Comparative transcriptomic approach to investigate differences in wine yeast physiology and metabolism during fermentation

Abstract

Commercial wine yeast strains of the species Saccharomyces cerevisiae have been selected to satisfy many different, and sometimes highly specific, oenological requirements. As a consequence, more than 200 different strains with significantly diverging phenotypic traits are produced globally. This genetic resource has been rather neglected by the scientific community because industrial strains are less easily manipulated than the limited number of laboratory strains that have been successfully employed to investigate fundamental aspects of cellular biology. However, laboratory strains are unsuitable for the study of many phenotypes that are of significant scientific and industrial interest. Here, we investigate whether a comparative transcriptomics and phenomics approach, based on the analysis of five phenotypically diverging industrial wine yeast strains, can provide insights into the molecular networks that are responsible for the expression of such phenotypes. For this purpose, some oenologically relevant phenotypes, including resistance to various stresses, cell wall properties, and metabolite production of these strains were evaluated and aligned with transcriptomic data collected during alcoholic fermentation. The data reveal significant differences in gene regulation between the five strains. While the genetic complexity underlying the various successive stress responses in a dynamic system such as wine fermentation reveals the limits of the approach, many of the relevant differences in gene expression can be linked to specific phenotypic differences between the strains. This is, in particular, the case for many aspects of metabolic regulation. The comparative approach therefore opens new possibilities to investigate complex phenotypic traits on a molecular level.

FIG. 1.

Survival response of the strains in this study under carbon (A), nitrogen (B), sulfur (C), and phosphorus (D) starvation conditions.

FIG. 2.

Assays for heat shock (A), oxidative stress (B), osmotic stress (C), hypersaline stress (D), copper toxicity (E), and ethanol (EtOH) tolerance (F) in VIN13, EC1118, BM45, 285, and DV10 strains.

FIG. 3.

PCA showing components 1 and 2 (PC1 and PC2, respectively). Time points are indicated by date of sampling (where D2 is day 2, for example), strain, and sample number. Strains can be identified as follows: EC1118, E (purple); VIN13, V (black); BM45, B (red); 285, 2 (blue); DV10, D (green).

FIG. 4.

Hierarchical clustering of transcripts encoding enzymes involved in glycolysis, fermentation, and trehalose metabolism (data log normalized to the day 2 gene expression average). Red bars denote an increase in expression while green bars indicate a decrease in expression for a given gene.

FIG. 5.

Intracellular metabolite concentrations measured in the five strains at three time points corresponding to the transcriptional analysis. DW, dry weight.