The Influence of Crowding Conditions on the Thermodynamic Feasibility of Metabolic Pathways

Abstract

Intracellular reactions are carried out in a crowded medium where the macromolecules occupy ∼40% of the total volume. This decrease in the available volume affects the activity of the reactants. Scaled particle theory is used for the estimation of the activity coefficients of the metabolites, and thereby for the assessment of the impact of the presence of background molecules, on the estimation of the Gibbs free energy change (ΔrG) of the reactions. The lactic acid pathway and the central carbon metabolism of Actinobacillus succinogenes for the production of succinic acid from glycerol have been used as illustrative case studies. Results suggest the importance of maintaining intracellular crowded regions to favor the feasibility of a pathway that in other circumstances would be infeasible. Moreover, the crowding conditions may change the directionality of reactions and can modify the feasible range of fluxes estimated for a metabolic system compared with those obtained at standard biological conditions.

Estimation of flux distribution in metabolic networks accounting for thermodynamic constraints: The effect of equilibrium vs. blocked reactions

“…a metabolon, and/or its presence helps to maintain specific crowding conditions required to convert an unfeasible pathway to a feasible one [32].…”

“…enhanced by several orders of magnitude.This enhancement in the metabolite's activity could affect the thermodynamic analysis and therefore alter the flux distribution predicted[32]. Besides, this reduction in the available volume of the molecules causes a decrease in their diffusion and the likely encounter-reaction between reactants[33].3.3.…”

Increased production of isobutanol from xylose through metabolic engineering of Saccharomyces cerevisiae overexpressing transcription factor Znf1 and exogenous genes

“…Several strategies have been demonstrated to direct metabolic flux toward improved isobutanol production. These include overcoming specificity of enzyme activity, obtaining sufficient substrate availability, deleted competing endogenous pathways, maintaining the balance of metabolic cofactors, and relieving or avoiding metabolic bottlenecks (Keasling 2010 , Angeles-Martinez and Theodoropoulos 2015 , Yadav et al 2018 , Kuroda et al 2019 ). Here, we combined the effect of transcriptional activation of genes required for biosynthesis of isobutanol, ribosomal proteins and Fe/S cluster by the Znf1 regulator with the above approach to enhance production.…”

Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants

“…No further compartmentalization is considered in the model; thus, no intracellular transport reactions are included in the analysis. The activity of all species is taken to be equal to their concentrations i.e., all activity coefficients equal one. This assumption can be waived with the inclusion of an appropriate activity model such as the Debye-Hückel law, though these calculations are frequently imperfect in biological systems due to crowding effects [40,41]. The only energy-recovering and conserving mechanisms within the cell are substrate-level phosphorylation (SLP) and chemiosmotic proton translocations [42].…”