The relationship of thermodynamic stability at a G•U recognition site to tRNA aminoacylation specificity

Abstract

The G x U pair at the third position in the acceptor helix of Escherichia coli tRNA(Ala) is critical for aminoacylation. The features that allow G x U recognition are likely to include direct interaction of alanyl-tRNA synthetase with distinctive atomic groups and indirect recognition of the structural and stability information encoded in the sequence of G x U and its immediate context. The present work investigates the thermodynamic stability and acceptor activity for a comprehensive set of variant RNAs with substitutions of the G x U pair of E. coli tRNA(Ala). The four RNAs with Watson-Crick substitutions had a lower acceptor activity and a higher stability relative to the G x U RNA. On the other hand, the RNAs with mispair substitutions had a lower stability, but either a higher or a lower acceptor activity. Thus, the entire set of variant RNAs does not exhibit a correlation between thermodynamic stability of the free, unbound tRNA and its acceptor activity. The substantial acceptor activity of tRNAs with particular mispair substitutions may be explained by their ability to assume the conformational preferences of alanyl-tRNA synthetase. Moreover, the G x U pair may provide a point of deformability for the substrate tRNA to adapt to the enzyme's active site.

Selection on codon bias in yeast: a transcriptional hypothesis

“…However, as shown in Figure 4A, with increasing expression levels, a wobble pairing (U:G) is favored over the Watson–Crick pairing (C:G) at the third codon position of cysteine sites, whereas the C-ending codons are preferred for aspartic acid and histidine. If codon usage is adapted to tRNA profile, these incongruent selections at the third codon position indicate that the choice between G:U and G:C should be under weak selection, in agreement with the wobble rules (40). In this case, we should consider this weak selective force stronger than any other possible mechanism influencing codon usage, such as mutational biases and mRNA structural constraints.…”

The p53 mRNA: an integral part of the cellular stress response

“…A fundamental characteristic of the secondary RNA structure is the highly conserved G·U wobble base pairs which have unique chemical, thermodynamic and structural properties (129). Such pairs allow conformational flexibility and are conserved in the acceptor helix of tRNA of Ala (130) and on mRNAs encoding ribosomal proteins (131–133) and are functionally associated with self-splicing ribozymes (i.e.…”

Surprising contribution to aminoacylation and translation of non-Watson–Crick pairs in tRNA

“…By analogy with prior biophysical work in other RNA system (25)(26)(27)(28), the mutant tRNAs probably are more active because their mispairs exhibit greater conformational heterogeneity and thermodynamic instability, whereas inactive W-C pairs and their helices are structurally rigid. Thus, the deformability of the mutant tRNAs allows their adaptability to the dynamics of synthetases and translation mechanisms at lower free energy costs relative to rigid W-C helices.…”