The function, formation, and carbon-source regulation of 3' truncated mRNAs in Saccharomyces cerevisiae

Abstract

The yeast gene CBP1 produces two transcripts with different 3' ends. Carbon source reciprocally regulates production of the two transcripts. The level of the longer transcript decreases upon induction of respiration while that of the shorter transcript increases; the total level of CBP1 transcripts remains constant. This result was unexpected since the longer transcript encodes an essential respiratory protein, while no protein translated from the short transcript was detected. To determine whether the short transcript has an essential respiratory function, production of the short transcript was abolished by mutagenesis, resulting in a constant level of the long transcript upon induction of respiration. A concomitant increase in the level of mitochondrial COB mRNA, which accumulates through the action of Cbp1, was also observed. Therefore, Cbp1 is limiting for the accumulation of COB mRNA; the function of short CBP1 transcript production is to downregulate the long transcript level upon induction of respiration. The mechanisms of formation and regulation of the short CBP1 transcripts are unknown. Measurement of the half-lives of the two CBP1 transcripts revealed that differential mRNA stability is not responsible for their reciprocal regulation. Deletion of the gene encoding the transcription elongation factor TFIIS did not alter the ratio of long to short transcripts. Therefore, carbon source-regulated alternative 3' end formation is the most plausible explanation for the reciprocal regulation of the two CBP1 transcripts. I considered whether other truncated transcripts are also regulated by carbon source. The steady-state levels of the shortest AEP2/ATP13 and RNA14 transcripts and the 2.3 kb truncated SIR1 transcript increase upon induction of respiration, while those of the longest transcripts of all three genes and the 1.5 kb truncated RNA14 transcript decrease. Mapping the 3' ends of the shortest transcripts of RNA14, SIR1, CBP1, and AEP2/ATP13, and also the 1.5 kb RNA14 transcript, revealed multiple 3' ends for each short transcript. Comparison of the sequences surrounding the 3' ends of all five short transcripts failed to reveal conserved motifs; however, putative 3' end formation signals for each short transcript were identified. I conclude that carbon source regulates mRNA 3' end formation in yeast.