Engineering Streptomyces bacteria for the sustainable manufacture of antibiotics

链霉菌制造抗生素，使它们能够在环境中生存，这些分子在临床上被用作抗生素，没有它们，许多现代医学将停止发挥作用。抗生素的工业生产是通过使用专门的培养基在大型发酵罐中培养链霉菌来实现的。使用的细菌不是野生型链霉菌，而是经过广泛“改进”以帮助它们有效地制造更多抗生素的菌株。链霉菌的“改良”过程可以被看作是植物或动物的选择性育种，其中那些表现出最佳性状的被选中以供将来使用。这意味着每一代都更适合发酵罐中的生长和人工生长培养基，而不是环境。然而最重要的是，它们产生了更多的抗生素。所有工业链霉菌菌株都是这样做的，生产商业数量的抗生素是一个漫长而艰苦的过程。在这些发酵中使用的生长培养基（通常称为原料）是高度精炼的，通常是昂贵的，并且可以与人类和动物营养竞争使用。为了应对气候危机，英国政府制定了雄心勃勃的净零目标，以提高工业过程的可持续性。实现这些目标和提高抗生素生产可持续性的一种方法是利用废物作为原料。近年来，面包垃圾作为可持续发酵原料引起了人们的关注，因为食品工业每年产生数百万吨的垃圾。实现这一目标的一个主要限制是链霉菌的抗生素生产受到原料中营养物质的严格调节，某些营养来源导致制造抗生素的细胞机制受到抑制。这意味着一些原料与高水平的生产不兼容，成为工业采用它们的障碍。我们相信这是一个解决方案，通过使用工程生物学的原理来合理地修改现有的高产链霉菌菌株。为了验证这一点，我们将与葛兰素史克（GSK）合作。葛兰素史克生产一种重要的抗生素——克拉维酸（clavulanic acid， CA），被世界卫生组织（World Health Organisation）视为基本药物之一。我们将采用工程中的设计-构建-测试-学习原则来分析gsk高产链霉菌菌株的基因组，并使用基因组规模建模来确定它们产生大量CA的原因。我们将利用这些信息修改限制抗生素生产的机制，设计遗传电路并引入其他细菌的基因，使它们能够利用食物垃圾中的原料而不损失任何生产力。然后，我们将在一系列规模上对我们的新工程菌株进行实验测试，并与GSK合作，我们将获得他们的工业开发设施来测试生产力。我们认为这种利用可持续碳源的链霉菌工程方法也将转化为其他工业生产的链霉菌抗生素。这是可能的，因为许多抗生素的构建模块来自与CA的构建模块相同的代谢部分。我们对这项工程生物学任务的方法将使工业抗生素生产更容易，更快速，更可持续。

Streptomyces bacteria make antibiotics to enable them to survive in the environment and it is these molecules that are used clinically as antibiotics, without which, much of modern medicine would cease to function. Industrial production of antibiotics is achieved by growing Streptomyces in large fermenters using specialised media. The bacteria used are not the wild-type Streptomyces, but strains that have undergone extensive rounds of 'improvement' to help them efficiently make more antibiotics. The 'improvement' process for Streptomyces can be thought of like selective breeding of plants or animals, where those exhibiting the best traits are selected for future use. This means that each generation is better adapted for growth and artificial growth media in the fermenter, rather than environment. Yet most importantly they produce more antibiotics. This has been done for all industrial Streptomyces strains and it is a long and laborious process to produce commercial amounts of antibiotic. The growth media (often called feedstocks) used in these fermentations is highly refined, often expensive and can have competing uses with human and animal nutrition. To address the climate crisis the UK government has set ambitious net zero goals to improve the sustainability of industrial processes. One way to address these targets and to increase the sustainability of antibiotic production is to utilise waste products as feedstocks. Recently bread waste has attracted attention as sustainable fermentation feedstock as millions of tons each year are produced as waste from the food industry. A major limitation to achieving this is that the production of antibiotics by Streptomyces is tightly regulated by availability of nutrients in the feedstock, with certain nutrition sources resulting in the repression of the cellular machinery that makes the antibiotic. This means that some feedstocks are not compatible with high levels of production, acting as a barrier to their adoption by industry. We believe there is a solution to this, by using the principles of engineering biology to rationally modify existing, high-producing Streptomyces strains. To test this, we will collaborate with GSK, who make an important antibiotic called clavulanic acid (CA), which the World Health Organisation considers as one of its essential medicines. We will employ the design-build-test-learn principles from engineering to analyse the genomes of GSKs high-producing strains of Streptomyces and use genome scale modelling to identify why they produce large amounts of CA. We will use this information to modify the machinery that constrains antibiotic production with certain feedstocks, design genetic circuits and introduce genes from other bacteria that will allow them to utilise feedstocks from food waste without any loss to productivity. We will then experimentally test our newly engineered strains at a range of scales and in collaboration with GSK, we will have access to their industrial development facilities to test productivity. We think that this approach to engineering Streptomyces to utilise sustainable carbon sources will also translate to other industrially produced Streptomyces antibiotics. This is possible because the building blocks for many antibiotics are derived from the same parts of metabolism as the building blocks for CA. Our approach to this engineering biology mission will make it easier and quicker to make industrial antibiotic production more sustainable.