Gene expression profile of yeast cells under stress [bulk RNA-seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE201385 | GEO | 2022/04/26
REPOSITORIES: GEO
Similar Datasets
Project description:To understand transcriptomic changes in baker’s yeast S. cerevisiae cells under stress conditions, we sequenced 117 yeast cells under three stress treatments (hypotonic condition, glucose starvation and amino acid starvation) using a full-length based single-cell RNA-Seq method. We found that though single cells from the same treatment showed varying degrees of uniformity, technical noise and batch effects can confound results significantly. However, upon careful selection of samples to reduce technical artifacts and account for batch-effects, we were able to capture distinct transcriptomic signatures for different stress conditions. Our results show that a full single cell based transcriptomic analysis of the yeast may help paint a clearer picture of how the model organism responds to stress than do bulk cell population-based methods.
2022-04-26 | GSE201386 | GEO
Project description:In this study, we focused on air-drying stress and analyzed the changes in gene expression of commercial baker’s yeast during the air-drying process. Changes in gene expression profiles of commercial baker’s yeast during an air-drying process at 37oC that simulated dried yeast production were analyzed using DNA microarrays. Keywords: Stress response
2008-06-25 | GSE6454 | GEO
Project description:Frozen dough baking is useful method in the modern bread-making industry. However, the fermentation activity of baker’s yeast dramatically decreased after thawing due to freeze injuries, because baker’s yeast cells contained in dough experience freeze injuries during freeze-thaw processes. Here, we performed genome-wide expression analysis to determine genetic response in baker’s yeasts under freeze-thaw condition using a DNA microarray analysis. Functional and clustering analyses in gene expression reveal that genes could be characterized by the term of freeze-thaw stress. Under short-term freeze stress (freeze treatment for 3 day), genes involved in ribosomal protein were up-regulated. Under long-term freeze stress (freeze treatment for longer than 7 day), genes involved in energy synthesis were up-regulated. In each phase, genes involved in protein damage, several stresses and trehalose and glycogen metabolism were also up-regulated. Through these freeze stress, yeast cells may improve reduced efficiency of translation and enhanced cell protection mechanism to survive under freeze stress condition. These regulations of these genes would be controlled by the cAMP-protein kinase A pathway. Keywords: baker’s yeast, freeze-thaw stress, gene expression, freezing period
2009-07-31 | GSE8673 | GEO
Project description:Freeze-thaw stress causes various cellular damages, survival and proliferation defects, and metabolic alterations, although how cells cope with it is poorly understood. In this study, model dough fermentations using two different strains of Saccharomyces cerevisiae baker’s yeast were compared after two-week cell preservation in the refrigerator or in the freezer. As a result, one strain specifically exhibited a decreased fermentation rate after exposed to freeze-thaw stress. A DNA microarray analysis of the cells during fermentation revealed that the genes involved in oxidative phosphorylation were upregulated after the freeze-thawing process in the stress-sensitive strain, suggesting a metabolism switching from glycolysis to respiration. In the identical strain, however, most of the genes that encode the components of the proteasome complex were commonly downregulated, and ubiquitinated proteins were highly accumulated by freeze-thaw stress. In the cells with a laboratory-strain background, treatment with a proteasome inhibitor MG132 or deletion of each transcriptional activator gene for the proteasomal genes (RPN4, PDR1, or PDR3) led to a marked decrease in the rate of model dough fermentation using the frozen cells. Based on these data, degradation of freeze-thaw damaged proteins by proteasome may guarantee the high fermentation performance. Furthermore, a heterozygous dominant-negative PDR3 allele (A148T/A229V/H336R/L541P) was found in the diploid genome of the stress-sensitive baker’s yeast strain, which may be associated with the decreased fermentation rate. Removal of such responsible mutations may improve the freeze-thaw stress tolerance and the fermentation performance of baker’s yeast strains, as well as other industrial S. cerevisiae yeast strains.
