Figure 3

Survival of Escherichia coli deletion mutants in genes where codon adaptation was linked to aerobicity. H₂O₂ shock survival of mutants in putative oxidative stress genes (those with changes in codon adaptation in aerotolerant or obligately aerobic microbes, false discovery rate (FDR) ≤9.6% and ≤11.8%, respectively), without or with pre-treatment with N-acetylcysteine (NAC). More H₂O₂ concentrations are shown in Additional file 8. Deleted genes are E. coli representatives of clusters of orthologous groups (COGs) with codon adaptation correlated with oxygen in the environment, after controlling for confounding phenotypes or taxonomy. Strains are ordered by H₂O₂ survival, normalized to the wild-type survival under the same stress (13.8% for H₂O₂ after normalization shown as 100% on the plot). The outcome of the NAC rescue experiment is shown as a fold change in H₂O₂ survival over the same strain without NAC (right x axis). Additionally, the survival of each strain after heat and osmotic shocks is given for comparison; normalization as above. The strains lon and recA showed non-specific sensitivity and were thus separated on the plot, alongside sodA, which was included as a positive control. Error bars show the 95% C.I. of the mean, determined over at least four replicates.