System level characterization of galactose mutants of yeast
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe
PROVIDER: GSE27185 | GEO | 2011/03/31
SECONDARY ACCESSION(S): PRJNA137359
REPOSITORIES: GEO
Similar Datasets
Project description:Adaptively evolved mutants of yeast on galactose were characterized by feremtation physiology and tools from systems biology. Three evolved mutants of yeast grown on aerobic batch with galactose as carbon source
2011-03-31 | E-GEOD-27185 | biostudies-arrayexpress
Project description:Exploring molecular details of carbon utilization trade-offs in galactose-evolved yeast Adaptively evolved yeast mutants on galactose for around 400 generations showed diminished growth and carbon uptake rates on glucose. Genome-scale approaches were applied to characterize the molecular genetic basis of these trade-offs in carbon source utilization. Engineered mutants showing trade-offs in a specific carbon uptake rate between both carbons were used as controls. The transcriptional responses of the evolved mutants were almost identical during growth on both carbon sources. These carbon-independent conserved patterns were clearly observed in specific pathways and genes. Up-regulation of PGM2, a confirmed beneficial genetic change for improving galactose utilization was preserved on both carbons. In addition, HXK1, GLK1 and genes involved in reserve carbohydrate metabolism were up-regulated, while HXK2 was down-regulated. Genes that have a transcription factor binding site for Gis1p, Rph1p, Msn2/4p and Nrg1p were up-regulated. These results indicated changes in the metabolic pathways involved in metabolism of both carbons and in nutrient signaling pathway. The concentration profile of trehalose and glycogen supported these findings. Mutations in RAS2 and ERG5 genes were selected because of their beneficial and neutral effect on galactose utilization, respectively in our previous study. Site-directed mutants containing galactose-beneficial mutations in RAS2 only resulted in a significant decrease in glucose utilization. Integration of all these analyses clearly suggest an antagonistic pleiotropic trade-off in carbon source utilization caused by changes in regulatory region, and we hereby demonstrate how systems biology can be used to gain insight into evolutionary processes at the molecular level. Yeast galactose evolved mutants having improved galactose availability were grown on aerobic batch with glucose as carbon source
2012-07-31 | E-GEOD-39065 | biostudies-arrayexpress
Project description:Exploring molecular details of carbon utilization trade-offs in galactose-evolved yeast Adaptively evolved yeast mutants on galactose for around 400 generations showed diminished growth and carbon uptake rates on glucose. Genome-scale approaches were applied to characterize the molecular genetic basis of these trade-offs in carbon source utilization. Engineered mutants showing trade-offs in a specific carbon uptake rate between both carbons were used as controls. The transcriptional responses of the evolved mutants were almost identical during growth on both carbon sources. These carbon-independent conserved patterns were clearly observed in specific pathways and genes. Up-regulation of PGM2, a confirmed beneficial genetic change for improving galactose utilization was preserved on both carbons. In addition, HXK1, GLK1 and genes involved in reserve carbohydrate metabolism were up-regulated, while HXK2 was down-regulated. Genes that have a transcription factor binding site for Gis1p, Rph1p, Msn2/4p and Nrg1p were up-regulated. These results indicated changes in the metabolic pathways involved in metabolism of both carbons and in nutrient signaling pathway. The concentration profile of trehalose and glycogen supported these findings. Mutations in RAS2 and ERG5 genes were selected because of their beneficial and neutral effect on galactose utilization, respectively in our previous study. Site-directed mutants containing galactose-beneficial mutations in RAS2 only resulted in a significant decrease in glucose utilization. Integration of all these analyses clearly suggest an antagonistic pleiotropic trade-off in carbon source utilization caused by changes in regulatory region, and we hereby demonstrate how systems biology can be used to gain insight into evolutionary processes at the molecular level.
2012-08-01 | GSE39065 | GEO
Project description:Transcriptional profiles of S. cerevisiae strains with deletions of mth1, std1, or both were compared to that of a wild-type strain during growth on synthetic complete media with galactose as the carbon source, with the intent to understand each protein's contribution to the cells' response to glucose.
