Comparative Transcriptomic and Proteomic Profiling of Industrial Wine Yeast Strains

Abstract

The geno-and phenotypic diversity of commercial Saccharomyces cerevisiae wine yeast strains provides an opportunity to apply the system-wide approaches that are reasonably well established for laboratory strains to generate insight into the functioning of complex cellular networks in industrial environments. We have previously analyzed the transcriptomes of five industrial wine yeast strains at three time points during alcoholic fermentation. Here, we extend the comparative approach to include an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis of two of the previously analyzed wine yeast strains at the same three time points during fermentation in synthetic wine must. The data show that differences in the transcriptomes of the two strains at a given time point rather accurately reflect differences in the corresponding proteomes independently of the gene ontology (GO) category, providing strong support for the biological relevance of comparative transcriptomic data sets in yeast. In line with previous observations, the alignment proves to be less accurate when assessing intrastrain changes at different time points. In this case, differences between the transcriptome and proteome appear to be strongly dependent on the GO category of the corresponding genes. The data in particular suggest that metabolic enzymes and the corresponding genes appear to be strongly correlated over time and between strains, suggesting a strong transcriptional control of such enzymes. The data also allow the generation of hypotheses regarding the molecular origin of significant differences in phenotypic traits between the two strains.Saccharomyces cerevisiae has long been a model organism to investigate the biology of the eukaryotic cell. The yeast genome, which is compact and contains only around 6,000 protein-encoding genes, was completely sequenced in 1996 (18), but nearly 10% of putative proteins remain without predicted functions. The majority, if not all of these remaining gene products, are nonessential, and the deletion of these genes in most cases does not lead to a detectable phenotype.A major limitation of most current approaches in this regard is that research is conducted using a limited number of laboratory yeast strains which, while displaying characteristics that are useful for genetic and molecular analyses, represent limited genetic and phenotypic diversity. These laboratory strains are furthermore significantly different from the strains that are used for industrial and commercial purposes. Industrial environments, however, constitute much of the evolutionary framework of the species S. cerevisiae in the past centuries, and many genes that appear not to be associated with a specific function in laboratory strains may be responsible for specific phenotypes in industrial strains. Such strains will therefore be better suited for the analysis of complex genetic and molecular networks and of their phenotypic relevance or biological meaning. The recent sequencing of wine yeast strains (9,3...

Review of Aroma Formation through Metabolic Pathways of Saccharomyces cerevisiae in Beverage Fermentations

“…The sheer amount of genomic and experimental data available for S. cerevisiae and its long history in industrial fermentation make this organism an ideal target for improving and enhancing its application in biotechnology, particularly for the production of small molecules. Systems biology approaches applied to S. cerevisiae fermentation have focused on differential gene expression (Rossouw and Bauer 2009), correlation of gene and protein expression (Rossouw et al 2010), differentiating phenotypes of industrial strains (Rossouw et al 2008, Rossouw and, and linking gene and protein expression to the production of secondary aroma compounds (Rossouw et al 2008, Rossouw et al 2010. Despite this volume of work, we are only beginning to understand how altering the fermentation environment may result in altered secondary metabolism of S. cerevisiae.…”

Geographic Origin and Diversity of Wine Strains ofSaccharomyces

“…A change in a transcription factor can result in the appearance of multiple compensatory cis changes throughout the genome (Bullard et al 2010). Proteomic and metabolite profiling has also been used to assess strain differences solely and in comparison to the transcriptome (Rossouw et al 2008(Rossouw et al , 2009(Rossouw et al , 2010. These analyses indicate that, depending upon gene function, transcript profiles have predictive value for protein and metabolic activity.…”

Transcriptional Regulation and the Diversification of Metabolism in Wine Yeast Strains

“…Studies of wine yeast strains have correlated differences in fermentation phenotypes to gene expression, protein levels, and metabolic regulation (Rossouw et al 2008(Rossouw et al , 2009(Rossouw et al , 2010. These studies focused on the aroma-relevant exometabolome as produced by different wine yeast strains, since this metabolome largely determines the aromatic perception of fruitiness and complexity of wines, and is therefore of particular interest to winemakers.…”