Background: Saccharomyces cerevisiae is a well-known popular model system for basic biological studies and to serve as host organism for heterologous production of commercially interesting small molecules and proteins. The central metabolism is at the core to provide building blocks and energy to support growth and survival in normal situations as well as during exogeneous stresses and forced heterologous protein production. Here, we present a comprehensive study of intracellular central metabolite pool profiling when growing S. cerevisiae on different carbon sources in batch cultivations and at different growth rates in nutrient limited glucose chemostats. Latest versions of absolute quantitative mass spectrometry-based metabolite profiling methodology were applied to cover glycolytic and pentose phosphate pathway metabolites, TCA, complete amino acid and deoxy-/nucleoside phosphate pools. We have attempted to correlate the total metabolite pool composition with growth rates and nutrient limitation in both batch and chemostat cultivations. We have also tried to dissect the Crabtree-effect, i.e. ethanol-producing cultivation conditions, based on metabolite pool composition.
Results: Glutamate, glutamine, alanine and citrate were the four most abundant metabolites for most conditions tested. Amino acid is the dominant metabolite class even though a marked relative reduction compared to the other metabolite classes was observed for nitrogen and phosphate limited chemostats. Interestingly, glycolytic and PPP metabolites display largest variation among the cultivation conditions while the nucleoside phosphate pools are more stable and vary within a closer concentration window. The overall trends for glucose and nitrogen limited chemostats were increased metabolite pools with increasing growth rate. Next, comparing the chosen chemostat reference growth rate (0.12 h -1 , approximate one-fourth of maximal unlimited growth rate) illuminates an interesting pattern: almost all pools are lower in nitrogen and phosphate limited conditions compared to glucose limitation, except for the TCA metabolites citrate, isocitrate and a-ketoglutarate.
Conclusions: This study provides new knowledge how the central metabolism is adapting to various cultivations conditions and growth rates which is essential for expanding our understanding of cellular metabolism and development of improved phenotypes in metabolic engineering.