Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA310648 | ENA |
REPOSITORIES: ENA
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Project description:Here, we explored natural variation in stress tolerance and in transcriptomic responses to synthetic hydrolysate, mimicking chemically pretreated plant material, to dissect the physiological effects hydrolysate components. Using six different Saccharomyces cerevisiae strains that together maximized phenotypic and genetic diversity, we explored transcriptomic differences between resistant and sensitive strains. We identified both common and strain-specific responses. Comparing responses of resistant and sensitive strains provided insights about primary cellular targets of hydrolysate toxins, implicating cell wall structure, protein and DNA stability, energy stores and redox balance. Importantly, we uncovered lower expression of thiamine genes while in the presence of toxins, which we argue are most likely an indirect effect that increases sensitivity. We also demonstrate synergistic interactions between the nutrient composition, osmolarity, pH, and classes of hydrolysate toxins. Together, this work provides a platform for further dissecting hydrolysate toxins and strain responses. RNA-seq and transcriptome analysis of six S. cerevisiae natural isolates having different resistant to lignocellulosic hydrolysate. Two biological replicate cell samples (collected on different days) were harvested for RNAseq analysis. Strains were grown in YPD, synthetic hydrolysate without toxins (SynH -HTs), and synthetic hydrolysate with toxins (SynH). Cells were grown for at least three generations to log phase (OD600 ~0.5) and collected by centrifugation.
2016-04-01 | E-GEOD-77505 | biostudies-arrayexpress
Project description:Here, we explored natural variation in stress tolerance and in transcriptomic responses to synthetic hydrolysate, mimicking chemically pretreated plant material, to dissect the physiological effects hydrolysate components. Using six different Saccharomyces cerevisiae strains that together maximized phenotypic and genetic diversity, we explored transcriptomic differences between resistant and sensitive strains. We identified both common and strain-specific responses. Comparing responses of resistant and sensitive strains provided insights about primary cellular targets of hydrolysate toxins, implicating cell wall structure, protein and DNA stability, energy stores and redox balance. Importantly, we uncovered lower expression of thiamine genes while in the presence of toxins, which we argue are most likely an indirect effect that increases sensitivity. We also demonstrate synergistic interactions between the nutrient composition, osmolarity, pH, and classes of hydrolysate toxins. Together, this work provides a platform for further dissecting hydrolysate toxins and strain responses.
2016-04-01 | GSE77505 | GEO
Project description:To reach an economically feasible bioethanol process from lignocellulose, efficient fermentation by yeast of all sugars present in the hydrolysate has to be achieved. However, when exposed to lignocellulosic hydrolysate, Saccharomyces cerevisiae is challenged with a variety of inhibitors that reduce yeast viability, growth and fermentation rate, and in addition damage cellular structures. In order to evaluate the yeast capability to adapt to lignocellulosic hydrolysates and to investigate the yeast molecular response to inhibitors, fed-batch cultivation of an industrial S. cerevisiae strain was performed using either spruce hydrolysate or a sugar medium as feed. The physiological effects of cultivating yeast in spruce hydrolysate was comprehensively studied by assessment of yeast performance in simultaneous saccharification and fermentation (SSF), measurement of furaldehyde reduction activity, assessment of conversion of phenolic compounds and genome wide transcription analysis. The yeast cultivated in spruce hydrolysate developed a rapid adaptive response to lignocellulosic hydrolysate, which significantly improved its fermentation performance in subsequent SSF experiments. Yeast adaptation to hydrolysate was shown to involve induction of NADPH-dependent aldehyde reduction activity and conversion of phenolic compounds during the fed-batch cultivation and these properties were correlated to the expression of several genes encoding oxido-reductase activities, notably AAD4, ADH6, OYE2/3 and YML131w. The other most significant transcriptional changes involved genes involved in transport mechanisms, such as YHK8, FLR1 or ATR1. A large set of genes were found to be associated to transcription factors involved in stress response (Msn2p, Msn4p, Yap1p but also cell growth and division (Gcr4p, Ste12p, Sok2p) that were most likely activated at the post-transcriptional level.
