Dependency of Gene Expression in Saccharomyces cerevisiae on extracellular Glucose Concentration
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE6358 | GEO | 2007/12/02
SECONDARY ACCESSION(S): PRJNA99567
REPOSITORIES: GEO
Similar Datasets
Project description:Dependency of Gene Expression in Saccharomyces cerevisiae on extracellular Glucose Concentration
| PRJNA99567 | ENA
Project description:NaCl-resistant Saccharomyces cerevisiae mutant was obtained by evolutionary engineering. EMS mutagenized culture was used as the initial population for the selection procedure. Gradually increasing levels of NaCl stress was applied through 40 successive batch cultivations. The reference strain could not grow even at 0.85 M NaCl whereas this mutant was shown to be resistant up to 1.45 M NaCl concentration. Whole-genome microarray analysis was used to identify the NaCl resistance mechanisms by comparing NaCl-resistant mutant strain and the reference strain in the absence of NaCl stress.
2014-09-30 | GSE61903 | GEO
Project description:Yeast cells can be affected during their growth to several stress conditions. One of the most known and characterised is the osmotic stress and most of the studies about osmotic sterss response in yeast have been focused on salt or sorbitol stress. However, during yeast growth in industrially relevant processes (for instance throughout alcoholic fermentation on the must to produce alcoholic beverages) the osmotic stress is mainly due to the high sugar(in particular glucose) concentration (200-250 g/L).
2011-03-22 | GSE13703 | GEO
Project description:Yeast cells can be affected during their growth to several stress conditions. One of the most known and characterised is the osmotic stress and most of the studies about osmotic sterss response in yeast have been focused on salt or sorbitol stress. However, during yeast growth in industrially relevant processes (for instance throughout alcoholic fermentation on the must to produce alcoholic beverages) the osmotic stress is mainly due to the high sugar(in particular glucose) concentration (200-250 g/L). In this study we want to know the transcriptional response of the Saccharomyces cerevisiae when it was grown in a medium with high glucose concentration. For this aim we have grown yeast in YP medium containing 2% of glucose in cultures overnight and after that we diluted this cultures to an OD600 of 0.1 in two differents mediums: YP containing 2% or 20% of glucose.One hour later of inoculation we collect the cells and quikly frozen in liquid nitrogen. We extracted the total mRNA of the cells and after that we did the microarrays, comparing cells were grown in YP2 media against the cells were grown in YP20 media.
2011-03-21 | E-GEOD-13703 | biostudies-arrayexpress
Project description:Expression data from batch cultivations of Aspergillus niger wild type strain ATCC 1015 and adrA, facB and creA deletion mutants constructed on ATCC 1015 background strain with glucose or glycerol as carbon sources. Genome-wide transcriptome analysis was used to identify genes either affected directly or indirectly by each transcription factor investigated during growth on a repressing or a derepressing carbon source. For this purpose, batch cultivations under well-controlled conditions were performed with Aspergillus niger wild type strain ATCC 1015 and the three deletion mutants of the corresponding transcription factors AdrA, FacB and CreA. Samples for RNA extraction were collected and further processed for hybridization in custom-designed Affymetrix microarrays containing probes for three Aspergillus species, including A. niger.
2011-01-31 | GSE19952 | GEO
Project description:Prolonged cultivation of Saccharomyces cerevisiae in aerobic, glucose-limited chemostat cultures (dilution rate, 0·10 h–1) resulted in a progressive decrease of the residual glucose concentration (from 20 to 8 mg l–1 after 200 generations). This increase in the affinity for glucose was accompanied by a fivefold decrease of fermentative capacity, and changes in cellular morphology. These phenotypic changes were retained when single-cell isolates from prolonged cultures were used to inoculate fresh chemostat cultures, indicating that genetic changes were involved. Kinetic analysis of glucose transport in an ‘evolved’ strain revealed a decreased Km, while Vmax was slightly increased relative to the parental strain. Apparently, fermentative capacity in the evolved strain was not controlled by glucose uptake. Instead, enzyme assays in cell extracts of the evolved strain revealed strongly decreased capacities of enzymes in the lower part of glycolysis. This decrease was corroborated by genome-wide transcriptome analysis using DNA microarrays. In aerobic batch cultures on 20 g glucose l–1, the specific growth rate of the evolved strain was lower than that of the parental strain (0·28 and 0·37 h–1, respectively). Instead of the characteristic instantaneous production of ethanol that is observed when aerobic, glucose-limited cultures of wild-type S. cerevisiae are exposed to excess glucose, the evolved strain exhibited a delay of 90 min before aerobic ethanol formation set in. This study demonstrates that the effects of selection in glucose-limited chemostat cultures extend beyond glucose-transport kinetics. Although extensive physiological analysis offered insight into the underlying cellular processes, the evolutionary ‘driving force’ for several of the observed changes remains to be elucidated Keywords: evolution
2007-08-31 | GSE8898 | GEO
Project description:Transcriptomics was performed on batch cultivations of A. niger grown on three monosaccharides and three complex carbohydrates with defined compositions as to allow the detection of cross-induction if present, and for demonstration of how enzyme interaction graphics can be used to visualize the global transcription response. Batch cultivations of A. niger were grown in shake-flasks on one of three monosaccharides (arabinose, glucose, xylose) or one of three complex carbohydrates (arabinan, starch, xylan). Three replicates were performed for each monosaccharide and complex carbohydrate, except for starch, where two replicates were performed.
