Dynamics of Storage Carbohydrates Metabolism in Saccharomyces cerevisiae

Abstract

Production of chemicals via biotechnological routes are becoming rapidly an alternative to oil-based processes. Several microorganisms including yeast, bacteria, fungi and algae can transform feedstocks into high-value molecules at industrial scale. Improvement of the bioprocess performance is a key factor for making this technology economically feasible. Despite the vast knowledge on microbial metabolism, some gaps still remain open. In Saccharomyces cerevisiae, metabolism of storage carbohydrates, trehalose and glycogen, is well documented. However, the lack of quantitative information limits our understanding on what is the actual role of these materials, especially regarding the in vivo reaction rates. Like in nature, in industrial bioreactors microorganisms may encounter fluctuating environments that lead to diverse metabolic responses, especially due to large-scale substrate mixing limitations. These dynamic scenarios are known to trigger the recycle of glucose through the storage carbohydrate nodes. The cyclic nature of storage carbohydrate metabolism (synthesis and degradation) can lead to a waste of metabolic energy decreasing biomass and product yields. Thus, the biological system needs to be robust enough to withstand this adverse scenario and maintain its metabolic functions. The scope of this thesis is to investigate the dynamics of storage carbohydrates, trehalose and glycogen, and its interaction with the central carbon metabolism in Saccharomyces cerevisiae from a quantitative perspective. In this work, it is proposed to use stimulus response experiments in combination with 13C-labeling and mathematical modeling for identifying reaction rates. In this direction, novel feast/famine experiments are proposed as a robust experimental platform for dynamic metabolic studies and estimating dynamic fluxes in time by piecewise function approximations. Hence, the main contribution of this thesis is not only the better understanding of storage carbohydrate metabolism through dynamic metabolic rates but also the used experimental platforms and modeling approach. The results obtained in this work clearly highlight the relevance of storage carbohydrates and its interaction with the central carbon metabolism. It is shown that storage carbohydrates are key metabolites for yeast robustness since these metabolites are involved in the regulation of the glycolytic flux. This work comprehensively presents the role of trehalose and glycogen metabolism in yeast from a quantitative point of view, and it is expected that this contribution will be of significant relevance for understanding yeast metabolism in both scientific and industrial environments.