This Small Business Innovation Research (SBIR) Phase I project is to develop a general process to enable microorganisms for rapid genome engineering. Current technologies to engineer cells are expensive and time consuming due to reliance on inefficient, serial modifications of DNA. Multiplex Automated Genome Engineering (MAGE) is a disruptive technology that allows for rapid engineering of microorganisms at substantially reduced cost. MAGE enables large-scale highly specific genome modifications via incorporation of synthetic oligonucleotides at multiple locations simultaneously - akin to massive parallel reprogramming of the genome. However, use of MAGE is currently limited to E. coli due to key genetic requirements. The goal of this project is a general process to identify and optimize the requisite genetic features for MAGE in new microorganisms. As a first step, the project will build on progress in making a MAGE-competent yeast strain, which is not yet efficient for use in commercial applications. Moreover, since potential industrial partners use their own strains for production, it will be necessary to quickly and reversibly endow existing strains of yeast with the capacity to undergo MAGE. The successful application of this process will result in the ability to rapidly and reversibly deploy MAGE-competence in existing commercial yeast strains.
The broader impact/commercial potential of this project, if successful, will be the rapid and reversible introduction of the capacity to reprogram numerous species of microorganisms for specific functions (e.g., production of specialty chemicals, enzymes, etc.). The successful application of this process to introduce MAGE-competence to strains of the widely utilized budding yeast, S. cerevisiae, will result in immediate commercial opportunities - making yeast genome engineering faster and significantly less expensive. Additionally, the demonstration of this process paves the way for deployment of MAGE-competence in other high-valued commercial yeasts, such as Pichia pastoris and Kluyveromyces lactis. This project will establish the basis for a generalized process to port MAGE to other yeasts, and ultimately other microorganisms. The introduction of MAGE engenders the ability to rewrite or edit novel genomes, making our process synergistic with the extraordinary decline in sequencing costs and increasing wealth of informatics tools. Each new MAGE-competent species confers the ability to rewrite, understand, and utilize sequence information at an extraordinary pace - opening the door to new opportunities for understanding and engineering biology.
