Daniel Amador-Noguez, Associate Professor, Department of Bacteriology, University of Wisconsin-Madison, will present.
In vivo thermodynamic analysis of metabolic networks
Abstract: Recent breakthroughs in genome editing and metabolic engineering expand the range of microorganisms and synthesis routes that may be used to produce biofuels and valuable bioproducts from renewable biomass resources. Thus, there is an increasing need for new approaches to characterize the metabolic capabilities of nascent industrial organisms and improve the efficiency of their biosynthetic pathways.
Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. A biochemical reaction with a strong thermodynamic driving force (i.e. with a large negative ΔG) will achieve a higher net flux given a fixed amount enzyme than one closer to equilibrium. Within a pathway, steps closer to equilibrium will be the least enzyme efficient. Thermodynamic analysis can therefore provide unique insights in synthetic pathway design by identifying bottlenecks, pinpointing the enzymes for which changes in activity will have the largest effect on flux, and predicting the most efficient route for product synthesis.
During this talk, I will discuss the development of experimental-computational approaches for in vivo determination of Gibbs free energies (ΔG) in metabolic networks. In our first iteration of this approach, we combined quantitative metabolomics with 2H and 13C metabolic flux analysis to measure step-by-step ΔG of central metabolic pathways in different microbes. This showed that the Entner-Doudoroff glycolytic pathway in Zymomonas mobilis, a prolific ethanol producer, is nearly twice as thermodynamically favorable as the classical glycolytic pathway in well-studied microbes such as E. coli or yeast, helping explain its rapid sugar catabolism. In a subsequent study, we found that the glycolytic pathway of Clostridium thermocellum, a cellulolytic biofuel producer, operates surprisingly close to thermodynamic equilibrium, allowing increased ATP yield per glucose molecule but at a slower glycolytic rate. Taken together, these results illustrate the tradeoff between energy yield, catabolic rate, and thermodynamic driving force across the glycolytic pathways of diverse organisms, reflecting evolutionary adaptations to distinct lifestyles and habitats. Our long-term goal is the construction of accurate metabolic models that incorporate thermodynamic constrains and guide rational engineering of microbial networks.
Bio: Daniel Amador-Noguez is an Associate Professor in the Department of Bacteriology at the University of Wisconsin-Madison. Dr. Amador-Noguez received his B.S. in Chemistry from Monterrey Institute of Technology (ITESM), Monterrey, Mexico. He earned his Ph.D. in Molecular Genetics from Baylor College of Medicine, Houston TX. He then worked as a post-doctoral associate with Joshua Rabinowitz at Princeton University. Daniel joined the faculty of the Department of Bacteriology at UW-Madison in 2013. His research program seeks to generate a quantitative and holistic understanding of how metabolic networks are regulated in microbes. The Amador-Noguez laboratory integrates systems-level approaches, especially LC-MS-based metabolomics, with computational modeling and genetic engineering to understand how metabolic fluxes are controlled and how microbes adapt their metabolism in response to environmental challenges and during developmental processes. His laboratory has three main research areas: 1) metabolic regulation in biofuel producers, and 2) metabolic remodeling during biofilm development, and 3) biochemical activities of the gut microbiome.
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