2017-07-11 | GSE101071 | GEO
Project description:Environmental conditions are quite effective during propagation and industrial application of Baker’s yeast (Saccharomyces cerevisiae). The change of temperature is one of the most important conditions which affects the dough-leaving capacity of yeast cells. Accordingly, heat changes play an essential role in the commercial and economic impact of the yeast. Recent technologies in genomics have been used for analysis of global gene expression profiles such as microarray and RNA sequencing to solve the problems related with industrial application of yeast. Hereby, the aim of this study is to explore the effects of heat stresses on global gene expression profiles and to identify the candidate genes for the heat stress response in commercial baker’s yeast by using microarray technology and comparative statistical data analyses. Data from all hybridizations and array normalization were analyzed using the GeneSpringGX 12.1 (Agilent) and the R 2.15.2 program language. In the analysis of this dataset, all required statistical methods are performed comparatively in each step and the best performed ones are used in further computations. Hence, as the first step of the analyses, different background normalization algorithms such as MAS5.0, RMA, MBEI and GC-RMA were applied and the algorithm which gives the most accurate findings was chosen for the normalization procedure. As a result, expression values, computed from CEL files, were processed by Robust Multiarray Analysis (RMA) which is the selected procedure for the normalization of the systematic differences between samples. In order to determine differentially expressed genes under heat stress treatments, two different methods, namely, the fold-change and the hypothesis testing approaches are executed. In the fold-change method, various cut-off values are implemented while different multiple testing procedures are performed for the hypothesis testing. Under the heat shock and temperature-shift stress conditions, up/down regulated differentially expressed probes were functionally categorized into the different groups via the cluster analyses. Transcriptome changes under the heat shock and temperature-shift stress treatments show that the number of differentially up-regulated genes among the heat shock proteins (HSPs) and transcription factors (TFs) changed significantly. Consequently, the identification of thousands of genes related with heat stress treatments via microarray technology and comparative statistical analysis resulted in the creation of big picture which provides the understanding of the importance for the baker’s yeast industrial applications.
2017-01-30 | E-MTAB-3459 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE3205: Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 1 GSE3206: Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 2 Abstract: We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited batch cultures of yeast go through two sequential exponential growth phases, beginning with a largely fermentative phase, followed by an essentially completely aerobic use of residual glucose and evolved ethanol. Judging from the patterns of gene expression, the state of the cells growing at steady state in glucose-limited chemostats corresponds most closely with the state of cells in batch cultures just before they undergo this "diauxic shift." Essentially the same pattern was found between chemostats having a fivefold difference in steady-state growth rate (the lower rate approximating that of the second phase respiratory growth rate in batch cultures). Although in both cases the cells in the chemostat consumed most of the glucose, in neither case did they seem to be metabolizing it primarily through respiration. Although there was some indication of a modest oxidative stress response, the chemostat cultures did not exhibit the massive environmental stress response associated with starvation that also is observed, at least in part, during the diauxic shift in batch cultures. We conclude that despite the theoretical possibility of a switch to fully aerobic metabolism of glucose in the chemostat under conditions of glucose scarcity, homeostatic mechanisms are able to carry out metabolic adjustment as if fermentation of the glucose is the preferred option until the glucose is entirely depleted. These results suggest that some aspect of actual starvation, possibly a component of the stress response, may be required for triggering the metabolic remodeling associated with the diauxic shift. Refer to individual Series
2006-03-07 | E-GEOD-4398 | biostudies-arrayexpress
Project description:Time-course transcriptomic profilling of the oleaginous yeast Yarrowia lipolytica, during a controlled fed-batch. A nitrogen limitation was applied during the course of the fed-batch to initiate de novo biolipid synthesis.
