Systems Biology of Metabolism

Metabolism is a complex system that encompasses all biochemical reactions and processes that occur in living organisms along with their interaction and regulation. Our incomplete knowledge of metabolism greatly limits our ability to engineer biological systems. To address this issue, our laboratory engages in fundamental studies that contribute to the creation of the knowledge base required for the effective engineering of metabolism.

Our discovery that the bacterium E. colican anaerobically ferment glycerol (Appl. Environ. Microbiol. 74: 1124, 2008; Biotechnol. Bioeng. 94: 821, 2006) led us to propose a new model for the fermentative utilization of glycerol in E. coliand other bacteria (Appl. Environ. Microbiol. 75: 5871, 2009; Metab. Eng. 10: 234, 2008). The knowledge base created by these studies enabled the engineering of bacteria for the synthesis of a wide arrange of products, as described under “Metabolic Engineering & Synthetic Biology“.

We have demonstrated that using a system-level approach provides an unprecedented understanding of microbial metabolism otherwise not achievable through classical biochemical and molecular genetic approaches. For example, using in silicoand in vivometabolic flux analysis we discovered the role of the pyruvate dehydrogenase complex on the fermentative metabolism of glucuronate and glucose in E. coli(J. Biol. Chem. 285: 31548, 2010; Microbiology-SGM 156: 1860, 2010). Prior to the work conducted in our laboratory, the role of PDHC in the fermentative metabolism of E. coli remained unknown and this enzyme was thought unable to support fermentative growth. In this area we have also developed new methods and tools that facilitate the system-level analysis of microbial and cellular metabolism (BMC Bioinformatics 7: 377, 2006; J. Theor. Biol. 263: 499, 2010).

We have used system-level methods and tools to elucidate key aspects of microbial and cellular metabolism. For example, we conducted a quantitative analysis of the fermentative metabolism of glycerolin E. colithrough the use of kinetic modeling and Metabolic Control Analysis and elucidated the control structure of the pathways involved in glycerol utilization and ethanol synthesis (Biotechnol. Bioeng. 109: 187, 2012). These findings were then used to identify key targets for genetic manipulation that enhanced product synthesis. Similar approaches enabled an improved understanding of apoptosis in Chinese Hamster Ovary (CHO) cell cultures during the production of recombinant proteins (PLoS ONE 9: e93865hem, 2014; Chem. Eng. Sci. 66: 2431, 2011) and the anaerobic metabolism of E. coliduring glucose fermentation (Biotechnol. Bioprocess. Eng. 16: 419, 2011). More recently, we performed a comparative proteomic analysis of E. coli under octanoic acid stress and identified the underlying mechanisms of short-chain fatty acids toxicity in this bacterium (J. Proteomics 122: 86, 2015).