Translation ability of mitochondrial tRNAsSer with unusual secondary structures in an in vitro translation system of bovine mitochondria

Background: Metazoan mitochondrial (mt) tRNAs are structurally quite different from the canonical cloverleaf secondary structure. The mammalian mt tRNA(Ser)GCU for AGY codons (Y = C or U) lacks the entire D arm, whereas tRNA(Ser)UGA for UCN codons (N = A, G, C or U) has an extended anti-codon stem. It has been a long-standing problem to prove experimentally how these tRNAs Ser work in the mt translation system. Results: To solve the above-mentioned problem, we examined their translational abilities in an in vitro, bovine mitochondrial translation system using transcripts of altered tRNA(Ser) analogues derived from bovine mitochondria. Both tRNA(Ser) analogues had almost the same ability to,form ternary complexes with mt EF-Tu and GTP. The D-arm-lacking tRNA(Ser) GCU analogue had considerably lower translational activity than the tRNA(Ser)UGA analogue and produced mostly short oligopeptides, up to a tetramer. In addition, tRNA(Ser)GCU analogue was disfavoured by the ribosome when other tRNAs capable of decoding the cognate codon were available. Conclusion: Both mt tRNA(Ser)GCU and tRNA(Ser)UGA analogues with unusual secondary structure were found to be capable of translation on the ribosome. However, the tRNA(Ser)GCU analogue has some molecular disadvantage on the ribosome, which probably derives from the lack of a D arm.