Evolutionary and molecular origins of a phenotypic switch in Pseudomonas fluorescens SBW25 : a thesis submitted in partial fulfilment of the requirements for the degree of Ph.D. in Evolutionary Genetics at Massey University, Auckland, New Zealand
Survival in the face of unpredictable environments is a challenge faced by all
organisms. One solution is the evolution of mechanisms that cause stochastic switching
between phenotypic states. Despite the wide range of switching strategies found in
nature, their evolutionary origins and adaptive significance remain poorly understood.
Recently in the Rainey laboratory, a long-term evolution experiment performed with
populations of the bacterium Pseudomonas fluorescens SBW25 saw the de novo
evolution of a phenotypic switching strategy. This provided an unprecedented
opportunity to gain insight into the evolution and maintenance of switching strategies.
The derived ‘switcher’ genotype was detected through colony level phenotypic
dimorphism. Further microscopic examination revealed the cellular basis of phenotypic
switching as the bistable (ON/OFF) expression of a capsule. Transposon mutagenesis
demonstrated that the structural basis of the capsule was a colanic acid-like polymer
encoded by the Pflu3656-wzb locus. Subsequently, whole genome re-sequencing
enabled elucidation of the series of mutational events underlying the evolution of
capsule bistability: nine mutations were identified in the switcher. Present in both forms
of the switcher, the final mutation – a point mutation in a central metabolic pathway –
was shown to be the sole mechanistic cause of capsule switching; it ‘set the stage’ for a
series of molecular events directly responsible for bistability.
Two models were proposed to explain capsule switching at the molecular level: the
genetic amplification-reduction model, and the epigenetic feedback model. Collective
results of biochemical and genetic assays proved consistent with the epigenetic model,
whereby a decrease in flux through the pyrimidine biosynthetic pathway activates an
already-present feedback loop. Subsequent analysis of a second switcher (evolved
independently of and in parallel with the first) revealed a radically different genetic
route leading to phenotypically and mechanistically similar capsule switching.
In addition to providing the first empirical insight into the evolutionary bases of
switching strategies, the work presented in this thesis demonstrates the power of natural
selection – operating on even the simplest of organisms – to forge adaptive solutions to
evolutionary challenges; in a single evolutionary step, selection took advantage of
inherent intracellular stochasticity to generate an extraordinarily flexible phenotype.