2011-05-15 | GSE29046 | GEO
Project description:Abstract: We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited batch cultures of yeast go through two sequential exponential growth phases, beginning with a largely fermentative phase, followed by an essentially completely aerobic use of residual glucose and evolved ethanol. Judging from the patterns of gene expression, the state of the cells growing at steady state in glucose-limited chemostats corresponds most closely with the state of cells in batch cultures just before they undergo this "diauxic shift." Essentially the same pattern was found between chemostats having a fivefold difference in steady-state growth rate (the lower rate approximating that of the second phase respiratory growth rate in batch cultures). Although in both cases the cells in the chemostat consumed most of the glucose, in neither case did they seem to be metabolizing it primarily through respiration. Although there was some indication of a modest oxidative stress response, the chemostat cultures did not exhibit the massive environmental stress response associated with starvation that also is observed, at least in part, during the diauxic shift in batch cultures. We conclude that despite the theoretical possibility of a switch to fully aerobic metabolism of glucose in the chemostat under conditions of glucose scarcity, homeostatic mechanisms are able to carry out metabolic adjustment as if fermentation of the glucose is the preferred option until the glucose is entirely depleted. These results suggest that some aspect of actual starvation, possibly a component of the stress response, may be required for triggering the metabolic remodeling associated with the diauxic shift. This SuperSeries is composed of the SubSeries listed below.
2006-03-08 | GSE4398 | GEO
Project description:Amino acid assimilation and metabolism are crucial for bacterial growth and survival and this is particularly obvious for lactic acid bacteria (LAB) that are generally auxotroph for various amino acids. However, amino acid assimilation is poorly characterized and a complete description of the response during amino acid starvation is still lacking in LAB. In this context, the global response of the LAB model Lactococcus lactis was characterized during isoleucine starvation in batch culture. The stress was imposed by isoleucine natural consumption in an initially rich chemically defined medium. Dynamic analyses were performed both using transcriptomic and proteomic approaches. The response was found to occur gradually and could be divided into three major parts that were firstly deduced from transcriptomic analysis and generally corroborated by proteomic results: (i) a global repression of biogenic processes (transcription, translation, and carbon metabolism and transport), (ii) a specific response related to the limiting nutrient (numerous pathways belonging to carbon or nitrogen metabolism and leading to isoleucine supply were activated) and (iii) an additional response connected to oxidative stress (induction of aerobic metabolism, electron transport, thioredoxin metabolism and pyruvate dehydrogenase). The involvement of various regulatory mechanisms such as growth rate regulation, stringent response, CodY, GlnR, and CcpA regulations, was discussed on the basis of transcriptomic data comparisons. Above the full description of L. lactis isoleucine starvation response, this work additionally provided a complex but realistic outlook of the regulation network involved in isoleucine starvation. Such integrated and comparative approach will allow, by its implementation to other regulations and environmental conditions, the whole regulatory network of L. lactis or any other microorganism to be deciphered. Batch cultivation of Lactococcus lactis IL1403 were carried out on a chemically defined medium and under controlled conditions (30 °C, pH 6.6, nitrogen atmosphere). Cell samples were harvested at steady state. Total RNA was extracted from these samples and radiolabelled cDNA were prepared and hybridized on nylon arrays. 1948 amplicons specific of Lactococcus lactis IL1403 genes were spotted twice on the array. Samples corresponding to various growth rates were analyzed simultaneously and 3 independent repetitions were performed.
2011-09-21 | E-GEOD-12962 | biostudies-arrayexpress
Project description:Phenylethanol-resistant S. cerevisiae mutants were obtained by using evolutionary engineering strategy. Briefly, a chemically mutagenized culture was used as the initial population for the selection procedure. Gradually increasing levels of phenylethanol stress was applied through 56 successive batch cultivations. Individual mutants were selected from the final population. The mutant with the highest phenylethanol resistance could resist up to 3 g/L phenylethanol concentrations. Whole-genome transcriptomic analyses of the phenylethanol-resistant mutant strain and the reference strain were performed by using DNA microarray technology, in the absence of phenylethanol stress. Agilent yeast DNA microarray systems were used for whole-genome transcriptomic analyses of the reference strain and the selected phenylethanol-resistant mutant. Three replicates of each culture were grown in 100 mL yeast minimal medium using 500 mL flasks, at 30°C and 150 rpm. Cells at logarithmic phase of growth (~1.0 OD600) were used for total RNA isolation.
2014-07-12 | E-GEOD-59353 | biostudies-arrayexpress