A transcriptomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
SUBMITTER: Sylvie Dequin
PROVIDER: E-GEOD-34810 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Experience 2: 59A vs. 59A NADH Bdh200 mM, 59A NADPH Bdh200mM and 59A NADPH Bdh300 mM Analysis used RNA samples of three replicates by strain extracted from cells harvested at mid-exponential phase of wine fermentation
2012-03-31 | E-GEOD-34809 | biostudies-arrayexpress
Project description:Experience 1: 59A vs. 59A NADPH Bdh100mM Analysis used RNA samples of three independent replicates by strain extracted from cells harvested at mid-exponential phase of oenological fermentation
2012-03-31 | E-GEOD-34808 | biostudies-arrayexpress
Project description:Resistance of Saccharomyces cerevisiae to high furfural concentration is based on NADPH-dependent reduction by at least two oxireductases. Biofuels derived from lignocellulosic biomass hold promises for a sustainable fuel economy, but several problems hamper their economical feasibility. One important problem is the presence of toxic compounds in processed lignocellulosic hydrolysates with furfural as a key toxin. While Saccharomyces cerevisiae has some intrinsic ability to reduce furfural to the less toxic furfuryl alcohol, higher resistance is necessary for process conditions. By comparing an evolved, furfural resistant strain and its parent in micro-aerobic, glucose-limited chemostats at increasing furfural challenge, we elucidate key mechanism and the molecular basis of both natural and high-level furfural resistance. At lower furfural concentrations, NADH-dependent oxireductases are the main defence mechanism. At concentrations above 15 mM, however, [1-13C]-flux and global array-based transcript analysis demonstrated that the NADPH-generating flux through pentose-phosphate pathway increases and that NADPH-dependent oxireductases became the major resistance mechanism. The transcript analysis further revealed that iron transmembrane transport is up-regulated in response to furfural. While these responses occur in both strains, high-level resistance in the evolved strain was based on strong induction of ADH7, the uncharacterised ORF YKL071W and 4 further, likely NADPH-dependent oxireductases. By overexpressing the ADH7 gene and the ORF YKL071W, we inverse engineered significantly increased furfural resistance in the parent strain, thereby demonstrating these two enzymes to be key elements of the resistance phenotype.
2009-09-29 | GSE18314 | GEO
Project description:EKD-13 is among the recently developed mannoprotein overproducing strains. It is a recombinant derivative of the well known EC1118 commercial strain, in which the ORF of all the alleles of KNR4/SMI1 was replaced by different integration cassettes. Lack of Knr4p resulted in a negligible impairment in fermentation kinetics and a net reduction in bentonite requirements to attain complete protein stabilization of white wines made out of natural grape must. In order to improve the technological characterization of this strain, and to better understand the mechanisms underlying mannoprotein oversecretion, we have analyzed kinetics of mannoprotein release and autolysis during fermentation and aging, and we have performed a genome wide expression analysis in two different steps of the fermentation process. The results give some additional clues on KNR4 function in S. cerevisiae as well as on the best application conditions for this recombinant strain. A comparative transcriptome analysis between the S. cerevisiae recombinant strain (EKD-13) defective for KNR4/SMI1 and the wild-type strain (EC1118) was implemented. At every step of the fermentation (mid-exponential growth phase of fermentation advancement as 10 g of released CO2 and stationary-growth phase as 70 g of CO2 released) a recombinant and a WT yeast samples are put on a slide. There are three biological replicates that are labeled in dye-switch way (sometimes called biological dye-swap) for each step of fermentation leading to 3 independent intensity values for each gene (spots) on the microarrays. This experimental design minimizes the intrinsic biological noise between identical culture conditions and the technical variations inherent to the DNA microarray technology. In summary, there are six samples, each corresponding to comparisons between independent fermentations of both strains.
