Collaborative Research: Synthetic integrons for continuous directed evolution of complex genetic ensembles

合作研究：用于复杂遗传整体连续定向进化的合成整合子

• 批准号: 0943390
• 负责人: Joshua Leonard
• 金额: $ 47.33万
• 依托单位: Northwestern University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-01 至 2013-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0943390&HistoricalAwards=false
• 关键词: Collaborative; Research; Synthetic; integrons; continuous

Synthetic biology is emerging scientific and engineering discipline that seeks to make it possible to build new biological systems (using building blocks gleaned from the natural world) that can be customized to meet pressing needs in areas such as renewable energy, specialty chemical production, and various areas of biotechnology. A grand challenge in this field is the need for technologies that enable the construction of novel complex functions in biological systems. When these functions involve the expression and coordination of multiple genes, building them becomes increasingly difficult. Assembling multigenic functions in an organism by an iterative approach is both laborious and difficult, since the engineered genes and their products often interact strongly with both one another and with the pre-existing native functions in the organism. For example, such complications have presented major challenges to efforts to engineer metabolism in microbes and plants. Moreover, many desirable applications of synthetic biology comprise complex novel functions and great genetic diversity, such as the assembly of genes from a metagenomic library in order to synthesize novel small molecules. In these cases, one might not know a priori which genetic elements need to be included in such a synthetic assembly, much less how they should be regulated in order to maximize the performance of a particular function. While these properties make linear engineering inefficient and difficult, sometimes prohibitively so, Nature has evolved mechanisms to deal with such complexity. This research project will develop a synthetic system that harnesses the power of these natural mechanisms to enable synthetic biologists to generate, diversify, and refine complex multigenic functions. The core of this technology will be based on a bacterial innovation called integrons, which are natural cloning and expression systems that assemble multiple open reading frames, in the form of gene cassettes, by using site-specific recombination and conversion to functional genes by expression from an internal promoter. The ability to capture disparate individual genes and physically link them in arrays suitable for co-expression is a trait unique to these genetic elements. The result is an assembly of functionally coordinated genes theoretically facilitating the rapid evolution of new phenotypes. This project will generate a novel technology platform based on synthetic integrons (syntegrons), including computational optimization and analysis tools, that will enable the engineering of complex multigenic functions (such as the biosynthesis of plant-derived small molecules like taxol) through continuous directed evolution.Broader impactsThis project will generate a robust technology enabling the engineering of biological systems, including both microbes and plants, for myriad useful purposes. Notable examples include the production of renewable bio-fuels and biomaterials, the synthesis of small biomolecules for applications in specialty chemicals, bioremediation, and improvement of crops for agriculture. This project will also provide a scientific tool for probing genome organization and dynamics in processes such as the emergence of microbial resistance to small-molecules and metabolic pathway evolution. In addition, this project will introduce students at both graduate and undergraduate levels to the potential of synthetic biology, including exposure through the annual International Genetically Engineered Machine (iGEM) competition. Finally, this project will engage the broader community (outside the university setting) through the Science, Art and Writing (SAW) initiative - a cross-curricular science education program that is particularly targeted towards school-age children (www.sawtrust.org). This initiative uses themes and images from science as the starting point for scientific experimentation, art and creative writing, and in doing so stimulates creativity and scientific curiosity.

合成生物学是新兴的科学和工程学科，试图使建立新的生物系统（使用自然界收集的构件）成为可能，以满足可再生能源，特种化学生产和各个生物技术领域等领域的紧迫需求。在该领域的一个巨大挑战是需要在生物系统中构建新​​型复杂功能的技术。当这些功能涉及多个基因的表达和协调时，构建它们就变得越来越困难。通过迭代方法在生物体中组装多基因功能既费力又困难，因为工程基因及其产物通常相互互动，并且在生物体中具有预先存在的天然功能。例如，这种并发症已经面临着在微生物和植物中设计代谢的努力的主要挑战。此外，许多合成生物学的理想应用包括复杂的新功能和巨大的遗传多样性，例如元基因组文库的基因组装以综合新的小分子。在这些情况下，人们可能不知道需要将遗传因素包括在这种合成组装中，更不用说应调节它们以最大程度地调节特定功能的性能。尽管这些特性使线性工程效率低下且困难，但有时是过时的，但自然已经发展出处理这种复杂性的机制。该研究项目将开发一个合成系统，该系统利用这些自然机制的力量使合成生物学家能够产生，多样化和完善复杂的多基因函数。该技术的核心将基于一种称为Integron的细菌创新，该创新是自然的克隆和表达系统，通过使用位点特异性的重组和转化为基因，以基因盒的形式组装多个开放式读取框，并通过内部启动子的表达来分配到功能基因。捕获不同单个基因并在适合共表达的阵列中物理联系的能力是这些遗传元素所特有的特征。结果是从理论上促进了新表型的快速演变的功能协调基因组装。 This project will generate a novel technology platform based on synthetic integrons (syntegrons), including computational optimization and analysis tools, that will enable the engineering of complex multigenic functions (such as the biosynthesis of plant-derived small molecules like taxol) through continuous directed evolution.Broader impactsThis project will generate a robust technology enabling the engineering of biological systems, including both microbes and plants, for myriad useful目的。值得注意的例子包括生产可再生生物燃料和生物材料，在特种化学物质中应用小生物分子的合成，生物修复以及农作物的农作物改善。该项目还将提供一个科学工具，用于探测基因组组织和过程中的动态，例如微生物对小分子的耐药性和代谢途径的演变。此外，该项目将向研究生和本科级别的学生介绍合成生物学的潜力，包括通过年度国际基因工程机器（IGEM）竞赛的接触。最后，该项目将通过科学，艺术和写作（SAW）倡议来吸引更广泛的社区（大学之外的社区） - 一项跨课程科学教育计划，特别针对学校时代的儿童（www.sawtrust.org）。该倡议使用科学的主题和图像作为科学实验，艺术和创造性写作的起点，并为此刺激了创造力和科学的好奇心。