Protein overabundance is driven by growth robustness

TL;DR

This study shows that bacteria often produce more essential proteins than needed, ensuring robust growth even when protein levels drop.

Contribution

The paper reveals that overabundance of essential proteins is a widespread mechanism for growth robustness in bacteria.

Findings

Most essential proteins are overabundant, with over 70% produced in excess.

Overabundance increases as protein expression levels decrease.

Low-abundance proteins are produced in more than 10× the amount needed for growth.

Abstract

Protein expression levels optimize cell fitness: Too low an expression level of essential proteins will slow growth by compromising essential processes, whereas overexpression slows growth by increasing the metabolic load. This trade-off naïvely predicts that cells maximize their fitness by sufficiency, expressing just enough of each essential protein for function. We test this prediction in the naturally competent bacterium Acinetobacter baylyi by characterizing the proliferation dynamics of essential-gene knockouts at a single-cell scale (by imaging) as well as at a genome-wide scale. In these experiments, cells proliferate for multiple generations as target protein levels are diluted from their endogenous levels. This approach facilitates a proteome-scale analysis of the fitness landscape with respect to protein abundance. We find that most essential proteins are subject to a threshold-like fitness landscape: Growth is independent of protein abundance above a critical threshold and arrests below that threshold. We have recently analyzed the implications of this landscape for growth robustness. Confirming signature predictions of this model, we find that (i) roughly 70% of essential proteins are overabundant, (ii) overabundance increases as the expression level decreases, and (iii) the lowest abundance proteins are in vast excess (>10×) of what is required for growth in the typical cell. These results reveal that robustness plays a fundamental role in determining the expression levels of essential genes and that overabundance is a key mechanism for ensuring robust growth.

Fitness optimization drives vast overabundance in low-expression proteins.

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