21EBTA: Engineering Biology with Synthetic Genomes (EBSynerGy)

21EBTA：合成基因组工程生物学 (EBsynerGy)

• 批准号: BB/W014483/1
• 负责人: Yizhi Cai
• 金额: $ 169.34万
• 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: 2022
• 资助国家: 英国
• 起止时间: 2022 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FW014483%2F1
• 关键词: 21EBTA; Engineering; Biology; Synthetic; Genomes

Yeast, Saccharomyces cerevisiae, has been used for centuries to bake bread and in brewing. Yeast is utilised across the world in many important industrial biotechnology applications, and is a model eukaryotic organism of great importance in fundamental research. Over the past decade, a large international consortium (Sc2.0) has been synthesising yeast chromosomes (16 in total). We aim to combine these chromosomes to create the world's first fully synthetic eukaryotic cell, which has a number of in-built design features to allow for its rapid optimization for new applications. For example, a genome scrambing function allows researchers to re-shuffle the genome like a deck of cards and can be applied to generate mutant strains with improved properties for industrial applications. However, genome scrambling can lead to the loss of essential genes which kills the cells. In light of this, we propose to relocate all the essential genes onto a dedicated "neochromosome" creating Sc3.0 cells. These new Sc3.0 cells will retain the essential genes during scrambling, so that more cells survive with desirable traits. We will exploit the synthetic yeast (Sc2.0/3.0), as a platform for the production of valuable natural products (e.g. antibiotics), cholesterol lowering agents (statins) and precursors required for manufacture of mRNA vaccines (e.g. Pfizer's COVID vaccine). Pathways to the target compounds will be introduced in the synthetic yeast and genome scrambling will be used to create large numbers of mutants producing the target compounds. We will also develop biosensors that can bind to the target products, triggering a fluorescent response to allow us to rapidly select the scrambled mutant cells that produce the highest levels of the target compound. In addition, we will develop novel imaging methods that can rapidly identify cells producing the desired compound. Finally, we will use the synthetic yeast to efficiently produce new generations of functionalized proteins. Nature produces proteins with an extraordinary range of functions, from enzymes that accelerate biochemical reactions needed for life to the antibodies that protect us from infectious diseases. These proteins are chains (polymers) made from only twenty building blocks called amino acids. In recent years an exciting technology has emerged called genetic code expansion (GCE) that allows us to produce proteins from more than these twenty building blocks. This technology is well developed for use in bacterial cells, but unfortunately many proteins can only be produced in higher organisms such as yeast - and here many of the important GCE tools do not operate effectively. Here we will develop yeast strains that are specifically optimized for the production of proteins with an expanded range of building blocks. These strains will underpin the development of new generations of protein therapies, catalysts and materials.

几个世纪以来，酵母（酿酒酵母）一直被用来烘烤面包和酿造。酵母在世界各地被用于许多重要的工业生物技术应用，并且是在基础研究中具有重要意义的模型真核生物。在过去的十年中，一个大型国际联盟（Sc2.0）一直在合成酵母染色体（总共16条）。我们的目标是将这些染色体结合起来，创造出世界上第一个完全合成的真核细胞，该细胞具有许多内置的设计功能，可以快速优化新应用。例如，基因组扰乱功能允许研究人员像一副纸牌一样重新洗牌基因组，并可用于生成具有改进特性的突变菌株以用于工业应用。然而，基因组扰乱可能导致必需基因的丢失，从而杀死细胞。有鉴于此，我们建议将所有必需基因重新定位到专用的“新染色体”上，以创建 Sc3.0 细胞。这些新的 Sc3.0 细胞将在扰乱过程中保留必需的基因，以便更多的细胞能够以所需的特性存活下来。我们将利用合成酵母（Sc2.0/3.0）作为生产有价值的天然产物（例如抗生素）、降胆固醇剂（他汀类药物）和制造 mRNA 疫苗（例如辉瑞的新冠疫苗）所需的前体的平台。通向目标化合物的途径将被引入合成酵母中，并且基因组加扰将用于产生大量产生目标化合物的突变体。我们还将开发可以与目标产物结合的生物传感器，触发荧光反应，使我们能够快速选择产生最高水平目标化合物的杂乱突变细胞。此外，我们将开发新的成像方法，可以快速识别产生所需化合物的细胞。最后，我们将使用合成酵母高效生产新一代功能化蛋白质。大自然产生的蛋白质具有一系列非凡的功能，从加速生命所需生化反应的酶到保护我们免受传染病侵害的抗体。这些蛋白质是仅由二十种称为氨基酸的结构单元组成的链（聚合物）。近年来出现了一种令人兴奋的技术，称为遗传密码扩展（GCE），它使我们能够从这二十多个构建模块中生产蛋白质。这项技术已经非常成熟，可以在细菌细胞中使用，但不幸的是，许多蛋白质只能在酵母等高等生物体中产生，而在这里，许多重要的 GCE 工具无法有效运行。在这里，我们将开发专门优化用于生产具有更多构建模块的蛋白质的酵母菌株。这些菌株将支持新一代蛋白质疗法、催化剂和材料的开发。

项目成果

Strategies for designing biocatalysts with new functions

设计具有新功能的生物催化剂的策略

• DOI: 10.1039/d3cs00972f
• 发表时间: 2024
• 期刊: Chemical Society Reviews
• 影响因子: 46.2
• 作者: Bell E

Synthetic yeast chromosome XI design enables extrachromosomal circular DNA formation on demand

• DOI: 10.1101/2022.07.15.500197
• 发表时间: 2022-07-16
• 期刊: bioRxiv
• 作者: Blount, B. A.;Lu, X.;Ellis, T.
• 通讯作者: Ellis, T.

Engineering stringent genetic biocontainment of yeast with a protein stability switch

• DOI: 10.1101/2022.11.24.517818
• 发表时间: 2023-02
• 期刊: Nature Communications
• 影响因子: 16.6
• 作者: Stefan A. Hoffmann;Yizhi Cai

Cellular Surveillance: DNA-Based Recording to Monitor and Memorize Biological Events

• DOI: 10.1089/genbio.2023.0018
• 发表时间: 2023-06-01
• 期刊: GEN BIOTECHNOLOGY
• 作者: David，Gabrielle;O'Keefe，Raymond T.;Cai，Yizhi
• 通讯作者: Cai，Yizhi

Reconstruct a eukaryotic chromosome arm by de novo design and synthesis

• DOI: 10.1101/2022.10.04.509869
• 发表时间: 2022-10
• 期刊: bioRxiv
• 作者: Shuangying Jiang;Zhouqing Luo;Kang Yu;Shijun Zhao;Zelin Cai;Wenfei Yu;Hong Wang;Li Cheng;Zhenzhen Liang;Hui Gao;M. Monti;Daniel Schindler;Linsen Huang;Cheng Zeng;Wei-Meng Zhang;Chun Zhou;Yuanwei Tang;Tianyi Li;Yingxin Ma;Yizhi Cai;J. Boeke;Junbiao Dai