Project description:The inhibitors hydroxymethylfurfural (HMF) and furfural were added to the feed-medium of carbon-limited anaerobic chemostat cultures. Samples were taken for transcriptome analysis at steady-state from cultures with inhibitors and without inhibitors.
Project description:This dataset contains global label-free proteomics data from Saccharomyces cerevisiae cultivated under carbon-limited chemostat conditions. Samples were collected under aerobic and anaerobic steady-state conditions and after establishment of a dynamic steady state induced by repetitive glucose pulses. Proteomic analysis was performed to investigate oxygen-dependent metabolic adaptation and long-term proteome reprogramming in response to transient carbon excess under nutrient-limited conditions. Raw mass spectrometry files and processed identification and quantification results are provided.
Project description:In the present study transcriptome and proteome of recombinant, xylose-utilising S. cerevisiae grown in aerobic batch cultures on xylose were compared with glucose-grown cells both in glucose repressed and derepressed states. The aim was to study at genome-wide level how signalling and carbon catabolite repression differed in cells grown on either glucose or xylose. The more detailed knowledge about is xylose sensed as a fermentable carbon source, capable of catabolite repression like glucose, or is it rather recognised as a non-fermentable carbon source is important in achieving understanding for further engineering this yeast for more efficient anaerobic fermentation of xylose.
Project description:We attempted to improve the resistance of taxadiene-producing yeast strain to oxidative stress to develop a more robust yeast cell factory for improved Taxol® drug oxyenated taxanes precursors production from taxadiene. To this end, we evolved a yeast strain on H2O2-containing defined growth medium, supplemented with galactose as carbon source to induce the heterologous taxadiene biosynthesis pathway genes in that strain. The oxidative stress re-induction effect on the expression profiles of the superior evolved yeast strain (E_LRS5) was then studied before (steady state I) and during its continous use (steady state II) in galactose-limited chemostats, in parallel with the parent strain (LRS5).
Project description:In contrast to batch cultivation, chemostat cultivation allows the identification of carbon source responses without interference by carbon-catabolite repression, accumulation of toxic products, and differences in specific growth rate. This study focuses on the yeast Saccharomyces cerevisiae, grown in aerobic, carbon-limited chemostat cultures. Genome-wide transcript levels and in vivo fluxes were compared for growth on two sugars, glucose and maltose, and for two C2-compounds, ethanol and acetate. In contrast to previous reports on batch cultures, few genes (180 genes) responded to changes of the carbon source by a changed transcript level. Very few transcript levels were changed when glucose as the growth-limiting nutrient was compared with maltose (33 transcripts), or when acetate was compared with ethanol (16 transcripts). Although metabolic flux analysis using a stoichiometric model revealed major changes in the central carbon metabolism, only 117 genes exhibited a significantly different transcript level when sugars and C2-compounds were provided as the growthlimiting nutrient. Despite the extensive knowledge on carbon source regulation in yeast, many of the carbon source-responsive genes encoded proteins with unknown or incompletely characterized biological functions. In silico promoter analysis of carbon source-responsive genes confirmed the involvement of several known transcriptional regulators and suggested the involvement of additional regulators. Transcripts involved in the glyoxylate cycle and gluconeogenesis showed a good correlation with in vivo fluxes. This correlation was, however, not observed for other important pathways, including the pentose-phosphate pathway, tricarboxylic acid cycle, and, in particular, glycolysis. These results indicate that in vivo fluxes in the central carbon metabolism of S. cerevisiae grown in steadystate, carbon-limited chemostat cultures are controlled to a large extent via post-transcriptional mechanisms. Keywords: medium composition
Project description:The inhibitors hydroxymethylfurfural (HMF) and furfural were added to the feed-medium of carbon-limited anaerobic chemostat cultures. Samples were taken for transcriptome analysis at steady-state from cultures with inhibitors and without inhibitors. Three biological replicates from each condition (inhibitors, no inhibitors) were analyzed.
