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Dancing to a Different Tune: Adaptive Evolution Fine-Tunes Protein Dynamics
[Technical Report, Doctoral Thesis]
University of Canterbury
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Molecular mechanisms that underpin adaptive evolution are not well understood. This thesis provides a case study exploring molecular changes underlying adaptive evolution. It builds upon a long-term evolution experiment by Richard Lenksi, where replicate populations of Escherichia coli have adapted in parallel to better fit their low-glucose environment. I determined structure 2.2 of wild-type enzyme for comparison with evolved enzymes. I demonstrate kinetic function of the recombinant enzyme is same as previously reported. I propose a new model for allosteric activation. Functional analyses demonstrated all eight evolved enzymes have reduced activity compared to the wildtype at physiological substrate concentrations. Evolved enzymes also showed changes to substrate binding affinity and seven showed an altered allosteric activation mechanism. These results suggest natural selection has selected for enzymes with reduced activity by altering functional mechanism of the evolved enzymes. However, structure characterization determined that all of the evolved enzymes have maintained same structural fold as wild-type. Although the fold is the same, substrate binding promiscuity suggested a change in the flexibility of the enzyme, allowing substrates of different sizes and shapes to bind. The study provides the first example of adaptive evolution fine-tuning protein dynamics to alter allostery. The thesis describes molecular mechanisms underlying the adaptation of Escherichia coli to the low-glucose environment. From a molecular perspective, natural selection has selected for adaptive mutations that alter the dynamics to produce an enzyme with reduced catalytic activity, thus decreasing phosphoenolpyruvate consumption. In addition, adaptive mutations have altered the enzymes affinity for the allosteric activator. Overall, this work describes the intricate relationship between genetic changes and the resulting phenotype and demonstrates parallel nature of adaptation.
[A, Approved For Public Release]