CAREER: Epigenetic Regulation of Gene Expression in Engineered Prokaryotes

职业：工程原核生物基因表达的表观遗传调控

• 批准号: 2338573
• 负责人: Natalie Farny
• 金额: $ 122.6万
• 依托单位: Worcester Polytechnic Institute
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2024
• 资助国家: 美国
• 起止时间: 2024-03-01 至 2029-02-28
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2338573&HistoricalAwards=false
• 关键词: CAREER; Epigenetic; Regulation; Gene; Expression

The soil contains a complex web of microbes, dominated by bacteria species, and these microbes are essential for soil health, soil stability and crop production. Engineered varieties of soil bacteria may help protect our soils by detecting and removing pollutants, or reducing the nitrogen needed to fertilize farmlands. To engineer soil bacteria efficiently and with minimal risk to the environment, a better understanding of how important genes are turned on and off is needed. This CAREER research focuses on epigenetic regulation – gene expression that is controlled by chemical modifications to the DNA-and its role in the survival and performance of native and engineered strains of soil bacteria. This work will be the source of projects for a research-oriented upper-level undergraduate course and for interactive educational resources that teach the principles of bioengineering to undergraduates. Epigenetic regulation of gene expression via genome methylation in prokaryotes has been vastly understudied. Differences in genome methylation have been observed under changing growth conditions, such as between exponential and stationary phase growth, which suggests that the growth environment significantly influences epigenetic regulation. However, understanding of epigenetic regulation in synthetic biology chassis organisms beyond E. coli, and in real-world environmental contexts, is extremely limited. Pseudomonas putida is a versatile Gram-negative organism that is native to soil, and is being developed as a chassis for numerous industrial and environmental applications. Yet, no comprehensive study of epigenetic regulation, nor any investigation of epigenetic effects on synthetic gene circuit function, has yet been reported in P. putida. This CAREER program will examine how genome methylation affects gene expression changes that are essential for the transition of P. putida from laboratory to soil conditions. These epigenetic changes may similarly affect the function of integrated synthetic gene circuits. The overall objective of this proposal is to investigate the impact of genome methylation on gene expression and synthetic gene circuit function in P. putida within its native soil environment. To achieve the overall objective, two specific objectives will be pursued: 1) Determine the effect of genome methylation on endogenous gene expression of P. putida in soil. 2) Control synthetic gene circuit expression in P. putida by modulation of DNA methylation. The proposed research will be complemented by educational activities that create new open-access higher education resources for teaching the core principles of synthetic biology. The research proposed in this CAREER program will uncover important epigenetic principles that permit engineered organisms to thrive within a complex environment. The knowledge will be broadly translatable to the optimization of genetically engineered microbes for a range of environmental and industrial applications.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.

土壤包含一个复杂的微生物网，以细菌为主，这些微生物对于土壤健康，土壤稳定性和作物产生至关重要。土壤细菌的工程变化可以通过检测和去除污染物或减少施肥农田所需的氮来帮助保护我们的土壤。为了有效地设计土壤细菌，对环境的风险很小，可以更好地理解如何打开和关闭基因的重要性。职业研究的重点是表观遗传调节 - 基因表达，该基因表达受到对DNA的化学修饰的控制，并且其在土壤细菌的天然和工程菌株的生存和性能中的作用。这项工作将是一个面向研究的上层本科课程的项目来源，以及互动的教育资源，这些教育资源教授生物工程的本科生原则。通过基因组甲基化对基因表达的表观遗传调节已广为人知。在不断变化的生长条件下，例如指数阶段生长和固定相生长之间已经观察到了基因组甲基化的差异，这表明生长环境显着影响表观遗传调节。然而，对大肠杆菌以外的合成生物学底盘生物以及在现实世界环境环境中的表观遗传调节的理解非常有限。假单胞菌putida是一种多功能的革兰氏阴性生物，原产于土壤，正在作为众多工业和环境应用的底盘开发。然而，尚未在P. p.putida中报道过对表观遗传调节的全面研究，也没有对合成基因回路功能的表观遗传作用进行的任何研究。该职业计划将研究基因组甲基化如何影响基因表达变化，这对于p. putida从实验室过渡到土壤条件至关重要。这些表观遗传变化可能同样影响综合合成基因回路的功能。该提案的总体目的是研究基因组甲基化对基因表达和合成基因回路功能在其天然土壤环境中的影响。为了实现总体目标，将实现两个特定的目标：1）确定基因组甲基化对土壤中p。putida的内源基因表达的影响。 2）通过调节DNA甲基化来控制P. p. p. p. p. p. p. p.的表达。拟议的研究将由教育活动完成，这些活动创造了新的开放式高等教育资源，以教授合成生物学的核心原则。该职业计划中提出的研究将揭示重要的表观遗传原则，使工程生物可以在复杂的环境中蓬勃发展。这些知识将可以广泛地翻译成针对各种环境和工业应用的一般工程微生物的优化。该奖项反映了NSF的法定任务，并通过使用基金会的知识分子优点和更广泛的影响审查标准来通过评估来评估。