Transfer RNA Recognition and Aminoacylation by Synthetases

Abstract

Fidelity of transfer ribonucleic acid (tRNA) charging by amino acids ensures correct translation of the genetic code into proteins. Charging is catalysed by a set of enzymes known as aminoacyl-tRNA synthetases. Owing to the degeneracy of the genetic code, some of the different tRNAs have the same amino acid attached to them. Specificity of charging obeys universal rules and is ensured by positive elements, the identity determinants unique to each tRNA and responsible for its recognition by the cognate synthetase, and negative elements, the antideterminants that prevent false recognitions. To fulfil the aminoacylation specificity and prevent noncognate aminoacyl-tRNA delivery to the ribosome, some synthetases also mediate proofreading reactions that increase fidelity of the tRNA charging. In such reactions, misactivated amino acids or mischarged tRNAs are checked in specific sites and noncognate products are hydrolysed. However, mischarging is beneficial under certain stress circumstances or when catalysed by nondiscriminatory synthetases, and represents a driving force in evolution. Key Concepts:•Translational expression of the genetic code refers to aminoacyl-tRNA-and ribosomedependent decoding of genes into proteins, a process highly dependent on fidelity of tRNA aminoacylation by synthetases.•The rules that account for the aminoacylation identity of tRNAs are referred to as the second genetic code.•The RNA operational code is encoded in the acceptor stem of tRNA and is crucial for recognition by aminoacyl-tRNA synthetases and specific aminoacylation.•Allostery in tRNA-synthetase systems concerns long-range transfer of chemical information (up to 75 Å) to the synthetase catalytic site (through the body of tRNA and/or synthetase) triggered by contacts of tRNA identity determinants with the synthetase.•Engineering the identity of tRNA-synthetase systems allows reprogramming the genetic code.

Optimization of Anticodon Edited Transfer RNAs (ACE-tRNAs) Function in Translation for Suppression of Nonsense Mutations

“…6). It has been noted that the anticodon serves as an anti-determinant between tRNA Arg and TrpRS 40 . By converting the anticodon of tRNA Trp to UCA along with alterations to the t-stem sequence, it appears the cognate specificity between tRNA Trp and RARS was lost.…”

Suppressor tRNAs at the interface of genetic code expansion and medicine

“…Most aaRSs select their cognate tRNA substrates via interactions with two of the tRNA's structural features: the anticodon loop and the acceptor stem (Figure 1). A dedicated anticodon binding domain generally mediates the anticodon recognition, while the aminoacylation domain recognizes the acceptor stem (Giegé and Eriani, 2023). The identity of tRNAs for a particular amino acid is defined by these unique sets of tRNA-aaRS interactions, preventing cross-reactions between non-cognate tRNAs and aaRSs.…”

“…Due to the stringent anticodon recognition, converting the anticodon sequence of a canonical tRNA into a suppressor sequence significantly decreases the interaction and affinity with the cognate aaRS. However, some aaRSs do not directly interact with tRNA anticodon or depend little on the anticodon bases (Giegé and Eriani, 2023). For example, leucyl-and seryl-tRNA synthetase do not recognize the anticodon, while arginyl-and tyrosyl-synthetase tolerate changes in their tRNA substrate's anticodons.…”

“…The intricacies of the tRNA-aaRS interactions go beyond the direct role of tRNA bases in binding and catalysis. Even changes in tRNA regions that do not directly contact the aaRS may influence aminoacylation (Giegé and Eriani, 2014). Finally, changes in the anticodon can cause unintended crossreactions between aaRSs (Normanly et al, 1990;Zheng et al, 2017;Giegé and Eriani, 2023;Osgood et al, 2023).…”

“…Even changes in tRNA regions that do not directly contact the aaRS may influence aminoacylation (Giegé and Eriani, 2014). Finally, changes in the anticodon can cause unintended crossreactions between aaRSs (Normanly et al, 1990;Zheng et al, 2017;Giegé and Eriani, 2023;Osgood et al, 2023). In bacteria, a tRNA Trp with CUA, but not with UCA, is aminoacylated by glutaminyl-tRNA synthetase (Italia et al, 2017a).…”