Saccharomyces cerevisiae
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PROVIDER: PRJNA137315 | ENA |
REPOSITORIES: ENA
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Project description:Though highly efficient at fermenting hexose sugars, the ethanologenic yeast Saccharomyces cerevisiae has limited ability to ferment five-carbon sugars. As a significant portion of sugars found in cellulosic biomasses is the five carbon sugar xylose, S. cerevisiae must be engineered to metabolize pentose sugars. Here we combined classical candidate gene approach with systems biology to develop xylose-utilising S. cerevisiae strains. The introduction of an exogenous xylose isomerase (XYLA) and an additional copy of the endogenous xylulokinase gene (XKS1) results in the significant improvement of xylose consumption. Microarray studies reveal that the introduction of XYLA and XKS1 results in the dramatic transcriptional remodelling of the cell under both glucose and xylose conditions. To further investigate the cellular processes impacted by the introduction of XYLA and XKS1, using genome-wide chemical and synthetic lethal screens we identified greater than 40 deletion mutants that impact xylose utilization. We identified four genes, ALP1, ISC1, RPL20B and BUD21, that when individually deleted allow S. cerevisiae to utilize xylose as the sole carbon source. When these mutants are combined with XYLA and XKS1, it results in strains with significant improvement in xylose consumption. We have demonstrated that systems biology techniques combined with candidate gene approaches can successfully lead to novel genetic strategies for the improvement of xylose utilization
2012-07-15 | GSE27325 | GEO
Project description:Though highly efficient at fermenting hexose sugars, the ethanologenic yeast Saccharomyces cerevisiae has limited ability to ferment five-carbon sugars. As a significant portion of sugars found in cellulosic biomasses is the five carbon sugar xylose, S. cerevisiae must be engineered to metabolize pentose sugars. Here we combined classical candidate gene approach with systems biology to develop xylose-utilising S. cerevisiae strains. The introduction of an exogenous xylose isomerase (XYLA) and an additional copy of the endogenous xylulokinase gene (XKS1) results in the significant improvement of xylose consumption. Microarray studies reveal that the introduction of XYLA and XKS1 results in the dramatic transcriptional remodelling of the cell under both glucose and xylose conditions. To further investigate the cellular processes impacted by the introduction of XYLA and XKS1, using genome-wide chemical and synthetic lethal screens we identified greater than 40 deletion mutants that impact xylose utilization. We identified four genes, ALP1, ISC1, RPL20B and BUD21, that when individually deleted allow S. cerevisiae to utilize xylose as the sole carbon source. When these mutants are combined with XYLA and XKS1, it results in strains with significant improvement in xylose consumption. We have demonstrated that systems biology techniques combined with candidate gene approaches can successfully lead to novel genetic strategies for the improvement of xylose utilization For this experiment samples (2 reference and 2 test samples), consisting of at least 3 biological reps were hybridized. Cy3 one-color labelling was used for each sample.
2012-07-14 | E-GEOD-27325 | 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:Three dimensional engineered culture systems are powerful tools to rapidly expand our knowledge of human biology and identify novel therapeutic targets for disease. Bioengineered skeletal muscle has been recently shown to recapitulate many features of native muscle biology. However, current skeletal muscle bioengineering approaches require large numbers of cells, reagents and labour, limiting their potential for high-throughput studies. Herein, we use a miniaturized 96-well micro-muscle platform to facilitate semi-automated tissue formation, culture and analysis of human skeletal micro muscles (hμMs). Utilising an iterative screening approach we define a serum-free differentiation protocol that drives rapid, directed differentiation of human myoblast to skeletal myofibres. The resulting hμMs comprised organised bundles of striated and functional myofibres, which respond appropriately to electrical stimulation. Additionally, we developed an optogenetic approach to chronically stimulate hμM to recapitulate known features of exercise training including myofibre hypertrophy and increased expression of metabolic proteins. Taken together, our miniaturized approach provides a new platform to enable high-throughput studies of human skeletal muscle biology and exercise physiology.
