Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from yeast strain VIN13 in pure-culture fermentations and in mixed fermentations with co-inoculated Oenococcus oeni strain S6

ABSTRACT: The yeast Saccharomyces cerevisiae is an important component of the wine fermentation process and determines various attributes of the final product. However, lactic acid bacteria (LAB) are also an integral part of the microflora of any fermenting must. Various wine microorganism engineering projects have been endeavoured in the past in order to change certain wine characteristics, namely aroma compound composition, ethanol concentration, levels of toxic/ allergenic compounds etc. Most of these projects focus on a specific gene or pathway, whereas our approach aims to understand the genetically complex traits responsible for these phenotypes in a systematic manner by implementing a transcriptomic analysis of yeast in mixed fermentations with the LAB O. oeni. Our aim is to investigate interactions between yeast and LAB on a gene expression level to identify targets for modification of yeast and O. oeni in a directed manner. Our goal was to identify the impact that the common wine microorganism O. oeni (malolactic bacteria) has on fermenting yeast cells on a gene expression level. To this end we co-inoculated the yeast and bacteria at the start of fermentation in a synthetic wine must, using yeast-only fermentations witout O. oeni as a control. Fermentations were carried out in synthetic wine must in triplicate for both the control S. cerevisiae VIN13 strain and the mixed fermentation of VIN13 and O. oeni (strain S5). Sampling of yeast for RNA extractions were performed at day 3 of fermentation, during the exponential growth phase of the yeast cells, and again at day 7 of fermentation, during the early stationary growth phase.

ORGANISM(S): Saccharomyces cerevisiae Vin13

SUBMITTER: Debra Rossouw

PROVIDER: E-GEOD-27085 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The yeast Dekkera bruxellensis is as ethanol tolerant as Saccharomyces cerevisiae and may be found in bottled wine. It causes the spoilage of wine, beer, cider and soft drinks. In wines, the metabolic products responsible for spoilage by Dekkera bruxellensis are mainly volatile phenols. These chemical compounds are responsible for the taints described as M-bM-^@M-^XM-bM-^@M-^XmedicinalM-bM-^@M-^YM-bM-^@M-^Y in white wines (due to vinyl phenols) and as M-bM-^@M-^XM-bM-^@M-^XleatherM-bM-^@M-^YM-bM-^@M-^Y, M-bM-^@M-^XM-bM-^@M-^Xhorse sweatM-bM-^@M-^YM-bM-^@M-^Y and M-bM-^@M-^XM-bM-^@M-^XstableM-bM-^@M-^YM-bM-^@M-^Y in red wines (due to ethyl phenols mainly 4-ethylphenol). Apart from the negative aroma nuances imparted by these yeasts, positive aromas such as M-bM-^@M-^XsmokyM-bM-^@M-^Y, M-bM-^@M-^XspicyM-bM-^@M-^Y and M-bM-^@M-^XtoffeeM-bM-^@M-^Y are also cited. Our goal was to identify the impact that the wine spoilage yeast Dekkera bruxellensis has on fermenting S. cerevisiae cells, especially on its gene expression level. To this end we co-inoculated both yeast species at the start of fermentation in a synthetic wine must, using S. cerevisiae-only fermentations without Dekkera bruxellensis as a control. All fermentations were employed in special membrane reactors (50 KDa pore size cut-off) physically separating Dekkera bruxellensis from wine yeast S. cerevisiae. Biomass separation with this membrane was done to abolish the possibility of hybridizing also D. bruxellensis probes on Agilent V2 (8x15K format) G4813 DNA microarrays designed just for S. cerevisiae ORF targets. The 50 KDa pore membrane separating both yeasts allowed the exchange of ethanol, metabolites and sugars during the fermentation. Fermentations were carried out in synthetic wine must in duplicate for both the control S. cerevisiae (strain Lalvin EC1118) and mixed fermentation. Sampling of yeast S. cerevisiae for RNA extractions were performed at 22 h of fermentation, during the exponential growth phase of S. cerevisiae, at 92 h and 144 h of fermentation, during its early and late stationary growth phase and at 187 h of fermentation, during its phase of growth decline.

Project description:Industrial wine yeast strains are geno- and phenotypically highly diversified, and have adapted to the ecological niches provided by industrial wine making environments. These strains have been selected for very specific and diverse purposes, and the adaptation of these strains to the oenological environment is a function of the specific expression profiles of their genomes. It has been proposed that some of the primary targets of yeast adaptation are functional binding sites of transcription factors (TF) and the transcription factors themselves. Sequence divergence or regulatory changes related to specific transcription factors would lead to far-reaching changes in overall gene expression patterns, which will in turn impact on specific phenotypic characteristics of different yeast species/ strains. Variations in transcriptional regulation between different wine yeast strains could thus be responsible for rapid adaptation to different fermentative requirements in the context of commercial wine-making. In this study, we compare the transcriptional profiles of five different wine yeast strains in simulated wine-making conditions: Comparative analyses of gene expression profiles in the context of TF regulatory networks provided new insights into the molecular basis for variations in gene expression in these industrial strains. We also show that the metabolic phenotype of one strain can indeed be shifted in the direction of another by modifying the expression of key transcription factors. SOK2 was one target transcription factor identified in this study. This expression factor was overexpressed in order to validate our hypotheses that altered expression levels of key transcription factors could shift metabolism in a directed, predicted manner. Fermentations were carried out in synthetic wine must in triplicate for both the control VIN13 strain and the SOK2 overexpressing strain. Sampling for RNA extractions were performed at day 2 of fermentation, during the exponential growth phase of the yeast cells.

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Expression data from yeast strain VIN13 in pure-culture fermentations and in mixed fermentations with co-inoculated Oenococcus oeni strain S6

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