Emergent, cost-free surplus of core biosynthesis governs bacterial fitness

Cells often express essential components in excess of the levels required to sustain steady-state growth. The concept of protein reserve or surplus has recently emerged as a strategy for long-term cell fitness in bacteria, typically assumed to reduce steady-state growth as a trade-off for faster adaptation to a new environment. However, the origin and physiological consequences of such surplus remain unclear, particularly for core cellular processes including transcription, translation, and central metabolism. Here, we establish a unified operational definition of surplus and quantify it for selected key components of transcription, translation, and central metabolism machinery in Escherichia coli at the single-cell level. By combining microfluidics, quantitative fluorescence imaging, and CRISPR interference-based gene knockdown, we demonstrate that substantial fractions of core biosynthetic components can be removed without affecting steady-state growth under nutrient-limited conditions. Unexpectedly, this surplus imposes no cost on steady-state growth, in contrast to prevailing trade-off models. Instead, we show that surplus emerges as a passive consequence of substrate limitation using a simple theoretical model, which is based on the universal autocatalytic-network structure of bacterial cells. Perturbation experiments confirm model predictions that surplus of transcription and translation machinery accelerates growth adaptation to nutrient-rich conditions, without affecting steady-state growth. Moreover, under slow-growth conditions, surplus suppresses cell death by reducing the risk of stochastic collapse of biosynthetic cycles, also in accord with our theoretical model prediction. Altogether, our results identify surplus as an intrinsic property of core biosynthesis and a key determinant of long-term bacterial fitness in fluctuating environments.