tRNA as an active chemical scaffold for diverse chemical transformations

Abstract

During protein synthesis, tRNA serves as the intermediary between cognate amino acids and their corresponding RNA trinucleotide codons. Aminoacyl-tRNA is also a biosynthetic precursor and amino acid donor for other macromolecules. AA-tRNAs allow transformations of acidic amino acids into their amide-containing counterparts, and seryl-tRNA(Ser) donates serine for antibiotic synthesis. Aminoacyl-tRNA is also used to cross-link peptidoglycan, to lysinylate the lipid bilayer, and to allow proteolytic turnover via the N-end rule. These alternative functions may signal the use of RNA in early evolution as both a biological scaffold and a catalyst to achieve a wide variety of chemical transformations.

Figure 1. Secondary roles of tRNA in cellular metabolism

The canonical roles of tRNA in protein synthesis are represented by “Chemistry of Aminoacylation and Editing” and “Ribosomal Protein Synthesis,” while other functions discussed in this review are arrranged in a circular fashion around a central tRNA molecule. Depending upon its role in a particular process, the tRNA molecule shown in the circle should be considered as either free tRNA (as shown) or an aminoacyl-tRNA. The details of these processes are discussed in the text.

Figure 2. Role of tRNA in facilitating key steps in protein synthesis

A., Substrate-assisted catalysis of peptide bond formation in the ribosome, adapted from Weinger at al (ref 20). The -amino group of the A-site tRNA (blue) serves as the nucleophile in the attack on the carbonyl carbon of the P-site tRNA (magenta). The specific function of the 2′OH as a general base in the reaction is still under investigation. B., Substrate assisted catalysis of aminoacyl transfer by threonyl-tRNA synthetase, adapted from Minajigi & Francklyn (ref. 23). The threonyl adenylate is depicted in blue, and the A76 group of incoming tRNA^Thr in magenta. C., Proposed role for the adjacent hydroxyl of A76 in stabilizing the geometry of the attacking water molecule in the deacylation of Thr-tRNA^Phe by phenylalanyl-tRNA synthetase, adapted from Ling et al. (ref 26). The decreases in aminoacyl transfer by threonyl synthetase and post transfer editing by phenylalanyl-tRNA synthetase associated with removal of the adjacent hydroxyl are of the same order (750 vs 300-fold, respectively), but several orders magnitude less than the effect of loss of the adjacent hydroxyl on peptidyltransferase (~10⁶).

Figure 3. A common fold for aminoacyl transfer in two different systems

A. Structure of FemX from Weisella viridecens, in complex with UDP-MurNAc-pentapeptide, as reported by Biarotte-Sorin et al (ref. 68). The enzyme is depicted in ribbon form in magenta, with the ligand rendered in stick form. B., Structure of the leucyl/phenylalanyl-tRNA protein transferase from Escherichia coli, as reported by Watanabe et al., (ref 80). The adenosine moiety of the rA-Phe substrate analog is rendered in stick form.