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Expression data from yeast strain VIN13 overexpressing the transcription factor SOK2

ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe Saccharomyces cerevisiae Vin13

PROVIDER: GSE26929 | GEO | 2011/02/11

SECONDARY ACCESSION(S): PRJNA136079

REPOSITORIES: GEO

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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.

Project description:The yeast Saccharomyces cerevisiae is a model for biology and is also one of the most important microorganisms for food and drink production. Surprisingly, only a few genes involved in the adaptation to anthropic niches have been described until now. Wine fermentation and flor aging, which are performed by strains from two closely related groups of yeast, are two technologies that have opposite approaches toward oxygen, which results in contrasting lifestyles for yeast: fermentation growth on grape for wine yeast, and biofilm aerobic growth on ethanol and glycerol contained in wine for flor strains. This pair of environments and the associated yeast populations can be a model for studying adaptation to anthropic environments. In this project, we have obtained high-quality genome sequences of 20 yeast strains from 9 flor yeast, 9 wine yeast as well as EC1118 and haploid derivative 59A. Phylogeny and population structure analysis, based on GATK genotyping, enable us to characterize a group of flor yeast that is clearly different from wine yeast. A comparison of the genomes of wine and flor yeasts using various methods (PCA, nucleotidic diversity, McDonald Kreitman test, potentially impacted genes according to SIFT) enabled us to note divergent regions, or genes, with potential non-neutral evolution, and highly variant genes. The results of these genomic comparisons are echoed by the comparison of a wine and a flor yeast transcriptome. These methods, as expected, highlight key genes that are involved in FLO11 regulation as well as in biofilm growth, but they also revealed the presence of many allelic variations in genes that are involved in the sensing and regulation of osmotic pressure (such as SLN1, HKR1, SSK22, AQY2) and specific metabolic traits, such as the fructophily of flor yeast, which carry a fructophile allele of HXT3. More remarkable is the accumulation of mutations in multiple genes, which creates a pattern of convergent mutations in regulatory networks, as seen in FLO11 regulation or the HOG MAP kinase pathway. The rewiring of these regulatory networks is clearly one of the hallmarks of domestication for the flor yeast genome. Data presented here correspond to the comparison of Flor yeast P3-D5 and wine yeast K1-280-2B transcriptomes under conditions potentially enabling the production of a biofilm.

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Expression data from yeast strain VIN13 overexpressing the transcription factor SOK2

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