Effects of tRNA modification on translational accuracy depend on intrinsic codon–anticodon strength

Abstract

Cellular health and growth requires protein synthesis to be both efficient to ensure sufficient production, and accurate to avoid producing defective or unstable proteins. The background of misreading error frequency by individual tRNAs is as low as 2 × 10−6 per codon but is codon-specific with some error frequencies above 10−3 per codon. Here we test the effect on error frequency of blocking post-transcriptional modifications of the anticodon loops of four tRNAs in Escherichia coli. We find two types of responses to removing modification. Blocking modification of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${\rm tRNA}_{{\rm UUC}}^{{\rm Glu}}$\end{document} and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${\rm tRNA}^{\rm Asp}_{\rm QUC}$\end{document} increases errors, suggesting that the modifications act at least in part to maintain accuracy. Blocking even identical modifications of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${\rm tRNA}^{\rm Lys}_{\rm UUU}$\end{document} and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${\rm tRNA}^{\rm Tyr}_{\rm QUA}$\end{document} has the opposite effect of decreasing errors. One explanation could be that the modifications play opposite roles in modulating misreading by the two classes of tRNAs. Given available evidence that modifications help preorder the anticodon to allow it to recognize the codons, however, the simpler explanation is that unmodified ‘weak’ tRNAs decode too inefficiently to compete against cognate tRNAs that normally decode target codons, which would reduce the frequency of misreading.

The Escherichia coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (preQ0) Transport

“…Modifications of the anticodon loop, contribute to the fidelity and efficiency of protein synthesis [2]. There is evidence that Queuosine does have a role in both of these processes [3,4,5]. Whereas the physiological role of Q is still not fully elucidated, there has been a renewed interest in this molecule, particularly as it appears to be a forgotten micronutrient in humans, discussed in recent reviews [1,6,7,8].…”

Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment

“…tRNA modification influences each level of the genetic code, including the interactions of mRNA codons with tRNA anticodons and the interactions of tRNAs with their aaRSs (6). In addition, modified tRNAs serve regulatory roles modulating the interactions between the process of translation and cellular stress and metabolism (7,8). The three levels of the genetic code are tightly connected: the pairing of tRNA anticodon to mRNA codon as a means of information transfer is limited by the efficiency of the joining of an amino acid to the appropriate tRNA, and the effectiveness of both processes are modulated by the modification of tRNA species.…”

Cross-Talk between Dnmt2-Dependent tRNA Methylation and Queuosine Modification

“…It was thus hypothesized that this might be due to the Q modification that is absent from tRNA Lys . However, for tRNA Asp , the Q modification did not affect Glu codon misreading, showing that Q modification is not essential to block wobble misreading by tRNA Asp of these codons [56]. In contrast, and contrary to expectation, for tRNA Tyr QUA , the absence of Q modification lowered rather than increased the mistranslation rates of the UAG stop codon, but had little effect on the UAA codon (Figure 4).…”

“…Importantly, the investigation of the role of Q modification in this scenario gave the surprising result that the error rate of tRNA Asp QUC on the glycine GGC, but not GGU codon, was strongly increased in the absence of Q modification, showing that Q modification here served to suppress translation errors. In contrast, the middle position mismatching in both cysteine codons by tRNA Tyr was decreased in the absence of Q modification, with the stronger effect being observed for the UGU codon, indicating that the modification actually increases error rates [56]. In short, the presence of Q decreased errors by tRNA Asp and increased errors by tRNA Tyr .…”

“…Here, the presence of Q at the first position led to the displacement of the mismatched cytosine at the third position from the codon-anticodon helix and to a distortion of the helix, thus enhancing the inability to form a stable C◦A interaction. In vivo, however, misreading rates of tRNA Tyr on the CAC codon were slightly higher in the presence of Q modification [56], thus contradicting the assumption that Q modification would prevent misreading.…”