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

This work presents a methodology to evaluate the bioenergetic feasibility of alternative metabolic pathways for a given microbial conversion, optimising their energy yield and driving forces as a function of the concentration of metabolic intermediates. The tool, based on thermodynamic principles and multi-objective optimisation, accounts for pathway variants in terms of different electron carriers, as well as energy conservation (proton translocating) reactions within the pathway. The method also accommodates other constraints, some of them non-linear, such as the balance of conserved moieties. The approach involves the transformation of the maximum energy yield problem into a multi-objective mixed-integer linear optimisation problem which is then subsequently solved using the epsilon-constraint method, highlighting the trade-off between yield and rate in metabolic reactions. The methodology is applied to analyse several pathway alternatives occurring during propionate oxidation in anaerobic fermentation processes, as well as to the reverse TCA cycle pathway occurring during autotrophic microbial CO2 fixation. The results obtained using the developed methodology match previously reported literature and bring about insights into the studied pathways.Author summary: In this study we have developed a method that evaluates the feasibility of various metabolic pathways in microbes and finds the optimum concentrations of metabolic intermediates modes in terms of energy efficiency (yield) and driving forces (rate). The method is based on thermodynamic principles and uses multi-objective optimization to evaluate numerous different pathway variants, including the use of different electron carriers and energy conservation reactions. It also considers other constraints, such as the balance of conserved components. A complex mathematical problem is solved that maps the trade-off between yield and rate in the pathways evaluated. We applied this methodology to analyse alternative pathways in propionate oxidation and CO2 fixation by microbes. This research has potential applications in biotechnology and environmental studies, advancing our understanding of the trade-offs between energy efficiency and rate in different microbial pathways and allowing for the design of synthetic pathways for engineered organisms based on optimality principles.