Speaker
Description
Gene regulatory networks are essential to organism survival as they allow rapid adaptation through altering gene expression profiles. These regulatory networks can be key sites of evolutionary change and they provide important insights into the adaptability of various organisms to environmental shifts such as climate change. Mutations drive their evolution, but mutation biases can drive adaptation down one particular route and may limit their ability to explore alternative (and potentially fitter) evolutionary trajectories. One cause of mutational biases are DNA secondary structures such as DNA hairpins that can cause the replication machinery to “trip” and generate a mutation. If this secondary structure is stable, it can create a mutational hotspot. Environmental signals can increase expression of certain genes, which in turn increases the chance of mutation events. This research looks at the evolutionary consequences of these interplaying factors on the evolution of gene regulatory networks by employing a model system that re-evolves motility in different nutrient environments across two bacterial strains of Pseudomonas fluorescens: one with a mutational hotspot in a gene regulatory network (AR2), and one without (Pf0-2x). We focus on the regulation of the motility phenotype of these bacteria, which is transient, only being essential when bacteria are searching for food or escaping toxins or predators and can therefore be easily selected for. By disrupting fleQ, the master regulator for the flagellum, we render them immotile. Under strong selection through starvation, the bacteria reliably re-evolve motility after just a few days, by co-opting a response regulator from another regulatory network (associated with nitrogen regulation) to take over the function of the missing FleQ. Co-option is achieved through mutations in the DNA of the nitrogen response regulator and associated regulatory genes within the network. AR2 has a mutational hotspot in one of these regulatory genes that funnels evolution down the same route nearly every time, with motility restored almost exclusively by a single repeatable SNP. The hotspot is predicted to be caused by a hairpin in the DNA, which can be abolished via the introduction of synonymous changes. Restoration of motility in Pf0-2x is via recruitment of the same nitrogen response regulator as AR2 but it does not contain a mutational hotspot, as such mutations conferring motility are observed across multiple loci but within the same regulatory network. When evolved in complex and simple nutrient environments we see that Pf0-2x has environmentally sensitive biases towards mutations in specific genes, whilst the mutation spectrum in AR2 remains constant across nutrient environments, suggesting the hotspot is a stronger force in determining adaptive outcomes within AR2. The types of mutations we see have varying pleiotropic costs despite restoring the same motility phenotype. The most common mutations typically are not the fittest, highlighting the important role that randomness and mutation bias can play in evolution, rather than selection and persistence of genotypes based purely on fitness.
