Genome Organisation for Optimising Synthetic Secondary Metabolism

用于优化合成次级代谢的基因组组织

• 批准号: BB/K006290/1
• 负责人: Thomas Ellis
• 金额: $ 43.45万
• 依托单位: Imperial College London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2013
• 资助国家: 英国
• 起止时间: 2013 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FK006290%2F1
• 关键词: Genome; Organisation; Optimising; Synthetic; Secondary

This project will research genome organisation and in particular how changing the location and arrangement of metabolic enzyme genes within a yeast genome can alter the amount of the metabolite they produce, in this case the antibiotic penicillin. Antibiotics are just one class of complex chemicals that the diverse array of organisms on Earth has naturally evolved to produce. The production of chemicals by life is known as metabolism and the more complex high-value chemicals that specialist cells produce (e.g. in plants) are called secondary metabolites and these include most therapeutic molecules known today. Production of secondary metabolites in cells requires specific enzymes which are encoded by genes usually under strict control (regulation). As our understanding of biology improves through many fundamental research breakthroughs, scientists are now looking to re-engineer secondary metabolism to produce valuable compounds in cellular systems that are easy to work with. Microbes like brewer's yeast are perfect as they are easy to culture and so could cheaply produce high yields of valuable compounds from renewable resources like sugar.The most promising way to perform this 'metabolic engineering' is to use what is known as a synthetic biology approach, where genes and their controllers are treated as modular components with well-defined behaviours and then combined in a rational design-based manner. So far the synthetic biology approach to metabolic engineering has been successful in producing compounds useful as anti-malarials, cosmetics and biofuels by taking genes for enzymes found in plants and exotic microbes and combining these inside industrially-used microbes such as yeast. Crucial for achieving high yields of production in these microbes is fine-control over the precise levels of enzymes in each cell.One method of tuning enzyme levels that is currently unexplored by scientists is how the genes for these enzymes are physically arranged within a cell's genome. It is already known that gene location and orientation within a genome plays an important role in gene expression in all forms of life. Recently, it has also been established that in cells that naturally perform secondary metabolism, such as plant cells, the location of genes that make up a pathway is often tightly conserved, usually in occurring in gene 'clusters' in areas known as 'sub-telomeric regions'. Clearly, if nature and evolution are correct, then the location of where pathway genes are added to a genome must affect the enzyme levels and therefore the pathway output.This project seeks to test the hypothesis that modifying pathway gene location within a genome can result in improved yields of a high-value secondary metabolite, in this case penicillin. The genes encoding the penicillin pathway will be added to the genome of a lab yeast strain and cells will be selected that produce the greatest amounts of penicillin. The amount produced will then be monitored in a series of experiments where the pathway genes are systematically rearranged around five different places in the genome. This will give valuable information on how the arrangement of genes in the genome affects the pathway. Finally, the pathway genes will be placed in an engineered lab strain specifically designed to shuffle parts of its genome when under an evolutionary pressure. The strain will be grown to compete against bacteria and in doing will automatically rearrange pathway genes to produce the most penicillin. This project will therefore provide an important new synthetic biology approach to metabolic engineering, and also uncover valuable new information on the fundamental science of genomes and genome evolution.

该项目将研究基因组组织，尤其是如何改变酵母基因组中代谢酶基因的位置和排列可以改变其产生的代谢物的量，在这种情况下为抗生素青霉素。抗生素只是一类复杂化学物质，地球上各种生物自然会产生。生命的化学物质的产生称为代谢，而专业细胞产生的更复杂的高价值化学物质（例如，在植物中）称为二级代谢产物，其中包括当今已知的大多数治疗分子。细胞中二级代谢产物的产生需要特定的酶，这些酶通常由严格控制（调节）在严格控制下编码。随着我们对生物学的理解通过许多基本研究的突破得到改善，科学家现在正在寻求重新设计二级代谢，以在易于使用的细胞系统中生产有价值的化合物。像啤酒酵母这样的微生物是完美的，因为它们易于培养，因此可以从糖等可再生资源（如糖）中廉价地产生高产量的有价值的化合物。到目前为止，代谢工程的合成生物学方法通过在植物和外来微生物中发现的酶来生产抗疟疾，化妆品和生物燃料的化合物成功，并将这些化合物（如酵母菌（如酵母））结合在一起。在每个细胞中精确水平的酶水平上，在这些微生物中实现高产量的至关重要。一种调谐酶水平的方法，科学家目前尚未探索的酶水平是这些酶的基因在细胞基因组中的物理排列。众所周知，基因组中的基因位置和取向在所有形式的生命中都在基因表达中起重要作用。最近，还已经确定，在自然执行次级代谢的细胞中，例如植物细胞，构成途径的基因的位置通常是紧密保守的，通常在称为“亚tel体区域”的基因“簇”中发生。显然，如果自然和进化是正确的，那么将途径基因添加到基因组中的位置必须影响酶水平，因此途径输出。该项目试图检验以下假设：在这种情况下，在这种情况下，在基因组中修改途径基因位置可以改善基因组中的基因位置，从而提高高价值代谢物的产量。编码青霉素途径的基因将被添加到实验室酵母菌菌株的基因组中，并选择产生最大量的青霉素的细胞。然后，将在一系列实验中监测所产生的量，其中途径基因在基因组中的五个不同位置进行了系统重排。这将提供有关基因在基因组中的排列如何影响途径的宝贵信息。最后，途径基因将被放置在专门设计的工程实验室菌株中，以在进化压力下进行基因组的各个部分。该菌株将成长以与细菌竞争，并且在执行过程中将自动重新排列途径基因，从而产生最多的青霉素。因此，该项目将为代谢工程提供一种重要的新合成生物学方法，并发现有关基因组和基因组进化基础科学的有价值的新信息。

项目成果

The Synthetic Genome Summer Course.

合成基因组暑期课程。

• DOI: 10.1093/synbio/ysy020
• 发表时间: 2018
• 期刊: Synthetic biology (Oxford, England)
• 作者: Blount BA

Burden-driven feedback control of gene expression

• DOI: 10.1101/177030
• 发表时间: 2017-08
• 期刊: Nature Methods
• 影响因子: 48
• 作者: Francesca Ceroni;Alice Boo;Simone Furini;T. Gorochowski;Olivier Borkowski;Y. Ladak;A. Awan;Charlie Gilbert;G. Stan;T. Ellis