Control strategies to manage trade-offs during microbial production

Abstract

When engineering microbes to overproduce a target molecule, engineers face multiple layers of trade-offs to allocate limited cellular resources between the target pathway and native cellular systems. These trade-offs arise from limited free ribosomes during translation, competition for metabolic precursors, as well as the negative relationship between production and growth rate. To achieve high production performance, microbes need to spontaneously make decisions in the dynamic and heterogeneous fermentation environment. In this review, we discuss recent advances in microbial control strategies that are used to manage these trade-offs and to improve microbial production. This review focuses on design principles and compares different implementations, with the hope to provide guidelines to future microbial engineering.

Figure 1

The presence of trade-offs during microbial production. (a) Ribosomal trade-offs. Overexpressing one protein decreases the number of free ribosomes available to synthesize native proteins and other target proteins within an engineered pathway. (b) Metabolic trade-offs. Precursor metabolites are used for the synthesis of cellular structures, energy supplies, as well as target pathways. Consumption of precursor metabolites by a target pathway can affect both cell growth and maintenance. (c) Growth rate trade-offs. Low producers usually grow faster than high producers. Without control, low producers gradually dominate the culture over time.

Figure 2

Design principles of control strategies that improve microbial production. (a) Feedback control of orthogonal rRNA provides robust gene expression from orthogonal ribosomes. (b) Stress-mediated feedback control to limit the burdensome protein synthesis. (c) Metabolic feedback control via MRTF to prevent metabolic overflow. (d) Stress-mediated feedback control to reduce the accumulation of the toxic intermediate. (e) Dynamics of trigger signals used to inhibit competing but essential pathways. (f) Setting an evolutionary stable point for high producers through population quality control. (g,h) Implement population quality control. Linking production and cell growth via sensor-selector (g) and by-product (h). GOI, gene of interests; o-rRNA, orthogonal rRNA; o-ribosome, orthogonal ribosome; MRTF, metabolite-responsive transcription factor; QS, quorum sensing.