A selection of Saccharomyces cerevisiae promoters for biotechnological applications aiming at the use of synthetic glycerol medium
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ABSTRACT:
PROVIDER: PRJNA429459 | ENA |
REPOSITORIES: ENA
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| Action | DRS | |||
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| SRR6458382.fastq.gz | Fastqsanger.gz |
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Project description:Glycerol offers several advantages as a substrate for biotechnological applications. An important step towards using the popular production host Saccharomyces cerevisiae for glycerol-based bioprocesses have been recent studies in which commonly used S. cerevisiae strains were engineered to grow in synthetic medium containing glycerol as the sole carbon source. In order to boost extensive S. cerevisiae metabolic engineering incentives aiming at the use of glycerol, we realized that promoters with predictable expression levels in synthetic glycerol medium were required. In the current study, we used transcriptome analysis and a yECitrine-based fluorescence reporter assay to select and characterize useful 25 promoters for driving expression of target genes in S. cerevisiae under the given conditions. The promoters of the genes ALD4 and ADH2 showed 4.2- and 3-fold higher activities compared to the well-known strong TEF1 promoter. Moreover, the collection contains promoters with graded activities in synthetic glycerol medium and different degrees of glucose repression. To demonstrate the general applicability of the promoter collection, we successfully used a subset of the characterized promoters with graded activities in order to optimize growth on glycerol in an engineered derivative of CEN.PK, in which glycerol catabolism exclusively occurs via a non-native DHA pathway.
2018-03-31 | GSE109036 | GEO
Project description:Exploring Ulva australis Areschoug for possible biotechnological applications: In vitro antioxidant and enzymatic inhibitory properties and fatty acids contents
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Project description:Biotechnology suggests that microorganisms can be used as chemical factories that transform renewable feedstock into value-added chemicals. Conversion of glycerol, using direct transformation or fermentation, into valuable products such as polymers, surfactants, solvents, and chemical intermediates has attained growing interest in recent years due to the dramatic growth of the biodiesel industry. However, the use of cell factories could be limited by low growth and uptake rates under certain environmental conditions, thus understanding microbial nutritional requirements is a critical point to use them as cell factories. Here, we compared E. coli ATCC 8739 transcriptomic responses to glycerol under aerobic conditions in an optimized culture medium (Condition 3) and one evolved strain in glycerol using as a reference a glycerol-based medium (Condition 11). Our analyses revealed 478 and 431 differentially expressed genes (DEGs) with log2 fold change (FC) > |2| and p Adjusted value < 0.05, for the bacteria growing in the optimized culture medium and the evolved strain, respectively. Among the DEGs, glp operon was found to be up-regulated as a response to glycerol uptake. Interestingly, between them, it was found genes that requires the use of phosphorous to ovoid the toxicity during glycerol consumption. Previously, we identified using a computational approach that phosphorous and nitrogen are essential compound that support high glycerol consumption in E. coli.
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Project description:Lactobacillus reuteri is a heterofermentative lactic acid bacterium best known for its ability to co-ferment glucose and glycerol. Its genome sequence has recently been deduced enabling the implementation of genome-wide analysis. In this study we developed a dedicated cDNA microarray platform and a genome-scale metabolic network model of L. reuteri and use them to revisit the co-fermentation of glucose and glycerol. The model was used to simulate experimental conditions and to visualize and integrate experimental data in particular the global transcriptional response of L. reuteri to the presence of glycerol. We show how the presence of glycerol affects cell physiology and triggers specific regulatory mechanisms allowing simultaneously a better yield and more efficient biomass formation. Furthermore we were able to predict and demonstrate for this well-studied condition the involvement of previously unsuspected metabolic pathways for instance related to amino acids and vitamins. These could be used as leads in future studies aiming at the increased production of industrially relevant compounds such as vitamin B12 or 1 3- propanediol. Keywords: cell type comparison
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Project description:Lactobacillus reuteri is a heterofermentative lactic acid bacterium best known for its ability to co-ferment glucose and glycerol. Its genome sequence has recently been deduced enabling the implementation of genome-wide analysis. In this study we developed a dedicated cDNA microarray platform and a genome-scale metabolic network model of L. reuteri and use them to revisit the co-fermentation of glucose and glycerol. The model was used to simulate experimental conditions and to visualize and integrate experimental data in particular the global transcriptional response of L. reuteri to the presence of glycerol. We show how the presence of glycerol affects cell physiology and triggers specific regulatory mechanisms allowing simultaneously a better yield and more efficient biomass formation. Furthermore we were able to predict and demonstrate for this well-studied condition the involvement of previously unsuspected metabolic pathways for instance related to amino acids and vitamins. These could be used as leads in future studies aiming at the increased production of industrially relevant compounds such as vitamin B12 or 1 3- propanediol. Keywords: cell type comparison
