Multiobjective strain design: A framework for modular cell engineering

Diversity of cellular metabolism can be harnessed to produce a large space of molecules. However, development of optimal strains with high product titers, rates, and yields required for industrial production is laborious and expensive. To accelerate the strain engineering process, we have recently introduced a modular cell design concept that enables rapid generation of optimal production strains by systematically assembling a modular cell with an exchangeable production module(s) to produce target molecules efficiently. In this study, we formulated the modular cell design concept as a general multiobjective optimization problem with flexible design objectives derived from mass balance. We developed algorithms and an associated software package, named ModCell2, to implement the design. We demonstrated that ModCell2 can systematically identify genetic modifications to design modular cells that can couple with a variety of production modules and exhibit a minimal tradeoff among modularity, performance, and robustness. Analysis of the modular cell designs revealed both intuitive and complex metabolic architectures enabling modular production of these molecules. We envision ModCell2 provides a powerful tool to guide modular cell engineering and sheds light on modular design principles of biological systems. •Formulate modular cell design as a multiobjective optimization problem.•Develop algorithm and computational platform, ModCell2, to streamline modular cell design.•Demonstrate ModCell2 to design modular cells using genome-scale E. coli metabolic model.•Show modular cells exhibit minimal tradeoff among modularity, performance, and robustness.•Reveal intuitive and complex metabolic architectures enabling modular design.