Intraspecific gene expression variability in the yeast revealed by micro-array analysis

Abstract

Using the Genolevures sequencing data, we developed an expression micro-array for the yeast Kluyveromyces lactis consisting of 482 genes, mainly involved in central metabolism, compound transport facilitators and stress response. The array was validated using the LAC/GAL system. By comparing gene expression in the laboratory reference strain CBS2359 and in an industrial strain B1, we demonstrated the influence of two carbon sources, glucose and lactose, on the expression of genes involved in the respiratory and in the fermentative metabolic pathways. We also showed that the two strains, although both originating from dairies, display unexpected differences in gene expression on each type of carbon source.

Transcriptomic Analysis of Extensive Changes in Metabolic Regulation in Kluyveromyces lactis Strains

“…RNA extraction, reverse transcription, and cDNA labeling were essentially as previously described (35). Briefly, total RNA was extracted from samples using the MIDIprep RNeasy kit (QIAGEN).…”

“…lactis microarray. The microarray we used in this study was previously described (35). It contains 482 70-mer nucleotides representing K. lactis genes, which cover a large number of cellular functions (Table 1).…”

“…Prehybridization and hybridization protocols were as described previously (35). For each slide, hybridization was performed with a mixture of the cDNAs obtained from the cells grown in glucose (just before lactose addition) and the cDNAs from each sample taken 2, 4, and 20 h after addition of lactose.…”

“…Cultures were performed twice independently with cytofluorophores reversed to test the statistical reproducibility. Scanning was performed using a robot Scanarray 4000 (Packard Biosciences, Boston, MA) with a resolution of 5 m. Two images, one for each cytofluorophore, were obtained that were analyzed with the Software Quantarray (Packard BioChip Technologies), as previously described (35). Low-quality spots were flagged at this step and were thus not taken into account for the following analysis.…”

“…Recently, growth in copper sulfate was shown to be associated with a finite number of genes when oenological strains of S. cerevisiae were compared (12). With a similar approach, we found differences in gene expression, some of them in response to the carbon sources, between two isolates of K. lactis, CBS2359 which is used as a reference for genetics studies, and B1, an industrial strain used in cheese making (35). Although K. lactis is the most studied and the best known of all the nonconventional yeasts, many aspects of its physiology remain to be understood.…”