The 3D rRNA modification maps database: with interactive tools for ribosome analysis

Abstract

The 3D rRNA modification maps database is the first general resource of information about the locations of modified nucleotides within the 3D structure of the full ribosome, with mRNA and tRNAs in the A-, P- and E-sites. The database supports analyses for several model organisms, including higher eukaryotes, and enables users to construct 3D maps for other organisms. Data are provided for human and plant (Arabidopsis) ribosomes, and for other representative organisms from eubacteria, archaea and eukarya. Additionally, the database integrates information about positions of modifications within rRNA sequences and secondary structures, as well as links to other databases and resources about modifications and their biosynthesis. Displaying positions of modified nucleotides is fully manageable. Views of each modified nucleotide are controlled by individual buttons and buttons also control the visibility of different ribosomal molecular components. A section called 'Paint Your Own' enables the user to create a 3D modification map for rRNA from any organism where sites of modification are known. This section also provides capabilities for visualizing nucleotides of interest in rRNA or tRNA, as well as particular amino acids in ribosomal proteins. The database can be accessed at http://people.biochem.umass.edu/fournierlab/3dmodmap/

Figure 1.

The positions of the modified nucleotides in the rRNA of several well-studied organisms can be visualized in linear, secondary structure and 3D structure formats. The menu bar (top) shows the sections of the database, and portions of the associated links are illustrated in exploded views. The examples shown are for modifications concentrated around the A site and PTC regions of E. coli and human (middle left; upper, view of the A site and PTC, lower, view of the PTC toward the exit tunnel). The 3D arrangements of the modified nucleotides in E. coli and human rRNAs are displayed using bioinformatics tools (middle right) available in a section named ‘Mod sites in 3D’. An interactive interface is provided for controlling the views of the ribosome model (both subunits, and the A-, P- and E-site tRNAs, and mRNA) and for selecting modifications, as follows: ‘pseudouridines’ (red), ‘2′-O-methylations’ (green) and ‘base methylations’ (orange). The web service is heavily linked to material in other databases and web resources, for example, snoRNA databases for human, yeast and plants, Modomics (a database of RNA modification pathways), EcoCyc (a comprehensive genome database for E. coli) and PubMed.

Figure 2.

Paint Your Own. Users may create 3D modification maps for rRNA from any organism. The ‘Paint Your Own’ section with an accompanying tutorial enables selection and highlighting of any site or segment within an rRNA, r-protein and tRNA. The example shown is for a deduced 3D arrangement of predicted 2′-O-methylations concentrated within the GTPase center of P. abyssi, using the ribosome model at 5.5 Å. Stepwise, visualization was achieved by: (i) determining the equivalent numbers of the rRNA nucleotides from the secondary structure of E. coli 23S rRNA (53) and, (ii) selecting and highlighting the GTPase center and the positions of the modified nucleotides, using a few commands provided in the Jmol console window. The rRNA fragment of the GTPase center is shown as a thick white backbone, and modified nucleotides are displayed as green dots. The tRNAs are placed in the A- (pink), P- (purple) and E- (cyan) sites of the LSU. A fragment of mRNA within the small ribosomal subunit (hidden) is displayed in yellow. Proteins of the LSU are also hidden.