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，以建立由模块化DNA零件编码的新型设备，途径和电路，最近又转向了活细胞中整个基因组的工程。合成生物学的许多工作的目的是设计和构建细胞以执行通常在自然界中不执行的有用的新功能。为了进一步进一步，重要的是要设计主力的活细胞，以便他们可靠和可重复地执行新任务。为此，人们对开发以最小基因组构建的简化细胞有很大的兴趣。通过基因组工程和合成，应该有可能创建不需要细胞执行其主要所需功能的许多基因驱动过程的基因组。这里提出的工作旨在加快此类最小基因组的工程和综合，这是第一个从仅仅是从仅被认为为其在实验室功能支持该单元的元素中构建工作染色体的项目。从理论上讲，用这种最小基因组生长的细胞在执行工程任务方面应该更有效，例如高产率的药物分子的生物合成。因此，我们的工作将能够生产出有价值用于生物技术的专业菌株。为了实现这一目标，我们计划使用从工作中获得的知识和工具作为国际SC2.0项目的一部分，该项目正在为贝克的酵母（酿酒酵母）建造一个完全合成的基因组。我们刚刚完成了该项目的一个染色体的结构，该项目现在编码通常在其自然对应物上发现的所有334个基因。在这个项目中，我们旨在用由DNA模块构建的最小版本替换整个染色体，每个版本都从该染色体中编码一个基因，认为这对于实验室的细胞生长至关重要。为此，我们将使用称为CRAMBLE的系统，该系统将其硬编码为我们最近完成的合成染色体的DNA。将此系统切换为导致基因自动从生长细胞中自动损失的基因。通过我们的工程酵母细胞进行大规模做到这一点，然后再进行基因组测序的整个种群，为我们提供丰富的数据，这些数据告诉我们实验室中酵母生长需要哪些基因。借助此重要的新数据集，我们将继续构建最小的合成染色体，并评估其在生长酵母细胞中替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性能，并确定它们是否可以比正常酵母更高的效率生长和表达基因，现在已经去除了冗余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演变为在其基因组上编码许多非必需基因。它还将使我们有机会生产新的专家细胞以用于生物技术，我们计划测试我们最少的染色体酵母，以便它们能够生产各种对工业，尤其是英国工业合作者有价值的药物分子的能力。

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