2012-03-28 | E-GEOD-11930 | biostudies-arrayexpress
Project description:A time series of whole-genome transcription profiling of E. coli K-12 W3110 was performed to study the dynamic physiological response of E. coli K-12 W3110 to limited carbon conditions. cDNA from eight time intervals after glucose limitation, representing different stages of glucose depletion, along with cDNA of an unrestricted growth were hybridized to whole-genome microarrays of E. coli K-12. Glucose concentrations were gradually reduced in a fed-batch cultivation process with constant feeding rate in a bioreactor. Major focus was put on the dynamic changes in the transcription level of genes involved in the central carbon metabolism (glycolysis, pentose phosphate pathway, TCA cycle and glyoxylate shunt), high-affinity glucose transport systems, movement, growth, and stress response. In total, 40 microarrays were hybridized. The data were statistically analysed using the software R (R, 2005) and the Limma package included (Smyth, 2005). The data were normalized â??print-tip-loessâ??. â??Multiple hypothesis testingâ?? correction was performed with the method of Benjamini and Hochberg (Benjamini and Hochberg, 1995), which controls the â??false discovery rateâ?? (fdr). Genes were regarded as differentially expressed when the â??adjusted p valuesâ?? were < 0.05, therefore nominally controlling the expected fdr to less than 0.05. The reproducibility of dye swap experiments as well as biological replicates was estimated by calculating â??Pearsonâ??s correlation coefficientsâ??. A high correlation was observed for the dye swap pairs (with averaged Pearsonâ??s correlation coefficients of 0.89 ± 0.06 for the reference samples and of 0.87 ± 0.08 for the different points of time) as well as for biological replicates (with averaged Pearsonâ??s correlation coefficients of 0.86 ± 0.04 for the red channel (Cy5) and 0.80 ± 0.09 for the green channel (Cy3)). Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B 57, 289-300. Smyth, G.K. (2005). Limma: Linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, Carrey, V., Dudoit, S., Irizzary, I., Huber, W., ed. (New York, Springer), pp. 397-420. R (2005). R: A language and environment for statistical computing. (R Development Core Team). Supplementary files: Data_table_A: TabelleA_Signifikante.txt Description: Data table with coefficients of the linear model for every gene which was differentially expressed for at least one point in time according to the reference sample. The statistical analysis was performed as described in Series section (GSE10307) based on the normalized log2(test/ref) ratios in the Sample records' VALUE columns. Data_table_B1: Tabelle_B1; /E. coli/, unlimited growth via glucose limitation (glucose concentration < 0.05 gL-1) Data_table_B2: Tabelle_B2; /E. coli/, unlimited growth via glucose limitation, acetate concentration = 0.35 gL-1 Data_table_B3: Tabelle_B3; /E. coli/, unlimited growth via glucose limitation, 30 min after depletion of extracellular acetate Data_table_B4: Tabelle_B4; /E. coli/, unlimited growth via glucose limitation, 50 min after depletion of extracellular acetate Data_table_B5: Tabelle_B5; /E. coli/, unlimited growth via glucose limitation, 110 min after depletion of extracellular acetate Data_table_B6: Tabelle_B6; /E. coli/, unlimited growth via glucose limitation, 170 min after depletion of extracellular acetate Data_table_B7: Tabelle_B7; /E. coli/, unlimited growth via glucose limitation, 230 min after depletion of extracellular acetate Data_table_B8: Tabelle_B8; /E. coli/, unlimited growth via glucose limitation, 350 min after depletion of extracellular acetate Description: Data_tables_B1-B8 report statistical values (A: average intensity value (1/2log2(test*ref)); M: average expression value (log2(test/ref)), t and P.value ('adjusted P.value')) for every point in time (studied conditions are described above for the corresponding table). Every differentially expressed gene of the corresponding point in time according to the reference sample is listed. Genes were regarded as differentially expressed when their 'adjusted P.values' were < 0.05, therefore nominally controlling the expected fdr to less than 0.05. The data are based on maximal three biological replicates (three independent fed-batch cultivations). RT-PCR_results_7genes.txt and RT-PCR_protocol.PDF Keywords: Time course, stress response Hybridization involved the hybridization of a common reference (unlimited growth, batch phase) on all arrays together with each sample of interest. This allowed the direct comparison of the transcripts of a time series taken during fed-batch cultivation with the unlimited reference sample. All samples were taken in duplicates and the experiments were performed as dye swap experiments. The first four samples of the time series (T1 - T4) were taken from three individual fed-batch cultivations (three biological replicates), the subsequent four samples (T5 - T8) were taken only from two individual fed-batch cultivations. On each array, the genes were spotted in duplicates. Therefore, twelve replicates (duplicates on dye swaps for three cultivations) were analyzed for T1 â?? T4 and eight replicates (duplicates on dye swaps for two cultivations) were analyzed for T5 â?? T8.
2010-05-19 | E-GEOD-10307 | biostudies-arrayexpress
Project description:Phenylethanol-resistant S. cerevisiae mutants were obtained by using evolutionary engineering strategy. Briefly, a chemically mutagenized culture was used as the initial population for the selection procedure. Gradually increasing levels of phenylethanol stress was applied through 56 successive batch cultivations. Individual mutants were selected from the final population. The mutant with the highest phenylethanol resistance could resist up to 3 g/L phenylethanol concentrations. Whole-genome transcriptomic analyses of the phenylethanol-resistant mutant strain and the reference strain were performed by using DNA microarray technology, in the absence of phenylethanol stress.
2014-07-12 | GSE59353 | GEO
Project description:The objective of the current study was to evaluate the performance of frequently used E. coli BL21 in the context of industrial cultivations. To meet this objective, we carried out batch cultivations with high-glucose media in computer-controlled bioreactors and applied transcriptome analysis to interpret phenotypic attributes at the molecular level. The resulting enhancement of knowledge about host physiology is expected to contribute to the acceleration of improvements and optimizations in related biotech processes.
2013-08-19 | E-MARS-21 | biostudies-arrayexpress