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.

酿酒酵母的酵母菌已经使用了几个世纪来烘烤面包和酿造。酵母在许多重要的工业生物技术应用中都在世界各地使用，并且是基础研究中非常重要的真核生物。在过去的十年中，一个大型国际财团（SC2.0）一直在综合酵母染色体（总共16个）。我们旨在将这些染色体结合起来，以创建世界上第一个完全合成的真核细胞，该染色体具有许多内置的设计功能，以允许其快速优化新应用。例如，基因组刮擦功能使研究人员可以像卡片甲板一样重新拆除基因组，并可以应用于具有改进特性的突变菌株用于工业应用。但是，基因组争夺可能导致杀死细胞的必需基因的丧失。鉴于此，我们建议将所有必需基因重新定位到创建SC3.0细胞的专用“新染色体”上。这些新的SC3.0细胞将在争夺过程中保留必需基因，从而使更多的细胞以理想的特征存活。我们将利用合成酵母（SC2.0/3.0），作为生产有价值的天然产品（例如抗生素），降低胆固醇降低剂（Statins）的平台和制造mRNA疫苗所需的前体（例如，辉瑞公司的同效疫苗）。将在合成酵母中引入靶化合物的途径，基因组争夺将用于产生大量产生靶化合物的突变体。我们还将开发可与目标产物结合的生物传感器，从而触发荧光响应，使我们能够迅速选择产生最高水平靶化合物的炒突变细胞。此外，我们将开发新的成像方法，这些方法可以快速鉴定产生所需化合物的细胞。最后，我们将使用合成酵母有效地生产新一代的功能化蛋白质。大自然产生具有非凡功能范围的蛋白质，从加速生命所需的生化反应的酶到保护我们免受传染病的抗体。这些蛋白质是仅由称为氨基酸的二十个构件制成的链（聚合物）。近年来，出现了一种令人兴奋的技术，称为遗传代码扩展（GCE），该技术使我们能够从超过20个构建基础中生产蛋白质。该技术用于细菌细胞中，但不幸的是，许多蛋白质只能在诸如酵母等较高生物体中生产 - 在这里，许多重要的GCE工具都无法有效运行。在这里，我们将开发酵母菌菌株，这些酵母菌菌株专门针对具有扩展构建块范围的蛋白质的生产进行了优化。这些菌株将支持新一代蛋白质疗法，催化剂和材料的发展。

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

The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering.

• DOI: 10.1038/s41467-022-32661-x
• 发表时间: 2022-08-29
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Herisson, Joan;Duigou, Thomas;du Lac, Melchior;Bazi-Kabbaj, Kenza;Azad, Mahnaz Sabeti;Buldum, Gizem;Telle, Olivier;El Moubayed, Yorgo;Carbonell, Pablo;Swainston, Neil;Zulkower, Valentin;Kushwaha, Manish;Baldwin, Geoff S.;Faulon, Jean-Loup
• 通讯作者: Faulon, Jean-Loup