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

Barbosa C, Mendes-Faia A, Lage P, Mira NP, Mendes-Ferreira A - Microb. Cell Fact. (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal. crbarbosa@utad.pt.

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.

No MeSH data available.


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])
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Fig1: 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])

Mentions: The transcriptomic profiling of the mixed-culture fermentations was performed at three different time-points (Fig. 1; Table 1): in mid-exponential growth phase (24 h), in early stationary-phase (48 h), and in late stationary growth-phase (96 h). To get a global view on how the presence of H. guilliermondii impacted the transcriptome of S. cerevisiae throughout the fermentation, the data obtained from the microarrays experiments were subjected to Principal Component Analysis (PCA). This multivariate statistical analysis revealed that gene expression differences between the fermentation stages were much greater than those observed between the two inoculum types (Fig. 2). The first two principal components (PCs) accounted for more than 75 % of the variation observed, with PC1 accounting for the majority (61.8 %) of the observed variability. Samples clustered together in a fermentation stage-specific manner, grouping along the first axes of variation, being observed minor variations between the independent biological replicates. Nevertheless, the separation of the samples collected at the same time-point rendered clear that the presence of H. guilliermondii affected S. cerevisiae transcriptome along fermentation. Notably, the maximal variation in S. cerevisiae genomic expression was reached at the later fermentation stages, in agreement with the much higher number of genes that was found to be differentially in the pair-wise comparisons performed between the two fermentations at the same time-point (see below, Additional file 1). As denoted by Maligoy et al. [27] caution should be taken when analyzing transcriptome data from two parallel cultures, since the variations of transcript levels observed could be either specific to the comparison of the two culture conditions or linked to a difference in the dynamics of the two cultures. To assure that the observed changes in the expression of S. cerevisiae genes truly reflects the influence of the presence of H. guilliermondii, rather than being attributable to different fermentation stages of the mixed and single cultures, the expression of a given gene in a given fermentation stage was compared to its mean expression (calculated taking the average of the expression levels obtained in the three time points analyzed). Although the mean expression value of each gene along the fermentation is merely an arbitrary reference point, such way of analyzing gene expression mitigates the influence exerted by fermentation dynamics, while maintaining the aptitude to identify expression differences [31]. Furthermore, this approach also has the advantage of providing information on how S. cerevisiae transcriptome adjusts to the different dynamics of the single or mixed-culture fermentation; an information that would be missed if only cross-comparisons between expression levels in single vs mixed cultures had been performed. Only genes having an increased or decreased expression of at least twofold were considered to be up- or down- regulated in a given fermentation stage. Using this criterion, two sets of 2224 genes and 1406 S. cerevisiae genes were considered to be differently expressed along the single- or mixed-fermentations, respectively (Additional files 2, 3). K-mean clustering analysis of these genes revealed that the modifications of S. cerevisiae genomic expression occurring throughout the wine fermentations showed similar patterns in the single and in the mixed culture since the gene clusters obtained for the two datasets are, in general, the same (Additional files 2, 3). A closer look into the functional categories of genes included in each cluster revealed that the herein observed alterations of the S. cerevisiae transcriptome along wine fermentation, either in single or in mixed-culture, are consistent with the results reported in other studies carried out with different S. cerevisiae strains and/or exploring different fermentation conditions [17, 19–21, 32]. In specific, genes involved in carbohydrate metabolism, mitochondrial respiration/oxidative phosphorylation, stress response were found to be induced at 48 h of fermentation, both in the single- (clusters II–IV; Additional file 2) and in the mixed-culture fermentation (clusters I–III and IX; Additional file 3), this being attributed to the higher fermentative activity exhibited by the yeast cells at this fermentation stage. Differently, genes involved in cell growth, protein biosynthesis and ribosomal processing, were found to have higher expression at the earlier fermentation stage being repressed afterwards in response to stress associated with alcoholic fermentation progression and entrance in stationary phase. The fact that S. cerevisiae in single-culture displayed more noticeable changes in its transcriptome, in terms of both the number of genes and the magnitude of expression changes, compared to mixed culture (Fig. 3), might reflect a higher need to adjust to a more challenging environment caused by the higher fermentative activity observed.Fig. 1


