Utilizing a cell-free protein synthesis platform for the biosynthesis of a natural product, caffeine

An efficient lysate-based approach for biosynthesis of the pyrrolobenzodiazepine natural product tilimycin

Many bacteria use nonribosomal peptide synthetases (NRPSs), a family of multidomain enzymes that produce peptide natural products using an assembly line strategy. One class of such compounds are pyrrolobenzodiazepines, which have DNA alkylating activity. One example is tilimycin, a compound produced by the human gut microbiota that plays a role in epithelial damage during antibiotic-associated dysbiosis. The production of analogs of these natural products may facilitate the discovery of novel bioactive molecules. However, the synthesis of these natural products typically requires significant resources and time to produce in sufficient amounts for microbial and biochemical testing. Biocatalysis offers an environmentally friendly approach, but enzyme yield and stability, particularly with large multidomain enzymes that are often used in natural product pathways, can limit biochemical reactions with purified protein. Here, we demonstrate a cell lysate-based method to synthesize the nonribosomal peptide natural product tilimycin directly from the substrates 3-hydroxyanthranilic acid and L-proline with lysates from E. coli cell lines that express the tilimycin biosynthetic proteins. We present our protocol optimization and scale-up to produce tilimycin in a fast, efficient manner.

Cell-free systems: A synthetic biology tool for rapid prototyping in metabolic engineering

Microbial cell factories provide sustainable alternatives to petroleum-based chemical production using cost-effective substrates. A deep understanding of their metabolism is essential to harness their potential along with continuous efforts to improve productivity and yield. However, the construction and evaluation of numerous genetic variants are time-consuming and labor-intensive. Cell-free systems (CFSs) serve as powerful platforms for rapid prototyping of genetic circuits, metabolic pathways, and enzyme functionality. They offer numerous advantages, including minimizing unwanted metabolic interference, precise control of reaction conditions, reduced labor, and shorter Design-Build-Test-Learn cycles. Additionally, the introduction of in vitro compartmentalization strategies in CFSs enables ultra-high-throughput screening in physically separated spaces, which significantly enhances prototyping efficiency. This review highlights the latest examples of using CFS to overcome prototyping limitations in living cells with a focus on rapid prototyping, particularly regarding gene regulation, enzymes, and multienzymatic reactions in bacteria. Finally, this review evaluates CFSs as a versatile prototyping platform and discusses its future applications, emphasizing its potential for producing high-value chemicals through microbial biosynthesis.

Synthetic Biology of Natural Products Engineering: Recent Advances Across the Discover-Design-Build-Test-Learn Cycle

Advances in genome engineering and associated technologies have reinvigorated natural products research. Here we highlight the latest developments in the field across the discover-design-build-test-learn cycle of bioengineering, from recent progress in computational tools for AI-supported genome mining, enzyme and pathway engineering, and compound identification to novel host systems and new techniques for improving production levels, and place these trends in the context of responsible research and innovation, emphasizing the importance of anticipatory analysis at the early stages of process development.

Cell-Free Synthesis: Expediting Biomanufacturing of Chemical and Biological Molecules

The increasing demand for sustainable alternatives underscores the critical need for a shift away from traditional hydrocarbon-dependent processes. In this landscape, biomanufacturing emerges as a compelling solution, offering a pathway to produce essential chemical materials with significantly reduced environmental impacts. By utilizing engineered microorganisms and biomass as raw materials, biomanufacturing seeks to achieve a carbon-neutral footprint, effectively counteracting the carbon dioxide emissions associated with fossil fuel use. The efficiency and specificity of biocatalysts further contribute to lowering energy consumption and enhancing the sustainability of the production process. Within this context, cell-free synthesis emerges as a promising approach to accelerate the shift towards biomanufacturing. Operating with cellular machinery in a controlled environment, cell-free synthesis offers multiple advantages: it enables the rapid evaluation of biosynthetic pathways and optimization of the conditions for the synthesis of specific chemicals. It also holds potential as an on-demand platform for the production of personalized and specialized products. This review explores recent progress in cell-free synthesis, highlighting its potential to expedite the transformation of chemical processes into more sustainable biomanufacturing practices. We discuss how cell-free techniques not only accelerate the development of new bioproducts but also broaden the horizons for sustainable chemical production. Additionally, we address the challenges of scaling these technologies for commercial use and ensuring their affordability, which are critical for cell-free systems to meet the future demands of industries and fully realize their potential.