Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of S. cerevisiae response to stress throughout a 15-day wine fermentation

ABSTRACT: We used genome-wide expression analyses to study the response of Saccharomyces cerevisiae to stress throughout a 15-day wine fermentation. Forty percent of the yeast genome significantly changed expression levels to mediate long-term adaptation to an environment in which ethanol is both a stressor and a carbon source. Within this set, we identify a group of 223 genes, designated as the Fermentation Stress Response (FSR), that are dramatically and permanently induced; FSR genes exhibited changes ranging from four-to eighty-fold. The FSR is novel; 62% of the genes involved have not been implicated in global stress responses and 28% of the genes have no functional annotation. Genes involved in respiratory metabolism and gluconeogenesis were expressed during fermentation despite the presence of high concentrations of glucose. Ethanol, rather than nutrient depletion, was responsible for entry of yeast cells into stationary phase. Ethanol seems to regulate yeast metabolism through hitherto undiscovered regulatory networks during wine fermentation. Experiment Overall Design: The main study is based on expression measurements at 0.5,2,3.5,7 and 10 % ethanol (corresponding to roughly 24,48,60,120 and 340 hours). Experiments were done in triplicate (biological replicates). This submission also includes the files at 1 hour and at 12 hours for completeness. (also in triplicate)

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Hennie JJ van Vuuren

PROVIDER: E-GEOD-8536 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response.

Marks Virginia D VD Ho Sui Shannan J SJ Erasmus Daniel D van der Merwe George K GK Brumm Jochen J Wasserman Wyeth W WW Bryan Jennifer J van Vuuren Hennie J J HJ

FEMS yeast research 20080201 1

In this study, genome-wide expression analyses were used to study the response of Saccharomyces cerevisiae to stress throughout a 15-day wine fermentation. Forty per cent of the yeast genome significantly changed expression levels to mediate long-term adaptation to fermenting grape must. Among the genes that changed expression levels, a group of 223 genes was identified, which was designated as fermentation stress response (FSR) genes that were dramatically induced at various points during ferme ...[more]

PMID: 18215224

Similar Datasets

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.

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.

Dataset Information

Transcription profiling of S. cerevisiae response to stress throughout a 15-day wine fermentation

Publications

Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets