21EBTA: Engineering Biology with Synthetic Genomes (EBSynerGy)

酵母，酿酒酵母，几个世纪以来一直被用来烘焙面包和酿造。酵母在世界上许多重要的工业生物技术应用中得到了广泛的应用，是一种在基础研究中具有重要意义的真核生物模型。在过去的十年里，一个大型的国际财团(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在一起，创造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功能，以便为新的应用快速优化。例如，基因组扰乱功能允许研究人员像一副牌一样重新洗牌基因组，并可以应用于产生具有更好性能的突变菌株，用于工业应用。然而，基因组混乱可能会导致必要基因的丢失，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一个专门的“新染色体”上，以创造Sc3.0细胞。这些新的Sc3.0细胞将在扰乱过程中保留必要的基因，以便更多的细胞以理想的特征存活下来。我们将利用合成酵母(Sc2.0/3.0)作为生产有价值的天然产品(如抗生素)、降胆固醇药物(他汀类药物)和制造信使核糖核酸疫苗(如辉瑞的COVID疫苗)所需前体的平台。通向目标化合物的途径将被引入合成酵母中，基因组扰乱将被用来创造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品结合的生物传感器，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，我们将使用合成酵母高效地生产新一代功能性蛋白质。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侵袭的抗体。这些蛋白质是链(聚合物)，仅由20个被称为氨基酸的构件组成。近年来，出现了一项令人兴奋的技术，称为遗传密码扩展(GCE)，它允许我们从这20多个构建块中生产蛋白质。这项技术在细菌细胞中得到了很好的应用，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工具并不能有效地运行。在这里，我们将开发专门针对蛋白质生产进行优化的酵母菌株，并扩大构建块的范围。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。

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.