The growth rate‐dependent regulation of cell size, ribosomal content, and metabolic efficiency follows a common pattern in unicellular organisms: with increasing growth rates, cell size and ribosomal content increase and a shift to energetically inefficient metabolism takes place. The latter two phenomena are also observed in fast growing tumour cells and cell lines. These patterns suggest a fundamental principle of design. In biology such designs can often be understood as the result of the optimization of fitness. Here we show that in basic models of self‐replicating systems these patterns are the consequence of maximizing the growth rate. Whereas most models of cellular growth consider a part of physiology, for instance only metabolism, the approach presented here integrates several subsystems to a complete self‐replicating system. Such models can yield fundamentally different optimal strategies. In particular, it is shown how the shift in metabolic efficiency originates from a tradeoff between investments in enzyme synthesis and metabolic yields for alternative catabolic pathways. The models elucidate how the optimization of growth by natural selection shapes growth strategies.

This paper examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes. In nongrowing, anaerobic, compressed Saccharomyces cerevisiae the values of the kinetic parameters of most glycolytic enzymes were determined. For the other enzymes appropriate literature values were collected. By inserting these values into a kinetic model for glycolysis, fluxes and metabolites were calculated. Under the same conditions fluxes and metabolite levels were measured.In our first model, branch reactions were ignored. This model failed to reach the stable steady state that was observed in the experimental flux measurements. Introduction of branches towards trehalose, glycogen, glycerol and succinate did allow such a steady state. The predictions of this branched model were compared with the empirical behavior. Half of the enzymes matched their predicted flux in vivo within a factor of 2. For the other enzymes it was calculated what deviation between in vivo and in vitro kinetic characteristics could explain the discrepancy between in vitro rate and in vivo flux.

Introduction: Cells use multilayered regulatory systems to respond adequately to changing environments or perturbations. Failure in regulation underlies cellular malfunctioning, loss of fitness, or disease. How molecular components dynamically interact to give rise to robust and adaptive responses is not well understood. Here, we studied how the model eukaryote Saccharomyces cerevisiae can cope with transition to high glucose levels, a failure of which results in metabolic malfunctioning and growth arrest. Methods: We combined experimental and modeling approaches to unravel the mechanisms used by yeast to cope with sudden glucose availability. We studied growth characteristics and metabolic state at population and single-cell levels (through flow cytometry and colony plating) of the wild type and of mutants unable to transit properly to excess glucose; such mutants are defective in trehalose synthesis, a disaccharide associated with stress resistance. Dynamic ¹³ C tracer enrichment was used to estimate dynamic intracellular fluxes immediately after glucose addition. Mathematical modeling was used to interpret and generalize results and to suggest subsequent experiments. Results: The failure to cope with glucose is caused by imbalanced reactions in glycolysis, the essential pathway in energy metabolism in most organisms. In the failure mode, the first steps of glycolysis carry more flux than the downstream steps, resulting in accumulating intermediates at constant low levels of adenosine triphosphate (ATP) and inorganic phosphate. We found that cells with such an unbalanced glycolysis coexist with vital cells with normal glycolytic function. Spontaneous, nongenetic metabolic variability among individual cells determines which state is reached and consequently which cells survive. In mutants of trehalose metabolism, only 0.01% of the cells started to grow on glucose; in the wild type, the success rate was still only 93% (i.e., 7% of wild-type yeast did not properly start up glycolysis). Mathematical models predicted that the dynamics of inorganic phosphate is a key determinant in successful transition to glucose, and that phosphate release through ATP hydrolysis reduces the probability of reaching an imbalanced state. ¹³ C-labeling experiments confirmed the hypothesis that trehalose metabolism constitutes a futile cycle that would provide proper phosphate balance: Upon a glucose pulse, almost 30% of the glucose is transiently shuttled into trehalose metabolism. Discussion: Our work reveals how cell fate can be determined by glycolytic dynamics combined with cell heterogeneity purely at the metabolic level. Specific regulatory mechanisms are required to initiate the glycolytic pathway; in yeast, trehalose cycling pushes glycolysis transiently into the right direction, after which cycling stops. The coexistence of two modes of glycolysis—an imbalanced state and the normal functional state—arises from the fundamental design of glycolysis. This makes the imbalanced state a generic risk for humans as well, extending our fundamental knowledge of this central pathway that is dysfunctional in diseases such as diabetes and cancer.