The ability to generate rapid phenotypic diversification and innovation is frequently the deciding factor for the survival or extinction of a population. From metazoa to microbes, gene regulatory networks (GRNs) determine phenotypic responses to sensed internal and external signals and are consequently the primary sites for phenotypic evolution. To better understand why some organisms adapt rapidly to environmental challenges and why others fail to do so, we need to determine sources of variation, bias and constraint in GRN evolution. In this thesis, a microbial experimental model of GRN evolution by transcription factor (TF) rewiring is used to investigate factors influencing network evolutionary dynamics. Firstly, I identify genetic and genomic features that form a mutational hotspot that strongly biases evolutionary innovation through a specific TF. Secondly, I identify alternatives to this TF that can also rewire, and through studying how this occurs find that pre-existing GRN structure has the potential to strongly influence which TFs undergo evolutionary innovation. I additionally simulate altered GRN structures by overexpressing alternative TFs, finding that several additional regulators can rewire following similar rules and demonstrating that evolutionary ‘preferences’ for which TF is rewired can be altered by changing TF expression levels. Finally, I lay the foundation for expanding this model system by constructing a set of gene duplication strains for the primary rewired TF in our model, to investigate the dynamics of rewiring for facilitate divergence of duplicated TF genes. The findings of this thesis build a framework of factors that generate or constrain variation and innovation within regulatory systems and can be applied toward predicting regulatory evolution or engineering regulatory systems with reduced evolvability for synthetic biology applications.
Sources of Variation and Bias in Bacterial Gene Regulatory Network Evolution: (Alternative Format Thesis)
Shepherd, M. (Author). 22 Feb 2023
Student thesis: Doctoral Thesis › PhD