COLLABORATIVE RESEARCH: Programming the rhizosphere through highly integrated genetic, spatio-temporal control systems

基因调控的研究是现代生物学的核心。新生的合成生物学领域的很大一部分都围绕着构建合成基因网络，以概括自然界中发现的调节机制或设计新的生物功能。然而，人工基因网络无论是在设计上还是在性能上都没有接近自然基因网络的复杂程度。目前有几个技术和科学挑战限制了大规模综合合成遗传网络的工程设计。这项研究的中心是开发一个框架，用于自动化基因网络设计的过程，方法是a)从大自然中获得基因调控机制的各种工作“部分”，b)应用工程科学来学习如何可靠地将它们组合成具有可预测行为的新系统。该项目的价值将通过“可编程根圈”的开发得到证明，“可编程根圈”是模式植物和土壤微生物物种之间的工程互惠关系的框架。可编程根圈将允许控制不同生物之间的相互作用，并代表着朝着我们操纵复杂生态系统的能力迈出的重要一步。广泛影响：该项目汇集了来自美国顶尖机构的研究人员，并与英国的主要大学建立了合作关系。与该项目相关的研究生和博士后研究人员将有机会参与一个多机构、多学科的研究项目。他们将有机会接受各种计算和分子生物学技术方面的培训。该项目的成果将通过编写宣传材料和动手演示向包括初中生在内的更广泛的公众传播，旨在教育公众有关合成生物学的技术和潜在影响。除了在理解工程学综合调控系统方面的进步外，可编程根际技术对农业的可持续性具有广泛的影响。特别是，这些技术可以用来设计有益的现象，如农作物的固氮，这将取代目前在农业生产中使用的石油基肥料。

The study of gene regulation is central to modern biology. A significant portion of the nascent field of synthetic biology has revolved around building synthetic gene networks to recapitulate regulatory mechanisms found in nature or to engineer novel biological functions. However, artificial gene networks have not approached the sophistication of their natural counterparts in either design or performance. There are several technical and scientific challenges that currently limit the engineering of large-scale integrated synthetic genetic networks. This research centers on developing a framework for automating the process of gene network design by a) obtaining various working "parts" of gene regulatory mechanisms from nature and b) by applying engineering sciences to learn how to compose them reliably into novel systems which have predictable behaviors. The value of this project will be demonstrated through the development of the ?Programmable Rhizosphere?, which is a framework for engineering mutualism between model plant and soil microbe species. The Programmable Rhizosphere will allow control of interactions between disparate organisms, and represents a significant step towards our ability to manipulate complex ecosystems.Broader impact: This project brings together researchers from top US institutions as well as establishes a collaboration with major universities in the UK. Graduate students and postdoctoral researchers associated with this project will get an opportunity to participate in a multi-institution, multidisciplinary research project. They will have the opportunity to train on a wide variety of techniques in computational and molecular biology. The results of the project will be disseminated to the broader public including middle and high school students through the development of informational materials and hands-on demonstrations designed for educating the public on the technologies and potential impact of synthetic biology. In addition to the advances in the understanding of engineering synthetic regulatory systems, the Programmable Rhizosphere technology has broad implications for sustainability in agriculture. In particular, these technologies could be used to engineer beneficial phenomena such as nitrogen fixation in agricultural crops, which would displace petroleum-based fertilizers currently used in agricultural production.