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Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling.

ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE29529 | GEO | 2011/05/26

SECONDARY ACCESSION(S): PRJNA141483

REPOSITORIES: GEO

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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.

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.

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Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling.

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