Environmental and Mutational Drivers of Gene Regulatory Network Evolution Across Pseudomonas spp.

: (Alternative Format Thesis)

Abstract

The organisation of life is no small feat. Ensuring the right components are made at the right time in each individual cell that makes up a living organism is a complex task. However, it is made possible through gene regulatory networks (GRNs), which respond to external and internal stimuli and ensure the correct genes are expressed at the right time and in the right place. While the proper functioning of these networks is essential for organismal survival, they themselves evolve over time, and can be a key source of evolutionary innovation. In order to study how these regulatory networks evolve, and what can drive their evolutionary trajectories, we have taken a sample of bacterial species across the Pseudomonas spp. clade and altered one part of their network. We remove the master regulator of their flagellar swimming phenotype, FleQ, rendering them immotile, and select for the re-evolution of swimmers through starvation. We study their adaptation in response to this catastrophic mutation on multiple levels. In Pseudomonas fluorescens Pf0-1, we use an almost identical strain containing a mutational hotspot site to ask the question, what happens when you select for the same phenotype but with different levels of mutational constraint? We find that having a mutational hotspot aids in restoring a swimming phenotype faster but also hinders the discovery of fitter mutant options by selection. We then extend our view across the clade and compare responses by Pseudomonas putida KT2440, Pseudomonas syringae pv tomato DC3000, and Pseudomonas ogarae F113. We see that when they restore swimming, mutations are targeted in the same nitrogen regulatory pathway. We also see differences in response to selection across simple and complex nutrient environments, with F113 and DC3000 not re-evolving swimming in a complex environment. Finally, we look more closely at the effect of nutrient environment on the restoration of the swimming phenotype. We found that mutations in certain genes that restored swimming in one environment were inviable in another but could eventually be restored (with varying success). This work shows the varying effects of mutational constraint and genetic background on evolution in GRNs, but perhaps more importantly it emphasises the influence that environment can have in the course of GRN evolution, something that is often overlooked in the field of experimental evolution.

Date of Award	26 Jun 2024
Original language	English
Awarding Institution	University of Bath
Supervisor	Tiffany Taylor (Supervisor) & Susanne Gebhard (Supervisor)