2019-03-12 | PXD011919 | Pride
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. Experiment Overall Design: Three aerobic batch fermentations were carried out both on 50 g l-1 glucose and on 50 g l-1 xylose to compare the yeast transcriptome and proteome of cells growing on xylose with that of glucose repressed and glucose derepressed cells. Samples of the xylose-grown cells were harvested at 72 h from the start of the xylose cultures with 32 g l-1 of residual xylose present. Samples of the glucose repressed cells were harvested at 5 h from the start of the glucose cultures with 37 g l-1 of residual glucose present. Samples of the glucose derepressed cells were harvested at 24 h from the start of the glucose cultures containing no glucose but 13 g l-1 of accumulated ethanol.
2008-10-26 | E-GEOD-12890 | biostudies-arrayexpress
Project description:Integrated systems-biology platform for power-to-gas technology
| PRJNA902403 | ENA
Project description:The ascomycetes Saccharomyces cerevisiae, Candida albicans and Scheffersomyces stipitis metabolize the pentose sugar xylose very differently. S. cerevisiae fails to grow on xylose, while C. albicans can grow, and S. stipitis can both grow and ferment xylose to ethanol. However, all three species contain highly similar genes that encode xylose reductase and xylitol dehydrogenase required to convert xylose to xylulose, on which all three fungi grow. We have created C. albicans strains deleted for either or both the xylose reductase gene GRE3, and the xylitol dehydrogenase gene XYL2. As expected, all the mutant strains cannot grow on xylose, while the gre3 mutant can grow on xylitol. The gre3 and xyl2 mutants are complemented efficiently by the XYL1 and XYL2 from S. stipitis respectively. Intriguingly, the S. cerevisiae GRE3 and SOR1 genes can complement the gre3 and xyl2 mutants respectively, showing that S. cerevisiae contains the enzymatic capacity for converting xylose to xylulose. In addition, the gre3 xyl2 double mutant is effectively rescued by the xylose isomerase (XI) gene of either Piromyces or Orpinomyces, suggesting that the XI provides an alternative to the missing oxido-reductase functions in the mutant required for the xylose-xylulose conversion. Overall this work establishes that C. albicans strains engineered to lack essential steps for xylose metabolism provide a platform for the analysis of xylose metabolism enzymes from a variety of species, and confirms that S. cerevisiae has the genetic potential to convert xylose to xylulose, although non-engineered strains cannot proliferate on xylose as the sole carbon source.
2013-10-30 | GSE50476 | GEO
Project description:Xylose induced effects on metabolism and gene expression during anaerobic growth of an engineered Saccharomyces cerevisiae on mixed glucose-xylose medium were quantified. Gene expression of S. cerevisiae harbouring an XR-XDH pathway for xylose utilisation was analysed from early cultivation when mainly glucose was metabolised, to times when xylose was co-consumed in the presence of low glucose concentrations, and finally, to glucose depletion and solely xylose being consumed. Cultivations on glucose as a sole carbon source were used as a control. Genome-scale dynamic flux balance analysis models were developed and simulated to analyse the metabolic dynamics of S. cerevisiae in the cultivations. Model simulations quantitatively estimated xylose dependent dynamics of fluxes and challenges to the metabolic network utilisation. Increased relative xylose utilisation was predicted to induce two-directionality of glycolytic flux and a redox challenge already at low glucose concentrations. Xylose effects on gene expression were observed also when glucose was still abundant. Remarkably, xylose was observed to specifically delay the glucose-dependent repression of particular genes in mixed glucose-xylose cultures compared to glucose cultures. The delay occurred during similar metabolic flux activities in the both cultures. Xylose is abundantly present together with glucose in lignocellulosic streams that would be available for the valorisation to biochemicals or biofuels. Yeast S. cerevisiae has superior characteristics for a host of the bioconversion except that it strongly prefers glucose and the co-consumption of xylose is yet a challenge. Further, since xylose is not a natural substrate of S. cerevisiae, the regulatory response it induces in an engineered yeast strain cannot be expected to have evolved for its utilisation. Dynamic cultivation experiments on mixed glucose-xylose medium having glucose cultures as control integrated with mathematical modelling allowed to resolve specific effects of xylose on the gene expression and metabolism of engineered S. cerevisiae in the presence of varying amounts of glucose.
2016-05-24 | GSE69966 | GEO
Project description:Snf1 and TORC1 are two global regulators that sense the nutrient availability and regulate the cell growth in yeast Saccharomyces cerevisiae. Here we undertook a systems biology approach to study the effect of deletion of these genes and investigate the interaction between Snf1 and TORC1 in regulation of gene expression and cell metabolism.
2011-10-20 | GSE24421 | GEO