Pre-optimized cell free lysates for rapid prototyping of genes and pathways

Recent advances in synthesis capacity place growing demands on the “test” portion of the design-build-test-analyze cycle. Traditionally, pathways are constructed by transferring newly synthesized or cloned DNA into a host strain and tested. Success or failure of this design is predicated on the strain background and capacity that can influence pathway titers by more than an order of magnitude. Unfortunately, designing background strains remains a tedious process that usually only benefits a singular subset of products. Collectively, these features along with transformation idiosyncrasies (especially for non-model hosts), motivate the need for new technology platforms for designing, building, and optimizing biosynthetic pathways to manufacture fuels and bioproducts of DOE bioenergy interest. Here, we will address this need in a new interdisciplinary venture to develop tools that re-conceive how we engineer complex biological systems by linking pathway design, prospecting, and validation into an integrated framework. Specifically, our vision seeks to advance and interweave high-throughput cell-based systems and rapid cell-free technologies in a way suitable for automation and microdroplet manipulation in a DOE JGI user facility setting. Scope of work: We will work with the team led by Dr. Alper to achieve the overall project goals. Specifically, we will focus on establishing a cell-free framework for rapid pathway prototyping and optimizing metabolic pathways. Our key objectives are to: (i) Establish a cell-free framework for rapid pathway prototyping and analysis based on CRISPR-modified platform lysates. Rewire Y. lipolytica for the production of new products. (ii) Establish a technology platform that leverages cell-free and cell-based systems to develop optimized production strains.