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Synthetic biology is defined by Design-Build-Test-Learn cycles. Recent advances in machine learning are changing the landscape; thus, we propose that “Learning” can precede “Design”. Moreover, adopting cell-free platforms can further accelerate “Building” and “Testing” for megascale data generation and models.

Access to recombinant proteins is vital in basic science and biotechnology research. Cell-free gene expression systems provide one approach to address this need, but widespread utilization remains limited by the cost, complexity, and inconsistency of current platforms. To address these limitations, we carry out a multi-dimensional definitive screening design to reduce the number of reagent components and remove costly secondary energy substrates. From 1,231 different reagent formulations, we discover a simple and reproducible system based on 12 components. The optimized reagent formulation can produce 2.4 ± 0.3 g/L of protein product at the 15-µL scale (~$60/g protein ) and 3.7 ± 0.2 g/L (~$39/g protein ) at the 4-mL scale with oxygen supplementation. This provides an average 95% reduction in cost over previous cell-free reagent formulations. We further show that the optimized reagent formulation can produce nucleoside triphosphates from nitrogenous bases and ribose and that it is robust to failure across batches of cell lysates, users/locations, and in the synthesis of more than 20 different proteins. For example, we demonstrate the production of fifteen therapeutically relevant products, including full-length aglycosylated monoclonal antibodies. We anticipate that our optimized reagent formulation will democratize the use of cell-free systems for protein manufacturing and synthetic biology applications. Recombinant proteins are a crucial product for basic science, biotechnology research, and biomanufacturing. Here, the authors develop a robust, low-cost, and high-yielding cell-free platform for protein production, decreasing cost per gram protein from ~$4,080 to ~$60 for multiple diverse products.

Access to recombinant proteins is vital in basic science and biotechnology research. Cell-free gene expression systems provide one approach to address this need, but widespread utilization remains limited by the cost, complexity, and inconsistency of current platforms. To address these limitations, we carry out a multi-dimensional definitive screening design to reduce the number of reagent components and remove costly secondary energy substrates. From more than 1,200 reagent formulations, we discover a simple and reproducible system based on 12 components. The optimized reagent formulation can produce 2.4 ± 0.3 g/L of protein product at the 15-μL scale (∼$55/gprotein) and 3.7 ± 0.2 g/L (∼$36/gprotein) at the 4-mL scale with oxygen supplementation. This provides an 84 to 99% reduction in cost over previous cell-free reagent formulations. We further show that the optimized reagent formulation can produce nucleoside triphosphates from nucleotides and ribose and that it is robust to failure across batches of cell lysates, users/locations, and in the synthesis of different proteins. Specifically, we demonstrate the production of fifteen therapeutically relevant products, including full-length aglycosylated monoclonal antibodies. We anticipate that our optimized reagent formulation will further democratize the use of cell-free systems for protein manufacturing and synthetic biology applications.