Transcriptional response of ethanol-stressed vs. non-stressed culture
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE15493 | GEO | 2009/09/01
SECONDARY ACCESSION(S): PRJNA115941
REPOSITORIES: GEO
Similar Datasets
Project description:The yeast Saccharomyces cerevisiae is well known for its high ethanol production performances. An original fermentation process that allows the yeast S. cerevisiae to produce in less than 45 h more than 150 g/l ethanol (i.e. 18.9°GL) was set up in our laboratory [1]. Under this condition, the yeast cells induce a dynamic process to adapt to increased ethanol concentration by a mechanism that is likely different to the stress response triggered by sudden ethanol addition to exponentially growing cells [2]. Kinetic analysis of the growth curve identified two main phases: a growth phase that ended up at 90 g/l ethanol and then an uncoupling phase during which non-growing cells kept producing ethanol. This latter phase is also characterized with an increased loss of viability. In order to investigate on a genome scale the expression changes occurring during this process, gene expression was quantified using DNA chips technology at six different time-points during fed-batch fermentation. [1] Alfenore et al, Appl. Microbiol. Biotechnol. 60 : 67-72, 2002. [2] Alexandre H. et al., FEBS Lett. 498(1) : 98-103, 2001. We measure the changes in the gene expression of ethanol stressed culture at five different time-points during fed-batch fermentation compared to a common reference consisting of exponentially growing yeast cells ( sample number 1 : growing cells ; low ethanol concentration of 17 g/l ; specific growth rate of 0.3 h-1) . The sets corresponded to sample number 2 : growing cells/ethanol concentration of 60 g/l ; sample number 3 : before growth arrest/ethanol concentration of 90 g/l ; sample number 4 : growth arrest/ethanol concentration of 95 g/l ; sample number 5 : 1 hour after growth arrest/ethanol concentration of 100 g/l and sample number 6 : uncoupling phase/ethanol concentration of 125 g/l. For each sample, total RNAs from one yeast culture (no biological replicate) were extracted three times (technical replicates -extract). For labelling, we labelled the common reference with dCTP-Cy5 and labelled the sample with dCTP-Cy3 and hybridized cDNA on three independent microarrays, given rise to six data value per gene (each gene is duplicate in the slide).
2009-09-01 | E-GEOD-15493 | biostudies-arrayexpress
Project description: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. Keywords: time course, stress response, fermentation
2008-04-17 | GSE8536 | GEO
Project description:The yeast Saccharomyces cerevisiae is an important component of the wine fermentation process and determines various attributes of the final product. However, lactic acid bacteria (LAB) are also an integral part of the microflora of any fermenting must. Various wine microorganism engineering projects have been endeavoured in the past in order to change certain wine characteristics, namely aroma compound composition, ethanol concentration, levels of toxic/ allergenic compounds etc. Most of these projects focus on a specific gene or pathway, whereas our approach aims to understand the genetically complex traits responsible for these phenotypes in a systematic manner by implementing a transcriptomic analysis of yeast in mixed fermentations with the LAB O. oeni. Our aim is to investigate interactions between yeast and LAB on a gene expression level to identify targets for modification of yeast and O. oeni in a directed manner. Our goal was to identify the impact that the common wine microorganism O. oeni (malolactic bacteria) has on fermenting yeast cells on a gene expression level. To this end we co-inoculated the yeast and bacteria at the start of fermentation in a synthetic wine must, using yeast-only fermentations witout O. oeni as a control. Fermentations were carried out in synthetic wine must in triplicate for both the control S. cerevisiae VIN13 strain and the mixed fermentation of VIN13 and O. oeni (strain S5). Sampling of yeast for RNA extractions were performed at day 3 of fermentation, during the exponential growth phase of the yeast cells, and again at day 7 of fermentation, during the early stationary growth phase.
2011-06-02 | E-GEOD-27085 | biostudies-arrayexpress
Project description:The yeast Dekkera bruxellensis is as ethanol tolerant as Saccharomyces cerevisiae and may be found in bottled wine. It causes the spoilage of wine, beer, cider and soft drinks. In wines, the metabolic products responsible for spoilage by Dekkera bruxellensis are mainly volatile phenols. These chemical compounds are responsible for the taints described as M-bM-^@M-^XM-bM-^@M-^XmedicinalM-bM-^@M-^YM-bM-^@M-^Y in white wines (due to vinyl phenols) and as M-bM-^@M-^XM-bM-^@M-^XleatherM-bM-^@M-^YM-bM-^@M-^Y, M-bM-^@M-^XM-bM-^@M-^Xhorse sweatM-bM-^@M-^YM-bM-^@M-^Y and M-bM-^@M-^XM-bM-^@M-^XstableM-bM-^@M-^YM-bM-^@M-^Y in red wines (due to ethyl phenols mainly 4-ethylphenol). Apart from the negative aroma nuances imparted by these yeasts, positive aromas such as M-bM-^@M-^XsmokyM-bM-^@M-^Y, M-bM-^@M-^XspicyM-bM-^@M-^Y and M-bM-^@M-^XtoffeeM-bM-^@M-^Y are also cited. Our goal was to identify the impact that the wine spoilage yeast Dekkera bruxellensis has on fermenting S. cerevisiae cells, especially on its gene expression level. To this end we co-inoculated both yeast species at the start of fermentation in a synthetic wine must, using S. cerevisiae-only fermentations without Dekkera bruxellensis as a control. All fermentations were employed in special membrane reactors (50 KDa pore size cut-off) physically separating Dekkera bruxellensis from wine yeast S. cerevisiae. Biomass separation with this membrane was done to abolish the possibility of hybridizing also D. bruxellensis probes on Agilent V2 (8x15K format) G4813 DNA microarrays designed just for S. cerevisiae ORF targets. The 50 KDa pore membrane separating both yeasts allowed the exchange of ethanol, metabolites and sugars during the fermentation. Fermentations were carried out in synthetic wine must in duplicate for both the control S. cerevisiae (strain Lalvin EC1118) and mixed fermentation. Sampling of yeast S. cerevisiae for RNA extractions were performed at 22 h of fermentation, during the exponential growth phase of S. cerevisiae, at 92 h and 144 h of fermentation, during its early and late stationary growth phase and at 187 h of fermentation, during its phase of growth decline.
