Programming Metabolic Dependency in Synthetic Cells Under Resource Scarcity

Abstract

Engineering synthetic cells where metabolism directly controls gene expression is one of the greatest challenges in synthetic biology. This coupling between metabolic activity and protein synthesis is also thought to have been a vital step in the evolution of the earliest cellular life. This fundamental process is essential for developing minimal, self-sustaining cells, both engineered for biotechnology applications and as models explaining the origins of life. Here, we present a programmable cell-free platform that links metabolic activity to translation under defined resource limitations. Using an engineered amino-acid-dependent cell-free translation system, we introduced a tunable metabolic bottleneck (depleting tyrosine). This enabled imposing a controlled metabolic constraint on protein synthesis. To alleviate this constraint, we then incorporated phenylalanine hydroxylase (PAH) as a minimal module for tyrosine synthesis. The PAH-driven tyrosine synthesis established a system in which protein expression is directly controlled by amino acid biosynthesis. This relationship was recapitulated in liposome compartments, resulting in three distinct synthetic cell populations. The metabolically active population had significantly higher fitness in protein production. Overall, this work establishes an experimentally tractable platform to investigate how primitive cells may have evolved internal metabolic capabilities, and it represents a foundational step toward constructing more autonomous and self-regulating synthetic cells.