Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA95713 | ENA |
REPOSITORIES: ENA
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Project description:In some of the earliest uses of genome-wide gene-expression microarrays and array-based Comparative Genomic Hybridization (aCGH), a set of diploid yeasts that had undergone experimental evolution under aerobic glucose limitation was used to explore how gene expression and genome structure had responded to this selection pressure. To more deeply understand how adaptation to one environment might constrain or enhance performance in another we have now identified the adaptive mutations in this set of clones using whole-genome sequencing, and have assessed whether the evolved clones had become generalists or specialists by assaying their fitness under three contrasting growth environments: aerobic and anaerobic glucose limitation and aerobic acetate limitation. Additionally, evolved clones and their common ancestor were assayed for gene expression, biomass estimates and residual substrate levels under the alternative growth conditions. Relative fitnesses were evaluated by competing each clone against a common reference strain in each environment. Unexpectedly, we found that the evolved clones also outperformed their ancestor under strictly fermentative and strictly oxidative growth conditions. We conclude that yeasts evolving under aerobic glucose limitation become generalists for carbon limitation, as the mutations selected for in one environment are advantageous in others. High-throughput sequencing of the evolved clones uncovered mutations in genes involved in glucose sensing, signaling, and transport that in part explain these physiological phenotypes, with different sets of mutations found in independently-evolved clones. Earlier gene expression data from aerobic glucose-limited cultures had revealed a shift from fermentation towards respiration in all evolved clones explaining increased fitness in that condition. However, because the evolved clones also show higher fitness under strictly anaerobic conditions and under conditions requiring strictly respirative growth, this switch cannot be the sole source of adaptive benefit. Furthermore, because independently evolved clones are genetically distinct we conclude that there are multiple mutational paths leading to the generalist phenotype. Strain Name: Parental strain (CP1AB) or evolved clones (E1 - E5) Media: aerobic / anaerobic
2011-11-02 | GSE25081 | GEO
Project description:In some of the earliest uses of genome-wide gene-expression microarrays and array-based Comparative Genomic Hybridization (aCGH), a set of diploid yeasts that had undergone experimental evolution under aerobic glucose limitation was used to explore how gene expression and genome structure had responded to this selection pressure. To more deeply understand how adaptation to one environment might constrain or enhance performance in another we have now identified the adaptive mutations in this set of clones using whole-genome sequencing, and have assessed whether the evolved clones had become generalists or specialists by assaying their fitness under three contrasting growth environments: aerobic and anaerobic glucose limitation and aerobic acetate limitation. Additionally, evolved clones and their common ancestor were assayed for gene expression, biomass estimates and residual substrate levels under the alternative growth conditions. Relative fitnesses were evaluated by competing each clone against a common reference strain in each environment. Unexpectedly, we found that the evolved clones also outperformed their ancestor under strictly fermentative and strictly oxidative growth conditions. We conclude that yeasts evolving under aerobic glucose limitation become generalists for carbon limitation, as the mutations selected for in one environment are advantageous in others. High-throughput sequencing of the evolved clones uncovered mutations in genes involved in glucose sensing, signaling, and transport that in part explain these physiological phenotypes, with different sets of mutations found in independently-evolved clones. Earlier gene expression data from aerobic glucose-limited cultures had revealed a shift from fermentation towards respiration in all evolved clones explaining increased fitness in that condition. However, because the evolved clones also show higher fitness under strictly anaerobic conditions and under conditions requiring strictly respirative growth, this switch cannot be the sole source of adaptive benefit. Furthermore, because independently evolved clones are genetically distinct we conclude that there are multiple mutational paths leading to the generalist phenotype. Strain Name: Parental strain (CP1AB) or evolved clones (E1 - E5) Media: aerobic / anaerobic 36 hybridizations
2011-11-02 | E-GEOD-25081 | biostudies-arrayexpress
Project description:In the present study transcriptome and proteome of recombinant, xylose-utilising S. cerevisiae grown in aerobic batch cultures on xylose were compared with glucose-grown cells both in glucose repressed and derepressed states. The aim was to study at genome-wide level how signalling and carbon catabolite repression differed in cells grown on either glucose or xylose. The more detailed knowledge about is xylose sensed as a fermentable carbon source, capable of catabolite repression like glucose, or is it rather recognised as a non-fermentable carbon source is important in achieving understanding for further engineering this yeast for more efficient anaerobic fermentation of xylose.
