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

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 sire (PBS) with ten nucleotides at the 3' end of tRNA(i)(Met), but three regions named boxes 0, 1 sind 2.1 interact with the T and D stems and loops of tRNA(i)(Met). Sequence comparison of 33 Tyl elements and 13 closely related Ty2 elements found in the yeast genome shows that the nucleotide sequence of all elements is highly conserved if 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 Tyl RNA. Our results show that the nucleotide sequence conservation of Tyl RNA is constrained not only by selection for Tyl 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. (C) 1997 by John Wiley & Sons, Ltd.