Sequence comparison of the Ty1 and Ty2 elements of the yeast genome supports the structural model of the tRNA(i)(Met)-Ty1 RNA reverse transcription initiation complex

Abstract

In the reverse transcription initiation complex of the yeast Ty1 retrotransposon, interaction between the template RNA and primer tRNA(i)(Met) is not limited to base pairing of the primer binding site (PBS) with ten nucleotides at the 3' end of tRNA(i)(Met), but three regions named boxes 0, 1 and 2.1 interact with the T and D stems and loops of tRNA(i)(Met). Sequence comparison of 33 Ty1 elements and 13 closely related Ty2 elements found in the yeast genome shows that the nucleotide sequence of all elements is highly conserved in the region spanning the PBS and the three boxes. Since this domain of the template RNA encodes a portion of protein TyA, we have calculated its amino acid profile and its nucleotide profile to evaluate the role played by nucleotide sequence conservation in the selection for TyA function and in the maintenance of base pairing interactions for the priming function of Ty1 RNA. Our results show that the nucleotide sequence conservation of Ty1 RNA is constrained not only by selection for Ty1 function but also by maintenance of a given nucleotide sequence able to base pair with the tRNA(i)(Met) in the primer-template initiation complex.