A nucleoside triphosphate-regulated, 3' exonucleolytic mechanism is involved in turnover of yeast mitochondrial RNAs.

We have employed cell-free transcription reactions with mitochondria isolated from Saccharomyces cerevisiae to study the mechanism of RNA turnover. The specificity of RNA turnover was preserved in these preparations, as were other RNA-processing reactions, including splicing, 3' end formation of mRNAs, and maturation of rRNAs. Turnover of nascent RNAs was found to occur exonucleolytically; endonucleolytic cleavage products were not detected during turnover of the omega intron RNA, which was studied in detail. However, these experiments still leave open the possibility that endonucleolytic cleavage products with very short half-lives are kinetic intermediates in the decay of omega RNA. Exonucleolytic turnover was regulated by nucleotide triphosphates and required their hydrolysis. A unique signature of this regulation was that any one of the eight standard ribo- or deoxyribonucleotide triphosphates supported RNA turnover. A novel hybrid selection protocol was used to determine the turnover rates of the 5', middle, and 3' portions of one mitochondrial transcript, the omega intron RNA. The results suggested that degradation along that transcript occurred with a 3'-->5' polarity. The similarity between features of mitochondrial RNA turnover and the properties of a nucleotide triphosphate-dependent 3' exoribonuclease that has been purified from yeast mitochondria suggests that this single enzyme is a key activity whose regulation is involved in the specificity of mitochondrial RNA turnover.