In large scale fermentors the cultivated cells are exposed to dynamic changes in the nutrient concentrations due to imperfect mixing. Based on the characterization of these nutrient gradients in space and time, a rational scale down design can be obtained. This study focuses on the combined gradients of dissolved sugar and oxygen concentrations. Based on a recent computational fluid dynamics (CFD) study, firstly a scale-down design was developed. From intracellular metabolite measurements during these scale-down experiments, the metabolic behavior of the cells under highly dynamic conditions was revealed. Under the combined influence of oscillating glucose and oxygen concentrations, the penicillin production declined to 50 % of the value under steady state conditions. This decline was similar as observed during glucose oscillations alone. The influence of oxygen oscillations on the levels of the majority of the intracellular metabolites analyzed was negligible, although these metabolites were strongly affected by the varying oxygen levels under solely oxygen oscillations. Additionally, a metabolic structured kinetic model was developed and validated with data from glucose and oxygen oscillation experiments. This model can be coupled to CFD simulations to obtain an accurate prediction of the performance of industrial strains in space and time in large industrial scale bioreactors.

Engineered strains of the yeast Saccharomyces cerevisiae are intensively studied as production platforms for aromatic compounds such as hydroxycinnamic acids, stilbenoids and flavonoids. Heterologous pathways for production of these compounds use L-phenylalanine and/or L-tyrosine, generated by the yeast shikimate pathway, as aromatic precursors. The Ehrlich pathway converts these precursors to aromatic fusel alcohols and acids, which are undesirable by-products of yeast strains engineered for production of high-value aromatic compounds. Activity of the Ehrlich pathway requires any of four S. cerevisiae 2-oxo-acid decarboxylases (2-OADCs): Aro10 or the pyruvate-decarboxylase isoenzymes Pdc1, Pdc5, and Pdc6. Elimination of pyruvate-decarboxylase activity from S. cerevisiae is not straightforward as it plays a key role in cytosolic acetyl-CoA biosynthesis during growth on glucose. In a search for pyruvate decarboxylases that do not decarboxylate aromatic 2-oxo acids, eleven yeast and bacterial 2-OADC-encoding genes were investigated. Homologs from Kluyveromyces lactis (KlPDC1), Kluyveromyces marxianus (KmPDC1), Yarrowia lipolytica (YlPDC1), Zymomonas mobilis (Zmpdc1) and Gluconacetobacter diazotrophicus (Gdpdc1.2 and Gdpdc1.3) complemented a Pdc⁻ strain of S. cerevisiae for growth on glucose. Enzyme-activity assays in cell extracts showed that these genes encoded active pyruvate decarboxylases with different substrate specificities. In these in vitro assays, ZmPdc1, GdPdc1.2 or GdPdc1.3 had no substrate specificity towards phenylpyruvate. Replacing Aro10 and Pdc1,5,6 by these bacterial decarboxylases completely eliminated aromatic fusel-alcohol production in glucose-grown batch cultures of an engineered coumaric acid-producing S. cerevisiae strain. These results outline a strategy to prevent formation of an important class of by-products in ‘chassis’ yeast strains for production of non-native aromatic compounds.