2009-09-03 | GSE17437 | GEO
Project description:We describe a transcriptional analysis platform consisting of a universal micro-array system (UMAS) combined with an enzymatic manipulation step that is capable of generating expression profiles from any organism without requiring a priori species-specific sequence information. The transcriptome is converted to cDNA and processed with restriction endonucleases to generate low-complexity pools (80–120) of equal length DNA fragments. The resulting material is amplified and detected with the UMAS system, comprising all possible 4,096 (4^6) DNA hexamers. Ligation to the arrays yields thousands of 14-mer sequence tags. The compendium of signals from all pools in the array-of-universal arrays comprises a full-transcriptome expression profile. The technology was validated by analysis of the galactose response of Saccharomyces cerevisiae, and the resulting profiles showed excellent agreement with the literature and real-time PCR assays. Keywords: other
2004-03-12 | GSE993 | GEO
Project description:We report high-throughput RNA sequencing of Δcrp and five adaptively evolved mutants of Δcrp in the batch exponential phase, IG116-Δcrp in batch exponential phase and Δcrp and two adaptively evolved mutants of Δcrp in chemostat cultivations
2021-12-31 | GSE152214 | GEO
Project description:Transcriptional landscape of MyceliopTranscriptional profiling of Myceliophthora thermophila on galactose and metabolic engineering for improved galactose utilization thora thermophila responding to soluble starch and the role of regulator AmyR on polysaccharide degradation Efficient biological conversion of all sugars from lignocellulosic biomass is necessary for cost-effective production of biofuels and commodity chemicals. Galactose is the next most abundant sugar in many hemicelluloses and it will be important to capture this carbon for an efficient bioconversion process of plant biomass. Thermophilic fugus Myceliophthora thermophila has been used as cell factory to produce biochemicals directly from renewable polysaccharides. This study determined the transcriptomic profiles of M. thermophila responding to galactose and identified the gene involved in the oxido-reductive pathway for galactose degradation, of which hexokinase might be the rate-limiting enzyme in this thermophilic fungus. Galactokinase was necessary for high induction of galactose transporter and disruption of galK resulted in decreased galactose utilization. Both of galactokinase deletion and sugar transporter overexpression could further activate the oxido-reductive pathway and led to improved galactose utilization. In addition, disruption of the Leloir pathway brought about reduced tolerance to cell wall perturbation, oxidative stress and high osmolality. In order to accelerate galactose consumption, the third galactose-degradation pathway- De Ley-Doudoroff pathway was successfully integrated into M. thermophila and the consumption rate of galactose was increased by 57%. This study will be benefit for the rational design of fungal strains to produce biofuels and biochemical from plant biomass, especially, marine plant biomass with the abundant of galactose, such as red seaweed and molasses.
2021-02-05 | GSE165516 | GEO
Project description:Reconstructed mutants of yeast by inverse metabolic engineering were characterized by fermentation physiology and tools from systems biology. Six reconstructed mutants of yeast were grown on aerobic batch with galactose as carbon source
2012-02-29 | E-GEOD-36118 | biostudies-arrayexpress
Project description:Metabolomic analysis of Wildtype, crp mutant and its five adaptively evolved populations evolved in glucose minimal media with 40 mM MOPS during its exponential phase of growth. Three biological and two technical replicate samples (n=6) were harvested for each of the strains while growing in a bioreactor aerobically at 37 degree Celsius and 700 rpm. This study aims to characterize and compare the metabolic profile of all these strains.
2020-06-06 | ST001394 | MetabolomicsWorkbench
Project description:Transcriptional profiles of S. cerevisiae strains with deletions of mth1, std1, or both were compared to that of a wild-type strain during growth on synthetic complete media with galactose as the carbon source, with the intent to understand each protein's contribution to the cells' response to glucose. Single-condition experiment, mth1 delete, std1 delete or the double mth1/std1 deletion strain vs. a wild type yeast strain. Biological replicates: 2. Rep. 1: Independently isolated RNA preps for each mutant was compared against a single WT sample. Rep. 2: A second set of mutant and WT samples was used to repeat the profiling. Two replicate spots representing each gene are present per array.
2010-05-06 | E-GEOD-17437 | biostudies-arrayexpress