Codon-by-Codon Modulation of Translational Speed and Accuracy Via mRNA Folding
Figure 5
Among residues encoded by the same codon within the same gene, those with higher demands for translational accuracy have lower elongation speeds. A total of 1,843 genes are used.
(A) Synonymous codon usage does not predict elongation speed. For each amino acid, OR2 is calculated for each gene and then combined across genes by the MH procedure. OR2>1 indicates that preferred codons are translated faster than unpreferred codons, and vice versa. The combined OR2 from all amino acids is not significantly different from 1 (p>0.2). (B) Among residues encoded by the same codon in the same gene, those that are more conserved are translated more slowly. For each codon, OR3 is calculated for each gene and then combined across genes by the MH procedure. OR3>1 indicates that conserved residues encoded by a codon are translated more slowly than unconserved ones encoded by the same codon, and vice versa. The combined OR3 from all codons is significantly greater than 1 (p<10−5). For both panels, error bar indicates one standard error, estimated by bootstrapping the genes 1,000 times. The standard error of OR3 for CGA cannot be estimated because CGA with relevant information occurred in only one gene. Nominal p values from the MH test are indicated by asterisks. * p<0.05; ** p<0.01; *** p<0.001.