Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of Escherichia coli

Abstract

Adaptation to novel environments is often associated with changes in gene regulation. Nevertheless, few studies have been able both to identify the genetic basis of changes in regulation and to demonstrate why these changes are beneficial. To this end, we have focused on understanding both how and why the lactose utilization network has evolved in replicate populations of Escherichia coli. We found that lac operon regulation became strikingly variable, including changes in the mode of environmental response (bimodal, graded, and constitutive), sensitivity to inducer concentration, and maximum expression level. In addition, some classes of regulatory change were enriched in specific selective environments. Sequencing of evolved clones, combined with reconstruction of individual mutations in the ancestral background, identified mutations within the lac operon that recapitulate many of the evolved regulatory changes. These mutations conferred fitness benefits in environments containing lactose, indicating that the regulatory changes are adaptive. The same mutations conferred different fitness effects when present in an evolved clone, indicating that interactions between the lac operon and other evolved mutations also contribute to fitness. Similarly, changes in lac regulation not explained by lac operon mutations also point to important interactions with other evolved mutations. Together these results underline how dynamic regulatory interactions can be, in this case evolving through mutations both within and external to the canonical lactose utilization network.

Author Summary

Differences in gene regulation underlie many important biological processes and are thought to be important for the adaption of organisms to novel environments. Here we focus on the regulation of a group of well-studied genes, the lac operon, that control the utilization of lactose sugar, and we examine how their regulation changes during the adaptation of populations of Escherichia coli bacteria to environments that differ only in the presence of lactose. We find that lac operon regulation is altered in almost all populations that evolve in the presence of lactose and identify two classes of mutations that explain a large part of this change and that confer significant fitness benefits. Interestingly, our study indicates that other mutations, lying outside of the commonly recognized control region, cause new regulation of the lac operon. Together these findings reinforce the importance of changes in gene regulation during evolution and suggest that the biological basis of these changes can be complex and involve novel interactions between genes.