Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms

Abstract

The specific aminoacylation of tRNA by tyrosyl-tRNA synthetases (TyrRSs) relies on the identity determinants in the cognate tRNATyrs. We have determined the crystal structure of Saccharomyces cerevisiae TyrRS (SceTyrRS) complexed with a Tyr-AMP analog and the native tRNATyr(GΨA). Structural information for TyrRS–tRNATyr complexes is now full-line for three kingdoms. Because the archaeal/eukaryotic TyrRSs–tRNATyrs pairs do not cross-react with their bacterial counterparts, the recognition modes of the identity determinants by the archaeal/eukaryotic TyrRSs were expected to be similar to each other but different from that by the bacterial TyrRSs. Interestingly, however, the tRNATyr recognition modes of SceTyrRS have both similarities and differences compared with those in the archaeal TyrRS: the recognition of the C1-G72 base pair by SceTyrRS is similar to that by the archaeal TyrRS, whereas the recognition of the A73 by SceTyrRS is different from that by the archaeal TyrRS but similar to that by the bacterial TyrRS. Thus, the lack of cross-reactivity between archaeal/eukaryotic and bacterial TyrRS-tRNATyr pairs most probably lies in the different sequence of the last base pair of the acceptor stem (C1-G72 vs G1-C72) of tRNATyr. On the other hand, the recognition mode of Tyr-AMP is conserved among the TyrRSs from the three kingdoms.

Identifying the ligated amino acid of archaeal tRNAs based on positions outside the anticodon

“…For tRNAs His , it was experimentally shown (see Table 3) that Aeropyrum pernix K1 uses position N73 (Nagatoyo et al 2005). Regarding tRNAs Tyr , it was found that three positions (other than the anticodon) are assumed to participate in the recognition process: N72, N1, and N73 (Fechter et al 2001;Iwaki et al 2002Iwaki et al , 2012Tsunoda et al 2007). This is in agreement with our results where positions N72 and N1 are found to be highly informative (both contain nearly the same information due to their Watson-Crick bonds).…”

“…For example, published work on the role of the paired positions N2:N71 in tRNAs for the aminoacylation of tyrosine shows that while bacteria's aaRS requires the G:C nucleotides pair in these positions for proper aminoacylation, such a structure does not enable the aminoacylation of tyrosine in humans or Archaea. Yet the simple switch to C:G in N2:N71, in the tRNA, does enable this species-specific aminoacylation (Quinn et al 1995;Wakasugi et al 1998;Tsunoda et al 2007). In our study, we found that Archaea species contain the relevant information in positions N1:N72, and not N2:N71 (as it was also found experimentally, see Table 3.).…”

Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog

“…Rv2275 reportedly forms a dimer, similar to the class Ic aaRSs, which must dimerize for tRNA binding (with the tRNA bound across both monomers) (15) (Fig. S5).…”

Decreased aminoacylation in pathology-related mutants of mitochondrial tRNATyr is associated with structural perturbations in tRNA architecture

“…In the case of mt-tRNA Tyr , a direct implication of G15 and A22 in the tyrosylation process is ruled out based on crystallographic knowledge of the mt-TyrRS (Bonnefond et al 2007b) and of T. thermophilus (Yaremchuk et al 2002), Methanococcus jannaschii (Kobayashi et al 2003), and cytosolic Saccharomyces cerevisiae (Tsunoda et al 2007) tRNA Tyr /TyrRS complexes. We show here that the aminoacylation deficiencies are due to structural perturbations and correspond to the initial impact of the mutations.…”