Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA141483 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptome analyses using a wild-type strain of Saccharomyces cerevisiae were performed to assess the overall pattern of gene expression during the transition from glucose-based fermentative to glycerol-based respiratory growth. These experiments revealed a complex suite of metabolic and structural changes associated with the adaptation process. Alterations in gene expression leading to remodeling of various membrane transport systems and the cortical actin cytoskeleton were observed. Transition to respiratory growth was accompanied by alterations in transcript patterns demonstrating not only a general stress response, as seen in earlier studies, but also the oxidative and osmotic stress responses. In some contrast to earlier studies, these experiments identified modulation of expression for many genes specifying transcription factors during the transition to glycerol-based growth. Importantly and unexpectedly, an ordered series of changes was seen in transcript levels from genes encoding components of the TFIID, SAGA (Spt-Ada-Gcn5-Acetyltransferase), and SLIK (Saga LIKe) complexes and all three RNA polymerases, suggesting a modulation of structure for the basal transcriptional machinery during adaptation to respiratory growth. In concert with data given in earlier studies, the results presented here highlight important aspects of metabolic and other adaptations to respiratory growth in yeast that are common to utilization of multiple carbon sources. Importantly, they also identify aspects specific to adaptation of this organism to growth on glycerol as sole carbon source. A time-series illustrating the transition from fermentation using glucose (dextrose) as sole carbon source to respiration using glycerol as sole carbon source. Time points of 15 minutes, 30 minutes and 60 minutes as well as growth on dextrose, glycerol or ethanol as sole carbon source from a starter culture. Three biological replicates of the 30 minute time point and growth on glycerol from starter culture.
2011-05-26 | E-GEOD-29529 | biostudies-arrayexpress
Project description:Transcriptome analyses using a wild-type strain of Saccharomyces cerevisiae were performed to assess the overall pattern of gene expression during the transition from glucose-based fermentative to glycerol-based respiratory growth. These experiments revealed a complex suite of metabolic and structural changes associated with the adaptation process. Alterations in gene expression leading to remodeling of various membrane transport systems and the cortical actin cytoskeleton were observed. Transition to respiratory growth was accompanied by alterations in transcript patterns demonstrating not only a general stress response, as seen in earlier studies, but also the oxidative and osmotic stress responses. In some contrast to earlier studies, these experiments identified modulation of expression for many genes specifying transcription factors during the transition to glycerol-based growth. Importantly and unexpectedly, an ordered series of changes was seen in transcript levels from genes encoding components of the TFIID, SAGA (Spt-Ada-Gcn5-Acetyltransferase), and SLIK (Saga LIKe) complexes and all three RNA polymerases, suggesting a modulation of structure for the basal transcriptional machinery during adaptation to respiratory growth. In concert with data given in earlier studies, the results presented here highlight important aspects of metabolic and other adaptations to respiratory growth in yeast that are common to utilization of multiple carbon sources. Importantly, they also identify aspects specific to adaptation of this organism to growth on glycerol as sole carbon source.
2011-05-26 | GSE29529 | GEO
Project description:When the yeast Saccharomyces cerevisiae is subjected to increasing glycolytic fluxes under aerobic conditions, there is a threshold value of the glucose uptake rate at which the metabolism shifts from being purely respiratory to mixed respiratory and fermentative. This shift is characterized by ethanol production, a phenomenon known as the Crabtree effect due to its analogy with lactate overflow in cancer cells. It is well known that at high glycolytic fluxes there is glucose repression of respiratory pathways resulting in a decrease in the respiratory capacity. Despite many years of detailed studies on this subject, it is not known whether the onset of the Crabtree effect (or overflow metabolism) is due to a limited respiratory capacity or caused by glucose-mediated repression of respiration. We addressed this issue by increasing respiration in S. cerevisiae by introducing a heterologous alternative oxidase, and observed reduced aerobic ethanol formation. In contrast, increasing non-respiratory NADH oxidation by overexpression of a water-forming NADH oxidase reduced aerobic glycerol formation. The metabolic response to elevated alternative oxidase occurred predominantly in the mitochondria, while NADH oxidase affected genes that catalyze cytosolic reactions. Moreover, NADH oxidase restored the deficiency of cytosolic NADH dehydrogenases in S. cerevisiae. These results indicate that NADH oxidase localizes in the cytosol, while alternative oxidase is directed to the mitochondria. The onset of aerobic ethanol formation is demonstrated to be a consequence of an imbalance in mitochondrial redox balancing. In addition to answering fundamental physiological questions, our findings are relevant for all biomass derived applications of S. cerevisiae. Experiment Overall Design: Heterologous gene expression in chemostats using Affymetrix Yeast Genome 2.0 arrays. Total RNA extraction and sample preparation, hybridization was done according to the manufacturer's protocol.