2011-02-28 | E-GEOD-26965 | biostudies-arrayexpress
Project description:Resistance of Saccharomyces cerevisiae to high furfural concentration is based on NADPH-dependent reduction by at least two oxireductases. Biofuels derived from lignocellulosic biomass hold promises for a sustainable fuel economy, but several problems hamper their economical feasibility. One important problem is the presence of toxic compounds in processed lignocellulosic hydrolysates with furfural as a key toxin. While Saccharomyces cerevisiae has some intrinsic ability to reduce furfural to the less toxic furfuryl alcohol, higher resistance is necessary for process conditions. By comparing an evolved, furfural resistant strain and its parent in micro-aerobic, glucose-limited chemostats at increasing furfural challenge, we elucidate key mechanism and the molecular basis of both natural and high-level furfural resistance. At lower furfural concentrations, NADH-dependent oxireductases are the main defence mechanism. At concentrations above 15 mM, however, [1-13C]-flux and global array-based transcript analysis demonstrated that the NADPH-generating flux through pentose-phosphate pathway increases and that NADPH-dependent oxireductases became the major resistance mechanism. The transcript analysis further revealed that iron transmembrane transport is up-regulated in response to furfural. While these responses occur in both strains, high-level resistance in the evolved strain was based on strong induction of ADH7, the uncharacterised ORF YKL071W and 4 further, likely NADPH-dependent oxireductases. By overexpressing the ADH7 gene and the ORF YKL071W, we inverse engineered significantly increased furfural resistance in the parent strain, thereby demonstrating these two enzymes to be key elements of the resistance phenotype. Experiment Overall Design: RNA levels were measured in glucose limited, micro-aerobic chemostat cultures with different concentrations of the growth inhibitor furfural. Two strains were compared: TMB3400-FT30-3 is a strain that has been evolutionary adapted to withstand high furfural concentrations. TMB3400 is its less resistant parent. Number of biological replicates: 2-3.
2009-10-03 | E-GEOD-18314 | biostudies-arrayexpress
Project description:A transcriptomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation [2010]
| PRJNA156291 | ENA
Project description:A transcriptomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation [2009]
| PRJNA156289 | ENA
Project description:Industrial wine yeast strains possess specific abilities to ferment under stressing conditions and give a suitable aromatic outcome. Although the fermentations properties of Saccharomyces cervisiae wine yeasts are well documented little is known on the genetic basis underlying the fermentation traits. Besides, although strain differences in gene expression has been reported, their relationships with gene expression variations and fermentation phenotypic variations is unknown. To both identify the genetic basis of fermentation traits and get insight on their relationships with gene expression variations, we combined fermentation traits QTL mapping and expression profiling in a segregating population from a cross between a wine yeast derivative and a laboratory strain. 40 samples are analysed with 2 technical replicates, using a unique reference named pool of the 30 segregants. The transcriptome of each segregant is compared to the transcriptome of the pool. The transcriptome of 5 biologic replicates of each parental strain is also compared to this reference. An haploid derivative of the commercialized wine yeast EC1118 which sequence is available (Novo et al. 2009. PNAS, 106:16333-16338) called 59A was used as industrial wine yeast. It is a prototroph strain and has a MATa sexual type. The haploid laboratory strain S288C (MATa) was used for crossing.
2011-01-19 | E-GEOD-26437 | biostudies-arrayexpress
Project description:The goal of this study was to compare the expression level of the whole genome of two wine yeast strains highly differing in their sulfite production (High producer strain: 10281A; Low producer strain: 1764A). Conditions maximizing SO2 production were selected: nitrogen rich media (425 mg/l assimilable nitrogen) and low temperature (16°C). This transcriptomic analysis was performed during the sulfite production phase, just after the entry in stationary phase. This analysis is part of a global work, aiming at the identification of the molecular basis of sulfite production by wine yeasts through physiologic, transcriptomic and genetic studies. Two strains compared in the same conditions with biological replicates following a dye-swap design.
2015-05-14 | E-GEOD-55083 | biostudies-arrayexpress