RNA-seq result of yeast cells grown in glucose and glycerol condition
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE301747 | GEO | 2025/08/01
REPOSITORIES: GEO
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.
2011-05-26 | GSE29529 | GEO
Project description:To get a global view of the impact of Hap4 and Hap5 on gene expression in the human pathogen Candida glabrata, we compared the transcriptomes of wild type starins with those of mutant strains in which either HAP4 or HAP5 were deleted. We performed these experiments in two different growth conditions: glycerol as sole carbon source (as Hap4 is supposed to be involved in the induction of respiratory genes in non-fermentative growth conditions) or glucose with iron excess (2 mM FeSO4) as Hap5 is supposed to be involved in the high iron response independently of Hap4.
2021-11-19 | E-MTAB-10544 | 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. 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:The goal of the study is to use Next generation sequencing (RNA-seq) to study the underlying regulation of glycerol metabolism in mixed culture fermentation (glucose and glycerol) of Rhodosporidium toruloides. We sequenced the RNA from 4 different samples in the mixed culture (glucose and glycerol) with 2 replicates each. Transcriptional profiles showed that glycerol might be produced intracellularly and glycerol kinase (GUT1) and glycerol 3–phosphate dehydrogenase (GUT2) enzymes were not down-regulated in the presence of glucose at the transcriptional level. It also showed that this yeast has a different regulation compared to S.cerevisiae. Certain insights into lipid biosynthesis on these mixed cultures are provided at systems level. This analysis provides interesting targets for metabolic engineering in this organism growing on glucose and glycerol.
2016-05-12 | GSE74307 | 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:The bloodstream forms of Trypanosoma brucei (BSF), responsible for the sleeping sickness, primarily evaluate in the blood of its mammalian hosts. The skin and the adipose tissues were recently identified as additional major sites for the parasite proliferation and transmission through its insect vector blood ingestion. Glucose is the only carbon source used by the blood parasites to feed its central metabolism, however, the metabolic behavior of the tissue-adapted parasites has not yet been addressed. Since production of glycerol is an important primary function of adipocytes, we have adapted the BSF trypanosomes to glucose-depleted and glycerol-rich growth medium (CMM_Gly/GlcNAc) and compared its metabolism and proteome with standard glucose-rich growth conditions (CMM_Glu). BSF consume 2-times more oxygen per carbon consumed in CMM_Gly/GlcNAc and is 11.5-times more sensitive to SHAM, a specific inhibitor of the alternative oxidase, which is consistent with the expected absolute requirement of the mitochondrial respiratory chain activity to convert glycerol into dihydroxyacetone phosphate. Metabolomic analyses by mass spectrometry showed that 13C-labeled glycerol is incorporated into hexose phosphates through gluconeogenesis. After several weeks of growth in CMM_Gly/GlcNAc, BSF adapt their metabolism by increasing and decreasing the rate of glycerol and glucose consumption, respectively. As expected RNAi-mediated down-regulation of glycerol kinase expression abolished glycerol degradation and is lethal for BSF growth in CMM_Gly/GlcNAc. However, the glycerol kinase activity is 7.8-fold decreased in CMM_Gly/GlcNAc, as confirms by western blotting and proteomic analyses, which suggests that the huge excess of glycerol kinase, which is not necessary for glycerol metabolism, is required for another yet undetermined non-essential function in glucose rich-conditions. Altogether these data shows that BSF trypanosomes are well adapted to glycerol-rich conditions, which could be encountered by the parasite in extravascular niches, such as skin and adipose tissues.
2018-10-22 | PXD009763 | Pride
Project description:Altered lipid metabolism in macrophages is associated with various important inflammatory conditions. Although lipid metabolism is an important target for therapeutic intervention, the metabolic requirement involved in lipid accumulation during pro-inflammatory activation of macrophages remains incompletely characterized. We show here that macrophage activation with IFNγ results in increased aerobic glycolysis, iNOS-dependent inhibition of respiration, and accumulation of triacylglycerol. Surprisingly, metabolite tracing with 13C-labeled glucose revealed that the glucose contributed to the glycerol groups in triacylglycerol (TAG), rather than to de novo synthesis of fatty acids. This is in stark contrast to the otherwise similar metabolism of cancer cells, and previous results obtained in activated macrophages and dendritic cells. Our results establish a novel metabolic pathway whereby glucose provides glycerol to the headgroup of TAG during classical macrophage activation.
2020-02-27 | PXD017148 | Pride
Project description:Clostridium sp. strain CT7 is a new emerging microbial cell factory with high butanol ratio owing to the non-traditional butanol fermentation mode with uncoupled acetone and 1,3-propanediol formation. Significant change of products profile was shown in glycerol- and glucose-fed strain CT7, especially much higher butanol and lower volatile fatty acids production from glycerol-fed one. However, the mechanism of this interesting phenomenon was still unclear. To better elaborate the bacterial response towards glycerol and glucose, the quantitative proteomic analysis through iTRAQ strategy was performed to reveal the regulated proteomic expression levels under different substrates. Proteomics data showed highly increased proteomic expression levels of proteins related with glycerol utilization and solvent generation under glycerol media. In addition, the up-regulation of hydrogenases, ferredoxins and electron-transferring proteins may attribute to the internal redox balance, while the earlier triggered sporulation response in glycerol-fed media may be associated with the higher butanol fermentation. This study will provide the platform for metabolic engineering of this emerging industrial microorganism for more efficient butanol production from glycerol.
2021-09-08 | PXD016848 | Pride
Project description:Conserved transcriptional regulation of glycerol metabolism was investigated in three Aspergillus species, A. nidulans, A. oryzae and A. niger. For this purpose, batch cultivations under well controlled conditions were performed with the three Aspergilli. Samples for RNA extraction were collected and further processed for hybridization in custom designed Affymetrix microarrays containing probes for the three Aspergillus species. Protein comparisons and cross analysis with gene expression data of all three species resulted in the identification of 88 genes having a conserved response across the three Aspergillus species. A promoter analysis of the up-regulated genes led to the identification of a conserved binding site for a putative regulator.
2009-10-21 | GSE15702 | GEO
Project description:The energy metabolism pathways are significantly influenced by the available carbon sources. In Saccharomyces cerevisiae, energy is primarily produced through aerobic respiration during glycerol cultivation, a process believed to depend on the yeast AMPK (AMP-activated protein kinase) homolog, Snf1. It has been reported that Snf1 increases the expression of respiratory genes by phosphorylating transcriptional activators in environments where glucose is unavailable. We discovered that Tda1, activated by Snf1, phosphorylates Hxk2. Hxk2 has been reported to function as a transcriptional repressor. Therefore, we analyzed how Tda1 affects the expression of respiratory genes by RNA-seq analysis of glycerol-cultured cells.
2025-03-23 | GSE290495 | GEO