Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts

Abstract

Background: Use of alternative non-Saccharomyces yeasts in wine and beer brewing has gained more attention the recent years. This is both due to the desire to obtain a wider variety of flavours in the product and to reduce the final alcohol content. Given the metabolic differences between the yeast species, we wanted to account for some of the differences by using in silico models.

Results: We created and studied genome-scale metabolic models of five different non-Saccharomyces species using an automated processes. These were: Metschnikowia pulcherrima, Lachancea thermotolerans, Hanseniaspora osmophila, Torulaspora delbrueckii and Kluyveromyces lactis. Using the models, we predicted that M. pulcherrima, when compared to the other species, conducts more respiration and thus produces less fermentation products, a finding which agrees with experimental data. Complex I of the electron transport chain was to be present in M. pulcherrima, but absent in the others. The predicted importance of Complex I was diminished when we incorporated constraints on the amount of enzymatic protein, as this shifts the metabolism towards fermentation.

Conclusions: Our results suggest that Complex I in the electron transport chain is a key differentiator between Metschnikowia pulcherrima and the other yeasts considered. Yet, more annotations and experimental data have the potential to improve model quality in order to increase fidelity and confidence in these results. Further experiments should be conducted to confirm the in vivo effect of Complex I in M. pulcherrima and its respiratory metabolism.

Keywords: Alternative pathways; Automated reconstructions; Complex I; Electron transport chain; Enzymatic constraints; Genome-scale models; Metabolic modelling; Metschnikowia pulcherrima; Yeast; decFBA; sMOMENT.

Fig. 1

dFBA simulations of the models without enzymatic constraints for the six yeast models, starting with $10\text{mmol}{\text{L}}^{-1}$ glucose. $\frac{\text{gDW}}{\text{L}}$: Grams of dry weight per liter

Fig. 2

dFBA simulations of the models without enzymatic constraints for Metschnikowia pulcherrima and Kluyveromyces lactis when artificially changing the stoichiometry of the number of protons pumped by Complex I

Fig. 3

decFBA simulations of the sMOMENT model of Metschnikowia pulcherrima when artificially changing the stoichiometry of the number of protons pumped by Complex I under different levels of the protein pool. $\frac{\text{gDW}}{\text{L}}$: Grams of dry weight per liter

Fig. 4

decFBA simulations of the sMOMENT models for Metschnikowia pulcherrima and Kluyveromyces lactis under different levels of the protein pool. $\frac{\text{gDW}}{\text{L}}$: Grams of dry weight per liter