Abstract
Existing computational tools for de novo metabolic pathway assembly, either based on mixed integer linear programming techniques or graph-search applications, generally only find linear pathways connecting the source to the target metabolite. The overall stoichiometry of conversion along with alternate co-reactant (or co-product) combinations is not part of the pathway design. Therefore, global carbon and energy efficiency is in essence fixed with no opportunities to identify more efficient routes for recycling carbon flux closer to the thermodynamic limit. Here, we introduce a two-stage computational procedure that both identifies the optimum overall stoichiometry (i.e., optStoic) and selects for (non-)native reactions (i.e., minRxn/minFlux) that maximize carbon, energy or price efficiency while satisfying thermodynamic feasibility requirements. Implementation for recent pathway design studies identified non-intuitive designs with improved efficiencies. Specifically, multiple alternatives for non-oxidative glycolysis are generated and non-intuitive ways of co-utilizing carbon dioxide with methanol are revealed for the production of C2+ metabolites with higher carbon efficiency.
Highlights
Graph-based pathway design approaches[35] begin from the target chemical and iteratively retrace back a path to the source metabolite using a retrosynthetic algorithm
The term overall stoichiometry/conversion abstracts the global elemental balance sheet for the chemical changes including metabolites, small molecules, ions and free energy equivalents required to achieve the design objective. Meeting this overall stoichiometry often requires the recruitment of many additional metabolites that help recycle carbon and redox resources in highly complex ways. This motivates the development of a stoichiometry and pathway design tool (Fig. 1) that first optimizes the overall stoichiometry by exploring exhaustively co-reactant/co-product combinations (Step 1)
We explored whether it is possible to construct the entire pathway in a single organism unlike the engineered non-oxidative glycolysis (NOG) pathway that requires at least one heterologous enzyme
Summary
Graph-based pathway design approaches[35] begin from the target chemical and iteratively retrace back a path to the source metabolite using a retrosynthetic algorithm. The term overall stoichiometry/conversion abstracts the global elemental balance sheet for the chemical changes including metabolites, small molecules, ions and free energy equivalents required to achieve the design objective. Meeting this overall stoichiometry often requires the recruitment of many additional metabolites that help recycle carbon and redox resources in highly complex ways. This motivates the development of a stoichiometry and pathway design tool (Fig. 1) that first optimizes the overall stoichiometry (e.g., aA + cC → bB + dD) by exploring exhaustively co-reactant/co-product combinations (Step 1). Overall conversion stoichiometries and pathway designs span a range of complex network topologies and provide valuable insight as to how the overall conversion pathway changes in response to alternate co-reactant and/or co-product scenarios
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