Figure 5.

Adaptive, low-cost, or suboptimal control of genes in Shewanella oneidensis MR-1. Among the genes with both fitness and expression data, we classified their control by the following criteria. If a gene fit into multiple categories, then it was counted only in the first (top-most) category. First, we classified genes as being under adaptive control if the fitness–expression correlation, across 15 matched conditions, was under −0.5. We used a threshold of −0.5 because this is roughly where the actual distribution of fitness–expression correlations diverges from the shuffled distribution (Figure 3B); also, 53% of amino-acid synthesis genes are below this threshold. We classified genes as constitutive and low cost if they had a low standard deviation of expression (in a large compendium), they were not detrimental to growth (in 38 groups of fitness experiments), and their absolute expression level was at most two-fold above the median gene in all of our 15 conditions. Genes that are significantly detrimental to growth in 1 or more of 38 groups of fitness experiments were subclassified into genes that are important for motility (motility ‘fitness’ below −0.4), selfish genes such as transposons, prophages, and restriction elements, or other unexplained genes. Genes were considered to change expression without being important for fitness if, in any of 14 comparisons between conditions, the expression changed by two-fold or more but the fitness value was between −0.4 and 0.4 in both conditions. The remaining genes were classified as having little phenotype or change in expression if their fitness value was between −0.75 and +0.75 in all 15 matched conditions.