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Combining systems and synthetic biology forin vivoenzymology
Abstract
Enzymatic parameters are classically determinedin vitro, under reaction conditions that are far from those encountered in cells, casting doubt on their physiological relevance. In this study, we developed a generic approach combining tools from synthetic and systems biology to measure enzymatic parametersin vivo. In the context of a synthetic pathway aiming to produce phytoene and lycopene inSaccharomyces cerevisiae, we focused on four membrane-associated enzymes, a phytoene synthase and three phytoene desaturases, which are difficult to studyin vitro. We designed, built, and analyzed a collection of yeast strains mimicking substantial variations in substrate concentration (> 200-fold change) by strategically manipulating the copy number and expression strength of the gene encoding geranyl-geranyl pyrophosphate (GGPP) synthase. We successfully determinedin vivo-equivalent Michaelis-Menten parameters (KM, Vmaxandkcat) for GGPP-converting phytoene synthase from quantitative metabolomics, fluxomics and proteomics data, highlighting differences betweenin vivoandin vitroparameters. Then, leveraging the versatility of the same set of strains to cover a wide range of phytoene concentrations, we successfully extracted enzymatic parameters for two of the three phytoene desaturases. Our approach demonstrates the feasibility of assessing enzymatic parameters along a pathway of interest directlyin vivo, providing a novel perspective on the kinetic characteristics of enzymes in real cellular conditions.
Product Used
Genes
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