EDGE: CT: Development of foundational multiplex genome engineering tools for non-conventional yeast

基因组多样性的广度赋予生物丰富的生物合成能力，使它们能够适应不同的环境。生物系统中的物种多样性具有解决全球挑战的巨大潜力，例如危险废物的补救，生产新药和设计细胞以减轻人类疾病，以及合成新的化学品和材料以确保环境的可持续性。这些挑战激发了开发全新功能基因组工具的需求，并使技术能够大规模修改基因组。具体而言，需要用于基因网络或基因组的平行和连续定向进化的方法，以增强理解并加快具有规定功能的生物体的设计和进化。在这个项目中，研究人员通过在非传统酵母物种中开发多重基因组工程技术来解决这些挑战。该项目还促进跨学科教育，包括具体扩大STEM教育和代表性不足的少数民族和妇女的职业机会。此外，研究人员还创建了体验式学习模块，将基因组工程研究带到K-12和本科课堂，并将学生与实验室中的科学联系起来。这个新的推广计划确保了该项目的进展使更广泛的社区受益，并有助于激励和培养年轻的科学家和工程师。在这个项目中，我们寻求开发跨物种的多重基因组工程技术，使非常规酵母（NCY）物种的基因功能发现成为可能。通过整合最先进的分子生物学、实验室进化和合成生物学技术，该项目为研究和产生遗传变异创建了一个新的框架。该框架的重点是在非传统酵母中建立跨物种基因组编辑能力，并提高在细胞中递送合成DNA的能力。以碱基对水平精确度引入许多靶向基因组修饰的能力建立了NCY中以及更广泛地用于真核生物的多重组合基因组工程的一般策略。这些进展使得能够构建靶向的遗传变异集，可以对其进行功能研究，以阐明基因型和表型之间的因果关系，并重新编程细胞行为。从长远来看，目前的工作将改变科学家在非传统酵母物种中进行大规模遗传修饰的方式，并开创一个时代，在这个时代，全球重新编程细胞行为将变得简单，廉价，并使研究人员能够发现新的生物现象，阐明基因型和表型之间的因果关系，并设计和重新编程生物体。总之，该项目为基因组工程相关的学术和工业努力提供了新的方向，同时培养下一代科学家和工程师成为劳动力的全面参与者。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

The breadth of genomic diversity endows organisms with rich biosynthetic capabilities and allows them to adapt to diverse environments. This species diversity in biological systems has tremendous potential to solve global challenges, such as the remediation of hazardous waste, producing new drugs and designer cells to alleviate human diseases, and the synthesis of novel chemicals and materials to ensure environmental sustainability. These challenges motivate the need to develop entirely new functional genomic tools, and enabling technologies to modify genomes on a large scale. Specifically, methods are needed for parallel and continuous directed evolution of gene networks or genomes to enhance understanding and expedite the design and evolution of organisms with prescribed functions. In this project, the investigators address these challenges through the development of multiplex genome engineering technologies in non-conventional yeast species. This project also promotes interdisciplinary education, including the specific expansion of STEM education and career opportunities for underrepresented minorities and women. Further, the investigators create experiential learning modules that bring genome engineering research to K-12 and undergraduate classrooms and connect students to the science in the laboratory. This new outreach program ensures that advances made in this project benefit a broader community and contribute to motivating and training young scientists and engineers.In this project, we seek to develop cross-species multiplex genome engineering technologies to enable gene function discovery in non-conventional yeast (NCY) species. By integrating state-of-the-art molecular biology, laboratory evolution, and synthetic biology technologies, this project creates a new framework for studying and generating genetic variation. This framework is focused on establishing cross-species genome editing capabilities in nonconventional yeast with improved capabilities of delivering synthetic DNA in cells. The ability to introduce many targeted genome modifications at base-pair level precision establishes a general strategy for multiplex combinatorial genome engineering in NCYs and more broadly for eukaryotes. These advances enable the construction of targeted sets of genetic variants that can be functionally studied to elucidate causal links between genotype and phenotype and reprogram cellular behavior. In the long-term, the present work will transform the way scientists perform large-scale genetic modifications in non-conventional yeast species and usher in an era wherein globally reprogramming cellular behavior will become simple, inexpensive, and empower researchers to uncover new biological phenomena, elucidate causal links between genotype and phenotype, and design and reprogram organisms. In sum, this project provides new directions for academic and industrial efforts related to genome engineering, while simultaneously training the next generation of scientists and engineers to be full participants in the work force.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.