Nucleotides U28-A42 and A37 in unmodified yeast tRNA(Trp) as negative identity elements for bovine tryptophanyl-tRNA synthetase

The tRNA identity landscape for aminoacylation and beyond

tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.

Interaction of aminoacyl-tRNA synthetases with tRNA: general principles and distinguishing characteristics of the high-molecular-weight substrate recognition

This review summarizes results of numerous (mainly functional) studies that have been accumulated over recent years on the problem of tRNA recognition by aminoacyl-tRNA synthetases. Development and employment of approaches that use synthetic mutant and chimeric tRNAs have demonstrated general principles underlying highly specific interaction in different systems. The specificity of interaction is determined by a certain number of nucleotides and structural elements of tRNA (constituting the set of recognition elements or specificity determinants), which are characteristic of each pair. Crystallographic structures available for many systems provide the details of the molecular basis of selective interaction. Diversity and identity of biochemical functions of the recognition elements make substantial contribution to the specificity of such interactions.

A previously unidentified activity of yeast and mouse RNA:pseudouridine synthases 1 (Pus1p) on tRNAs

Mouse pseudouridine synthase 1 (mPus1p) was the first vertebrate RNA:pseudouridine synthase that was cloned and characterized biochemically. The mPus1p was previously found to catalyze Psi formation at positions 27, 28, 34, and 36 in in vitro produced yeast and human tRNAs. On the other hand, the homologous Saccharomyces cerevisiae scPus1p protein was shown to modify seven uridine residues in tRNAs (26, 27, 28, 34, 36, 65, and 67) and U44 in U2 snRNA. In this work, we expressed mPus1p in yeast cells lacking scPus1p and studied modification of U2 snRNA and several yeast tRNAs. Our data showed that, in these in vivo conditions, the mouse enzyme efficiently modifies yeast U2 snRNA at position 44 and tRNAs at positions 27, 28, 34, and 36. However, a tRNA:Psi26-synthase activity of mPus1p was not observed. Furthermore, we found that both scPus1p and mPus1p, in vivo and in vitro, have a previously unidentified activity at position 1 in cytoplasmic tRNAArg(ACG). This modification can take place in mature tRNA, as well as in pre-tRNAs with 5' and/or 3' extensions. Thus, we identified the protein carrying one of the last missing yeast tRNA:Psi synthase activities. In addition, our results reveal an additional activity of mPus1p at position 30 in tRNA that scPus1p does not possess.

An unusual tryptophanyl tRNA synthetase interacts with nitric oxide synthase in Deinococcus radiodurans

In mammals, nitric oxide synthases (NOSs) produce nitric oxide for signaling and defense functions; in Streptomyces, NOS proteins nitrate a tryptophanyl moiety in synthesis of a phytotoxin. We have discovered that the NOS protein from the radiation-resistant bacterium Deinococcus radiodurans (deiNOS) associates with an unusual tryptophanyl tRNA synthetase (TrpRS). D. radiodurans contains genes for two TrpRSs: the first has approximately 40% sequence identity to typical TrpRSs, whereas the second, identified as the NOS-interacting protein (TrpRS II), has only approximately 29% identity. TrpRS II is induced after radiation damage and contains an N-terminal extension similar to those of proteins involved in stress responses. Recombinantly expressed TrpRS II binds tryptophan (Trp), ATP, and D. radiodurans tRNA(Trp) and catalyzes the formation of 5' adenyl-Trp and tRNA(Trp), with approximately five times less activity than TrpRS I. Upon coexpression in Escherichia coli, TrpRS II binds to, copurifies with, and dramatically enhances the solubility of deiNOS. Dimeric TrpRS II binds dimeric deiNOS with a stoichiometry of 1:1 and a dissociation constant of 6-30 muM. Upon forming a complex, deiNOS quenches the fluorescence of an ATP analog bound to TrpRS II, and increases its affinity for substrate l-arginine. Remarkably, TrpRS II also activates the NOS activity of deiNOS. These findings reveal a link between bacterial NOS and Trp metabolism in a second organism and may indicate yet another novel biological function for bacterial NOS.