2012-06-12 | E-GEOD-38582 | biostudies-arrayexpress
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.
2011-05-31 | E-GEOD-29273 | biostudies-arrayexpress
Project description:In our previous work, we showed the positive effect of the magnesium and the negative effect of the copper on yeast fermentation performance. The magnesium increases the ethanol yield and a faster glucose consumption by the yeast, on the other hand, the copper provides an opposite effect in yeast under fermentation condition. Therefore, from this contrasting effect we performed the gene-wide expression analysis in the industrial yeast Saccharomyces cerevisiae JP1 under fermentation condition in order to reveal the gene expression profile upon magnesium and copper supplementation.
2015-12-09 | GSE75803 | GEO
Project description: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)
2008-06-16 | E-GEOD-8536 | biostudies-arrayexpress
Project description:In our previous work, we showed the positive effect of the magnesium and the negative effect of the copper on yeast fermentation performance. The magnesium increases the ethanol yield and a faster glucose consumption by the yeast, on the other hand, the copper provides an opposite effect in yeast under fermentation condition. Therefore, from this contrasting effect we performed the gene-wide expression analysis in the industrial yeast Saccharomyces cerevisiae JP1 under fermentation condition in order to reveal the gene expression profile upon magnesium and copper supplementation. Fermentation assays was performed with the industrial yeast S. cerevisiae JP1 in reference medium (mineral concentration balanced), in the medium supplemented with 500 mg/L of magnesium (Mg2+ medium) and in the medium supplemented with 1 mg/L of copper (Cu2+ medium).
2015-12-09 | E-GEOD-75803 | biostudies-arrayexpress
Project description:The yeast Dekkera bruxellensis is as ethanol tolerant as Saccharomyces cerevisiae and may be found in bottled wine. It causes the spoilage of wine, beer, cider and soft drinks. In wines, the metabolic products responsible for spoilage by Dekkera bruxellensis are mainly volatile phenols. These chemical compounds are responsible for the taints described as ‘‘medicinal’’ in white wines (due to vinyl phenols) and as ‘‘leather’’, ‘‘horse sweat’’ and ‘‘stable’’ in red wines (due to ethyl phenols mainly 4-ethylphenol). Apart from the negative aroma nuances imparted by these yeasts, positive aromas such as ‘smoky’, ‘spicy’ and ‘toffee’ are also cited. Our goal was to identify the impact that the wine spoilage yeast Dekkera bruxellensis has on fermenting S. cerevisiae cells, especially on its gene expression level. To this end we co-inoculated both yeast species at the start of fermentation in a synthetic wine must, using S. cerevisiae-only fermentations without Dekkera bruxellensis as a control. All fermentations were employed in special membrane reactors (1.2 um pore size cut-off) physically separating Dekkera bruxellensis from wine yeast S. cerevisiae. Biomass separation with this membrane was done to abolish the possibility of hybridizing also D. bruxellensis probes on Agilent V2 (8x15K format) G4813 DNA microarrays designed just for S. cerevisiae ORF targets. The 1.2 um pore membrane separating both yeasts allowed the exchange of ethanol, metabolites and sugars during the fermentation.
2012-06-13 | GSE38582 | GEO
Project description:We have previously shown that fed-batch processes with the longest uncoupling phase (ethanol adapted) were characterized by induction of storage carbohydrates, a metabolic event typical of yeast cells experiencing nutrient limitation, at the onset of this phase, whereas this metabolic event was not seen in processes with a short uncoupling phase (ethanol non adapted culture). Taken together, our results suggested that reproducible high bioethanol performance in aerated fed-batch process may be linked to the ability of yeast cells to impede ethanol toxicity by triggering a metabolic remodelling reminiscent to that of cells entering a quiescent G0/G1 state. The aim of this study was to search for genes implicated in the induction an ethanol adapted culture vs ethanol non-adapted culture. We measure the changes in the gene expression of Ethanol adapted culture (Test : fermentation I in ref 17005001[PMID]) and Ethanol non-adapted (reference : Fermentation II in ref 17005001[PMID]) at the same ethanol concentration of 60 g/l and the same growth rate of the cells (0,14 h-1 :Test) and (0,13 h-1 : reference) to reduce the risk of observing secondary effects due to growth and ethanol stress. For each sample, total RNAs from one yeast culture (no biological replicate) were extracted four times (technical replicates -extract). For labelling, we employed a dye-switch (dCTP-Cy3 and dCTP-Cy5) repeated 2 times and hybridized cDNA on four independent microarrays, given rise to eight data value per gene (each gene is duplicate on the slide).
2009-08-31 | E-GEOD-15321 | biostudies-arrayexpress