Development of a continuous genome shuffling approach to expedite adaptive laboratory evolution
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abstract
This project will develop a novel methodology to study how microbes evolve. All biological systems have the capacity to adapt and to evolve. Adaptive evolution can be used as a tool for the development of effective strains for the conversion of renewable feedstock to fuels and chemicals for a more sustainable route of production. Due to the complexity of biological systems, the process of how microbes adapt and evolve is not fully understood. The researchers will address this challenge by developing a strain of Escherichia coli that can be used to expedite the process of adaptive evolution via the continuous recombination of beneficial mutations while removing neutral or deleterious mutations from the population. The tools to be developed in the proposed work can also be applied to gain fundamental understandings of the emergence and development of antibiotic drug resistance. The ability of biological systems to adapt and evolve is both an advantage and disadvantage in the field of biotechnology. This evolutionary potential of microbial systems presents opportunities for developing strains with desired traits. On the other hand, undesired adaptation can cause strain instability and loss of performance. The goal of this project is to address this limitation by developing an enabling methodology towards the fundamental study of evolutionary processes in microbial systems. Adaptive laboratory evolution (ALE) is a powerful inverse engineering tool that can be used to generate microbes with desired traits and to uncover the underlying mechanisms of how microbes evolve and adapt. Specifically, this project aims to develop a continuous in situ genome shuffling system that expedites ALE experiments in Escherichia coli, which will allow beneficial mutations from different clones to recombine to form superior genotypes and deleterious mutations to be removed from an otherwise superior strain. Therefore, the overarching hypothesis of the proposed work is that inclusion of sexual recombination will expedite the rate of adaptive evolution. This hypothesis will be tested via three objectives: (i) characterization of the benefit of an efficient bi-directional conjugation system in E. coli, (ii) development of a conditional mutator version of the genderless system, and (iii) application of the system to develop E. coli strains that exhibit multiple desired characteristics and that elucidate the impacts of adaptive evolutionary strategies and recombination on the rates of adaptation, evolutionary trajectories, and mechanisms of adaptation. The work will involve team members from engineering and plant pathology and microbiology, allowing students at all levels to gain experience in interdisciplinary research. This award by the Biotechnology and Biochemical Engineering Program of the CBET Division is co-funded by the Genetic Mechanisms Program of the Division of Molecular and Cellular Biosciences.
