Dispensability of Escherichia coli's latent pathways

TL;DR

This study computationally investigates whether latent metabolic pathways in E. coli aid growth and adaptation after perturbations, finding that they generally do not provide benefits and may inhibit growth, challenging previous assumptions.

Contribution

It demonstrates through computational analysis that latent pathways in E. coli do not enhance growth post-perturbation and may be detrimental, suggesting they are not beneficial for adaptation.

Findings

Latent pathways do not improve growth after genetic perturbations.

Activation of latent pathways can inhibit growth.

Latent pathways may be a suboptimal adaptive response.

Abstract

Gene-knockout experiments on single-cell organisms have established that expression of a substantial fraction of genes is not needed for optimal growth. This problem acquired a new dimension with the recent discovery that environmental and genetic perturbations of the bacterium Escherichia coli are followed by the temporary activation of a large number of latent metabolic pathways, which suggests the hypothesis that temporarily activated reactions impact growth and hence facilitate adaptation in the presence of perturbations. Here we test this hypothesis computationally and find, surprisingly, that the availability of latent pathways consistently offers no growth advantage, and tends in fact to inhibit growth after genetic perturbations. This is shown to be true even for latent pathways with a known function in alternate conditions, thus extending the significance of this adverse effect beyond apparently nonessential genes. These findings raise the possibility that latent pathway activation is in fact derivative of another, potentially suboptimal, adaptive response.