2008-09-24 | GSE12890 | GEO
Project description:Physiological effects of carbon dioxide and impact on genome-wide transcript profiles were analysed in chemostat cultures of Saccharomyces cerevisiae. In anaerobic, glucose-limited chemostat cultures grown at atmospheric pressure, cultivation under CO2-saturated conditions had only a marginal (<10%) impact on the biomass yield. Conversely, a 25% decrease of the biomass yield was found in aerobic, glucose-limited chemostat cultures aerated with a mixture of 79% CO2 and 21% O2. This observation indicated that respiratory metabolism is more sensitive to CO2 than fermentative metabolism. Consistent with the more pronounced physiological effects of CO2 in respiratory cultures, the number of CO2-responsive transcripts was higher in aerobic cultures than in anaerobic cultures. Many genes involved in mitochondrial functions showed a transcriptional response to elevated CO2 concentrations. This is consistent with an uncoupling effect of CO2 and/or intracellular bicarbonate on the mitochondrial inner membrane. Other transcripts that showed a significant transcriptional response to elevated CO2 included NCE103 (probably encoding carbonic anhydrase), PCK1 (encoding PEP carboxykinase) and members of the IMD gene family (encoding isozymes of inosine monophosphate dehydrogenase Keywords: Dose reponse
2007-08-31 | GSE8900 | GEO
Project description:Transcriptional response of S.cerevisiae to aeration after anaerobic growth
| PRJNA98177 | ENA
Project description:The goal of this study was to study this interaction by analyzing genome-wide transcriptional responses to four different nutrient-limitation regimes under aerobic and anaerobic conditions in chemostat cultures of S. cerevisiae. This ‘two-dimensional’ approach resulted in a new, robust set of ‘anaerobic’ and ‘aerobic’ signature transcripts for S. cerevisiae, as well as to a refinement of previous reports on nutrient-responsive genes. Moreover, the identification of genes regulated both by nutrient and oxygen availability provided new insight in cross-regulated network and hierarchy in the control of gene expression. Keywords = S. cerevisiae Keywords = oxygen availability Keywords = anaerobiosis Keywords = chemostat Keywords = transcriptome Keywords = nutrient limitation Keywords = carbon Keywords = nitrogen Keywords = sulfur Keywords = phosphorus. Keywords: other
2004-09-03 | GSE1723 | GEO
Project description:In this study we focus on two Saccharomyces cerevisiae strains with varying production of heterologous α-amylase and we compare the metabolic fluxes and transcriptional regulation at aerobic and anaerobic conditions, in particular with the objective to identify the final electron acceptor for protein folding. We found that anaerobic conditions showed high amount of amylase productions when comparing to aerobic conditions and the genome-scale transcriptional analysis suggested that genes related to the endoplasmic reticulum (ER), lipid synthesis and stress responses were generally up-regulated at anaerobic conditions. Moreover, we proposed a model for the electron transfer from ER to the final electron acceptor, fumarate under anaerobic conditions.
2013-01-17 | GSE38848 | GEO
Project description:The inhibitors hydroxymethylfurfural (HMF) and furfural were added to the feed-medium of carbon-limited anaerobic chemostat cultures. Samples were taken for transcriptome analysis at steady-state from cultures with inhibitors and without inhibitors.
2012-10-18 | GSE41659 | GEO
Project description:Microorganisms are exposed to large variations in nutrient availability in nature. To cope with these variations and sustain growth, they maximize the utility of the available nutrients and adapt to nutritional deficiencies. We studied the transcriptional and metabolic dynamics in Saccharomyces cerevisiae in response to a gradual transition from glucose-limited growth to ammonia-limited growth under aerobic or anaerobic conditions. Through exposing yeast to a gradual increase in glucose availability, we discovered new aspects of regulation that ensured a balanced metabolism of glucose and ammonia to sustain growth. This required tight coordination of metabolism with different cellular processes. The coordinated expression of the genes involved in key cellular processes implicated the role of signaling pathways mediated by Tor1, Pka1 and Hog1. This is in contrast to the rapid increase in glucose availability, when Snf1 appeared to be the key regulator. The results presented here provide clear insight into key cellular processes that are affected by nutrient limitation and have direct implications in further studies on genome-scale regulation of metabolism. Gene expression was measured in Saccharomyces cerevisiae as it was exposed to gradualy increasing amounts of glucose under aerobic or anaerobic conditions. Eight samples were collected in each case and gene expression measured.
2010-07-23 | E-GEOD-23012 | biostudies-arrayexpress
Project description:Investigation of lipid metabolism as a function of three experimental factors: 1) aerobicity (aerobic vs anaerobic, or 'A' vs 'O'), 2) nutrient limitation (carbon vs nitrogen limitation, or 'C' vs 'N'), 3) temperature (30C vs 15C, or 'T' vs 't') using a full factorial design.
2013-01-31 | E-MEXP-3704 | biostudies-arrayexpress