Genomic expression program of Saccharomyces cerevisiae along a mixed-culture wine fermentation with Hanseniaspora guilliermondii

Abstract

Background: The introduction of yeast starter cultures consisting in a blend of Saccharomyces cerevisiae and non-Saccharomyces yeast strains is emerging for production of wines with improved complexity of flavor. The rational use of this approach is, however, dependent on knowing the impact that co-inoculation has in the physiology of S. cerevisiae. In this work the transcriptome of S. cerevisiae was monitored throughout a wine fermentation, carried out in single culture or in a consortium with Hanseniaspora guilliermondii, this being the first time that this relevant yeast-yeast interaction is examined at a genomic scale.

Results: Co-inoculation with H. guilliermondii reduced the overall genome-wide transcriptional response of S. cerevisiae throughout the fermentation, which was attributable to a lower fermentative activity of S. cerevisiae while in the mixed-fermentation. Approximately 350 genes S. cerevisiae genes were found to be differently expressed (FDR < 0.05) in response to the presence of H. guilliermondii in the fermentation medium. Genes involved in biosynthesis of vitamins were enriched among those up-regulated in the mixed-culture fermentation, while genes related with the uptake and biosynthesis of amino acids were enriched among those more expressed in the single-culture. The differences in the aromatic profiles of wines obtained in the single and in the mixed-fermentations correlated with the differential expression of S. cerevisiae genes encoding enzymes required for formation of aroma compounds.

Conclusions: By integrating results obtained in the transcriptomic analysis performed with physiological data our study provided, for the first time, an integrated view into the adaptive responses of S. cerevisiae to the challenging environment of mixed culture fermentation. The availability of nutrients, in particular, of nitrogen and vitamins, stands out as a factor that may determine population dynamics, fermentative activity and by-product formation.

Fig. 1

Fermentation kinetics (a) and growth profiles (b) of single- or mixed-cultures of S. cerevisiae and H. guilliermondii in natural grape-juice. Values presented are the means from triplicate fermentations. Arrows indicate the sampling points for transcriptomic analysis (The data stem from Lage et al. [6])

Fig. 2

Principal Component Analysis of the alterations registered in the transcriptome of S. cerevisiae along a wine fermentation performed in single culture or in consortium with H. guilliermondii. The PCA plot shows variation in expression levels of S. cerevisiae genes either in single- (Sc) or mixed-culture (Mc) at each fermentation stage (24, 48 and 96 h)

Fig. 3

Variation of the expression of S. cerevisiae genes in single or in mixed culture with H. guilliermondii. The expression of each S. cerevisiae gene after 24, 48 or 96 h of single or mixed wine fermentation was compared with its mean expression value along the fermentation. Genes exhibiting at least twofold difference in expression were considered to be differently expressed and were included in this analysis

Fig. 4

Association between S. cerevisiae genes whose expression changed along the single or mixed wine fermentations with their documented regulators. The entire dataset of genes found to change their expression throughout the single or the wine fermentations was searched for documented targets of all described S. cerevisiae transcription factors using the tools and information available in the YEASTRACT database. The activity of each transcription factor was predicted based on the number of targets present in each dataset only considering direct regulatory associations in which binding of the transcription factor to the target gene promoter. The dataset of up-regulated genes was only searched for targets of transcriptional activators (a) while the dataset of down-regulated genes was only searched for targets of transcriptional repressors (b). Transcriptional regulators found to work both as transcriptional activators or repressors were included in both analyses. In this figure only a selected set of regulatory associations is shown but the full list is available in Additional file 1

Fig. 5

Biochemical pathways involved in flavor-active compounds formation. a Yeast genes encoding the enzymes that catalyze each step in the different pathways are shown in italic. b Expression of genes involved in aroma compounds formation: (1) comparison of Sc vs Mc gene expression at each fermentation stage, T1 (24 h), T2 (48 h) and T3 (96 h) red higher expressed in Sc and green higher expressed in Mc—Comparative analysis; and dynamics of genes expression along each fermentation. In this case ratios were obtained using the corresponding T1 as reference—Time-course analysis (red up-regulated and green down-regulated)

Fig. 6

Biochemical pathways involved sulfur amino acid biosynthesis in S. cerevisiae. a Yeast genes encoding the enzymes that catalyze each step in the different pathways are shown in italic. b Expression of genes involved in hydrogen sulfide (H₂S) formation: (1) comparison of Sc vs Mc gene expression at each fermentation stage, T1 (24 h), T2 (48 h) and T3 (96 h)—Comparative analysis (red higher expressed in Sc and green higher expressed in Mc) and dynamics of genes expression along each fermentation. In this case ratios were obtained using the corresponding T1 as reference—Time-course analysis (red up-regulated and green down-regulated)

Fig. 7

Hydrogen sulfide (H₂S) liberation in single-culture—Sc (red) and mixed-culture—Mc (green) fermentations. Data points are the mean from triplicate fermentations ± SD