A single base change in the intron of a serine tRNA affects the rate of RNase P cleavage in vitro and suppressor activity in vivo in Saccharomyces cerevisiae

Differences in the processing of dimeric tRNA(Ser)-tRNA(Met) precursors derived from the Schizosaccharomyces pombe sup9 wild-type and opal suppressor genes can be attributed to conformational alterations in the tRNA(Ser) anticodon/intron domain. A comparison of the patterns obtained upon transcription of the sup9⁺ (wild-type) and sup9-e (opal suppressor) genes in a coupled transcription/processing extract from Saccharomyces cerevisiae reveals that the latter exhibits a greatly reduced efficiency of 5'-end maturation and is susceptible to specific endonucleolytic cleavage(s) within the intron. Free energy calculations indicate that these effects coincide with a destabilization of the wild-type anticodon/intron stem and suggest that the predominant sup9-e conformer lacks secondary structure in this region. Evidence in support of this hypothesis was obtained by (i) analyzing the processing of sup9⁺ and sup9-e precursors carrying the intron base substitution, G37:10, which destroys and restores, respectively, the base-pairing potential of the proposed secondary structure and (ii) comparing the strength and temperature sensitivity of sup9-e and sup9-e G37:10 suppression in vivo in S. cerevisiae. The data indicate that the anticodon/intron structure of tRNA precursors can influence the rate of RNase P cleavage in vitro and affect tRNA expression in vivo.