Metabolic shifts: a fitness perspective for microbial cell factories

Abstract

Performance of industrial microorganisms as cell factories is limited by the capacity to channel nutrients to desired products, of which optimal production usually requires careful manipulation of process conditions, or strain improvement. The focus in process improvement is often on understanding and manipulating the regulation of metabolism. Nonetheless, one encounters situations where organisms are remarkably resilient to further optimization or their properties become unstable. Therefore it is important to understand the origin of these apparent limitations to find whether and how they can be improved. We argue that by considering fitness effects of regulation, a more generic explanation for certain behaviour can be obtained. In this view, apparent process limitations arise from trade-offs that cells faced as they evolved to improve fitness. A deeper understanding of such trade-offs using a systems biology approach can ultimately enhance performance of cell factories.

Fig. 1

Yield and rate. a Why flux balance analysis (FBA) is in fact a yield optimization problem rather than a rate optimization problem. b Trade-off between biomass yield and substrate uptake rate for a number of exponentially growing yeast species: Reprinted by permission from Macmillan Publishers Ltd: [Heredity] (MacLean 2008)

Fig. 2

Different hypotheses and trade-offs involved, for growth rate (and substrate (S)) related ATP-efficient and inefficient metabolism. a Chemical warfare: at the cost of ATP production, toxic compounds are produced in order to inhibit the growth of competitors. b The danger of reactive oxygen species (ROS): additional ATP production via respiration concomitantly generates ROS that can damage DNA. c Spatial structure: spatial structure promotes ATP-efficient substrate usage but lone individual cells can grow faster as long as sufficient substrate is available. d Ethanol as an inhibitor of fermentation: substrate can be used efficiently but slowly or fast but inefficiently and the latter strategy produces toxic compounds that are exported but nonetheless accumulate more inside the cells producing them. e Limited intracellular space: due to limited intracellular space and bulky respiratory machinery, the flux through respiration cannot match high substrate uptake rates and a gradual shift to inefficient metabolism occurs. f Limited membrane space: the membrane can be used to produce additional ATP from substrate via the electron transport chain (ETC.) or to take up more substrate. g An economical approach: substrate can be used slowly and efficiently but this requires a lot of proteins, or it can be consumed fast but inefficiently which requires much less proteins

Fig. 3

The cycle of systems biology. Defined as the quantitative study of biological processes as whole systems, instead of isolated parts, systems biology comprises utilizing knowledge bases and experimental data to develop and construct computational models to propose new hypotheses. The field is characterized by synergistic integration of data and theory that can be combined to produce a model. Model analysis leads to predictions of physiological functions which might be difficult to obtain otherwise. Validation of these predictions helps identify novel components or interactions, which in turn refine the model. Ultimately, the effectiveness of a model does not necessarily depend on goodness-of-fit, but on its usefulness in, for example, (i) providing new hypotheses/leads as predictions, (ii) providing a data integration platform as a formal representation of current knowledge, or (iii) helping to discriminate between alternative explanations