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

改变调节模块成员资格如何影响中央代谢内模块功能的实证检验

• 批准号: 1906486
• 负责人: Daniel Kliebenstein
• 金额: $ 103.3万
• 依托单位: University of California-Davis
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1906486&HistoricalAwards=false
• 关键词: Empirical; testing; how; changing; regulatory

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.

在团队合作中，一个团队使用协调的方向来最大限度地取得成功。这个概念也被认为是新陈代谢在生活中如何发挥作用的核心。一组基因/酶按照转录因子的指示组织起来，作为一个内聚单元发挥作用。了解生物模块的功能对于工程或改善生物体的所有努力都是至关重要的。然而，这一概念实际上尚未得到检验。该项目使用基因组工程方法使单个基因失去作为基因的功能，并测试模块如何发挥作用。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学的本科生研究人员提供直接的研究经验，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调节，以优化网络产生的特性，并最大限度地提高效率。然而，目前尚不清楚全酶或代谢途径中的所有基因是否需要协调，或者是否存在某种阈值，在该阈值下基因可以从调控模块中脱落而不产生功能性后果。该项目使用基因组工程直接测试这一理论，通过操纵启动子从特定的调节子中去除基因和通路。这些操作的效果是用一系列表型分析平台来测量的，以测试从转录物到代谢物到整个生物体的所有水平的性状的结果。这些结果允许一个直接的经验测试如何在全酶，通路或超通路水平的模块成员影响这些模块的功能。该项目直接测量调节子中有多少成员必须协调才能产生适当的特质反应。这些结果有助于发展新的理论和概念，以提高对生物体功能的理解。该奖项反映了NSF的法定使命，并被认为是值得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的支持。

项目成果

Innovation, conservation, and repurposing of gene function in root cell type development

• DOI: 10.1016/j.cell.2021.04.024
• 发表时间: 2021-06-10
• 期刊: CELL
• 影响因子: 64.5
• 作者: Kajala, Kaisa;Gouran, Mona;Brady, Siobhan M.
• 通讯作者: Brady, Siobhan M.