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Fitness-enhancing adaptations of protein expression and its regulation are an important aspect of bacterial evolution. A key question is whether evolution has led to optimal protein expression that maximizes immediate growth rate (short-term fitness) in a robust manner (consistently across diverse conditions). Alternatively, they could display suboptimal short-term fitness, because they cannot do better or because they instead strive for long-term fitness maximization by, for instance, preparing for future conditions. To address this question, we focus on the ATP-producing enzyme F1F0 H+-ATPase, which is an abundant enzyme and ubiquitously expressed across conditions. Its expression is highly regulated and dependent on growth rate and nutrient conditions. For instance, during growth on sugars, when metabolism is overflowing acetate, glycolysis supplies most ATP, while H+-ATPase is the main source of ATP synthesis during growth on acetate. We tested the optimality of H+-ATPase expression in Escherichia coli across different nutrient conditions. In all tested conditions, wild-type E. coli expresses its H+-ATPase remarkably close (within a few per cent) to optimal concentrations that maximize immediate growth rate. This work indicates that bacteria can indeed achieve robust optimal protein expression for immediate growth-rate maximization.

Overflow metabolism is ubiquitous in nature, and it is often considered inefficient because it leads to a relatively low biomass yield per consumed carbon. This metabolic strategy has been described as advantageous because it supports high growth rates during nutrient competition. Here, we experimentally evolved bacteria without nutrient competition by repeatedly growing and mixing millions of parallel batch cultures of Escherichia coli. Each culture originated from a water-in-oil emulsion droplet seeded with a single cell. Unexpectedly we found that overflow metabolism (acetate production) did not change. Instead, the numerical cell yield during the consumption of the accumulated acetate increased as a consequence of a reduction in cell size. Our experiments and a mathematical model show that fast growth and overflow metabolism, followed by the consumption of the overflow metabolite, can lead to a higher numerical cell yield and therefore a higher fitness compared with full respiration of the substrate. This provides an evolutionary scenario where overflow metabolism can be favorable even in the absence of nutrient competition.

Overflow metabolism is ubiquitous in nature, and it is often considered inefficient because it leads to a relatively low biomass yield per consumed carbon. This metabolic strategy has been described as advantageous because it supports high growth rates during nutrient competition.Here we experimentally evolved bacteria without nutrient competition by repeatedly growing and mixing millions of parallel batch cultures of E. coli. Each culture originated from a water-in-oil emulsion droplet seeded with a single cell. Unexpectedly we found that overflow metabolism (acetate production) did not change. Instead the numerical cell yield during the consumption of the accumulated acetate increased as a consequence of a reduction in cell size. Our experiments and a mathematical model show that fast growth and overflow metabolism followed by the consumption of the overflow metabolite, leads to a higher numerical cell yield and therefore a higher fitness compared to full respiration of the substrate. This provides an evolutionary scenario where overflow metabolism can be favourable even in the absence of nutrient competition.

Improved protein expression is an important evolutionary adaptation of bacteria. A key question is whether evolution has led to optimal protein expression that maximizes immediate growth rate (short-term fitness) across conditions. Alternatively, fitter genetic variants could display suboptimal short-term fitness, because they cannot do better or because they strive for long-term fitness maximization by, for instance, anticipating future conditions. To answer this question, we focus on the ATP-producing enzyme F1F0 H+-ATPase, which is an abundant enzyme and ubiquitously expressed across conditions. We tested the optimality of H+-ATPase expression in Escherichia coli across 27 different nutrient conditions. In all tested conditions, wild-type E. coli expresses its H+- ATPase remarkably close to optimal concentrations that maximize immediate growth rate. This work indicates that bacteria can achieve robust optimal protein expression for immediate growth- rate.

Epithelial branching morphogenesis drives the development of organs such as the lung, salivary gland, kidney and the mammary gland. It involves cell proliferation, cell differentiation and cell migration. An elaborate network of chemical and mechanical signals between the epithelium and the surrounding mesenchymal tissues regulates the formation and growth of branching organs. Surprisingly, when cultured in isolation from mesenchymal tissues, many epithelial tissues retain the ability to exhibit branching morphogenesis even in the absence of proliferation. In this work, we propose a simple, experimentally plausible mechanism that can drive branching morphogenesis in the absence of proliferation and cross-talk with the surrounding mesenchymal tissue. The assumptions of our mathematical model derive fromin vitroobservations of the behaviour of mammary epithelial cells. These data show that autocrine secretion of the growth factor TGFβ1 inhibits the formation of cell protrusions, leading to curvature-dependent inhibition of sprouting. Our hybrid cellular Potts and partial-differential equation model correctly reproduces the experimentally observed tissue-geometry-dependent determination of the sites of branching, and it suffices for the formation of self-avoiding branching structures in the absence and also in the presence of cell proliferation.This article is part of the theme issue ‘Multi-scale analysis and modelling of collective migration in biological systems’.

Epithelial branching morphogenesis drives the development of organs such as the lung, salivary gland, kidney and the mammary gland. It involves cell proliferation, cell differentiation and cell migration. An elaborate network of chemical and mechanical signals between the epithelium and the surrounding mesenchymal tissues regulates the formation and growth of branching organs. Surprisingly, when cultured in isolation from mesenchymal tissues, many epithelial tissues retain the ability to exhibit branching morphogenesis even in absence of proliferation. In this work, we propose a simple, experimentally-plausible mechanism that can drive branching morphogenesis in absence of proliferation and cross-talk with the surrounding mesenchymal tissue. The assumptions of our mathematical model derive fromin vitroobservations of the behavior of mammary epithelial cells. These data show that autocrine secretion of the growth factor TGFβ1 inhibits the formation of cell protrusions, leading to curvature dependent inhibition of sprouting. Our hybrid cellular Potts and partial-differential equation model correctly reproduces the experimentally observed tissue-geometry dependent determination of the sites of branching, and it suffices for the formation of self-avoiding branching structures in absence and also in presence of cell proliferation.

Metabolism is generally required for cellular maintenance and for the generation of offspring under conditions that support growth. The rates, yields (efficiencies), adaptation time and robustness of metabolism are therefore key determinants of cellular fitness. For biotechnological applications and our understanding of the evolution of metabolism, it is necessary to figure out how the functional system properties of metabolism can be optimized, via adjustments of the kinetics and expression of enzymes, and by rewiring metabolism. The trade-offs that can occur during such optimizations then indicate fundamental limits to evolutionary innovations and bioengineering. In this paper, we review several theoretical and experimental findings about mechanisms for metabolic optimization.