Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbonsources

We describe a genome-wide characterization of mRNA transcript levels in yea st grown on the fatty acid oleate, determined using Serial Analysis of Gene Expression (SAGE). Comparison of this SAGE library with that reported for glucose grown cells revealed the dramatic adaptive response of yeast to a c hange in carbon source. A major fraction (>20%) of the 15,000 mRNA molecule s in a yeast cell comprised differentially expressed transcripts, which wer e derived from only 2% of the total number of similar to 6300 yeast genes. Most of the mRNAs that were differentially expressed code for enzymes or fo r other proteins participating in metabolism (e.g., metabolite transporters ). In oleate-grown cells, this was exemplified by the huge increase of mRNA s encoding the peroxisomal beta-oxidation enzymes required for degradation of fatty acids. The data provide evidence for the existence of redox shuttl es across organellar membranes that involve peroxisomal, cytoplasmic, and m itochondrial enzymes. We also analyzed the mRNA profile of a mutant strain with deletions of the PIP2 and OAF1 genes, encoding transcription factors r equired for induction of genes encoding peroxisomal proteins. Induction of genes under the immediate control of these factors was abolished; other gen es were up-regulated, indicating an adaptive response to the changed metabo lism imposed by the genetic impairment. We describe a statistical method fo r analysis of data obtained by SAGE.