From genetic parts to neochromosome in yeast

从酵母的遗传部分到新染色体

• 批准号: BB/P02114X/1
• 负责人: Yizhi Cai
• 金额: $ 50.41万
• 依托单位: University of Manchester
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2018
• 资助国家: 英国
• 起止时间: 2018 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FP02114X%2F1
• 关键词: genetic; parts; neochromosome; yeast

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.

该项目旨在开发可用于快速生成和测试工程酵母菌株的工具，这些工具可利用合成生物学工具应用于许多不同的工业和医疗保健需求。合成生物学，也称为生物工程，是一门快速发展的学科，旨在应用工程技术来创建新的有用的生物系统。对于此类项目最有用的生物体之一是普通面包酵母，酿酒酵母。酵母在人类食品和饮料技术中的应用已有数千年的历史，目前在全球范围内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制造抗疟疾药物青蒿素，作为植物来源的替代品，以及碳氢化合物燃料法呢烯的制造，以及最近证明可以在改良酵母中生产重要的止痛药，例如氢可酮。由于生物学工程仍然是一门艺术和一门科学，因此组装和测试系统的许多不同变体非常有用， 查看哪些变体效果最好，作为进一步工程的起点。要大规模进行这种“快速原型制作”，需要使用自动化系统，该系统使用机器人来执行所有必要的操作，从 DNA 组装到菌株构建再到最终测试。此类自动化的主要制造商之一是 Thermo-Fisher，它是该项目的工业合作伙伴。 Thermo-Fisher 自动化系统构成了一个可以大规模组装和测试 DNA 构建体的平台，以促进快速创建可用于解决工业和医疗保健问题的新菌株。为了帮助这一过程，使用了许多不同的技术。例如，酵母 DNA“部件”库以一种名为“YeastFab”的格式提供，它允许快速自动组装，以不同的组合将部件连接在一起。还需要软件工具来帮助设计过程并跟踪零件及其属性。 Thermo-Fisher 的自动化由名为“Momentum”的软件控制。在这个项目中，我们的目标是开发一套工具，可用于将所有这些流程连接在一起，使用户能够充分利用自动化组装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 库管理软件连接到控制自动化系统的 Momentum 软件，从而实现从设计到构建和测试的无缝过渡。我们将使用这些工具来扩展我们的 YeastFab 天然酵母启动子库（DNA“控制”序列，对于构建遗传机器至关重要）并生成可用于控制工程系统的新合成启动子，从而提高系统的实用性。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全新的染色体，从而组装生产许多生物产品（例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展示这些技术的有效性。所有开发的软件工具都将在开源基础上提供，以造福用户社区。

项目成果

Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods.

使用体外和体内合成基因组 SCRaMbLE-in 方法进行快速途径原型设计和工程设计

• DOI: 10.1038/s41467-018-04254-0
• 发表时间: 2018-05-22
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Liu W;Luo Z;Wang Y;Pham NT;Tuck L;Pérez-Pi I;Liu L;Shen Y;French C;Auer M;Marles-Wright J;Dai J;Cai Y
• 通讯作者: Cai Y

EMMA assembly explained: A step-by-step guide to assemble synthetic mammalian vectors.

EMMA 组装说明：组装合成哺乳动物载体的分步指南。

• DOI: 10.1016/bs.mie.2018.12.017
• 发表时间: 2019
• 期刊: Methods in enzymology
• 作者: Jones S

EMMA-CAD: Design Automation for Synthetic Mammalian Constructs

EMMA-CAD：合成哺乳动物结构的设计自动化

• DOI: 10.1021/acssynbio.1c00433
• 发表时间: 2022
• 期刊: ACS Synthetic Biology
• 影响因子: 4.7
• 作者: Luo Y