tRNA ligase is a form of RNA ligase that is thought to function in all eukaryotic cells. Its biological role is to catalyze the splicing of the precursor to transfer RNA. In contrast to the RNA splicing that occurs with messenger RNA, which proceeds via transesterification, without a protein to catalyze the cleaving and ligating reactions, tRNA splicing requires both latter enzyme activities. The tRNA ligase of Saccharomyces cerevisiae, which is the most-studied (1), is a single polypeptide chain of 95.4 kDa comprised of domains that correspond to cyclic phosphodiesterase, kinase, and adenylylation activities. The overall reaction is quite similar to those of T4 polynucleotide kinase plus T4 RNA ligase, the only difference being that a 2′-phosphate group occurs with tRNA ligase, rather than a 2′-hydroxyl (see Fig. 2 of RNA Ligases). The mechanism of the reaction involves (i) opening of the 2′,3′-cyclic phosphate to a 2′-phosphomonoester (phosphodiesterase activity), (ii) addition of a phosphate group to the 5′-hydroxyl of the donor (kinase activity), (iii) transfer of an adenylyl group from an adenylylated enzyme, which is produced in advance by another kinase activity of the same enzyme, to the 5′-phosphate of the donor (adenylylation activity), and (iv) attack of the acceptor 3′-hydroxyl on the activated donor phosphoanhydride, to form a 3′,5′-phosphodiester bond (bond formation activity). The mature tRNA is then generated by the action of a distinct enzyme, 2′-phosphotransferase, which removes the 2′-phosphate from the product.
Yeast tRNA ligase has a rather strong substrate-specificity, while wheat germ tRNA ligase, another well-studied tRNA ligase, has less specificity and can also ligate oligo(A) and oligo(UnG), in addition to tRNA precursors. The wheat germ and other plant (such as tobacco and Chlamydomonas) tRNA ligases are assumed to be exploited by viroids and virusoids for circularizing their genomic RNAs after rolling-circle replication and self-cleavage.
In addition to its catalytic function, tRNA ligase may play a role in transport within the nucleus of the precursor molecule that is to be spliced; this process seems to be performed by a group of PRP (precursor RNA processing) proteins in the case of mRNA splicing (2). Another novel function of yeast tRNA ligase is that it is involved in the splicing of the mRNA of Hac1 protein (a transcription factor required for the unfolded protein response) (3). This might unveil another important function of tRNA ligase, having a role in a crucial regulatory process.
Structural analysis of tRNA ligase is underway. In yeast tRNA ligase, Lys114 is responsible for accepting an adenylyl group by a phosphoamide bond. The region of the primary structure surrounding this lysine is well-conserved among tRNA ligases and T4 RNA ligase (see RNA Ligases) (Fig. 1). The region involved in nucleoside triphosphate-binding is also fairly well conserved among tRNA ligases, T4 polynucleotide kinase, and human 3′-cyclic nucleotide 3′-phosphodiesterase (4), implying that they have an evolutionary relationship.
Figure 1. Optimal alignment of a conserved region of RNA ligases. S. cer., Saccharomyces cerevisiae; S.pom., Schizosa lysine (K) residue that accepts an adenylyl group is indicated by an arrow.
