EAGER: Engineering synthetic organelles to power formate-based microbial cell factories

Michigan State University, East Lansing MI

Investigators

Abstract

Industrial scale biotechnology is a potential growth industry in the US. One area of particular interest is the development of specialized bacteria that can consume industrial waste products and convert these compounds into molecules that can be used to produce fuels, plastic monomers and other commercially important chemicals. This project focuses on re-purposing a naturally occurring subcellular factory found in common bacteria into a specialized compartment for the conversion of an industrial byproduct (formate) into a versatile molecule (pyruvate) that can be used by bacteria as a precursor to many desirable compounds. The project exemplifies a "build it to understand it" approach, by emphasizing bioengineering based on structural information. Moreover, it will provide a crucial test of our understanding of bacterial microcompartment assembly and whether enhancement of enzyme function can be achieved by encapsulation in a microcompartment. The project will provide interdisciplinary training to early career scientists in computational, structural, molecular, and synthetic biology. The project involves computational protein and microcompartment design via structure-based modeling to engineer a synthetic metabolic pathway, the PFK-PKT pathway. The project is grounded in a theoretical pathway that can be realized with pyruvate formate lyase, an oxygen-sensitive enzyme that restricts the synthetic pathway to anaerobic or microaerophilic conditions. To solve this limitation, an organelle to encapsulate pyruvate formate lyase and the requisite supporting enzymes will be built and the permeability of the repurposed bacterial microcompartment shell engineered. Several complementary strategies will be pursued, including a top-down approach to repurpose naturally occurring glycyl radical enzyme microcompartments and a bottom-up approach to construct the requisite protein core for encapsulation in the microcompartment shell. The Broader Impacts of the project include the training of undergraduates and Postdoctoral Fellow who will take part in an international collaboration between the groups of an established synthetic biologist and a theoretician. Moreover, the project demonstrates modular engineering based on structural synthetic biology, an approach that is poised to play a significant part in the development of sustainable chemistries to meet pressing global needs.