2008-09-15 | GSE11861 | GEO
Project description:Lactobacillus reuteri is a heterofermentative lactic acid bacterium best known for its ability to co-ferment glucose and glycerol. Its genome sequence has recently been deduced enabling the implementation of genome-wide analysis. In this study we developed a dedicated cDNA microarray platform and a genome-scale metabolic network model of L. reuteri and use them to revisit the co-fermentation of glucose and glycerol. The model was used to simulate experimental conditions and to visualize and integrate experimental data in particular the global transcriptional response of L. reuteri to the presence of glycerol. We show how the presence of glycerol affects cell physiology and triggers specific regulatory mechanisms allowing simultaneously a better yield and more efficient biomass formation. Furthermore we were able to predict and demonstrate for this well-studied condition the involvement of previously unsuspected metabolic pathways for instance related to amino acids and vitamins. These could be used as leads in future studies aiming at the increased production of industrially relevant compounds such as vitamin B12 or 1 3- propanediol. Keywords: cell type comparison Dye swap
2010-05-20 | E-GEOD-11860 | biostudies-arrayexpress
Project description:Lactobacillus reuteri is a heterofermentative lactic acid bacterium best known for its ability to co-ferment glucose and glycerol. Its genome sequence has recently been deduced enabling the implementation of genome-wide analysis. In this study we developed a dedicated cDNA microarray platform and a genome-scale metabolic network model of L. reuteri and use them to revisit the co-fermentation of glucose and glycerol. The model was used to simulate experimental conditions and to visualize and integrate experimental data in particular the global transcriptional response of L. reuteri to the presence of glycerol. We show how the presence of glycerol affects cell physiology and triggers specific regulatory mechanisms allowing simultaneously a better yield and more efficient biomass formation. Furthermore we were able to predict and demonstrate for this well-studied condition the involvement of previously unsuspected metabolic pathways for instance related to amino acids and vitamins. These could be used as leads in future studies aiming at the increased production of industrially relevant compounds such as vitamin B12 or 1 3- propanediol. Keywords: cell type comparison Loop design
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Project description:The conservation and growth of natural capital accumulated in the seas and oceans is essential for the provision of sustainable ecosystem services and for the achievement of the EU’s Sustainable Development Goals (SDGs) set by the UN for 2030. Therefore, Marine Strategy Framework Directive (MSFD) offers a comprehensive and holistic approach for the protection of the European sea, acting as an environmental pillar of the EU’s broader maritime strategy. The blue economy conveys that a healthier sea is a more productive sea. Concretely, blue biotechnology, which uses, among others, shellfish, bacteria and algae for development in health care and energy production, needs a healthy ocean, biodiversity and biomass abundance to provide innovative substances that help in the production in innovative medicines for the maintenance of human health. Moreover, marine biomass has become a potent source of new and innovative biotechnological tools for new therapeutic strategies and compounds that will increases the utility of marine biomass valorization processes and the quest of new solutions to present diseases. Recently, proteomics approaches has highlighted its potential use to discover new activities with potential biotechnological applications from proteome data through “applied proteomics”. Finally, in the context of global climate change, it is also becoming more and more demanding to anticipate alterations and responses of bioindicator species and to create a database to prevent and predict the environmental and climatic changes before the damage being irreversible. In this project, The proteome analysis of the sea anemone, Anemonia sulcata and its symbiont will lead to the identification of gene expression biomarkers (GEBs), as emerging powerful diagnostic tools, for identifying and characterizing climate change drivers (temperature and irradiance) stress and improving monitoring techniques. In addition, By the application of novel algorithms to detect bioactive compounds based on the analysis of proteome marine-derived molecules will enable the identification of proteins with potential applications in agri-food and biomedicine fields.
2023-10-24 | PXD043202 | Pride
Project description:Diatoms are prominent marine microalgae, interesting not only from an ecological point of view, but also for their possible use for biotechnology applications. They can be cultivated in phototrophic conditions, using sunlight as the only energy source. Some diatoms, however, can also grow in mixotrophic mode, where both light and external reduced carbon contribute to biomass accumulation. In this study, we investigated the consequences of mixotrophy on the growth and metabolism of the pennate diatom Phaeodactylum tricornutum, using glycerol as a source of reduced carbon. Transcriptomic, metabolomic and physiological data indicate that glycerol affects the central-carbon, carbon-storage and lipid metabolism of the diatom. In particular, glycerol addition mimics some typical responses of nitrogen limitation on lipid metabolism at the level of TAG accumulation and fatty acid composition. However, this compound does not diminish photosynthetic activity and cell growth, at variance with nutrient limitation, revealing essential aspects of the metabolic flexibility of these microalgae and suggesting possible biotechnological applications of mixotrophy.
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