2008-06-14 | E-GEOD-6277 | biostudies-arrayexpress
Project description:When the yeast Saccharomyces cerevisiae is subjected to increasing glycolytic fluxes under aerobic conditions, there is a threshold value of the glucose uptake rate at which the metabolism shifts from being purely respiratory to mixed respiratory and fermentative. This shift is characterized by ethanol production, a phenomenon known as the Crabtree effect due to its analogy with lactate overflow in cancer cells. It is well known that at high glycolytic fluxes there is glucose repression of respiratory pathways resulting in a decrease in the respiratory capacity. Despite many years of detailed studies on this subject, it is not known whether the onset of the Crabtree effect (or overflow metabolism) is due to a limited respiratory capacity or caused by glucose-mediated repression of respiration. We addressed this issue by increasing respiration in S. cerevisiae by introducing a heterologous alternative oxidase, and observed reduced aerobic ethanol formation. In contrast, increasing non-respiratory NADH oxidation by overexpression of a water-forming NADH oxidase reduced aerobic glycerol formation. The metabolic response to elevated alternative oxidase occurred predominantly in the mitochondria, while NADH oxidase affected genes that catalyze cytosolic reactions. Moreover, NADH oxidase restored the deficiency of cytosolic NADH dehydrogenases in S. cerevisiae. These results indicate that NADH oxidase localizes in the cytosol, while alternative oxidase is directed to the mitochondria. The onset of aerobic ethanol formation is demonstrated to be a consequence of an imbalance in mitochondrial redox balancing. In addition to answering fundamental physiological questions, our findings are relevant for all biomass derived applications of S. cerevisiae. Keywords: Genetic Modification
2007-02-01 | GSE6277 | GEO
Project description:The ability of the yeast Saccharomyces cerevisiae to convert glucose, even in the presence of oxygen, via glycolysis and the fermentative pathway to ethanol has played an important role in its domestication. Despite the extensive knowledge on these pathways in S. cerevisiae, relatively little is known about these pathways in other industrially-relevant Saccharomyces yeast species. In this study we explore the diversity of the glycolytic and fermentative pathways within the Saccharomyces genus using S. cerevisiae, S. kudriavzevii and S. eubayanus as paradigms. Sequencing data revealed a highly conserved genetic makeup of the glycolytic and fermentative pathways in the three species in terms of number of paralogous genes. Although promoter regions were less conserved between the three species as compared to coding sequences, binding sites for Rap1, Gcr1 and Abf1, main transcriptional regulators of glycolytic and fermentative genes, were highly conserved. Transcriptome profiling of these three strains grown in aerobic batch cultivation in chemically defined medium with glucose as carbon source, revealed a remarkably similar expression of the glycolytic and fermentative genes across species, and the conserved classification of genes into major and minor paralogs. Furthermore, transplantation of the promoters of major paralogs of S. kudriavzevii and S. eubayanus into S. cerevisiae demonstrated not only the transferability of these promoters, but also the similarity of their strength and response to various environmental stimuli. The relatively low homology of S. kudriavzevii and S. eubayanus promoters to their S. cerevisiae relatives makes them very attractive alternatives for strain construction in S. cerevisiae, thereby expanding S. cerevisiae molecular toolbox.
2018-07-21 | GSE117404 | GEO
Project description:Glycerol offers several advantages as a substrate for biotechnological applications. An important step towards using the popular production host Saccharomyces cerevisiae for glycerol-based bioprocesses have been recent studies in which commonly used S. cerevisiae strains were engineered to grow in synthetic medium containing glycerol as the sole carbon source. In order to boost extensive S. cerevisiae metabolic engineering incentives aiming at the use of glycerol, we realized that promoters with predictable expression levels in synthetic glycerol medium were required. In the current study, we used transcriptome analysis and a yECitrine-based fluorescence reporter assay to select and characterize useful 25 promoters for driving expression of target genes in S. cerevisiae under the given conditions. The promoters of the genes ALD4 and ADH2 showed 4.2- and 3-fold higher activities compared to the well-known strong TEF1 promoter. Moreover, the collection contains promoters with graded activities in synthetic glycerol medium and different degrees of glucose repression. To demonstrate the general applicability of the promoter collection, we successfully used a subset of the characterized promoters with graded activities in order to optimize growth on glycerol in an engineered derivative of CEN.PK, in which glycerol catabolism exclusively occurs via a non-native DHA pathway.
