Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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).

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Stefano Campanaro

PROVIDER: E-GEOD-44845 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Second fermentation in a bottle supposes such specific conditions that undergo yeasts to a set of stress situations like high ethanol, low nitrogen, low pH or sub-optimal temperature. Also, yeast have to grow until 1 or 2 generations and ferment all sugar available while they resist increasing CO2 pressure produced along with fermentation. Because of this, yeast for second fermentation must be selected depending on different technological criteria such as resistance to ethanol, pressure, high flocculation capacity, and good autolytic and foaming properties. All of these stress factors appear sequentially or simultaneously, and their superposition could amplify their inhibitory effects over yeast growth. Considering all of the above, it has supposed interesting to characterize the adaptive response of commercial yeast strain EC1118 during second-fermentation experiments under oenological/industrial conditions by transcriptomic profiling. We have pointed ethanol as the most relevant environmental condition in the induction of genes involved in respiratory metabolism, oxidative stress, autophagy, vacuolar and peroxisomal function, after comparison between time-course transcriptomic analysis in alcoholic fermentation and transcriptomic profiling in second fermentation. Other examples of parallelism include overexpression of cellular homeostasis and sugar metabolism genes. Finally, this study brings out the role of low-temperature on yeast physiology during second-fermentation. S. cerevisiae EC1118 pre-adapted to ethanol cells and sucrose (20 g/L) were added to 20 L of base wine (Cavas Freixenet, Sant Sadurní D’Anoia, Spain). Complete volume was bottled with 350 mL each one. All were sealed and incubated in static conditions at 16ºC for approximately 40 days after tirage. Three samples were taken during the process for transcriptional study of the physiological adaptation of yeast cells to industrial second fermentation conditions. A sample corresponding to exponential-growth phase under unstressed conditions (in YPD at 28ºC) was used as an external reference. Three timepoints from second-fermentation were monitored and three biological replicates from each timepoint were analyzed.

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

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