Optimizing Metabolite Production Using Periodic Oscillations

Abstract

Methods for improving microbial strains for metabolite production remain the subject of constant research. Traditionally, metabolic tuning has been mostly limited to knockouts or overexpression of pathway genes and regulators. In this paper, we establish a new method to control metabolism by inducing optimally tuned time-oscillations in the levels of selected clusters of enzymes, as an alternative strategy to increase the production of a desired metabolite. Using an established kinetic model of the central carbon metabolism of Escherichia coli, we formulate this concept as a dynamic optimization problem over an extended, but finite time horizon. Total production of a metabolite of interest (in this case, phosphoenolpyruvate, PEP) is established as the objective function and time-varying concentrations of the cellular enzymes are used as decision variables. We observe that by varying, in an optimal fashion, levels of key enzymes in time, PEP production increases significantly compared to the unoptimized system. We demonstrate that oscillations can improve metabolic output in experimentally feasible synthetic circuits.

Dynamic metabolic engineering: New strategies for developing responsive cell factories

“…Oscillatory patterns of enzyme expression are another potential route to minimize protein expression burden or to match expression with systems showing a natural oscillatory cycle, such as the cyanobacterial Kai proteins [23]. A kinetic model incorporating oscillatory expression of sets of glycolytic proteins showed that this strategy could be used to increase phosphoenolpyruvate pools by 1.86‐fold [24]. Aside from protein expression burden, a number of pathway‐specific constraints also make temporal control of enzyme expression favorable, including instability of downstream enzymes, toxic pathway intermediates, and product inhibition of upstream enzymes.…”

A chemical engineer's perspective on health and disease

“…By and large in these situations the periodicity in the operations is a means to recover from naturally occurring events which damage the catalyst's activity. Interestingly, an optimization-based study by chemical engineers recently indicated that the intrinsic dynamic of enzyme catalysed reactions can be manipulated by means of imposing optimal, oscillatory, profiles in enzyme activity likely balancing growth trade-offs (Sowa et al, 2014). …”

Synthetic small RNAs: Current status, challenges, and opportunities

“…Protein synthesis consists of the two major steps of transcription and translation. 21 These circuits are currently being implemented for higher order applications such as the rewiring of natural systems, [22][23][24][25] the coupling of intracellular networks, 26 and the manipulation of cellular functions at various scales. The understanding of RNA biology has been significantly improved over time, and a number of cellular pathways, which are involved in gene regulation by repression and activation mechanisms, have been elucidated.…”