Studying the evolutionary systems biology of the lac operon

Gaining an understanding of how biological regulation evolves is a fundamental research question in both evolutionary biology and molecular genetics. In order to gain more insight into this topic, we focus on studying the simple gene regulatory system of the lac operon in E. coli. We show that simple population genetic models can shed light on evolution experiments and that this combined approach of modelling the experimental system gives insight to better understand the causes of evolutionary change in the experiment. We also study the natural diversity in the lac operon from 308 publicly available E. coli genomes that come from various host species and different regions of the world. Evidence that selection is generally maintaining the function of the lac operon across the sample regardless of host species is provided and we show that different protein coding genes in the operon are under different selective constraints on protein sequence preservation. A similar frameshift mutation found in experimental evolution studies is shown to be present in the sample we analyzed, indicating that selectively relevant variants in evolution experiments are also present in natural populations. We show that there is no simple phylogenetic relationship between host species, geographical location and the lac operon sequence. Finally, we argue that a combined approach of comparative genomics, experimental evolution and theoretical modelling contributes to a more complete understanding of molecular evolution.