Robust identification of metabolic control for microbial l-methionine production following an easy-to-use puristic approach

- Metabolic control in l-Met-producing E. coli studied by stimulus response experiments.
- Pool efflux capacity (PEC) criterion was applied to unravel flux control.
- Compared to conventional metabolic control analysis same key control steps are identified.
- Consideration of 13C labeling signals increase information content significantly.
- Enable the easy use of the approach for identifying metabolic engineering targets.

The identification of promising metabolic engineering targets is a key issue in metabolic control analysis (MCA). Conventional approaches make intensive use of model-based studies, such as exploiting post-pulse metabolic dynamics after proper perturbation of the microbial system. Here, we present an easy-to-use, purely data-driven approach, defining pool efflux capacities (PEC) for identifying reactions that exert the highest flux control in linear pathways. Comparisons with linlog-based MCA and data-driven substrate elasticities (DDSE) showed that similar key control steps were identified using PEC. Using the example of l-methionine production with recombinant Escherichia coli, PEC consistently and robustly identified main flux controls using perturbation data after a non-labeled 12C-l-serine stimulus. Furthermore, the application of full-labeled 13C-l-serine stimuli yielded additional insights into stimulus propagation to l-methionine. PEC analysis performed on the 13C data set revealed the same targets as the 12C data set. Notably, the typical drawback of metabolome analysis, namely, the omnipresent leakage of metabolites, was excluded using the 13C PEC approach.