Bioprocess engineering through dynamic control of metabolic pathways

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The common practice in metabolic engineering is strong overexpression of enzymes in the production pathway without feedback control. The lack of dynamic control becomes problematic when an individual cell finds itself in suboptimal conditions that would require lower synthesis and redistribution of chemical precursors. Although the required mechanisms like allosteric feedback regulation are known since decades, our incomplete understanding of their function in a living cell stands in the way to implement this type of regulation. In my recent work I developed a method to investigate the function of allosteric feedback regulation in bacteria using metabolomics and computational modeling.The goal of this project is to apply these tools to search and implement structural principles that coordinate natural metabolism with high overproduction of a chemical in a production host. Notably, I will consider conditions of industrial scale bioprocesses, that suffer from premature decrease of yields and not ideally stirred zones that might be detrimental to the production host. Specifically, I plan to use computational modeling in order to search for feedback regulation that achieves optimal coordination of the production pathway with metabolism of the production strain in the environment of a bioreactor. In order to implement the control circuits in a cell, I plan to construct synthetic allosteric enzymes using existing approaches of enzyme design. Therefore established procedures of protein fragment complementation, domain insertion and modular recombination will be evaluated. The activity and function of the synthetic allosteric enzymes in the production strain is determined with our novel method that combines metabolomics and computational modeling. With this approach I plan to achieve autonomous regulation of amino acid overproduction in the bacterium Escherichia coli.The long-term goal of this research is that we understand fundamental design principles of metabolic control circuits and transfer them to biotechnological relevant systems that require autonomous regulation. Dynamic control can improve overall fitness of production strains and thereby maintains high productivity of bioprocesses. One opportunity is to engineer cells that respond to not ideally stirred zones present in large-scale bioreactors, whenever a cell is in a zone with low supply of carbon source or oxygen, a metabolic signal could switch off the production pathway until the cell has recovered.