Empirical testing of how changing regulatory module membership affects module function within central metabolism

在团队合作中，团队使用协调的方向来最大化他们的成功。这一概念也被认为是新陈代谢如何在生活中发挥作用的核心。一组基因/酶根据转录因子的指示进行组织，以发挥凝聚力单位的作用。了解生物模块是如何发挥作用的，对于为几乎任何目的设计或改进生物体的所有努力都是至关重要的。然而，这一概念实际上还没有得到检验。该项目使用基因组工程方法来导致单个基因失去作为一个基因的功能，并测试该模块如何发挥作用。这项工作培养研究生和博士后研究员将合成生物学工程与基因组学和计算数据分析相结合。该项目为第一代和转校的本科生研究人员提供了直接的研究经验，以扩大未来的研究人员队伍。该项目测试了生物学的一个基本假设，即网络的成员受到协调的调节，以优化网络产生的特征并最大化效率。然而，目前还不清楚全酶或代谢途径中的所有基因是否需要协调，或者是否有某个阈值可以从调控模块中删除基因而不会产生功能后果。这个项目使用基因组工程来直接测试这一理论，方法是操纵启动子，从特定的调节子中移除基因和途径。这些操作的效果是通过一系列广泛的表型平台来衡量的，以测试从转录本到代谢物再到整个生物体的所有特征水平的后果。这些结果允许对全酶、途径或超途径水平上的模块成员如何影响这些模块的功能进行直接的经验测试。该项目直接测量一个规则的多少成员必须被协调才能产生适当的特征反应。这些结果有助于发展新的理论和概念，以提高对有机体如何运作的理解。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

In teamwork a group uses coordinated directions to maximize their success. This concept is also thought to be at the core of how metabolism functions in life. A team of genes/enzymes are organized by directions from a transcription factor to function as a cohesive unit. Understanding how biological modules function is essential for all efforts to either engineer or improve organisms for nearly any purpose. However, this concept has not actually been tested. This project uses genome engineering approaches to cause individual genes to lose their ability to function as a gene and test how the module functions. This effort trains graduate students and postdoctoral fellows to integrate synthetic biology engineering with genomics and computational data analysis. The project provides direct research experience to first-generation and transfer undergraduate researchers to broaden the future pool of researchers.This project tests a foundational assumption of biology, that the members of a network are coordinately regulated to optimize the trait being produced by the network and to maximize efficiency. However, it is not clear that all of the genes in a holoenzyme or metabolic pathway need to be coordinated or that there is some threshold at which genes can be dropped from a regulatory module without functional consequence. This project uses genome engineering to directly test this theory by manipulating promoters to remove genes and pathways from specific regulons. The effect of these manipulations is measured with a wide array of phenotyping platforms to test consequences at all levels of a trait from transcript to metabolite to whole organism. These results allow a direct empirical test of how module membership at the holoenzyme, pathway or super-pathway level influences those modules' function. The project directly measures how many members of a regulon must be coordinated to create the proper trait response. These results contribute to the development of new theories and concepts to improve the understanding of how organisms function.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.