Towards Genomes-to-Design: Building and Testing a Minimal Essential Chromosome

迈向基因组设计：构建和测试最小必需染色体

• 批准号: BB/R002614/1
• 负责人: Thomas Ellis
• 金额: $ 50.23万
• 依托单位: Imperial College London
• 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%2FR002614%2F1
• 关键词: Towards; Genomes; Design; Building; Testing

Synthetic biology follows engineering principles to build novel devices, pathways and circuits encoded by modular DNA parts, and more recently has turned to the engineering of entire genomes in living cells. The aim of much of the work of synthetic biology is to design and build cells to perform useful new functions they typically don't perform in nature. To further this field, it is important to engineer the workhorse living cell so that they perform their new tasks reliably and reproducibly. To this end there is significant interest in developing simplified cells built with minimal genomes. Through genome engineering and synthesis, it should be possible to create genomes that do not encode the many genes driving processes unnecessary for the cell to perform its main desired function. The work proposed here aims to accelerate the engineering and synthesis of such minimal genomes, by being the first project to build a working chromosome from just the elements deemed essential to support the cell for its function in the lab. Cells growing with this minimal genome should theoretically be more efficient at performing engineered tasks, such as the biosynthesis of a drug molecule at high yields. Our work will therefore be able to produce specialist strains valuable for use in biotechnology.To achieve this, we plan to use knowledge and tools gained from our work as part of the international Sc2.0 project, which is constructing an entirely synthetic genome for baker's yeast (Saccharomyces cerevisiae). We have just completed construction of one chromosome for this project, which now encodes all 334 genes normally found on its natural counterpart. In this project, we aim to replace this entire chromosome with a much smaller minimal version built-up from modules of DNA that each encode one of the genes from this chromosome deemed essential for cell growth in the lab. To do this we will use system called SCRaMbLE that is hard-coded into the DNA of our recently completed synthetic chromosome. Switching this system on leads to genes unnecessary for growth being automatically lost from the growing cells. Doing this at a large scale with our engineered yeast cells and then genome-sequencing whole populations, should provide us with a rich set of data that tells us which genes are required for growth of the yeast in the lab. With this important new dataset in hand, we will then proceed to building our minimal synthetic chromosome and assessing its ability to replace a full chromosome in growing yeast cells. We plan to measure how cells with the minimal chromosome perform in a variety of conditions and determine whether they can grow and express genes with greater efficiency than normal yeast, now that redundant DNA has been removed. This will generate important new insights for understanding how cells consume resources efficiently and have evolved to encode many non-essential genes on their genomes. It will also give us an opportunity to produce new specialist cells for use in biotechnology, and we plan to test our minimal chromosome yeast for their ability to produce a variety of drug molecules that are valuable for industry and particularly for UK industrial collaborators.

合成生物学遵循工程原理，构建由模块化DNA部分编码的新型装置、通路和电路，最近又转向活细胞中整个基因组的工程。合成生物学的大部分工作的目的是设计和构建细胞，以执行它们在自然界中通常不执行的有用的新功能。为了进一步推进这一领域，重要的是要工程化的主力活细胞，使他们可靠地和可重复地执行他们的新任务。为此，人们对开发用最少的基因组构建的简化细胞非常感兴趣。通过基因组工程和合成，应该可以创建不编码许多基因的基因组，这些基因驱动细胞执行其主要功能所不必要的过程。本文提出的工作旨在加速这种最小基因组的工程和合成，成为第一个仅从被认为对支持细胞在实验室中发挥功能至关重要的元素构建工作染色体的项目。从理论上讲，具有这种最小基因组的细胞在执行工程任务时应该更有效，例如以高产率生物合成药物分子。因此，我们的工作将能够产生在生物技术中有价值的专业菌株。为了实现这一目标，我们计划将从我们的工作中获得的知识和工具作为国际Sc2.0项目的一部分，该项目正在构建面包酵母（酿酒酵母）的完全合成基因组。我们刚刚为这个项目完成了一条染色体的构建，它现在编码了所有334个基因，这些基因通常在其天然对应物上发现。在这个项目中，我们的目标是用一个更小的最小版本来取代整个染色体，这个最小版本是由DNA模块组成的，每个DNA模块编码一个来自这个染色体的基因，这些基因被认为是实验室中细胞生长所必需的。为此，我们将使用一个名为SCRaMbLE的系统，它被硬编码到我们最近完成的合成染色体的DNA中。打开这个系统会导致生长不必要的基因从生长的细胞中自动丢失。用我们的工程酵母细胞大规模地做这件事，然后对整个种群进行基因组测序，应该会为我们提供一组丰富的数据，告诉我们哪些基因是酵母在实验室中生长所必需的。有了这个重要的新数据集，我们将继续构建我们的最小合成染色体，并评估其在生长的酵母细胞中取代完整染色体的能力。我们计划测量具有最小染色体的细胞在各种条件下的表现，并确定它们是否能够以比正常酵母更高的效率生长和表达基因，现在已经去除了多余的DNA。这将产生重要的新见解，以了解细胞如何有效地消耗资源，并进化到编码其基因组上的许多非必需基因。这也将使我们有机会生产用于生物技术的新的专业细胞，我们计划测试我们的最小染色体酵母菌生产各种药物分子的能力，这些药物分子对工业，特别是对英国工业合作者有价值。

项目成果

Screening microbially produced ?9-tetrahydrocannabinol using a yeast biosensor workflow.

使用酵母生物传感器工作流程筛选微生物产生的 9-四氢大麻酚。

• DOI: 10.17863/cam.89822
• 发表时间: 2022
• 作者: Shaw W

Synthetic designs regulating cellular transitions: Fine-tuning of switches and oscillators

• DOI: 10.1016/j.coisb.2020.12.002
• 发表时间: 2021-03-01
• 期刊: CURRENT OPINION IN SYSTEMS BIOLOGY
• 影响因子: 3.7
• 作者: Zorzan，Irene;Lopez，Alejandra Rojas;Barberis，Matteo
• 通讯作者: Barberis，Matteo