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These findings raise the possibility that latent pathway activation is in fact derivative of another, potentially suboptimal, adaptive response.Living cells are surprisingly robust against mutations and, in particular, against gene knockouts (1–5).We emphasize that because the modified organism lacks only transiently active (latent) metabolic reactions, the optimal steady states are identical to those of the unmodified strain both before and after the perturbation.

Yet, apart from chemical stress-based assays (10), studies designed to test whether nonessential genes become essential under different conditions have failed to identify a phenotype for more than a small fraction of additional genes (11).

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.

Even for genes with known functions under different conditions, this hypothesis is appealing as it suggests the possibility of an alternate phenotype that would not be detected in traditional high-throughput screens of knockout mutants (14).

Here, we test this hypothesis using the most complete in silico reconstruction of the metabolic network of K-12 MG1655 (15, 16) and perturbations caused by single-gene knockouts.

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The statistics are summarized in the left and center columns of Table 1 for MOMA and ROOM, respectively.

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