Evolutionary optimization of speed and accuracy of decoding on the ribosome

Abstract

Speed and accuracy of protein synthesis are fundamental parameters for the fitness of living cells, the quality control of translation, and the evolution of ribosomes. The ribosome developed complex mechanisms that allow for a uniform recognition and selection of any cognate aminoacyl-tRNA (aa-tRNA) and discrimination against any near-cognate aa-tRNA, regardless of the nature or position of the mismatch. This review describes the principles of the selection-kinetic partitioning and induced fit-and discusses the relationship between speed and accuracy of decoding, with a focus on bacterial translation. The translational machinery apparently has evolved towards high speed of translation at the cost of fidelity.

Figure 1.

Schematic of EF-Tu-dependent aa-tRNA binding to the A site. Kinetically resolved steps are indicated by the rate constants k₁–k₇ (forward reactions) and k₋₁ and k₋₂ (backward reactions). The rate of codon reading (presumably a readily reversible step [19]) could not be determined by rapid kinetics; the values available from single-molecule fluorescence resonance energy transfer (FRET) experiments [19,20] are not comparable with the values obtained in bulk experiments owing to differences in experimental conditions. Rate constants of the two chemical steps that are rate-limited by the respective preceding step are designated k_GTP and k_pep.

Figure 2.

Effect of codon–anticodon mismatches on the crucial steps of (a,b) initial selection (rate constants of dissociation k₋₂, GTPase activation k₃) and (c,d) proofreading (dissociation k₇, accommodation k₅). Cognate codons are UUC and UUU (black bars). Near-cognate codons contain a single mismatch in the first (CUC, CUU, GUC, light grey), second (UCC, white) or third (UUA, UUG, dark grey) codon position [30].

Figure 3.

Accuracy and speed of decoding in vitro. (a) Contributions of initial selection and proofreading to combined error frequency at optimized conditions in polymix (black bars) and HiFi (grey bars) buffers (adapted from Wohlgemuth et al. [37]). (b) Rates (k_app) of GTP hydrolysis (circles) and dipeptide formation (diamonds) were measured upon addition of increasing concentrations of competing near- and non-cognate ternary complexes (TC).