CAREER: Model-Guided Optimization and Autonomous Control of a Synthetic Biodetoxification Pathway for Harnessing Lignocellulosic Feedstock

萨利斯：有一个全国性的目标是用不与我们的食物供应竞争的生物可再生替代品取代汽油、柴油和塑料材料。工程微生物可以将糖转化为广泛的生物可再生产品，包括燃料和材料。然而，这种糖必须非常便宜，才能与现有的石油基产品竞争。非粮食农业副产品，如玉米秸秆和小麦秸秆，以及快速生长的树木可以通过多步骤生物质转化过程转化为廉价的糖。这种转化过程中最具挑战性的一个方面是产生有毒的抑制剂，这些抑制剂会杀死微生物，从而阻止它们产生产物。特别是糠醛和羟甲基糠醛（HMF）是两种对微生物毒性最大的抑制剂。本文建议设计和优化一种合成生物解毒途径，使工业微生物能够消耗糠醛和羟基甲基糠醛，将它们转化为有用的细胞构建块，并使使用廉价纤维素糖制造产品成为可能。这项工作还将呋喃生物传感器与遗传电路结合起来，在生物反应器条件变化的情况下自动调整途径的活性。活细胞只会在需要的时候激活这条通路。此外，本工作将开发新的生物物理建模和计算优化方法，使工程细胞代谢更加高效和可靠。提出的模型指导方法将大大减少优化新代谢途径所需的实验量，并根据代谢物生物传感器控制其活性。新的方法将通过用户友好的网络界面提供。研究者将通过三个有针对性的项目促进高中生、本科生和研究生的奖学金和教育。第一个项目将招募高中教师创建新的设计-建造-测试工程实验室，这些实验室将展示关键的工程原理，同时说明生物技术与我们日常生活之间的交集。在第二个项目中，PI将增加本科生的早期研究机会，特别是来自代表性不足群体的学生，作为提高毕业率和鼓励追求高等教育的一种方式。在第三个项目中，PI将开发一门新的合成生物学研究生课程。这门研究生水平的课程将是现有本科课程的高级版本，将遗传、代谢和蛋白质工程课程与生物能源和生物制药领域的研究课题结合起来。

CBET-1253641 SalisThere is a national objective to replace gasoline, diesel, and plastic materials with biorenewable alternatives that do not compete with our food supply. Engineered micro-organisms can convert sugars into a broad cornucopia of biorenewable products, including fuels and materials. However, the sugar must be very inexpensive to compete with existing petroleum-based products. Non-food agricultural byproducts, such as corn stover and wheat straw, and fast growing trees can be converted to inexpensive sugar through a multi-step biomass conversion process. One of the most challenging aspects of this conversion process is the generation of toxic inhibitors that kill the micro-organism, and thus prevent them from producing a product. In particular, furfural and hydroxy-methyl furfural (HMF) are two of the most toxic inhibitors to micro-organisms. It is proposed to engineer and optimize a synthetic biodetoxification pathway that enables industrial micro-organisms to consume furfural and hydroxy-methyl furfural, converting them into useful cellular building blocks, and enabling the manufacturing of products using inexpensive cellulosic sugars. This work will also combine furan biosensors with genetic circuitry to automatically tune the pathway's activity in the presence of changing bioreactor conditions. The living cell will only activate the pathway when it needs it. Further, this work will develop new biophysical modeling and computational optimization approaches to make engineering cellular metabolism more efficient and reliable. The proposed model-guided approach will substantially reduce the amount of experimentation that will be necessary to optimize new metabolic pathways, and control their activity according to a metabolite biosensor. New methods will be available through a user-friendly web interface.The investigator will promote the scholarship and education of high school students, undergraduate students, and graduate students through three targeted programs. The first program will recruit high school teachers to create new design-build-test engineering labs that will demonstrate key engineering principles while illustrating the intersection between biotechnology and our daily lives. In the second program, the PI will enhance the early-stage research opportunities for undergraduate students, especially ones from under-represented groups, as a way to increase graduation rates and encourage the pursuit of higher education. In the third program, the PI will develop a new graduate-level course on Synthetic Biology. This graduate-level course will be a higher-level version of an existing undergraduate course that integrates a genetic, metabolic, and protein engineering curriculum with research topics from the bioenergy and biopharmaceuticals fields.