A General Process-Based Model for Describing the Metabolic Shift in Microbial Cell Cultures.

Fabrizio Carteni,Emanuela Palomba,Alessio Occhicone,Christian E Vincenot,Francesco Giannino,Elisabetta De Alteriis,Stefano Mazzoleni

doi:10.3389/fmicb.2020.521368

Abstract

The metabolic shift between respiration and fermentation at high glucose concentration is a widespread phenomenon in microbial world, and it is relevant for the biotechnological exploitation of microbial cell factories, affecting the achievement of high-cell-densities in bioreactors. Starting from a model already developed for the yeast Saccharomyces cerevisiae, based on the System Dynamics approach, a general process-based model for two prokaryotic species of biotechnological interest, such as Escherichia coli and Bacillus subtilis, is proposed. The model is based on the main assumption that glycolytic intermediates act as central catabolic hub regulating the shift between respiratory and fermentative pathways. Furthermore, the description of a mixed fermentation with secondary by-products, characteristic of bacterial metabolism, is explicitly considered. The model also represents the inhibitory effect on growth and metabolism of self-produced toxic compounds relevant in assessing the late phases of high-cell density culture. Model simulations reproduced data from experiments reported in the literature with different strains of non-recombinant and recombinant E. coli and B. subtilis cultured in both batch and fed-batch reactors. The proposed model, based on simple biological assumptions, is able to describe the main dynamics of two microbial species of relevant biotechnological interest. It demonstrates that a reductionist System Dynamics approach to formulate simplified macro-kinetic models can provide a robust representation of cell growth and accumulation in the medium of fermentation by-products.

Highlights

Glucose is the main carbon and energy source for microbial metabolism
In this work, considering the similarity of the metabolic shift between S. cerevisiae and prokaryotic cells as determined by the level of the glycolytic intermediates, we extend the model by Mazzoleni et al (2015) to simulate the growth of different strains of E. coli and B. subtilis cultured in batch and fed-batch bioreactors under aerobic conditions, with glucose as carbon and energy source
The resulting model is composed of a set of 7 ordinary differential equations representing glucose in the growth medium (G), glycolysis intermediates from glucose-6-phosphate to pyruvate (P), acetate produced by fermentation (A), cellular components produced by either fermentation or respiration (CM), reserve compounds (R), growth-associated inhibitory byproducts (I), and dead cells (D)

Summary

Introduction

Glucose is the main carbon and energy source for microbial metabolism. Glucose uptake supplies the glycolytic process producing different intermediates, with pyruvate representing a central catabolic hub, followed by the respiratory or fermentative pathway, depending on oxygen availability.Modeling Metabolic Shift in Microbial CulturesRespiration is able to maximize ATP production and biomass yield. Despite the fully aerobic conditions, in several microbial species when glucose concentration is high, the respiratory metabolism is replaced by a fermentative one, which produces partially oxidized products (Molenaar et al, 2009; Goel et al, 2012). Such metabolic shift between two different ATP producing metabolisms, respiration and fermentation, is a widespread phenomenon in the biological world (Molenaar et al, 2009; Goel et al, 2012). It has been shown how the overexpression of a single transcription factor (the ortholog of S. cerevisiae GAL4) in Komagataella phaffii results in a switch of the Crabtree phenotype from negative to positive with an increase in specific glucose uptake (Ata et al, 2018)

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Conclusion