Experimental And Computational Approaches To Engineer Microbial Metabolism

Experimental and Computational Approaches to Engineer Microbial Metabolism

In this thesis, I have demonstrated the utility and benefits of using both computational and experimental approaches to engineer metabolism. Specifically, I have shown that metabolic flux analysis with labeled tracers is a powerful tool to accurately estimate in vivo fluxes. Using this tool, I have successfully estimated the in vivo thermodynamics and fluxes of both wild-type and 8b Z. mobilis, information that can then be integrated with additional multi-omics datasets to generate a kinetic model of Z. mobilis metabolism. Furthermore, the concept of kinetic modeling is promising; however, advancements in user-friendly computational tools to minimize the amount of data needed to fully parameterize any given kinetic model are needed, as collecting high-quality, multi-omics datasets is the rate-limiting step toward more published kinetic models in the literature. Additionally, this thesis demonstrates how rational metabolic engineering approaches can be applied to produce an industrially relevant chemical, valine, starting from a precursor-abundant platform strain at the highest yields in E. coli reported in the literature. Lastly, it is demonstrated that an active learning algorithm, ActiveOpt, is capable of leading metabolic engineers to superior strains faster than rational approaches alone. In the near future, more user-friendly computational tools (e.g., ActiveOpt) will be needed to assist metabolic engineers-especially those who don't have access to high throughput capabilities-in generating superior strains, that produce renewable bioproducts, faster than traditional methods, to meet increasing demands for a sustainable future.

Fluxomics and Metabolic Analysis in Systems Microbiology

Metabolic Pathway Engineering

Metabolic systems engineering combines the tools and approaches of systems biology, synthetic biology, and evolutionary engineering. This book reviews studies on metabolism, from the earliest work of Lavoisier and Buchner to current cutting-edge research in metabolic systems engineering. This technology has been used in bioengineering applications to create high-performing microbes and plants that produce important chemicals, pharmaceuticals, crops, and other natural products. Current applications include optimizing metabolic pathways to enhance degradation of biomass for biofuel production and accelerated processing of environmental waste products and contaminants. The book includes examples to illustrate the applications of this technology in the optimization of metabolic pathways to create robust industrial strains as well as in the engineering of biological processes involving health and diseases of humans, animals, and plants. Written by a seasoned computational biologist with many years of experience in genomics, bioinformatics, and systems biology, this book will appeal to anyone interested in metabolic systems analysis and metabolic pathway engineering.