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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Impact of PDR8 allelic variation on yeast transcriptome profile in wine fermentation condition.

ABSTRACT: An eQTL analysis show that mutations in PDR8 gene in 59A strain versus S288c could trigger expressions variations of QDR2. In order to confirm this result and highlight other gene expression variations associated to PDR8 allelic variation, we performed an allele switch of PDR8 in 59A background (59A PDR8-S288c) and compared the transcriptomic profile of this strain to 59A. The analysis was performed in wine alcoholic fermentation conditions in stationary phase during nitrogen starvation and in alcoholic stress. PDR8 allelic variation: 9 non synonymous SNP (S288c->59A) 9(K->T), 17(S->L), 79(P->S), 198(G->D), 263(H->R), 267(T->S), 371(L->F), 550(A->G), 601(I->V). 6 transcriptomic profiles were performed with Agilent mono-color array: 3 hybridizations were performed for each strain corresponding to 3 biological replicated samples. Using mono-color array, the intensity was used after normalization to calculate logarithm base 2 of expression ratios.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Bruno Blondin

PROVIDER: E-GEOD-41738 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Impact of PDR8 allelic variation on yeast transcriptome profile in wine fermentation condition.

Project description:An eQTL analysis show that mutations in PDR8 gene in 59A strain versus S288c could trigger expressions variations of QDR2. In order to confirm this result and highlight other gene expression variations associated to PDR8 allelic variation, we performed an allele switch of PDR8 in 59A background (59A PDR8-S288c) and compared the transcriptomic profile of this strain to 59A. The analysis was performed in wine alcoholic fermentation conditions in stationary phase during nitrogen starvation and in alcoholic stress. PDR8 allelic variation: 9 non synonymous SNP (S288c->59A) 9(K->T), 17(S->L), 79(P->S), 198(G->D), 263(H->R), 267(T->S), 371(L->F), 550(A->G), 601(I->V).

2013-10-21 | GSE41738 | GEO

eQTL linkages in wine yeasts to decipher regulatory networks in wine fermentation

Project description:We performed here the transcriptomic profile of 44 segregants from a cross between S288c and 59A (a spore of EC1118 strain). The analysis was performed in wine fermentation condition in stationary phase during nitrogen starvation and in alcoholic stress. These data, associated with an individual genotyping by Affymetrix array allow us to highlight genetic variations involved in perturbation of regulatory network and fermentative behavior. 56 transcriptomic profiles were performed with Agilent mono-color array. 6 hybridizations were performed for each parental strains: 3 technical replicates for 2 biological replicated samples (59As1 and 59As5; S288Cs1 and S288Cs5). One hybridization was performed for each of the 44 segregants. Using mono-color array, the logarithm base 2 of intensity was directly used after normalization.

2013-10-21 | E-GEOD-41025 | biostudies-arrayexpress

eQTL linkages in wine yeasts to decipher regulatory networks in wine fermentation

2013-10-21 | GSE41025 | GEO

Impact of nutrient unbalances on wine alcoholic fermentation: nitrogen excess enhances yeast cell death in lipid-limited must

Project description:In this work we evaluated the impact of nutritional unbalances, as lipids/nitrogen unbalances, on wine yeast survival during alcoholic fermentation. We showed that lipids limitations (actually ergosterol limitation) lead to a rapid loss of viability during the stationary phase of fermentation but that cell death rate is strongly modulated by the amount of nitrogen sources. Yeast survival is reduced when an excess of nitrogen is available in lipid-limited fermentations. Such rapid dying yeast cells fermenting with high nitrogen level and lipids-limited amounts displayed a low storage of carbohydrate trehalose and glycogen compared to nitrogen limited cells. Consistently, examination of the cells stress response using an HSP12 promoter-driven GFP expression showed that lipids limitation triggered a weaker stress response than nitrogen limitation. We examined the involvement of nitrogen signalling pathway in the triggering of cell death using a sch9-deleted strain. We showed that deletion of SCH9 restored a high yeast viability indicating that the signaling pathway acting through Sch9p is involved in the enhanced cell death triggered by nitrogen excess. In addition we showed that various nitrogen sources provoked cell death but that histidine and proline did not trigger a similar effect. As a whole our data indicate that lipids limitation does not elicit a transcriptional program leading to a stress response which protects yeast cells and that nitrogen excess triggers cell death through a modulation of this stress response, but not by HSP12. These results point a potential negative role of nitrogen in fermentation which has until now never been described and taken into account in the management of alcoholic fermentations. 2 conditions with 2 biological replicates compared: 59A and 59A-Sch9

2013-03-31 | E-GEOD-42027 | biostudies-arrayexpress

Transcriptomic analysis of the metabolic impact of higher oligopeptide assimilation mediated by horizontally acquired oligopeptide transporters Fot1/2 in wine strains.

Project description:To assess the impact of a higher oligopeptide assimilation mediated by Fot1/2, oligopeptides transporters acquired by HGT on wine yeast cell metabolism in winemaking conditions,we carried out a comparison of transcriptomic profiles of the wine wild type strain 59A and the deletion mutant of FOT1/2 genes during exponential growth. Two strains (59A and 59A FOT-deleted) at 2 released CO2 time point (5g/L and 10g/L) are analyzed. Each condition are in quadriplicate.

2016-01-19 | E-GEOD-62446 | biostudies-arrayexpress

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

Project description: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.

2011-01-19 | E-GEOD-26437 | biostudies-arrayexpress

A transcriptomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation [2010]

Project description:Experience 2: 59A vs. 59A NADH Bdh200 mM, 59A NADPH Bdh200mM and 59A NADPH Bdh300 mM Analysis used RNA samples of three replicates by strain extracted from cells harvested at mid-exponential phase of wine fermentation

2012-03-31 | E-GEOD-34809 | biostudies-arrayexpress

A transcriptomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation [2009]

Project description:Experience 1: 59A vs. 59A NADPH Bdh100mM Analysis used RNA samples of three independent replicates by strain extracted from cells harvested at mid-exponential phase of oenological fermentation

2012-03-31 | E-GEOD-34808 | biostudies-arrayexpress

A transcriptomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation [2010]

Project description:Experience 2: 59A vs. 59A NADH Bdh200 mM, 59A NADPH Bdh200mM and 59A NADPH Bdh300 mM

2012-04-01 | GSE34809 | GEO

Comparison of the metabolic response to over-production of p-coumaric acid in two yeast strains

Project description:We aimed to study how production of p-coumaric acid, a precursor of multiple secondary aromatic metabolites, influences the cellular metabolism of Saccharomyces cerevisiae. We evaluated the growth and p-coumaric acid production in batch and chemostat cultivations and analyzed the transcriptome and intracellular metabolome during steady state in low- and high-producers of p-coumaric acid in two strain backgrounds, S288c or CEN.PK. For analysis of the differential gene expression, we did pairwise comparisons between the optimized and non-optimized strains for p-CA production: CEN.PK strains (ST4288 and ST4408) and the S288c strains (ST4353 and ST4397). Transcriptome analysis showed that the CEN.PK strain was less affected by engineering towards higher p-CA production than the S288c strain, as the number of significantly up-/down-regulated genes was correspondingly 652 and 1927 amongst others, strain S288c had downregulations in gene sets involved in amino acid and protein biosynthesis. This suggests that CEN.PK may be a better platform strain for production of aromatic compounds than the S288c strain.

2017-11-21 | E-MTAB-6208 | biostudies-arrayexpress

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