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.

链霉菌是使抗生素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三分之二，没有现代药物就无法发挥作用。它们用于治疗感染，但在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）中也被广泛使用，以防止感染。近年来，抗生素耐药性感染的增加表明，我们迫切需要提高现有抗生素的生产效率，以帮助消除抵抗危机。通过使用专业培养基在大型发酵罐中种植链霉菌来实现抗生素的工业生产。所使用的细菌不是野生型链霉菌，而是经过大量“改进”的菌株，以帮助它们有效地产生更多的抗生素。可以将链霉菌的“改进”过程视为植物或动物的选择性繁殖或驯化过程，在这些植物或动物中，选择最佳特征的人是为了将来的繁殖。这意味着每一代都更好地适应发酵罐的生长，而不是土壤，并产生更多的抗生素。为了产生改善的菌株，链霉菌暴露于在其DNA中导致变化（突变）的化学物质，并且所得的菌株选择了抗生素产生增加的菌株以进行进一步的改进（也称为诱变和选择）。这是针对所有工业链霉菌菌株所做的，但是我们对最佳菌株具有的各种变化几乎没有理解或了解，因此使它们成为抗生素的过度生产剂。这意味着每种新的抗生素都必须经历漫长而费力的过程，以产生商业量的抗生素。 GSK一直在用链霉菌菌株进行诱变和选择超过35年，这使得一种称为clavulanic酸（CA）的重要抗生素。世界卫生组织将CA视为其必不可少的药物之一，并且了解CA的产生对于反对抗菌耐药性很重要。理解抗生素产生的细菌如何增加抗生素的产生，这对我们对更好地利用人类药物和农业的利用。为了实现这一目标，我们一直在分析链霉菌的GSK CA产生谱系的基因组，并鉴定出使它们产生的Ca比野生型菌株高五倍的突变。我们将通过实验测试这些突变中的每一个，以查看哪些是造成CA产量增加的原因，以及任何突变是否限制了可以产生多少Ca。可能是，尽管总体上这些突变有助于增加CA产量，但某些突变可能会损害代谢的某些部分，从而阻止菌株发挥其全部潜力。这些突变发生的顺序也可以决定产生链霉菌的良好状况。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效果。最后，一旦我们确定了增加CA产量的一些重要突变，我们将尝试在其他重要的链霉菌中进行相同的突变，以查看这些变化是否也增加了抗生素的产生。我们认为这是可能的，因为许多抗生素的基础是与CA的基础相同的代谢部分得出的。我们相信，这种方法将使将来将新的抗生素带入诊所，以帮助打击不断增长的抗菌抗菌感染感染危机。