Project description:This SuperSeries is composed of the following subset Series: GSE3205: Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 1 GSE3206: Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 2 Abstract: We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited batch cultures of yeast go through two sequential exponential growth phases, beginning with a largely fermentative phase, followed by an essentially completely aerobic use of residual glucose and evolved ethanol. Judging from the patterns of gene expression, the state of the cells growing at steady state in glucose-limited chemostats corresponds most closely with the state of cells in batch cultures just before they undergo this "diauxic shift." Essentially the same pattern was found between chemostats having a fivefold difference in steady-state growth rate (the lower rate approximating that of the second phase respiratory growth rate in batch cultures). Although in both cases the cells in the chemostat consumed most of the glucose, in neither case did they seem to be metabolizing it primarily through respiration. Although there was some indication of a modest oxidative stress response, the chemostat cultures did not exhibit the massive environmental stress response associated with starvation that also is observed, at least in part, during the diauxic shift in batch cultures. We conclude that despite the theoretical possibility of a switch to fully aerobic metabolism of glucose in the chemostat under conditions of glucose scarcity, homeostatic mechanisms are able to carry out metabolic adjustment as if fermentation of the glucose is the preferred option until the glucose is entirely depleted. These results suggest that some aspect of actual starvation, possibly a component of the stress response, may be required for triggering the metabolic remodeling associated with the diauxic shift. Refer to individual Series

Project description:Time course of batch growth. Reference (channel 1) was a culture grown in MD medium with 2.4 g/L glucose, with 5 slpm air-flow, stirring at 400 rpm and a constant 300C temperature, dilution 0.25 volumes/hour. The experimental (channel 2) time course samples were grown in batch for the indicated time. The "Low-D chemostat vs. High-D chemostat" hybridization's channel 2 sample was grown in a chemostat, with a dilution rate of 0.05 volumes/hour; it is most similar to the time course samples taken between 8 and 9 hours. Groups of assays that are related as part of a time series. FactorCategory: Elapsed Time; name: Elapsed Time; Measurement: time(absolute) 0 h; name: 45181_Elapsed Time; Measurement: time(absolute) 8.5 h; name: 38150_Elapsed Time; Measurement: time(absolute) 8.75 h; name: 38151_Elapsed Time; Measurement: time(absolute) 9 h; name: 38152_Elapsed Time; Measurement: time(absolute) 9.25 h; name: 38153_Elapsed Time; Measurement: time(absolute) 7.25 h; name: 38145_Elapsed Time; Measurement: time(absolute) 9.5 h; name: 38154_Elapsed Time; Measurement: time(absolute) 7.5 h; name: 38146_Elapsed Time; Measurement: time(absolute) 9.75 h; name: 38155_Elapsed Time; Measurement: time(absolute) 7.75 h; name: 38147_Elapsed Time; Measurement: time(absolute) 10 h; name: 38156_Elapsed Time; Measurement: time(absolute) 8 h; name: 38148_Elapsed Time; Measurement: time(absolute) 8.25 h; name: 38149_Elapsed Time FactorCategory: Growth Condition; name: Growth Condition; Growth Condition: chemostat dilution control; name: 45181_Growth Condition; Growth Condition: batch; name: 38150_Growth Condition; Growth Condition: batch; name: 38151_Growth Condition; Growth Condition: batch; name: 38152_Growth Condition; Growth Condition: batch; name: 38153_Growth Condition; Growth Condition: batch; name: 38145_Growth Condition; Growth Condition: batch; name: 38154_Growth Condition; Growth Condition: batch; name: 38146_Growth Condition; Growth Condition: batch; name: 38155_Growth Condition; Growth Condition: batch; name: 38147_Growth Condition; Growth Condition: batch; name: 38156_Growth Condition; Growth Condition: batch; name: 38148_Growth Condition; Growth Condition: batch; name: 38149_Growth Condition Keywords: time_series_design

