Abstract
Over evolutionary time, bacteria face changing environments, which may require different sets of genes for survival. As they adapt to a specific constant environment, some genes are modified and lost, which can increase fitness while also modulating the effects of further gene losses. However, whether evolutionary specialization leads to systematic changes in robustness to gene loss is largely unexplored. Here, we compare the effects of insertion mutations in Escherichia coli between ancestral and 12 independently derived strains after 50,000 generations of growth in a simple, uniform environment. We find that epistasis between insertion mutations and genetic background is common, but the overall distribution of fitness effects is largely unchanged. In particular, we see systematic changes in gene essentiality, with more genes becoming essential over evolution than vice versa. The resulting changes often occurred in parallel across the independently evolving populations. A few of the changes in gene essentiality are associated with large structural variations, but most are not. Taken together, our results demonstrate that gene essentiality is a dynamic, evolvable property, and they suggest that changes in gene essentiality are a result of natural selection in this long-term evolution experiment, rather than a mere byproduct of structural changes.
Competing Interest Statement
The authors have declared no competing interest.
