Comparative transcriptome analysis between original and evolved recombinant lactose-consuming S. cerevisiae strains

The engineering of Saccharomyces cerevisiae strains for lactose utilization has been attempted with the intent of developing high productivity processes for alcoholic fermentation of cheese whey. A recombinant S. cerevisiae flocculent strain that efficiently ferments lactose to ethanol was previously obtained by evolutionary engineering of an original recombinant that displayed poor lactose fermentation performance. In this study, we compared the transcriptomes of the original and the evolved recombinant strains (T1 and T1-E, respectively) growing in lactose, using cDNA microarrays. Microarray data revealed 173 genes whose expression levels differed more than 1.5-fold. About half of these genes were related to RNA mediated transposition. We also found genes involved in DNA repair and recombination mechanisms, response to stress, chromatin remodelling, cell cycle control, mitosis regulation, glycolysis and alcoholic fermentation. These transcriptomic data are in agreement with some of the previously identified physiological and molecular differences between the recombinants, and point to further hypotheses to explain those differences. Four samples, each corresponding to independent biological cultivations of the two strains (T1 and T1-E), were analysed. To reduce the bias due to unequal incorporation or differences in quantum efficiency of the two dyes, RNA samples from a second independent experiment were labeled by opposite dye to the first experiment (method called dye switch), and this procedure was repeated 4 times, leading to 4 independent intensity values for each gene (spots) on the microarray. This experimental design minimizes the intrinsic biological noise between identical culture conditions and the technical variations inherent to the DNA microarray technology.