Project description:Fungal electron transport systems (ETS) are branched, involving alternative NADH dehydrogenases and an alternative terminal oxidase. These alternative respiratory enzymes were reported to play a role in pathogenesis, production of antibiotics and excretion of organic acids. The activity of these alternative respiratory enzymes strongly depends on environmental conditions. Functional analysis of fungal ETS under highly standardised conditions for cultivation, sample processing and respirometric assay are still lacking. We developed a highly standardised protocol to explore in vivo the ETS-and in particular the alternative oxidase-in Penicillium ochrochloron. This included cultivation in glucose-limited chemostat (to achieve a defined and reproducible physiological state), direct transfer without any manipulation of a broth sample to the respirometer (to maintain the physiological state in the respirometer as close as possible to that in the chemostat), and high-resolution respirometry (small sample volume and high measuring accuracy). This protocol was aimed at avoiding any changes in the physiological phenotype due to the high phenotypic plasticity of filamentous fungi. A stable oxygen consumption (< 5% change in 20 minutes) was only possible with glucose limited chemostat mycelium and a direct transfer of a broth sample into the respirometer. Steady state respiration was 29% below its maximum respiratory capacity. Additionally to a rotenone-sensitive complex I and most probably a functioning complex III, the ETS of P. ochrochloron also contained a cyanide-sensitive terminal oxidase (complex IV). Activity of alternative oxidase was present constitutively. The degree of inhibition strongly depended on the sequence of inhibitor addition. This suggested, as postulated for plants, that the alternative terminal oxidase was in dynamic equilibrium with complex IV-independent of the rate of electron flux. This means that the onset of activity does not depend on a complete saturation or inhibition of the cytochrome pathway.

Project description:Time course of batch growth. Reference (channel 1) was a culture grown in MD medium with 2.4 g/L glucose, with 5 slpm air-flow, stirring at 400 rpm and a constant 300C temperature, dilution 0.25 volumes/hour. The experimental (channel 2) time course samples were grown in batch for the indicated time. The "Low-D chemostat vs. High-D chemostat" hybridization's channel 2 sample was grown in a chemostat, with a dilution rate of 0.05 volumes/hour; it is most similar to the time course samples taken between 8 and 9 hours. Groups of assays that are related as part of a time series. FactorCategory: Elapsed Time; name: Elapsed Time; Measurement: time(absolute) 0 h; name: 45181_Elapsed Time; Measurement: time(absolute) 8.5 h; name: 38150_Elapsed Time; Measurement: time(absolute) 8.75 h; name: 38151_Elapsed Time; Measurement: time(absolute) 9 h; name: 38152_Elapsed Time; Measurement: time(absolute) 9.25 h; name: 38153_Elapsed Time; Measurement: time(absolute) 7.25 h; name: 38145_Elapsed Time; Measurement: time(absolute) 9.5 h; name: 38154_Elapsed Time; Measurement: time(absolute) 7.5 h; name: 38146_Elapsed Time; Measurement: time(absolute) 9.75 h; name: 38155_Elapsed Time; Measurement: time(absolute) 7.75 h; name: 38147_Elapsed Time; Measurement: time(absolute) 10 h; name: 38156_Elapsed Time; Measurement: time(absolute) 8 h; name: 38148_Elapsed Time; Measurement: time(absolute) 8.25 h; name: 38149_Elapsed Time FactorCategory: Growth Condition; name: Growth Condition; Growth Condition: chemostat dilution control; name: 45181_Growth Condition; Growth Condition: batch; name: 38150_Growth Condition; Growth Condition: batch; name: 38151_Growth Condition; Growth Condition: batch; name: 38152_Growth Condition; Growth Condition: batch; name: 38153_Growth Condition; Growth Condition: batch; name: 38145_Growth Condition; Growth Condition: batch; name: 38154_Growth Condition; Growth Condition: batch; name: 38146_Growth Condition; Growth Condition: batch; name: 38155_Growth Condition; Growth Condition: batch; name: 38147_Growth Condition; Growth Condition: batch; name: 38156_Growth Condition; Growth Condition: batch; name: 38148_Growth Condition; Growth Condition: batch; name: 38149_Growth Condition Computed

Dataset Information

Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate.

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Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate.

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