2023-02-21 | GSE218764 | GEO
Project description:CRISPR interference screening of 129 protein kinases and 161 transcription factors in S. cerevisiae. Repression effects on yeast growth in oxygen-limited conditions were quantified in synthetic complete media (SCM), SCM supplemented with 10% lignocellulose hydrolysate and SCM supplemented with 45% of a mixture of growth-inhibiting lignocellulosic compounds. The aim of this project was to determine the reproducibility of CRISPRi effects across studies and to characterize CRISPRi for screening of phenotypes relevant for industrial biotechnology. We identify gene functions in general growth in oxygen-limited conditions, and specific for cellular fitness in lignocellulose hydrolysate. A further screen with a cocktail of lignocellulosic compounds enables us to explain hydrolysate-specific gene functions with roles in toxicity.
2021-02-15 | GSE155590 | GEO
Project description:Analysis of genomic variation in several Saccharomyces cerevisiae x S. kudriavzevii natural hybrids
2009-04-23 | GSE12774 | GEO
Project description:The physiology of ethanologenic Escherichia coli grown anaerobically in alkaline-pretreated plant hydrolysates is not well studied. To gain insight into how E. coli responds to such hydrolysates, we studied an E. coli K-12 ethanologen fermenting a hydrolysate prepared from corn stover pre-treated by ammonia fiber expansion. Despite the high sugar content (~6% glucose, 3% xylose) and relatively low toxicity of this hydrolysate, E. coli ceased growth long before glucose was depleted. Nevertheless, the cells remained metabolically active and continued conversion of glucose to ethanol until all glucose was consumed. Gene expression profiling revealed complex and changing patterns of metabolic physiology and cellular stress responses throughout the different stages of growth. During the exponential and transition phases of growth, high cell maintenance and stress response costs were mitigated, in part, by free amino acids available in the hydrolysate media. However, after the majority of amino acids were depleted from the media cells entered stationary phase and ATP derived from glucose fermentation was consumed entirely by the demands of cell maintenance in the hydrolysate. Comparative gene expression profiling and metabolic modeling of the ethanologen suggested that the high energetic cost of mitigating osmotic, lignotoxin and ethanol stress collectively limits growth, sugar utilization rates and ethanol yields in alkaline-pretreated lignocellulosic hydrolysates. 38 samples in total. 24 samples were derived from biological replicate fermentations of alkaline-pretreated cornstover hydrolysate (12 datapoint time-series per fermentation). The remaining samples were obtained from fermentations conducted in defined media (Glucose Minimal Media (GMM, n=7), Synthetic Hydrolysate media (SynH, n=7)).
2012-06-17 | E-GEOD-35049 | biostudies-arrayexpress
Project description:The physiology of ethanologenic Escherichia coli grown anaerobically in alkaline-pretreated plant hydrolysates is not well studied. To gain insight into how E. coli responds to such hydrolysates, we studied an E. coli K-12 ethanologen fermenting a hydrolysate prepared from corn stover pre-treated by ammonia fiber expansion. Despite the high sugar content (~6% glucose, 3% xylose) and relatively low toxicity of this hydrolysate, E. coli ceased growth long before glucose was depleted. Nevertheless, the cells remained metabolically active and continued conversion of glucose to ethanol until all glucose was consumed. Gene expression profiling revealed complex and changing patterns of metabolic physiology and cellular stress responses throughout the different stages of growth. During the exponential and transition phases of growth, high cell maintenance and stress response costs were mitigated, in part, by free amino acids available in the hydrolysate media. However, after the majority of amino acids were depleted from the media cells entered stationary phase and ATP derived from glucose fermentation was consumed entirely by the demands of cell maintenance in the hydrolysate. Comparative gene expression profiling and metabolic modeling of the ethanologen suggested that the high energetic cost of mitigating osmotic, lignotoxin and ethanol stress collectively limits growth, sugar utilization rates and ethanol yields in alkaline-pretreated lignocellulosic hydrolysates.
2012-06-18 | GSE35049 | GEO
Project description:Six strains of Saccharomyces cerevisiae were grown in four different environments representing a continuum of rich and poor natural conditions Keywords: Stress response, genetic diversity
2006-01-01 | GSE3021 | GEO
Project description:Natural S. cerevisiae isolates were evaluated for tolerance to a complex mixture of lignocellulosic inhibitors. Two isolates, with intermediate and superior tolerance characteristics, were investigated to determine the proteomic changes required for tolerance to lignocellulosic inhibitors.
2018-11-02 | PXD010868 | Pride