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.

酵母，酿酒酵母，几个世纪以来一直被用于烘烤面包和酿造。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非常重要的真核生物模型。在过去的十年中，一个大型国际财团（Sc2.0）一直在合成酵母染色体（共16条）。我们的目标是将这些染色体联合收割机创造出世界上第一个完全合成的真核细胞，它具有许多内置的设计特征，可以快速优化新的应用。例如，基因组打乱功能允许研究人员像一副牌一样重新洗牌基因组，并可用于产生具有改进特性的突变菌株，以供工业应用。然而，基因组混乱可能导致杀死细胞的必需基因的丢失。有鉴于此，我们建议将所有必需基因重新定位到专门的“新染色体”上，从而创建Sc3.0细胞。这些新的Sc3.0细胞将在混乱过程中保留必要的基因，以便更多的细胞以理想的性状存活。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COVID疫苗）所需的前体的平台。将在合成酵母中引入目标化合物的途径，并使用基因组加扰来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乱序突变细胞。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有效地生产新一代功能化蛋白质。自然界产生的蛋白质具有非常广泛的功能，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。这些蛋白质是由20种氨基酸组成的链（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），它允许我们从这20多个构建模块中生产蛋白质。这项技术在细菌细胞中得到了很好的发展，但不幸的是，许多蛋白质只能在酵母等高等生物中产生，而在这里，许多重要的GCE工具不能有效地运行。在这里，我们将开发酵母菌株，这些酵母菌株专门为生产具有扩大范围的构建模块的蛋白质而优化。这些菌株将为新一代蛋白质疗法、催化剂和材料的开发奠定基础。

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

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

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

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

Safety by design: Biosafety and biosecurity in the age of synthetic genomics.

• DOI: 10.1016/j.isci.2023.106165
• 发表时间: 2023-03-17
• 期刊: ISCIENCE
• 影响因子: 5.8
• 作者: Hoffmann, Stefan A.;Diggans, James;Densmore, Douglas;Dai, Junbiao;Knight, Tom;Leproust, Emily;Boeke, Jef D.;Wheeler, Nicole;Cai, Yizhi
• 通讯作者: Cai, Yizhi