Ontology highlight
ABSTRACT:
PROVIDER: PRJNA521450 | ENA |
REPOSITORIES: ENA
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Project description:Our study involves a transcriptomic approach to the analysis of industrial yeast metabolism. Historically, among the hundreds of yeast species, Saccharomyces cerevisiae has played an important role in scientific investigations and industrial applications, and it is universally acknowledged as one of the model systems for eukaryotic organisms. Yeast is also an important component of the wine fermentation process and determines various attributes of the final product. Our research takes a holistic approach to the improvement of industrial yeast strains by integrating large data sets from various yeast strains during fermentation. This means that analysis can be done in such a way as to co-evaluate several parameters simultaneously to identify points of interest and target genes for metabolic engineering. Eventually we hope to construct an accurate information matrix and a more complete cellular map for the fermenting yeast. This will enable accurate model-building for industrial yeast and facilitated the design of intelligent yeast improvement strategies which can be applied via traditional avenues of molecular biology.
2008-07-01 | GSE11651 | GEO
Project description:Our study involves a transcriptomic approach to the analysis of industrial yeast metabolism. Historically, among the hundreds of yeast species, Saccharomyces cerevisiae has played an important role in scientific investigations and industrial applications, and it is universally acknowledged as one of the model systems for eukaryotic organisms. Yeast is also an important component of the wine fermentation process and determines various attributes of the final product. Our research takes a holistic approach to the improvement of industrial yeast strains by integrating large data sets from various yeast strains during fermentation. This means that analysis can be done in such a way as to co-evaluate several parameters simultaneously to identify points of interest and target genes for metabolic engineering. Eventually we hope to construct an accurate information matrix and a more complete cellular map for the fermenting yeast. This will enable accurate model-building for industrial yeast and facilitated the design of intelligent yeast improvement strategies which can be applied via traditional avenues of molecular biology. Experiment Overall Design: Five different Saccharomyces cerevisiae strains used in industrial winemaking processes were used in synthetic must (MS300) fermentations. All fermentations were carried out in triplicate, so each sample is represented by three completely independent biological repeats. Samples for microarray analysis were taken at three different time points during fermentation, representative of the exponential (day2), early stationary (day5) and late stationary (day14) growth stages.
2008-10-21 | E-GEOD-11651 | biostudies-arrayexpress
Project description:Petite-negative ascomycete yeast used for genetic studies and industrial applications
| PRJNA12363 | ENA
Project description:Myceliophthora thermophila is a thermophilic fungus with great biotechnological characteristics for industrial applications, which can degrade and utilize all major polysaccharides in plant biomass. Nowadays, it has been developing into a platform for production of enzyme, commodity chemicals and biofuels. Therefore, an accurate genome-scale metabolic model would be an accelerator for this fungus becoming a universal chassis for biomanufacturing. Here we present a genome-scale metabolic model for M. thermophila constructed using an auto-generating pipeline with consequent thorough manual curation. Temperature plays a basic and critical role for the microbe growth. we are particularly interested in the genome wide response at metabolic layer of M. thermophilia as it is a thermophlic fungus. To study the effects of temperature on metabolic characteristics of M. thermophila growth, the fungus was cultivated under different temperature. The metabolic rearrangement predicted using context-specific GEMs integrating transcriptome data.The developed model provides new insights into thermophilic fungi metabolism and highlights model-driven strain design to improve biotechnological applications of this thermophilic lignocellulosic fungus.
2022-09-14 | GSE184074 | GEO
Project description:Due to the high capacity of their secretion machinery Gram-positive bacteria from the genus Bacillus are important expression hosts for the high-yield production of enzymes in industrial biotechnology. However, to date strains from only a few Bacillus species are used for enzyme production at the industrial scale. In this work, we introduce with Paenibacillus polymyxa DSM 292 a member of a different genus as a novel host for secretory protein production. The model gene cel8A from Clostridium thermocellum was chosen as an easily detectable reporter gene with industrial relevance to demonstrate efficient heterologous expression and secretion in P. polymyxa. The yield of the secreted cellulase Cel8A was increased by optimizing the expression medium and testing various promoter sequences on the expression plasmid pBACOV. To identify promising new promoter sequences from the genome of P. polymyxa itself, quantitative mass spectrometry was used to analyze the secretome. The most strongly secreted host proteins were identified and the promoters regulating the expression of the corresponding genes were selected. Eleven promoter sequences were cloned and tested, including well-characterized promoters from B. subtilis and B. megaterium. The best result was achieved with the promoter of the hypothetical protein PPOLYM_03468 from P. polymyxa, which in combination with the improved expression medium enabled the production of 5,475 U/l Cel8A which represents a 6.2-fold increase compared to the reference promoter PaprE. The set of promoters described in this work covers a broad range of promoter strengths useful for heterologous expression in the new host P. polymyxa.
2018-09-05 | PXD009882 | Pride
Project description:Trichoderma reesei is the main industrial producer of cellulases and hemicellulases used to depolymerize biomass in many biotechnical applications. Many production strains in use have been generated by classical mutagenesis. In this study we characterized genomic alterations in hyperproducing mutants of T. reesei by high-resolution comparative genomic hybridisation tiling array. We carried out aCGH analysis of four hyperproducing strains (QM9123, QM9414, NG14 and RutC-30) using QM6a genome as a reference. ArrayCGH analysis identified dozens of mutations in each strain analyzed.
2010-11-26 | GSE19606 | GEO
Project description:This study evaluated the variability of methylxanthine content of Ilex guayusa under different geographical, light, and age conditions, as an opportunity to emphasize the value of the chakra agroforestry system in the search for sustainable use of natural products with potential industrial applications.
2024-04-11 | MSV000094519 | MassIVE
Project description:Oxidative stress is a key attribute that one should considered when using yeast cells for industrial applications due to its direct impact on yeast growth, viability, and productivity. However, little information is currently available regarding the molecular mechanisms of oxidative stress induction and the antioxidant response to increased reactive oxygen species (ROS) in yeasts. In this study, we generated experimentally evolved and genetically stable oxidative stress-resistant S. cerevisiae strain. This evolved strain has elevated trehalose and glycogen production, and up-regulated gene expression profile for that related to stress response, transport, carbohydrate, lipid and co-factor metabolic processes, protein phosphorylation, cell wall organization or biogenesis. In contrast, down-regulated genes were related to ribosome and RNA processing, nuclear transport, tRNA, cell cycle etc. In addition to that, comparative physiological, transcriptomic, and genomic analyses revealed that this oxidative stress resistant strain was also cross-resistant against other stress types including heat, freeze-thaw, ethanol, copper, and salt stress. Single variants identified via whole genome sequencing were primarily related to stress response, cell wall organization, carbohydrate metabolism/transport which support the physiological and transcriptomic results. Overall, this shed light how yeast cells can cope with oxidative stress pressure using their complex molecular mechanisms for the stress resistance and hints on how oxidative stress resistant S. cerevisiae strain can be generated for industrial applications.
2022-02-14 | GSE184952 | GEO
Project description:This study evaluated the variability of methylxanthine content of Ilex guayusa under different geographical, light, and age conditions, as an opportunity to emphasize the value of the chakra agroforestry system in the search for sustainable use of natural products with potential industrial applications.
2024-04-11 | MSV000094519 | GNPS