Modeling a Minimal Ribosome Based on Comparative Sequence Analysis

• Published in: Journal of molecular biology 2002-08, Vol.321 (2), p.215-234
• Main Authors: Mears, Jason A., Cannone, Jamie J., Stagg, Scott M., Gutell, Robin R., Agrawal, Rajendra K., Harvey, Stephen C.
• Format: Article
• Language: English
• Subjects: Animals; Archaea - cytology; Archaea - genetics; Bacteria - cytology; Bacteria - genetics; Base Sequence; Binding Sites; Caenorhabditis elegans - chemistry; Caenorhabditis elegans - cytology; Caenorhabditis elegans - genetics; Chloroplasts - chemistry; Chloroplasts - genetics; Computer Simulation; conservation; Conserved Sequence; Eukaryotic Cells - cytology; evolution; Evolution, Molecular; Mitochondria - chemistry; Mitochondria - genetics; Models, Molecular; Molecular Conformation; Molecular Sequence Data; Movement; phylogenetics; Phylogeny; Protein Structure, Tertiary; Protein Subunits; ribosome; Ribosomes - chemistry; Ribosomes - genetics; RNA, Ribosomal - chemistry; RNA, Ribosomal - genetics; RNA, Ribosomal - metabolism; RNA, Transfer - chemistry; RNA, Transfer - genetics; RNA, Transfer - metabolism; rRNA; Sequence Alignment; Sequence Deletion
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/S0022-2836(02)00568-5

We have determined the three-dimensional organization of ribosomal RNAs and proteins essential for minimal ribosome function. Comparative sequence analysis identifies regions of the ribosome that have been evolutionarily conserved, and the spatial organization of conserved domains is determined by mapping these onto structures of the 30 S and 50 S subunits determined by X-ray crystallography. Several functional domains of the ribosome are conserved in their three-dimensional organization in the Archaea, Bacteria, Eucaryotic nuclear, mitochondria and chloroplast ribosomes. In contrast, other regions from both subunits have shifted their position in three-dimensional space during evolution, including the L11 binding domain and the α-sarcin–ricin loop (SRL). We examined conserved bridge interactions between the two ribosomal subunits, giving an indication of which contacts are more significant. The tRNA contacts that are conserved were also determined, highlighting functional interactions as the tRNA moves through the ribosome during protein synthesis. To augment these studies of a large collection of comparative structural models sampled from all major branches on the phylogenetic tree, Caenorhabditis elegans mitochondrial rRNA is considered individually because it is among the smallest rRNA sequences known. The C. elegans model supports the large collection of comparative structure models while providing insight into the evolution of mitochondrial ribosomes.