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

链霉菌是一种制造抗生素的细菌，使它们能够在土壤中生存。正是这些分子构成了临床上使用的抗生素的三分之二，没有它们，现代医学就无法发挥作用。它们用于治疗感染，但也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）中广泛使用，以预防感染。近年来抗生素耐药感染的增加表明，我们迫切需要提高现有抗生素的生产效率，以帮助对抗耐药性危机。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“改进”过程可以被认为是植物或动物的选择性育种或驯化过程，在这些过程中，那些表现出最佳特征的物种被选择用于未来的育种。这意味着每一代都更适合在发酵罐中生长，而不是在土壤中生长，并产生更多的抗生素。为了产生改良的菌株，链霉菌暴露在化学物质中，使其DNA发生变化（突变），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）。我们已经对所有的工业链霉菌菌株进行了研究，但我们对最佳菌株的变化种类知之甚少，因此也不知道是什么使它们成为抗生素的良好过度生产者。这意味着每一种新的抗生素都必须经历一个漫长而艰苦的过程，才能生产出商业数量的抗生素。35年来，葛兰素史克一直在对链霉菌进行诱变和选择，以生产一种重要的抗生素——克拉维酸（CA）。世界卫生组织将CA视为其基本药物之一，了解CA的生产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增加抗生素的产量对我们能够更好地利用链霉菌用于人类医学和农业非常重要。为了实现这一目标，我们一直在分析链霉菌产生GSK CA的谱系的基因组，并确定使它们产生比野生型菌株多5倍CA的突变。我们将通过实验测试这些突变中的每一个，看看哪些是导致CA产量增加的原因，以及是否有任何突变限制了CA的产量。这可能是，虽然总的突变有助于增加CA的产生，但一些突变可能会破坏代谢的某些部分，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的顺序积累才能产生有益的影响。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增加了抗生素的产量。我们相信这是可能的，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，我们相信这种方法将使未来更容易和更快地将新抗生素引入临床，以帮助应对日益严重的抗菌素耐药性感染危机。

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.