Regulation of glycolysis in Lactococcus lactis: an unfinished systems biological case study

The unexpectedly long, and still unfinished, path towards a reliable mathematical model of glycolysis and its regulation in Lactococcus lactis is described. The model of this comparatively simple pathway was to be deduced from in vivo nuclear magnetic resonance time-series measurements of the key glycolytic metabolites. As to be expected from any nonlinear inverse problem, computational challenges were encountered in the numerical determination of parameter values of the model. Some of these were successfully solved, whereas others are still awaiting improved techniques of analysis. In addition, rethinking of the model formulation became necessary, because some generally accepted assumptions during model design are not necessarily valid for in vivo models. Examples include precursor-product relationships and the homogeneity of cells and their responses. Finally, it turned out to be useful to model only some of the metabolites, while using time courses of ubiquitous compounds such as adenosine triphosphate, inorganic phosphate, nicotinamide adenine dinucleotide (oxidised) and nicotinamide adenine dinucleotide (reduced) as unmodelled input functions. With respect to our specific application, the modelling process has come a long way, but it is not yet completed. Nonetheless, the model analysis has led to interesting insights into the design of the pathway and into the principles that govern its operation. Specifically, the widely observed feedforward activation of pyruvate kinase by fructose 1,6-bisphosphate is shown to provide a crucial mechanism for positioning the starving organism in a holding pattern that allows immediate uptake of glucose, as soon as it becomes available.