Optimization of ribosome structure and function by rRNA base modification

• Published in: PloS one Vol. 2; no. 1; p. e174
• Main Authors: Baxter-Roshek, Jennifer L, Petrov, Alexey N, Dinman, Jonathan D
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 24.01.2007; Public Library of Science (PLoS)
• Subjects: Alleles; Amino acids; Baking yeast; Base Sequence; Biochemistry/RNA Structure; Biology; Cell Biology/Gene Expression; Chemical analysis; Defects; E coli; Escherichia coli; Gene sequencing; Genes; Genetics; Genetics and Genomics/Gene Expression; Genomics; GTP; Guanosine triphosphatases; Guanosine triphosphate; Guanosinetriphosphatase; Humans; Microbiology; Models, Molecular; Molecular Biology/Translation Mechanisms; Molecular Sequence Data; mRNA; Mutagenesis; Mutants; Mutation; Nucleic Acid Conformation; Optimization; Peptidyl Transferases - chemistry; Peptidyl Transferases - genetics; Peptidyltransferase; Plasmids; Propagation; Protein Biosynthesis; Protein Conformation; Proteins; Puromycin; Ribosomal peptidyltransferase; Ribosome Subunits, Large, Eukaryotic - chemistry; Ribosome Subunits, Large, Eukaryotic - genetics; Ribosomes; Ribosomes - chemistry; Ribosomes - genetics; RNA modification; RNA, Ribosomal - chemistry; RNA, Ribosomal - genetics; RNA, Transfer, Amino Acid-Specific - chemistry; RNA, Transfer, Amino Acid-Specific - genetics; rRNA; Saccharomyces cerevisiae; Structure-function relationships; Telomerase; Translation; tRNA; Viability; Virology/Antivirals, including Modes of Action and Resistance; Yeast; Maryland
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0000174

Translating mRNA sequences into functional proteins is a fundamental process necessary for the viability of organisms throughout all kingdoms of life. The ribosome carries out this process with a delicate balance between speed and accuracy. This work investigates how ribosome structure and function are affected by rRNA base modification. The prevailing view is that rRNA base modifications serve to fine tune ribosome structure and function. To test this hypothesis, yeast strains deficient in rRNA modifications in the ribosomal peptidyltransferase center were monitored for changes in and translational fidelity. These studies revealed allele-specific sensitivity to translational inhibitors, changes in reading frame maintenance, nonsense suppression and aa-tRNA selection. Ribosomes isolated from two mutants with the most pronounced phenotypic changes had increased affinities for aa-tRNA, and surprisingly, increased rates of peptidyltransfer as monitored by the puromycin assay. rRNA chemical analyses of one of these mutants identified structural changes in five specific bases associated with the ribosomal A-site. Together, the data suggest that modification of these bases fine tune the structure of the A-site region of the large subunit so as to assure correct positioning of critical rRNA bases involved in aa-tRNA accommodation into the PTC, of the eEF-1A.aa-tRNA.GTP ternary complex with the GTPase associated center, and of the aa-tRNA in the A-site. These findings represent a direct demonstration in support of the prevailing hypothesis that rRNA modifications serve to optimize rRNA structure for production of accurate and efficient ribosomes.