Evolutionary engineering of Saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass Samples vs Reference
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
SUBMITTER: Maria Almario
PROVIDER: E-GEOD-44085 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Adaptive evolution experiment for enhaced tolerance to hydrolysates of lignocellulosic biomass in S. cerevisiae. The samples involves a batch culture in YNB and Hydrolysates. Cells were harvested at mid-exponential phase.
2013-04-26 | GSE44085 | GEO
Project description:The capacity of respiring cultures of Saccharomyces cerevisiae to instantaneously switch to fast alcoholic fermentation upon a transfer to anaerobic sugar-excess conditions is a key characteristic of Saccharomyces cerevisiae in many of its industrial applications. This transition was studied by exposing aerobic glucose-limited chemostat cultures grown at a low specific growth rate to two simultaneous perturbations: oxygen depletion and relief of glucose limitation. This shift towards fully fermentative conditions caused a massive transcriptional response, where one third of all genes within the genome were transcribed differentially. During the first 30 min, most of these changes were driven by relief from glucose limitation. An anaerobic induction response was only observed after the initial response to glucose excess. By comparing this study with public datasets representing dynamic and steady conditions, 14 up-regulated and 11 down-regulated genes were determined to be anaerobiosis specific and can therefore be use as âsignatureâ transcripts for anaerobicity under dynamic as well as under steady state conditions Experiment Overall Design: To invoke rapid and full induction of fermentative capacity, respiratory, aerobic glucose-limited chemostat cultures (D=0.1â¢h-1) were shifted to fully fermentative conditions by sudden depletion of oxygen and addition of glucose. The glucose was added two min after sparging the continuous culture with pure nitrogen, when the dissolved oxygen concentration had decreased from 75-80% to 10-15% of air saturation. Samples for micro-arrays were taken for each time point after the perturbation (5, 10, 30, 60 and 120 min) from two independently cultured replicates, while steady state data were taken from three independent chemostats. The complete dataset therefore comprised 13 samples.
2008-10-18 | E-GEOD-8187 | biostudies-arrayexpress
Project description:Study of the short term (within the first 330 seconds) transcriptional response of S.cerevisiae upon a sudden addition of glucose. Experiment Overall Design: Chemostat cultivation â Saccharomyces cerevisiae (CEN PK 113-7D) was cultivated in an aerobic carbon-limited chemostat culture in a 7-litres fermentor (Applikon, The Netherlands) with a working volume of 4-l on the adapted doubled mineral medium (Verduyn et al., 1992) with 27.1 g.l-1 of glucose and 1.42 g.l-1 of ethanol, to support a biomass concentration of about 15 g dry weight.l-1. The dilution rate was set to be 0.05 hr-1 and the airflow rate was set to be 200 l.hr-1. Other fermentation parameters are: a pH controlled at 5, a temperature controlled at 30ËC, an overpressure of 0.3 bar and stirrer speed of 600 rpm. The chemostat was considered to obtain its stable steady state condition 5 resident times after the end of its batch phase. Experiment Overall Design: Glucose pulse experiment - At the age of 7 dilution times, the steady state chemostat culture was perturbed by the addition of 20 ml of glucose solution (200 g/l) to the fermentor so that the residual glucose concentration was suddenly increased to about 1 g/l (5.56 mM). The glucose solution was rapidly injected by a pneumatic system (< 1 s). Samples were taken prior to the glucose pulse (steady state samples) and within 360 s transient after the perturbation. Experiment Overall Design: Verduyn,C., Postma,E., Scheffers,W.A., and van Dijken,J.P. (1992). Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8, 501-517.
2008-06-12 | E-GEOD-3821 | biostudies-arrayexpress
Project description:When evaluating the quantitative performance of label-free proteomics method(s), samples with known compositions are necessary to define key parameters such as reproducibility, missing data levels, accuracy, precision, as well as sensitivity/specificity for biomarker discovery. Here, we provide a carefully-designed multi-species spike-in sample set for such purposes, which was prepared by spiking small, variable amounts of E. Coli (for mimicking significant protein changes, i.e., true positives) and yeast (for balancing the variable levels of E. coli proteins) proteins into a large, constant background of human proteins (representing unchanged proteins). The sample set encompasses a total of 25 LC-MS sample runs (5 E.coli-level groups, 5 LC-MS replicate runs in each group). The proportion of human proteins is 60% across all samples, and each group contains the following percentage of E. coli and yeast proteins : A: 5%/35%, B: 7.5%/32.5%, C: 10%/30%, D: 15%/25%, E: 20%/20%. These files were used to comprehensively evaluate the quantitative performances by ultra-high-resolution (UHR)-IonStar and SWATH-MS in Result 3.2 of “Ultra-High-Resolution IonStar Strategy Enhancing Accuracy and Precision of MS1-Based Proteomics and an Extensive Comparison with State-of-the-Art SWATH-MS in Large-Cohort Quantification (DOI: 10.1021/acs.analchem.0c05002)”.
