21EBTA: Engineering Biology with Synthetic Genomes (EBSynerGy)

酵母（Saccharomyces cerevisiae）几个世纪以来一直被用来烤面包和酿酒。酵母在世界范围内广泛应用于许多重要的工业生物技术应用，是一种在基础研究中具有重要意义的真核生物模型。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，它具有许多内置的设计特征，可以快速优化新的应用。例如，基因组搅乱功能允许研究人员像洗牌一样重新洗牌基因组，并可用于产生具有改进性能的突变株，以供工业应用。然而，基因组混乱会导致基本基因的丢失，从而杀死细胞。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细胞将在争夺过程中保留必要的基因，因此更多的细胞存活下来并具有理想的性状。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mRNA疫苗生产所需的前体（例如辉瑞的COVID疫苗）的平台。将在合成酵母中引入目标化合物的途径，并使用基因组混乱来产生大量产生目标化合物的突变体。我们还将开发能够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混乱突变细胞。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，我们将利用合成酵母高效生产新一代功能化蛋白。大自然产生的蛋白质具有一系列非凡的功能，从加速生命所需的生化反应的酶到保护我们免受传染病侵害的抗体。这些蛋白质是链（聚合物），仅由20个称为氨基酸的构建块组成。近年来出现了一项令人兴奋的技术，称为遗传密码扩展（GCE），它使我们能够从这20多种构建块中产生蛋白质。这项技术已经发展得很好，可以用于细菌细胞，但不幸的是，许多蛋白质只能在酵母等高等生物中产生——在这里，许多重要的GCE工具不能有效地运作。在这里，我们将开发酵母菌株，专门为生产具有扩展范围的构建块的蛋白质而优化。这些菌株将支持新一代蛋白质疗法、催化剂和材料的发展。

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.