A Computational Analysis of Stoichiometric Constraints and Trade-Offs in Cyanobacterial Biofuel Production

Henning Knoop, Ralf Steuer

Cyanobacteria are a promising biological chassis for the synthesis of renewable fuels and chemical bulk commodities. Significant efforts have been devoted to improve the yields of cyanobacterial products. However, while the introduction and heterologous expression of product-forming pathways is often feasible, the interactions and incompatibilities of product synthesis with the host metabolism are still insufficiently understood. In this work, we investigate the stoichiometric properties and trade-offs that underlie cyanobacterial product formation using a computational reconstruction of cyanobacterial metabolism. First, we evaluate the synthesis requirements of a selection of cyanobacterial products of potential biotechnological interest. Second, the large-scale metabolic reconstruction allows us to perform in silico experiments that mimic and predict the metabolic changes that must occur in the transition from a growth-only phenotype to a production-only phenotype. Applied to the synthesis of ethanol, ethylene, and propane, these in silico transition experiments point to bottlenecks and potential modification targets in cyanobacterial metabolism. Our analysis reveals incompatibilities between biotechnological product synthesis and native host metabolism, such as shifts in ATP/NADPH demand and the requirement to reintegrate metabolic by-products. Similar strategies can be employed for a large class of cyanobacterial products to identify potential stoichiometric bottlenecks.