Taming of the Streptomycete: Understanding the rules of domestication in antibiotic-producing bacteria

驯服链霉菌：了解产生抗生素的细菌的驯化规则

• 批准号: BB/Y00082X/1
• 负责人: Paul Hoskisson
• 金额: $ 59.47万
• 依托单位: University of Strathclyde
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2024
• 资助国家: 英国
• 起止时间: 2024 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FY00082X%2F1
• 关键词: Taming; Streptomycete; Understanding; rules; domestication

Streptomyces are bacteria that make antibiotics to enable them to survive in soil. It is these molecules that comprise around two-thirds of our clinically used antibiotics, without which modern medicine would cease to function. They are used to treat infections, but they are also used extensively prior to surgery and in immunocompromised patients (cancer, transplant patients, HIV/AIDS etc) to prevent infections. The rise in antibiotic resistant infections in recent years has indicated that there is an urgent need for us to increase the production efficiency of existing antibiotics to help combat the resistance crisis. 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 a selective breeding or domestication process for plants or animals, where those exhibiting the best traits are selected for future breeding. This means that each generation is better adapted for growth in the fermenter, rather than soil, and produces more antibiotics. To generate the improved strains, the Streptomyces are exposed to chemicals that bring about changes (mutations) in their DNA, and the resulting strains which show an increase in antibiotic production are chosen for further rounds of improvement (also known as mutagenesis and selection). This has been done for all industrial Streptomyces strains, yet we have very little understanding or knowledge of the kinds of changes the best strains have and therefore what makes them good overproducers of antibiotics. This means that every new antibiotic has to undergo a long and laborious process to produce commercial amounts of antibiotic. GSK have been performing mutagenesis and selection with a strain of Streptomyces for more than 35 years that makes an important antibiotic called clavulanic acid (CA). The World Health Organisation consider CA as one of its essential medicines and understanding the production of CA is important in the fight against antimicrobial resistance.Understanding how antibiotic-producing bacteria can increase the production of antibiotics is important for us to be able to better exploit Streptomyces for human medicine and agriculture. To achieve this, we have been analysing the genomes of the GSK CA-producing lineage of Streptomyces and identifying the mutations that allow them to produce up to five-times more CA than the wild-type strain. We will experimentally test each of these mutations to see which are responsible for the increase in CA production and if any of the mutations limit how much CA can be produced. It may be that while overall the mutations help increase CA production, some mutations may damage certain parts of metabolism, preventing strains from reaching their full potential. It is also possible that the order in which these mutations occurred could determine how good at producing CA the Streptomyces can become. We will use genome editing to test if the mutations need to accumulate in a specific order to have a beneficial effect. Finally, once we have identified some important mutations for increasing CA production, we will try and make the same mutations in other industrially important Streptomyces to see if these changes also increase antibiotic production. We believe that this is possible because the building blocks for many antibiotics are derived from the same parts of metabolism as the building blocks for CA.We believe this approach will make it easier and quicker to bring new antibiotics to the clinic in the future to help combat the growing antimicrobial resistant infection crisis.

链霉菌是产生抗生素以使其能够在土壤中生存的细菌。正是这些分子构成了我们临床使用的抗生素的约三分之二，没有它们，现代医学将无法发挥作用。它们用于治疗感染，但也广泛用于手术前和免疫功能低下的患者（癌症、移植患者、艾滋病毒/艾滋病等）以预防感染。近年来抗生素耐药性感染的上升表明，我们迫切需要提高现有抗生素的生产效率，以帮助应对耐药性危机。抗生素的工业生产是通过使用专用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，而是经过多轮“改进”以帮助它们有效制造更多抗生素的菌株。链霉菌的“改良”过程可以被认为是植物或动物的选择性育种或驯化过程，其中表现出最佳性状的那些被选择用于未来的育种。这意味着每一代都更适应发酵罐而不是土壤中的生长，并产生更多的抗生素。为了产生改良菌株，将链霉菌暴露于会导致其 DNA 变化（突变）的化学物质中，并选择产生的抗生素产量增加的菌株进行进一步的改良（也称为诱变和选择）。所有工业链霉菌菌株都这样做了，但我们对最好的菌株所发生的变化以及是什么使它们成为抗生素的良好生产者知之甚少。这意味着每种新抗生素都必须经历漫长而费力的过程才能生产出商业数量的抗生素。 35 年多来，葛兰素史克 (GSK) 一直在利用链霉菌菌株进行诱变和选择，从而制造出一种名为克拉维酸 (CA) 的重要抗生素。世界卫生组织将 CA 视为基本药物之一，了解 CA 的产生对于对抗抗菌素耐药性非常重要。了解产生抗生素的细菌如何提高抗生素的产量对于我们能够更好地利用链霉菌非常重要用于人类医学和农业。为了实现这一目标，我们一直在分析 GSK 链霉菌产 CA 谱系的基因组，并鉴定出使它们能够比野生型菌株产生最多五倍 CA 的突变。我们将通过实验测试这些突变中的每一个，看看哪些突变导致了 CA 产量的增加，以及是否有任何突变限制了 CA 的产量。虽然总体上突变有助于增加 CA 产量，但某些突变可能会损害新陈代谢的某些部分，从而阻止菌株充分发挥其潜力。这些突变发生的顺序也可能决定链霉菌产生 CA 的能力。我们将使用基因组编辑来测试突变是否需要以特定顺序积累才能产生有益的效果。最后，一旦我们确定了一些增加 CA 产量的重要突变，我们将尝试在其他工业上重要的链霉菌中进行相同的突变，看看这些变化是否也会增加抗生素的产量。我们相信这是可能的，因为许多抗生素的组成部分与 CA 的组成部分源自相同的代谢部分。我们相信这种方法将使未来更容易、更快捷地将新抗生素引入临床，以帮助应对日益严重的抗菌药物耐药性感染危机。