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Effects of SO2 on yeast metabolism and changes in the transcriptional profiles

ABSTRACT: Here we report the massively parallel cDNA sequencing (RNA-seq) analysis performed using high throughput sequencing of a vineyard yeast strain collected from the vineyards of the Piave AO (Appellation of origin) (R008 strains) region in North East of Italy and 3 commercial yeast strains (EC1118, VL3 and AWRI796). Yeast cells were collected at the same step of the fermentation curve: at the beginning of the process, when the CO2 produced by the cells was 6 g/l (middle exponential growth phase). The fermentations have been performed for each strain with no SO2 added and with SO2 added at a final concentration of 25 mg/l. Three biological replicates of the fermentations were performed for each strain and samples for RNA-seq were gathered at the beginning of the process. The aim of this experiment was the comparison of the transcriptomes of the four yeast strains to identify the genes characterizing sulphites response.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE57282 | GEO | 2015/04/28

SECONDARY ACCESSION(S): PRJNA246167

REPOSITORIES: GEO

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Effects of SO2 on yeast metabolism and changes in the transcriptional profiles

Project description:Here we report the massively parallel cDNA sequencing (RNA-seq) analysis performed using high throughput sequencing of a vineyard yeast strain collected from the vineyards of the Piave AO (Appellation of origin) (R008 strains) region in North East of Italy and 3 commercial yeast strains (EC1118, VL3 and AWRI796). Yeast cells were collected at the same step of the fermentation curve: at the beginning of the process, when the CO2 produced by the cells was 6 g/l (middle exponential growth phase). The fermentations have been performed for each strain with no SO2 added and with SO2 added at a final concentration of 25 mg/l. Three biological replicates of the fermentations were performed for each strain and samples for RNA-seq were gathered at the beginning of the process. The aim of this experiment was the comparison of the transcriptomes of the four yeast strains to identify the genes characterizing sulphites response. Eight samples were analyzed: R008 strain at middle exponential growth phase (6 g/l CO2 produced) with no SO2 added (previously submitted with ID GSM1092510, experiment GSE44845), R008 strain at middle exponential growth phase (6 g/l CO2 produced) with 25mg/l of SO2 added, EC1118 strain at middle exponential growth phase (6 g/l CO2 produced) with no SO2 added (previously submitted with ID GSM1092506, experiment GSE44845), EC1118 strain at middle exponential growth phase (6 g/l CO2 produced) with 25mg/l of SO2 added, VL3 strain at middle exponential growth phase (6 g/l CO2 produced) with no SO2 added, VL3 strain at middle exponential growth phase (6 g/l CO2 produced) with 25mg/l of SO2 added, AWRI796 strain at middle exponential growth phase (6 g/l CO2 produced) with no SO2 added, AWRI796 strain at middle exponential growth phase (6 g/l CO2 produced) with 25mg/l of SO2 added.

2015-04-28 | E-GEOD-57282 | biostudies-arrayexpress

Comparison of vineyard, enological and laboratory yeast transcriptomes at different steps of the fermentation curve

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Comparison of vineyard, enological and laboratory yeast transcriptomes at different steps of the fermentation curve

Project description:Here we report the massively parallel cDNA sequencing (RNA-seq) analysis performed using high throughput sequencing of four vineyard yeast strains collected from the vineyards of the M-bM-^@M-^\Prosecco di Conegliano-ValdobbiadeneM-bM-^@M-^] (P283 and P301 strains) and Piave AO (Appellation of origin) (R008 and R103 strains) regions in North East of Italy. Results were compared with RNA-seq performed on a commercial yeast strain (EC1118) and a laboratory strain (S288c). Yeast cells were collected at two different steps of the fermentation curve: at the beginning of the process, when the CO2 produced by the cells was 6 g/l (middle exponential growth phase), and in the middle of fermentation, at 45 g/l (early stationary phase). Three biological replicates of the fermentations were performed for each strain and samples for RNA-seq were gathered at the beginning of the process. The aim of this experiment was the comparison of the transcriptomes of the six yeast strains to identify the genes characterizing wild type yeast isolates, "commercial" and laboratory strains. Twelve samples were analyzed: S288c strain at middle exponential growth phase (6 g/l CO2 produced), S288c strain in the middle of fermentation (45 g/l CO2 produced), EC1118 strain at middle exponential growth phase (6 g/l CO2 produced), EC1118 strain in the middle of fermentation (45 g/l CO2 produced), P283 strain at middle exponential growth phase (6 g/l CO2 produced), P283 strain in the middle of fermentation (45 g/l CO2 produced), R008 strain at middle exponential growth phase (6 g/l CO2 produced), R008 strain in the middle of fermentation (45 g/l CO2 produced), R103 strain at middle exponential growth phase (6 g/l CO2 produced), R103 strain in the middle of fermentation (45 g/l CO2 produced), P301 strain at middle exponential growth phase (6 g/l CO2 produced), P301 strain in the middle of fermentation (45 g/l CO2 produced).

2014-03-31 | E-GEOD-44845 | biostudies-arrayexpress

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2010-02-13 | E-GEOD-16941 | biostudies-arrayexpress

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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

eQTL Mapping of the Yeast Ethanol Response

Project description:In a previous study, we identified extensive natural variation in the response to acute ethanol treatment in three yeast strains: a lab strain derived from the commonly used S288c (DBY8268), vineyard isolate M22, and oak soil strain YPS163. Many expression differences persisted across several modules of co-regulated genes, implicating trans-acting systemic differences in ethanol sensing and/or response. To understand the genetic basis for these expression differences, we performed eQTL mapping analysis of the response to acute ethanol stress in ~100 F2 strains from two crosses: DBY8268x M22 and DBY8268 x YPS163.

2014-10-02 | GSE54196 | GEO

Transcriptomics of cryophilic Saccharomyces kudriavzevii reveals the key role of gene translation efficiency in cold stress adaptations

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