UCLA

Simulation of metabolic systems with kinetic models requires a large number of parameter values, which are either difficult or impossible to obtain experimentally. Network information, such as stoichiometry, reversibility and steady state flux, can be used to determine mechanistically realistic rate laws, and these can be used to constrain the parameter space to only those values which satisfy the constraints. Until now, stability has been overlooked when considering kinetic metabolic models. However, dynamical stability and robustness to perturbation are important qualities for living organisms, since they may encounter changing environments or stochastic variation across time or within populations. Considering stability can both provide constraints on the parameter space and be used to interpret the response of the model to queries about the performance of the metabolic system under various perturbations. I have used stability analysis to predict the performance of many metabolic systems, with an emphasis on providing guidance for experimental efforts and uncovering biological significance.

The uses of stability analysis have encompassed several projects. Optimization of a novel methanol condensation cycle (MCC) was accomplished by tuning the amount of an irreversible phosphoketolase enzyme to a local productivity and stability maximum, as predicted by stability analysis and confirmed by in vitro experimentation. Several other in vitro enzymatic were subjected to stability analysis, and predictions matched previously published experimental results.

Stability analysis was also applied to several microbial systems to maximize production of a desired compound: n-butanol in Escherichia coli, isobutanol in Clostridium thermocellum and lipids in Yarrowia lipolytica. In these systems, production simulations matched the observations and predictions for further production improvements were made.

Stability analysis was also applied to gain biological understanding of the significance of structural features of the Calvin-Bassham-Benson (CBB) pathway in plants. The phosphate/glyceraldehyde-3-phosphate translocator was identified as more important for stability than a proposed glucose-6-phosphate shunt. Further, productivity was increased after overexpression of sedoheptulose-1,7-biosphosphatase, but not RuBiSCO, in agreement with previous experimental reports.

The importance of stability in analysis of metabolic systems is affirmed by this work, and the techniques demonstrated here pave the way for even further explorations.