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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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To study gene expression of PHO80-deleted yeast strain in xylose fermentation

ABSTRACT: The main objective is to improve xylose fermentation by deletion of PHO80 gene in recombinant xylose-fermenting yeast strains. Microarray analysis was performed to investigate effects of PHO80 deletion on the gene expression profile of xylose-fermenting strains. Samples for 2 strains (wild-type control, PHO80-deleted strain) were taken after 6h of xylose fermentation. Each sample was triplicated, resulting in a total of 6 samples.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Akihiko Kondo

PROVIDER: E-GEOD-46309 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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To study gene expression of PHO80-deleted yeast strain in xylose fermentation

Project description:The main objective is to improve xylose fermentation by deletion of PHO80 gene in recombinant xylose-fermenting yeast strains. Microarray analysis was performed to investigate effects of PHO80 deletion on the gene expression profile of xylose-fermenting strains.

2013-04-24 | GSE46309 | GEO

To study gene expression of PHO13 deleted Xylose isomerase (XI) harboring strain in xylose fermentation

Project description:The main objective is to improve xylose fermentation by deletion of PHO13 gene in Xylose isomerase (XI) harboring yeast strains. Microarray analysis was performed to investigate effects of PHO13 deletion on the gene expression prolife of xylose-fermenting strains.

2015-10-08 | GSE73814 | GEO

APJ1 and GRE3 Homologs Work in Concert to Allow Growth in Xylose in a Genetically Intractable Natural Saccharomyces sensu stricto Hybrid Yeast

Project description:Creating Saccharomyces yeasts capable of efficient fermentation of pentoses such as xylose remains a key challenge in the production of ethanol from lignocellulosic biomass. Metabolic engineering of industrial Saccharomyces cerevisiae strains has yielded xylose-fermenting strains, but these strains have not yet achieved industrial viability due largely to xylose fermentation being prohibitively slower than that of glucose. Recently, it has been shown that naturally occurring xylose-utilizing Saccharomyces species exist. Uncovering the genetic architecture of such strains will shed further light on xylose metabolism, suggesting additional engineering approaches or possibly even the development of xylose-fermenting yeasts that are not genetically modified. We previously identified a hybrid yeast strain, the genome of which is largely Saccharomyces uvarum, which has the ability to grow on xylose as the sole carbon source. Despite the sterility of this hybrid strain, we were able to develop novel methods to genetically characterize its xylose utilization phenotype, using bulk segregant analysis in conjunction with high-throughput sequencing. We found that its growth in xylose is governed by at least two genetic loci: one of the loci maps to a known xylose-pathway gene, a novel allele of the aldo-keto reductase gene GRE3, while a second locus maps to an allele of APJ1, a chaperonin gene not previously connected to xylose metabolism. Our work demonstrates that the power of sequencing combined with bulk segregant analysis can also be applied to a non-genetically-tractable hybrid strain that contains a complex, polygenic trait, and it identifies new avenues for metabolic engineering as well as for construction of non-genetically modified xylose-fermenting strains.

2012-07-19 | GSE35528 | GEO

To study gene expression by xylose fermenting strains in the presence and absence of furfural

Project description:The main objective is to develop a strain tolerant to furfural for ethanol production from lignocellulosic hydrolysates. We compare gene expressions among three genetically modified S. cerevisiae (control, TAL-expressing and TAL-ADH expressing strain) under the presence and absence of furfural. Samples for 3 strains (control, TAL-expressing and TAL-ADH expressing strain) were taken after 6h of exposure to furfural. Furfural concentration were 0 and 70 mM. Each samples were duplicated resulting in total of 12 samples.

2013-06-01 | E-GEOD-45273 | biostudies-arrayexpress

Merging candidate gene approach with high throughput systems biology technology for the development of xylose utilising S. cerevisiae strains

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

The transcriptome comparison data between Saccharomyces cerevisiae cells in thi2p deletion strains and the control strains BSGX001 in xylose consumption phase after glucose depleted in glucose-xylose co-fermentation.

Project description:The xylose fermentation rate of thi2p deletion strains was higher than the control strains BSGX001 during xylose consumption phase after glucose depleted in glucose-xylose co-fermentation (defined as GX stage). BSGX001 was derived from the haploid strain CEN.PK113-5D, which is a engineered strains that have the xylose-utilizing capacity. Here,we investigate the transcriptional differences between BSGX001 (thi2Δ) and BSGX001 in GX stage.

2018-10-01 | GSE119333 | GEO

Transcriptomic analysis of a novel Saccharomyces cerevisiae strain with improved xylose fermentation ability under heat and acid co-stress

Project description:Xylose-utilizing yeasts with tolerances to fermentation inhibitors (such as weak organic acids) and high temperature are needed for cost-effective simultaneous saccharification and co-fermentation (SSCF) of lignocellulosic materials. We constructed a novel xylose-assimilating Saccharomyces cerevisiae strain with improved fermentation performance under heat and acid co-stress using the genome shuffling technique. Two xylose-utilizing diploid yeasts with different genetic backgrounds were used as the parental strains for genome shuffling. The hybrid strain Hyb-8 showed significantly higher xylose fermentation ability than both parental strains (Sun049T-Z and Sun224T-K) under co-stress conditions of heat and acids. To screen for genes that might be important for fermentation under heat and acid co-stress, a transcriptomic analysis of hybrid strain Hyb-8 and its parental strains was performed.

2017-07-25 | GSE101786 | GEO

Selection of yeast Saccharomyces cerevisiae promoters available for xylose cultivation and fermentation

Project description:To select candidate promoters that function in the presence of xylose, we performed comprehensive gene expression analyses using xylose-utilizing yeast strains both during xylose and glucose fermentation.

2017-04-11 | GSE97580 | GEO

The transcriptome comparison data between Saccharomyces cerevisiae cells in xylose consumption phase after glucose depleted in glucose-xylose co-fermentation and when xylose was the sole carbon source.

Project description:The xylose fermentation rate during xylose consumption phase after glucose depleted in glucose-xylose co-fermentation (defined as GX stage) was much lower than that when xylose was the sole carbon source (defined as X stage). BSGX001 and XH7 are two engineered strains that have the xylose-utilizing capacity. Here,we investigate the transcriptional differences between GX stage and X stage of BSGX001 and XH7, respectively.

2018-04-25 | GSE95076 | GEO

Regulation involved in difference in nitrogen requirements of Saccharomyces cerevisiae wine yeasts in alcoholic fermentation

Project description:The objective of this work is to identify, in enological condition, differences in transcriptomic regulation that may explain the differences in strains fermentation properties. For this, we compared the global expression patterns of 8 Saccharomyces cerevisiae strains with different nitrogen requirement (L2868, 4CAR1, Fermiflor, Zymasil, MTF1782, 7013, K1M, EC1118). The transcriptome was analyzed on cells fermenting in a nitrogen limited medium containing 100mg.l-1 assimilable nitrogen (SM100) and harvested at stationary phase (45g/L of CO2 produced and corresponding to 6% ethanol). At this stage the strains exhibited differences in fermentation rates. Moreover, the transcriptome was shown to be rather stable at this stage since growth was stopped for all cells and nutrients have been depleted (Rossignol et al. 2003). Eight strains with different nitrogen requirement were analyzed (L2868, 4CAR1, Fermiflor, Zymasil, MTF1782, 7013, K1M, EC1118). This analysis includes two biological replicates for each strain.

2013-12-31 | E-GEOD-50626 | biostudies-arrayexpress

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