E. coli transcriptome evolution on the path to a major metabolic innovation

In the Lenski long-term evolution experiment, one population of E. coli evolved the ability to utilize a new nutrient (citrate) after 15 years of propagation in the laboratory in a glucose-limited growth medium. This metabolic innovation allowed these bacteria to tap into a previously unexploited niche, greatly increase their population size, and dominate. Despite the large benefit of evolving this capacity, the evolution of citrate utilization took many generations and has not occurred in the 11 other populations of the Lenski experiment, even after 34 years. This RNA-seq dataset tracks how gene expression changed due to mutations on the E. coli lineage leading to the evolution of citrate utilization with the aim of understanding whether there were any unique changes in regulation of its metabolism that acted as stepping stones to evolving citrate utilization. Understanding how rare evolutionary innovations like this one can occur provides general insights into predicting evolutionary outcomes and the pathways by which pathogens evolve.