In silico Determination of Some Conditions Leading to Glycolytic Oscillations and Their Interference With Some Other Processes in E. coli Cells.

Gheorghe Maria

doi:10.3389/fchem.2020.526679

Abstract

Autonomous oscillations of species levels in the glycolysis express the self-control of this essential cellular pathway belonging to the central carbon metabolism (CCM), and this phenomenon takes place in a large number of bacteria. Oscillations of glycolytic intermediates in living cells occur according to the environmental conditions and to the cell characteristics, especially the adenosine triphosphate (ATP) recovery system. Determining the conditions that lead to the occurrence and maintenance of the glycolytic oscillations can present immediate practical applications. Such a model-based analysis allows in silico (model-based) design of genetically modified microorganisms (GMO) with certain characteristics of interest for the biosynthesis industry, medicine, etc. Based on our kinetic model validated in previous works, this paper aims to in silico identify operating parameters and cell factors leading to the occurrence of stable glycolytic oscillations in the Escherichia coli cells. As long as most of the glycolytic intermediates are involved in various cellular metabolic pathways belonging to the CCM, evaluation of the dynamics and average level of its intermediates is of high importance for further applicative analyses. As an example, by using a lumped kinetic model for tryptophan (TRP) synthesis from literature, and its own kinetic model for the oscillatory glycolysis, this paper highlights the influence of glycolytic oscillations on the oscillatory TRP synthesis through the PEP (phosphoenolpyruvate) glycolytic node shared by the two oscillatory processes. The numerical analysis allows further TRP production maximization in a fed-batch bioreactor (FBR).

Highlights

The study of glycolytic oscillations might, prove crucial for the general understanding of the cell metabolism regulation and the connections among different parts of metabolism
Repeated simulations of the bioreactor dynamics using the fed-batch bioreactor (FBR)/MGM kinetic models, with the initial conditions of Table 1 and the parametric ranges of [GLC]ex ∈ [0.01–1.5] mM, and k6 ∈ [10–5-20] min−1 lead to the following results (Maria et al, 2018a,b,c): i) “Several glycolytic stationary oscillations domains exist in the E. coli cells, as indicated by the thick lines of Figure 3F plotted in the {[GLC]ex vs. k6} coordinates
This is due to the quick consumption of GLC by the cells following a more rapid adenosine triphosphate (ATP) recovery system (Maria et al, 2018c).” v) FBR dynamic simulations “have identified glycolytic oscillations with a period of 0.4–1 min, depending on the k6 value and on the [Glc]ex level

Summary

Introduction

The study of glycolytic oscillations might, prove crucial for the general understanding of the cell metabolism regulation and the connections among different parts of metabolism. A model able to simulate the dynamics of the cell CCM must include linked modules relating to (i) the glycolysis (Figures 1, 2); (ii) the phosphotransferase (PTS) system for GLC import into the cell (Figure 1); (iii) the pentose-phosphate pathway (PPP) to generate NADPH and pentoses (5-carbonsugars), as well as ribose 5-phosphate (R5P, a precursor for the synthesis of nucleotides); (iv) the tricarboxylic acid cycle (TCA); (v) the ATP recovery system, and several other pathways” (Palsson, 2005; Kadir et al, 2010; KEGG, 2011; Maria, 2018). “To cope with the very high complexity of cell metabolic processes, involving ca. 104 species concentrations, 103 gene expression transcription factors, and ca. 105 enzymatic reactions, adaptable reduced dynamic models, of ‘building-blocks’ like modular construction, have been developed over the last decades (reviews of Maria, 2017a,b), with including individual/lumped species and/or reactions

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Conclusion