From genetic parts to neochromosome in yeast

该项目旨在开发工具，可用于快速生成和测试工程酵母菌株，这些酵母菌株可应用于许多不同的工业和医疗保健需求，使用合成生物学工具。合成生物学，也被称为生物工程，是一门快速发展的学科，其目的是应用工程技术来创造新的和有用的生物系统。对这类工程最有用的生物之一是普通的面包酵母，即酿酒酵母。酵母已经在人类食品和饮料技术中使用了数千年，目前在世界范围内被大规模用于生产面包、酒精饮料和生物燃料等产品。由于其安全使用的悠久历史，大规模生产技术的可用性，以及在实验室中广泛应用于研究生命的基本过程，酵母是许多生物工程项目的理想起点。最近的一些例子包括在酵母中生产抗疟疾药物青蒿素，作为植物来源的替代品，以及生产碳氢化合物燃料法尼烯，以及最近证明可以在改性酵母中生产氢可酮等重要止痛药。因为生物工程既是一门科学，也是一门艺术，所以组装和测试一个系统的许多不同变体，看看哪些变体效果最好，作为进一步工程的起点，是非常有用的。为了大规模地进行这种“快速原型”，需要使用自动化系统，使用机器人来执行从DNA组装到应变构建到最终测试的所有必要操作。这类自动化设备的主要制造商之一是赛默飞世尔，该项目的工业合作伙伴。赛默飞世尔自动化系统构成了一个可以大规模组装和测试DNA结构的平台，以促进新菌株的快速创建，这些菌株可用于解决工业和医疗保健问题。为了帮助这个过程，使用了许多不同的技术。例如，一个名为“YeastFab”格式的酵母DNA“部件”库可以使用，它允许快速自动组装以不同的组合将部件连接在一起。软件工具也需要在设计过程中提供帮助，并跟踪零件及其属性。赛默飞世尔的自动化由一种名为“动量”的软件控制。在这个项目中，我们的目标是开发一套工具，可用于将所有这些过程连接在一起，使用户能够充分利用自动化装配和测试平台的速度和灵活性。具体来说，我们将开发和测试软件工具，将生物设计工具和DNA库管理软件与控制自动化系统的动量软件连接起来，实现从设计到施工和测试的无缝过渡。我们将利用这些工具，通过扩展我们的YeastFab天然酵母启动子库（DNA“控制”序列，对构建遗传机器至关重要）和生成新的可用于控制工程系统的合成启动子，来增加系统的实用性。我们还将开发和测试“新染色体”技术，该技术允许在酵母中构建完整的新染色体，允许组装生产许多生物产品（如抗生素和抗癌药物）所需的非常大的代谢途径。最后，我们将通过组装一些演示路径来演示这些技术的有效性。为了用户社区的利益，所有开发的软件工具都将在开源的基础上提供。

This project aims to develop tools which can be used for the rapid generation and testing of engineered yeast strains which can be applied to many different industrial and healthcare needs, using the tools of synthetic biology. Synthetic biology, also known as biological engineering, is a rapidly developing discipline which aims to apply the techniques of engineering to the creation of new and useful biological systems. One of the most useful organisms for such projects is ordinary baker's yeast, Saccharomyces cerevisiae. Yeast has been used in human food and beverage technology for thousands of years, and is currently used on an enormous scale worldwide for the production of bread, alcoholic beverages, and biofuels, among other products. Because of its long history of safe use, the availability of very large scale production technologies, and its widespread use in laboratories to study the basic processes of life, yeast is an ideal starting point for many biological engineering projects. Some recent examples include the manufacture of the anti-malarial drug artemisinin in yeast, as an alternative to plant sources, as well as the manufacture of the hydrocarbon fuel farnesene, and the recent demonstration that important pain-killers such as hydrocodone can be produced in modified yeast.Because engineering of biology is still as much an art as a science, it can be very useful to assemble and test many different variants of a system, to see which variants work best, as a starting point for further engineering. To do this kind of 'rapid prototyping' on a large scale requires the use of automated systems, which use robots to perform all of the necessary operations, from DNA assembly through strain construction to final testing. One major manufacturer of such automation is Thermo-Fisher, the industrial partner in this project. Thermo-Fisher automation systems constitute a platform which can assemble and test DNA constructs on a very large scale, to facilitate the rapid creation of new strains which can be applied to solve industrial and healthcare problems. To aid in this process, many different technologies are used. For example, a library of yeast DNA 'parts' is available in a format called 'YeastFab', which allows rapid automated assembly to join parts together in different combinations. Software tools are also required to aid in the design process and to keep track of parts and their properties. Thermo-Fisher's automation is controlled by software called 'Momentum'.In this project, we aim to develop a suite of tools which can be used to join all of these processes together, to enable users to take full advantage of the speed and flexibility of automated assembly and testing platforms. Specifically, we will develop and test software tools which link biological design tools and DNA library curation software to the Momentum software which controls the automated systems, enabling a seamless transition from design to construction and testing. We will use these tools to increase the usefulness of the system by expanding our YeastFab library of natural yeast promoters (DNA 'control' sequences, essential for building genetic machines) and generating new synthetic promoters which can be used to control engineered systems. We will also develop and test 'neochromosome' technology which allows the construction of entire new chromosomes in yeast, allowing the assembly of the very large metabolic pathways required for the production of many biological products such as antibiotics and anti-cancer drugs. Finally, we will demonstrate the effectiveness of these technologies by assembling a number of demonstration pathways. All of the software tools developed will be made available on an open source basis for the benefit of the user community.