Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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A combined genetic and genomic approach uncovers molecular basis of wine yeast fermentation traits

ABSTRACT: Industrial wine yeast strains possess specific abilities to ferment under stressing conditions and give a suitable aromatic outcome. Although the fermentations properties of Saccharomyces cervisiae wine yeasts are well documented little is known on the genetic basis underlying the fermentation traits. Besides, although strain differences in gene expression has been reported, their relationships with gene expression variations and fermentation phenotypic variations is unknown. To both identify the genetic basis of fermentation traits and get insight on their relationships with gene expression variations, we combined fermentation traits QTL mapping and expression profiling in a segregating population from a cross between a wine yeast derivative and a laboratory strain. 40 samples are analysed with 2 technical replicates, using a unique reference named pool of the 30 segregants. The transcriptome of each segregant is compared to the transcriptome of the pool. The transcriptome of 5 biologic replicates of each parental strain is also compared to this reference. An haploid derivative of the commercialized wine yeast EC1118 which sequence is available (Novo et al. 2009. PNAS, 106:16333-16338) called 59A was used as industrial wine yeast. It is a prototroph strain and has a MATa sexual type. The haploid laboratory strain S288C (MATa) was used for crossing.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Bruno Blondin

PROVIDER: E-GEOD-26437 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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:Wine produced at low temperature is often considered to improve sensory qualities. However, there are certain drawbacks to low temperature fermentations: e.g. low growth rate, long lag phase, and sluggish or stuck fermentations. Selection and development of new Saccharomyces cerevisiae strains well adapted at low temperature is interesting for future biotechnological applications. This study aimed to select and develop wine yeast strains that well adapt to ferment at low temperature through evolutionary engineering, and to decipher the process underlying the obtained phenotypes. To this end, we used a pool of 27 commercial yeast strains and set up batch serial dilution experiments to mimic wine fermentation conditions at 12 ºC. Evolutionary engineering was accomplished by using the natural yeast mutation rate and mutagenesis procedures. One strain (P5) outcompeted the others under both experimental conditions and was able to impose after 200 generations. The evolved strains showed improved growth and low-temperature fermentation performance compared to the ancestral strain. This improvement was acquired only under inositol limitation. The transcriptomic comparison between the evolved and parental strains showed the greatest up-regulation in four mannoprotein coding genes, which belong to the DAN/TIR family (DAN1, TIR1, TIR4 and TIR3). Genome sequencing of the evolved strain revealed the presence of a SNP in the GAA1 gene and the construction of a site-directed mutant (GAA1Thr108) in a derivative haploid of the ancestral strain resulted in improved fermentation performance. GAA1 encodes a GPI transamidase complex subunit that adds GPI, which is required for inositol synthesis, to newly synthesized proteins, including mannoproteins. Thus we demonstrate the importance of inositol and mannoproteins in yeast adaptation at low temperature and the central role of the GAA1 gene by linking both metabolisms. The first aim of this study was to assess the most competitive strains that grow under wine fermentation conditions at low temperature. To this end, we performed a growth competition assay with 27 commercial wine strains inoculated at equal population size in synthetic grape must. In spite of the economical and industrial importance of these strains, their phenotypic variation in the main enological traits, particularly those related to optimum growth temperature, and their ability to adapt to low temperature fermentation have been poorly investigated. The second goal was to obtain an improved strain to grow and ferment at low temperature by evolutionary engineering. For this purpose, we maintained growth competition in synthetic grape must during 200 generations to select for the mutations that produce phenotypes with improved growth in this medium. One of these evolved cultures was previously treated with ethyl methanesulfonate (EMS) to increase the mutation rate. Finally, we aimed to decipher the molecular basis underlying this improvement by analyzing the genomic and transcriptional differences between the parental strain and the strain evolved at low temperature.

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A combined genetic and genomic approach uncovers molecular basis of wine yeast fermentation traits

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