2018-03-31 | GSE109036 | GEO
Project description:RSC is a growth essential ATP-dependent chromatin-remodeling complex of Saccharomyces cerevisiae. Nps1/Sth1 is the ATPase subunit of the complex. A temperature-sensitive mutant allele of NPS1, nps1-13 and the null mutation of the RSC2 or RSC7 gene showed growth defect on a medium containing non fermentable carbon source, such as lactate or ethanol-glycerol (YPEG), suggested a possibility that RSC plays a role on mitochondria function. We used microarrays to compare the global gene expression profiles between the wild type and nps1-13 mutant under respiratory condition.
2015-03-10 | GSE66685 | GEO
Project description:RSC is a growth essential ATP-dependent chromatin-remodeling complex of Saccharomyces cerevisiae. Nps1/Sth1 is the ATPase subunit of the complex. A temperature-sensitive mutant allele of NPS1, nps1-13 and the null mutation of the RSC2 or RSC7 gene showed growth defect on a medium containing non fermentable carbon source, such as lactate or ethanol-glycerol (YPEG), suggested a possibility that RSC plays a role on mitochondria function. We used microarrays to compare the global gene expression profiles between the wild type and nps1-13 mutant under respiratory condition. WT (BY4743) and nps1-13 strains pre-grown in YPD medium were inoculated in YPEG medium for RNA extraction and hybridization on Affymetrix microarrays. In order to obtain more global insights into the role of RSC under respiratory conditions, we perfomed the genome-wide expression analysis of nps1-13 in YPEG medium.
2015-03-10 | E-GEOD-66685 | biostudies-arrayexpress
Project description:We performed whole genome analysis of the DNA binding of five Saccharomyces cerevisiae transcription factors involved in lipid biosynthesis, Ino2, Ino4, Hap1, Oaf1 and Pip2, in response to four different environmental conditions. Using chromatin immunoprecipitation with lambda exonuclease digestion (ChIP-exo) we discovered a large number of so-far unidentified targets with nucleotide resolution. Based on the newly identified targets we document expanded functions for all five transcription factors, e.g. glutamate biosynthesis as a target of Oaf1 and Pip2. Moreover, condition-dependent binding of transcription factors in response to cell metabolic state, e.g. differential binding of Ino2 between fermentative and respiratory metabolic conditions was clearly suggested. Using our data we build a comprehensive transcriptional regulatory network for lipid metabolism in yeast.
2018-07-05 | GSE88941 | GEO
Project description:The capacity of respiring cultures of Saccharomyces cerevisiae to instantaneously switch to fast alcoholic fermentation upon a transfer to anaerobic sugar-excess conditions is a key characteristic of Saccharomyces cerevisiae in many of its industrial applications. This transition was studied by exposing aerobic glucose-limited chemostat cultures grown at a low specific growth rate to two simultaneous perturbations: oxygen depletion and relief of glucose limitation. This shift towards fully fermentative conditions caused a massive transcriptional response, where one third of all genes within the genome were transcribed differentially. During the first 30 min, most of these changes were driven by relief from glucose limitation. An anaerobic induction response was only observed after the initial response to glucose excess. By comparing this study with public datasets representing dynamic and steady conditions, 14 up-regulated and 11 down-regulated genes were determined to be anaerobiosis specific and can therefore be use as âsignatureâ transcripts for anaerobicity under dynamic as well as under steady state conditions Experiment Overall Design: To invoke rapid and full induction of fermentative capacity, respiratory, aerobic glucose-limited chemostat cultures (D=0.1â¢h-1) were shifted to fully fermentative conditions by sudden depletion of oxygen and addition of glucose. The glucose was added two min after sparging the continuous culture with pure nitrogen, when the dissolved oxygen concentration had decreased from 75-80% to 10-15% of air saturation. Samples for micro-arrays were taken for each time point after the perturbation (5, 10, 30, 60 and 120 min) from two independently cultured replicates, while steady state data were taken from three independent chemostats. The complete dataset therefore comprised 13 samples.
2008-10-18 | E-GEOD-8187 | biostudies-arrayexpress