Integrated Sustainability Score Implementation as an Objective Function in Sustainable Metabolic Engineering

Abstract

The sustainable metabolic engineering (SME) concept was defined by Stalidzans and Dace as an approach to the selection of the most sustainable metabolic engineering designs taking the economic, environmental and social components of sustainability into account. At the centre of the sustainability calculations is a genome-scale metabolic model that provides full balance of all incoming and outgoing metabolic fluxes at steady state. Therefore, sustainability indicators are assigned for each exchange reaction, enabling the calculation of sustainability features of consumption or production of each metabolite. The further development of the SME concept depends on its implementation at the computational level to acquire applicable results—sustainable production strain designs. This study proposes for the first time a workflow and tools of SME implementation using constraint-based stoichiometric modelling, genome-scale metabolic models and growth-coupled product synthesis approach. To demonstrate the application of SME, a relatively simple engineering task has been carried out. The most sustainable designs have been identified using Escherichia coli as the chassis organism, glucose as a substrate and gene deletions as a metabolic engineering tool. A growth-coupled production design tool has been used to reduce the variability of sustainability. The 10,000 most sustainable designs are found to produce succinate as the main product with the number of deleted genes ranging from two to seven. Many similar designs were identified due to the combinatorial explosion of different alternative combinations of gene deletion sets that have the same impact on the metabolism.