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

Barbosa C, Mendes-Faia A, Lage P, Mira NP, Mendes-Ferreira A - Microb. Cell Fact. (2015)

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])
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4552253&req=5

Fig1: 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])
Mentions: The transcriptomic profiling of the mixed-culture fermentations was performed at three different time-points (Fig. 1; Table 1): in mid-exponential growth phase (24 h), in early stationary-phase (48 h), and in late stationary growth-phase (96 h). To get a global view on how the presence of H. guilliermondii impacted the transcriptome of S. cerevisiae throughout the fermentation, the data obtained from the microarrays experiments were subjected to Principal Component Analysis (PCA). This multivariate statistical analysis revealed that gene expression differences between the fermentation stages were much greater than those observed between the two inoculum types (Fig. 2). The first two principal components (PCs) accounted for more than 75 % of the variation observed, with PC1 accounting for the majority (61.8 %) of the observed variability. Samples clustered together in a fermentation stage-specific manner, grouping along the first axes of variation, being observed minor variations between the independent biological replicates. Nevertheless, the separation of the samples collected at the same time-point rendered clear that the presence of H. guilliermondii affected S. cerevisiae transcriptome along fermentation. Notably, the maximal variation in S. cerevisiae genomic expression was reached at the later fermentation stages, in agreement with the much higher number of genes that was found to be differentially in the pair-wise comparisons performed between the two fermentations at the same time-point (see below, Additional file 1). As denoted by Maligoy et al. [27] caution should be taken when analyzing transcriptome data from two parallel cultures, since the variations of transcript levels observed could be either specific to the comparison of the two culture conditions or linked to a difference in the dynamics of the two cultures. To assure that the observed changes in the expression of S. cerevisiae genes truly reflects the influence of the presence of H. guilliermondii, rather than being attributable to different fermentation stages of the mixed and single cultures, the expression of a given gene in a given fermentation stage was compared to its mean expression (calculated taking the average of the expression levels obtained in the three time points analyzed). Although the mean expression value of each gene along the fermentation is merely an arbitrary reference point, such way of analyzing gene expression mitigates the influence exerted by fermentation dynamics, while maintaining the aptitude to identify expression differences [31]. Furthermore, this approach also has the advantage of providing information on how S. cerevisiae transcriptome adjusts to the different dynamics of the single or mixed-culture fermentation; an information that would be missed if only cross-comparisons between expression levels in single vs mixed cultures had been performed. Only genes having an increased or decreased expression of at least twofold were considered to be up- or down- regulated in a given fermentation stage. Using this criterion, two sets of 2224 genes and 1406 S. cerevisiae genes were considered to be differently expressed along the single- or mixed-fermentations, respectively (Additional files 2, 3). K-mean clustering analysis of these genes revealed that the modifications of S. cerevisiae genomic expression occurring throughout the wine fermentations showed similar patterns in the single and in the mixed culture since the gene clusters obtained for the two datasets are, in general, the same (Additional files 2, 3). A closer look into the functional categories of genes included in each cluster revealed that the herein observed alterations of the S. cerevisiae transcriptome along wine fermentation, either in single or in mixed-culture, are consistent with the results reported in other studies carried out with different S. cerevisiae strains and/or exploring different fermentation conditions [17, 19–21, 32]. In specific, genes involved in carbohydrate metabolism, mitochondrial respiration/oxidative phosphorylation, stress response were found to be induced at 48 h of fermentation, both in the single- (clusters II–IV; Additional file 2) and in the mixed-culture fermentation (clusters I–III and IX; Additional file 3), this being attributed to the higher fermentative activity exhibited by the yeast cells at this fermentation stage. Differently, genes involved in cell growth, protein biosynthesis and ribosomal processing, were found to have higher expression at the earlier fermentation stage being repressed afterwards in response to stress associated with alcoholic fermentation progression and entrance in stationary phase. The fact that S. cerevisiae in single-culture displayed more noticeable changes in its transcriptome, in terms of both the number of genes and the magnitude of expression changes, compared to mixed culture (Fig. 3), might reflect a higher need to adjust to a more challenging environment caused by the higher fermentative activity observed.Fig. 1

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Escola de Ciências da Vida e Ambiente, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal. crbarbosa@utad.pt.

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.

No MeSH data available.