2022-01-06 | PXD030780 | Pride
Project description:This is parallel comparison of gene regulation by Gcn5 in evolutionarily divergent yeasts S. pombe and S. cerevisiae. Our study showed Gcn5 is required for a similar spectrum of stress responses in both organisms, including the response to KCl. This DNA microarray studies is to find conserved or diverged gene regulation pattern under KCl stress condition in the two yeasts. There are 6 subsets in total, 3 subsets in each evolutionarily divergent yeasts including the following: 1 gcn5 mutant compared to wt under rich medium without treatment, 2 gcn5 mutant compared to wild type both under KCl treatment, 3 wild type strains under KCl treatment compared to wild type without treatment. Keywords: stress response, Gcn5, Comparative genomics, Transcriptional co-activator Gene expression profiling experiment in which gene expression in logarithmically growing cultures of test groups was compared to that of the control groups in rich medium at 25C. There are 6 subsets in total, 3 subsets in each yeast including the following: 1 gcn5 mutant compared to wt under rich medium without treatment, 2 gcn5 mutant compared to wild type both under KCl treatment, 3 wild type strains under KCl treatment compared to wild type without treatment. RNA was extracted and subjected to cDNA expression profiling analysis using the established protocols (Xue et al, 2004). Independent RNA preparations were used to hybridize to microarray slides with dye swap. Data normalized with 'Lowess' per chip per spot normalization.
2010-06-24 | E-GEOD-5218 | biostudies-arrayexpress
Project description:Homozygous deletion mutants of drug resistance genes QDR3 and PDR3 and the homozygous deletion of HO (control) were grown in ammonium limited or glucose limited synthetic defined medium in aerated, pH controlled chemostats at a dilution rate of 0.1hr-1. Samples were collected at steady state.
2013-10-23 | E-MTAB-707 | biostudies-arrayexpress
Project description:We did transcription profiling on the effect of pmt1 pmt4 deletion, genes involved in the O-glycosylation process. These mutants cells show inhibition of mating, filamentation and induction of cell wall compensatory mechanism. Two biological samples were analyzed for each condition, and a microarray experiment were carried out for each sample 1. wild type cells SEY6210 2. pmt1 pmt2 cells from SEY6210 background
2010-09-29 | E-GEOD-12182 | biostudies-arrayexpress
Project description:Methyl ketone production by P. putida with A. thaliana and switchgrass hydrolysates obtained by dilute acid pretreatment led to the identification of plant-derived amino acids, rather than mono-aromatics, as key stimulative components of these hydrolysates. Shotgun proteomics indicated that the amino acids had a specific inductive effect on proteins involved in fatty acid biosynthesis, leading to a 9-fold increase in methyl ketone titer when amending glucose-containing minimal medium with a defined set of amino acids.
2019-06-27 | PXD012013 | Pride
Project description:We did transcription profiling on the effect of pmt1 pmt2 deletion. These genes are involved in the O-glycosylation process. These mutants cells show inhibition of mating, filamentation and induction of cell wall compensatory mechanism. Two biological samples were analyzed for each condition, and a microarray experiment were carried out for each sample 1. wild type cells SEY6210 2. pmt1 pmt2 cells from SEY6210 background
2010-09-29 | E-GEOD-12181 | biostudies-arrayexpress
Project description:The Saccharomyces cerevisiae SFP1 is required for proper regulation of ribosome biogenesis and cell size in response to nutrients. A mutant deleted for SFP1 shows specific traits among which a slow growth phenotype, which is particularly evident during growth on glucose. To assess the effects of nutrients on the activity of Sfp1 independent by growth rate related feedback we grew an sfp1Πmutant and its isogenic reference strain in chemostat cultures, at the same specific growth rate, under glucose/ethanol-limitation. Our data show that Sfp1 is involved in the modulation of cell size and RiBi gene expression and that these two functions are differently influenced by nutrients. The continuous cultures were then pulsed with a glucose excess generating a situation of batch growth similar to shake flask cultures. The dynamic analysis of the metabolic and transcriptional response following the glucose addition suggested that Sfp1 plays a role at the crossroads of ribosome biogenesis and central carbon metabolism regulation. Finally, we show that the down-regulation of RP genes, which was observed in an sfp1Πstrain during shake flask growth, cannot be directly ascribed to the absence of Sfp1 but is most probably a secondary effect due to the low growth potential of the mutant strain. Experiment Overall Design: After ten volume changes, few seconds after the samples for the steady state analysis were collected, the anaerobic glucose pulse experiments were started by sparging the medium reservoir and the fermenter with pure nitrogen gas (airflow of 0.5 L min-1, Hoek-Loos, Schiedam, <5 ppm O2). NorpreneTM tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic culture. Two minutes after nitrogen sparging and just before the addition of glucose, the medium and the effluent pumps were switched off. At this time point (which we will refer to as time T=0) the 200 mM glucose pulse was injected aseptically through a rubber septum. Experiment Overall Design: Sampling from chemostats, total RNA extraction, probe preparation and hybridization to Affymetrix Genechip® microarrays were performed as previously described (1). Samples were collected at steady state and then at 5, 10, 30, 60 and 120 minutes after the pulse. The results relative to steady state samples were derived from three independent cultures, those relative to the time course analysis were derived from two independent cultures. Experiment Overall Design: 1) Cipollina C., van den Brink J., Daran-Lapujade P., Pronk J.T., Vai M. and de Winde J.H. (2007) Revisiting the role of yeast Sfp1 in ribosome biogenesis and cell size control: A chemostat study. Microbiology. In press.
2008-06-18 | E-GEOD-9644 | biostudies-arrayexpress