  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.
