Human mitochondrial TyrRS disobeys the tyrosine identity rules

Abstract

Human tyrosyl-tRNA synthetase from mitochondria (mt-TyrRS) presents dual sequence features characteristic of eubacterial and archaeal TyrRSs, especially in the region containing amino acids recognizing the N1-N72 tyrosine identity pair. This would imply that human mt-TyrRS has lost the capacity to discriminate between the G1-C72 pair typical of eubacterial and mitochondrial tRNA Tyr Tyrosyl-tRNA synthetase (TyrRS) is distinguished from other aminoacyl-tRNA synthetases by its ambiguous assignation to class I of synthetases (Bedouelle 2004). Indeed, this homodimeric enzyme with typical class I motifs binds its homologous tRNA Tyr across its inferface (Bedouelle and Winter 1986) via the major groove side of the amino acid acceptor stem, as occurs for class II synthetases (Lee and RajBhandary 1991;Bedouelle et al. 1993;Fechter et al. 2000;Yaremchuk et al. 2002). Furthermore, tyrosylation reactions are peculiar in that no cross-aminoacylation between eubacterial tRNA Tyr and eukaryal TyrRS is possible and viceversa (Kleeman et al. 1997;Wakasugi et al. 1998). This strong and unusual phylogenetic barrier mainly relies on the properties of the N1-N72 base pair at the top of the acceptor stem that was assigned as the major tyrosine identity element in eukarya (C1-G72) (Fechter et al. 2000) and a minor element in eubacteria (G1-C72) (Quinn et al. 1995). Sequence alignments reveal strict conservation of the G1-C72 pair in all eubacterial tRNA Tyr species and its replacement by the reverse C1-G72 pair in eukaryal and archaeal tRNA Tyr molecules, an uncommon pair at this position in other tRNAs (Sprinzl and Vassilenko 2005). Recently, the crystallographic structures of Thermus thermophilus and Methanococcus jannaschii tRNA Tyr /TyrRS complexes brought to light the specific interactions established between the N1-N72 pair and TyrRS (Yaremchuk et al. 2002;Giegé 2003;Kobayashi et al. 2003). The differences seen in these interactions provide a structural support accounting for the absence of cross-tyrosylation. In this context, the correlation between two specific sequence clusters in the catalytic domain of TyrRSs and the N1-N72 identity pair can be recalled (Nair et al. 1997). Indeed, cluster 1, within the connective peptide domain, contains the main amino acids contacting the bases of the N1-N72 identity pair (Yaremchuk et al. 2002;Kobayashi et al. 2003). The functional role of these amino acids (Fig. 1) was already supported by peptide transplantation experiments enabling an identity switch in heterologous tyrosylation systems (Wakasugi et al. 1998). Likewise, cluster 2 is involved in N1 recognition (Yaremchuk et al. 2002;Kobayashi et al. 2003).On the other hand, beside a few studies on yeast mtTyrRSs involved in splicing events (Akins and Lambowitz 1987;Kamper et al. 1992), nothing is known concerning other mt-TyrRSs, in particular in relation to tyrosine identity. In the frame of a global approach to study human mitochondrial synthetases, the human mt-TyrRS has been purified (Bonnefond et al. 2005). Sequence comp...

Structural Divergence of the Group I Intron Binding Surface in Fungal Mitochondrial Tyrosyl-tRNA Synthetases That Function in RNA Splicing

“…The other corresponds to five residues of H9 and the loop connecting H9 to H10, which is near the previously mentioned stabilized 15-residue loop. Similar ordering of regions near the active site upon binding of L-tyrosine has been observed for other TyrRSs (53,58).…”

“…Four of these residues (Tyr-99, Tyr-247, Gln-251, and Asp-254 in CYT-18) are conserved in all TyrRSs, with the remaining residue (Asp-143 in CYT-18) is specific to mt and bacterial TyrRSs (Fig. 3C) (58). Although the Cp NTDs crystallized with one monomer in the asymmetric unit, the An NTDs had two monomers of neighboring dimers in the asymmetric unit.…”

Identification and evolution of fungal mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity

“…17 and genome sequence data). The human mtTyrRS was shown to charge tRNA Tyr containing an alternate N1-N72 pair with an Ϸ10-fold decrease in catalytic efficiency (18).…”

Translation in Mammalian Mitochondria: Order and Disorder Linked to tRNAs and Aminoacyl-tRNA Synthetases

“…A mutagenic analysis of the enzyme has confirmed this view (Fender et al 2006). Another example of the peculiarity of identity elements in a mitochondrial system concerns human mt-tRNA Tyr (Bonnefond et al 2005b). Base-pair G1-C72, forms an important identity element in archaeal and eukaryal tRNA Tyr (Bonnefond et al 2005b).…”

“…Mt-tRNAs are expressed in cells to very low levels as compared to their cytosolic counterparts (estimated as 1 mt-tRNA per 160 cytosolic tRNA), rendering access for biochemical investigation of these RNAs very limited (Enriquez and Attardi 1996). Detailed experimental secondary structures were however established on in vitro transcripts and revealed large structural flexibility, with alternative folds to the cloverleaf co-existing in equilibrium (Bonnefond et al 2005b;Helm et al 1998;Sohm et al 2003). This is due to a severe bias in nucleotide content (A, U, and C-rich, and G-poor) especially for the 14 tRNAs coded by the light DNA strand, leading to very low numbers of stable G-C base-pairs, and at opposite, to high levels of weaker A-U and G-U pairs.…”