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.Keywords: ribosome; protein synthesis; translation fidelity; tRNA; error frequency; mRNA decoding SPEED AND ACCURACY OF TRANSLATIONProtein synthesis on the ribosome is a fundamentally important process that consumes a large part of the energy resources of the cell. Ribosomes are universal macromolecular machines built of two subunits, the small subunit (30S subunit in bacteria), where mRNA decoding takes place, and the large subunit (50S subunit in bacteria), which harbours the catalytic site for peptide bond formation. The decoding and peptidyl transferase centres consist of RNA, suggesting that the ribosome originates from the RNA world. Intuitively, one would expect that the ribosome has evolved to produce proteins with maximum speed and accuracy at minimum metabolic cost. The aim of this review is to discuss the mechanisms by which this is achieved and potential limits to the optimization of the ribosome performance. Protein synthesis entails four major phases: initiation, elongation, termination and recycling. During initiation, the ribosome selects an mRNA and, assisted by initiation factors, places the initiator tRNA on the appropriate start codon in the P site. In the subsequent elongation phase, amino acids are added to the growing peptide in a cyclic process. Aminoacyl-tRNAs (aa-tRNAs) enter the ribosome in a tight complex with elongation factor Tu (EF-Tu) and guanosine-5 0 -triphosphate (GTP). Following the recognition of the codon by the anticodon of aa-tRNA and GTP hydrolysis by EF-Tu, aa-tRNA is accommodated in the A site of the 50S subunit and takes part in peptide bond formation. The rate of protein elongation in bacteria is between 4 and 22 amino acids per second at 378C [1-5]; thus, a protein of an average length of 330 amino acids [6] is completed in about 10-80 s. The times required for initiation, termination and ribosome recycling (around 1 s each [3]) are short enough to make elongation rate-limiting for protein synthesis [7]. Translation of a particular codon depends on both the nature and abundance of the respective tRNAs, particularly on the non-random use of synonymous codons and the availability of the respective isoacceptor tRNAs [8]. The overall rate of translation is limited by the codon-specific rates of cognate ternary complex delivery to the A site and is further attenuated ...

tRNA residues evolved to promote translational accuracy

“…In contrast, the nonconsensus U31-A39 mutation functions normally on the GCC codon but shows substantial amounts of product accumulating at a similar rate on the near-cognate GUC codon. This behavior is consistent with a substantial fraction of the mutant tRNA molecules being able to escape proofreading by having a faster rate of accommodation and/or a slower rate of rejection compared to wild-type tRNA (Wohlgemuth et al 2011). While additional experiments will be required Table 1. tRNA accuracy residues www.rnajournal.org 511 to determine the individual rate constants for these mutations, more thorough kinetic analyses of other tRNA misreading mutations indicate that changes in the rate constants of several steps in the decoding mechanism are altered (Cochella and Green 2005;Ledoux et al 2009).…”

“…A tRNA sequence that is too "stiff" will not be able to access the bent state sufficiently easily to decode its cognate codon, while a tRNA sequence that is too flexible will read near-cognate codons too well. The offsetting needs of speed and accuracy is a common theme in the design of the translational machinery (Thompson and Karim 1982;Wohlgemuth et al 2011;Johansson et al 2012), so it is not surprising that it is critical in dictating the evolution of tRNA sequences.…”

Functional Role of Methylation of G518 of the 16S rRNA 530 Loop by GidB in Mycobacterium tuberculosis

“…Under some conditions, mistranslation can be beneficial for the cell, for example, under growth conditions where amino acids are in limited supply, by allowing the cell to continue to produce proteins with a more limited repertoire of precursors (29). The ribosome has evolved in the face of pressure to maximize speed while achieving reasonable accuracy (30). Our experiments suggest the possibility that the organism normally methylates G518 at a lower level of translational accuracy at the wobble position, possibly to improve translational speed, although we have not yet formally tested that.…”

Reorganization of an intersubunit bridge induced by disparate 16S ribosomal ambiguity mutations mimics an EF-Tu-bound state

“…Basically, the functionally irreversible GTP hydrolysis step of the pathway provides a second independent opportunity for rejection of near-cognate aa-tRNA. It is clear, however, that kinetic proofreading is not maximally exploited for fidelity (6,10). Instead, the ribosome additionally employs an induced-fit mechanism to achieve both high speed and fidelity in decoding.…”

“…Extensive biochemical studies have shed light on the kinetics of this decoding process (reviewed in ref. 6). The aa-tRNA is delivered to the ribosome as part of a ternary complex (TC) with elongation factor thermo unstable (EF-Tu) and GTP.…”