally useful secondary structures in combination, along with relevant 3D structures. For E. coli, H. marismortui, T. thermophilus and S. cerevisiae there are two LSU directories and an SSU directory. There is no SSU directory for H. marismortui because there is no available 3D structure of the H. marismortui SSU. The recommended LSU directories and all SSU directories contain 3D-based secondary structures, which accurately represent the base pairing interactions as observed in the 3D structures. The alternative covariation-based' LSU galleries contain historical secondary structures, which lack many noncanonical base pairs and are not fully consistent with 3D structures. For the large eukaryotic ribosomes (D. melanogaster and H. sapiens.) we have constructed the 3D-based secondary structures only. Accuracy: E. coli, H. marismortui, T. thermophilus and S. cerevisiae are derived from x-ray diffraction data, which generally provides resolution sufficient for defining all base pairing interactions. The drosophila and human 3D structures are derived from cryo-EM data, which do not define all base pairs. So some base pairing interactions are omitted from the drosophila and human secondary structures. File Size & Format: The images are high resolution PNGs (so please be patient when viewing and downloading). SVG versions of all of the images are located in zipped directories observable on the top level. SVG images are fully editable in object-oriented programs such as Inkscape (free) or Adobe Illustrator (not free). With the SVG images one can change fonts, move individual objects such as nucleotides, etc. For ease of editing and manipulation, the SVG images are set up so that once imported into Illustrator, various object classes (nucleotide letters, nucleotide circles, molecular interactions, etc) are each partitioned to individual sublayers. License: The images here are licensed under Creative Commons and can be modifed and reproduced. We don't mind being cited (see next page for citation). Source: The software used to generate the images is available at apollo.chemistry.gatech.edu/RiboVision. Funding: This effort was supported by NASA NAI. Site Contents: The names of the files give the species and the information that is mapped onto the rRNAs. For example H_marismortui_Base_Stacking_1.png contains all base stacking interactions mapped onto the H. marismortiu rRNA secondary structure. Descriptions of the files, in the same order as in the gallaries, are elaborated in the list on the next page. For E. coli only there are secondary structures mapped with additional data including protein interactions, SHAPE reactivity, etc.

List of files in each gallery o Species_Domains_1.png: This file shows the partitioning of nucleotides into domains, which are indicated by color. Nucleotides are numbered and are represented by colored circles. Helices are numbered. Species_Domains_2.png: Same as the previous image except that nucleotide types (CGAU) are indicated. o Species.png: Basic secondary structure of the 23S and 5S rRNAs. Nucleotide labels are maroon, helix labels are blue. Domain labels are shown by roman numerals. o Species_Classic_Onion_1.png: The classic Onion Model as described in reference 2. Nucleotides are partitioned into 20 concentric shells based on their distance from the origin [peptidyl trasferase center (LSU) or deconding center (SSU)]. All nucleotides greater than 80 from the origin are in the same shell. Species_Classic_Onion_2.png: Same as the previous image except that nucleotide types (CGAU) are indicated. o Species_Fine_Grained_Onion_1.png: Nucleotides are partitioned into 64 concentric shells based on their distance from the origin [peptidyl trasferase center (LSU) or deconding center (SSU)]. Dark blue nucleotides are very close to the origin. Red nucleotides are far from the origin. Species_Fine_Grained_Onion_2.png: Same as the previous image except that nucleotide types (CGAU) are indicated. o Species_Helices_1.png:This image partitions nucleotides into'helicoids'. A helicoid is a helix plus the most closely associated ss rRNA. Each nucleotide is uniquely contained in one helicoid. The collection of all helicoids contain all rRNA. A helicoid is an in-house construct invented by Eli Hershkovits that is useful networking analysis, evolutionary pathways, etc. Species_Helices_2.png: Same as the previous image except that nucleotide types (CGAU) are indicated. o Species_Shannon_Entropy_1.png: This image contains information of phylogenetic conservation. Shannon entropies are mapped onto the rRNA. The Shannon entropies are obtained from a multiple sequence alignment of 122 species (reference 1). Dark blue corresponds to low entropy (highly conserved). Red represents high entropy (most variable). Note that the 5S rRNA and the eukyotic expansion elements are colored arbitrarily, as they were not included in the alignment. Species_Shannon_Entropy_2.png: Same as the previous image except that nucleotide types (CGAU) are indicated. o Species_Base_Pairs_1.png: All base-pairing interactions between nucleotides are depicted by lines. Secodary interactions are short lines. Tertiary interactions are long lines. Species_Base_Pairs_2.png: Same as the previous image except that nucleotide types (CGAU) are indicated. o Species_Base_Phosphate_1.png: All base-phosphate interactions are depicted by lines. Species_Base_Phosphate_2.png: Same as the previous image except that nucleotide types (CGAU) are indicated. o Species_Base_Stacking_1 .png: All base stacking interactions are depicted by lines. Species_Base_Stacking_2.png: Same as the previous image except that nucleotide types (CGAU) are indicated. o Species_Base_Sugar_1.png: All base-sugar interactions are depicted by lines. Species_Base_Sugar_2.png: Same as the previous image except that nucleotide types (CGAU) are indicated. References and Citations 1) Petrov et al., (2013) "Secondary Structure and Domain Architecture of the23S rRNA", Nucleic Acids Res. doi: 10.1093/nar/gkt513. 2) Hsiao et al., (2009) "Peeling the Onion: Ribosomes Are Ancient Molecular Fossils", Mol. Biol. Evol. 26, 2415-2425, doi 10.1093/molbev/msp163