Development of a continuous genome shuffling approach to expedite adaptive laboratory evolution

[1605347]这个项目将开发一种新的方法来研究微生物是如何进化的。所有的生物系统都有适应和进化的能力。适应性进化可以作为一种工具，用于开发有效菌株，将可再生原料转化为燃料和化学品，以实现更可持续的生产路线。由于生物系统的复杂性，微生物如何适应和进化的过程尚未完全了解。研究人员将通过开发一种大肠杆菌菌株来解决这一挑战，这种菌株可以通过不断重组有益的突变来加速适应性进化的过程，同时从种群中去除中性或有害的突变。在拟议工作中开发的工具也可用于获得对抗生素耐药性的出现和发展的基本理解。生物系统的适应和进化能力是生物技术领域的优势和劣势。微生物系统的这种进化潜力为开发具有所需特性的菌株提供了机会。另一方面，不期望的适应可能导致应变不稳定和性能损失。该项目的目标是通过开发一种对微生物系统进化过程的基础研究的使能方法来解决这一限制。适应性实验室进化（ALE）是一种强大的逆向工程工具，可用于产生具有所需特征的微生物，并揭示微生物如何进化和适应的潜在机制。具体来说，该项目旨在开发一种连续原位基因组洗牌系统，加速大肠杆菌的ALE实验，这将允许来自不同克隆的有益突变重新组合形成优越的基因型，并从其他优良菌株中去除有害突变。因此，提出的工作的首要假设是，包括性重组将加快适应进化的速度。这一假设将通过三个目标进行检验：(i)表征大肠杆菌中高效双向偶联系统的益处，（ii）开发无性别系统的条件突变版本，以及（iii）应用该系统开发具有多种所需特征的大肠杆菌菌株，并阐明适应性进化策略和重组对适应速率、进化轨迹和适应机制的影响。这项工作将涉及来自工程、植物病理学和微生物学的团队成员，使各个层次的学生都能获得跨学科研究的经验。该奖项由CBET部生物技术与生化工程项目颁发，由分子与细胞生物科学部遗传机制项目共同资助。

1605347Kao, Katy C.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.