Rapid phenotypic switching in a natural isolate of Escherichia coli : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University, Albany, New Zealand

Abstract

The survivability of any given bacterial population is dependent on its genetic and phenotypic makeup. When cells replicate they usually produce genetically identical daughter cells through a process called binary fission. Although these daughter cells may remain genetically identical and form isogenic populations, bacteria also possess the ability to alter their phenotype independently of other cells in their population. This can result in subpopulations of phenotypically variable cells forming within a larger population, rendering them phenotypically heterogeneous. Phenotypic heterogeneity can arise from multiple molecular mechanisms that cause either genetic or epigenetic changes. Genetic mechanisms include site-specific DNA inversion, slipped-strand mispairing and homologous recombination. Epigenetic changes involve modifications to DNA at the structural level, and in bacteria most commonly refer to methylation. Heterogeneity can provide evolutionary advantages through processes like bet-hedging or the division of labour. A well documented example of evolutionarily advantageous phenotypic heterogeneity is the formation of persister cells within bacterial strains, a leading cause of antibiotic treatment failure. In this study, we have identified an Escherichia coli natural isolate strain (SC375) that is able to rapidly switch between two phenotypes. The phenotypic heterogeneity demonstrated in this strain results in varying colony morphologies influenced by their cellular composition. We initially proposed a DNA inversion mechanism for this switching but subsequently confirmed that all cells remain isogenic regardless of cell phenotype. Through RNA-sequencing we identified three virulence genes that were differentially regulated in both phenotypes, suggestive of an epigenetic regulatory mechanism. We then show, using reporter assays, that two of these genes are expressed in variable levels across subpopulations. We suggest that the rapid phenotypic reversibility of this strain is a possible indicator of epigenetic memory.