Manipulating two-component systems to activate cryptic antibiotic pathways in filamentous actinomycete bacteria

操纵双组分系统激活丝状放线菌中的神秘抗生素途径

• 批准号: BB/Y005724/1
• 负责人: Matthew Hutchings
• 金额: $ 127.72万
• 依托单位: John Innes Centre
• 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%2FY005724%2F1
• 关键词: Manipulating; two; component; systems; activate

Most of the antibiotics we use in human medicine are derived from the natural products of soil bacteria and fungi. We call these natural products "specialised metabolites" because they have specialised functions that help the producing organisms survive in their highly competitive soil environment, but they are not required for the organism to grow in the laboratory. These molecules are often toxic to other bacteria and fungi, but some of them can also kill worms, insects and even plants and many have been used as medicines and as herbicides and pesticides in agriculture. They are incredibly useful and valuable to humans.The biggest producers of specialised metabolites are a genus of bacteria called Streptomyces, which make 55% of the antibiotics we use as medicines. These bacteria are important to human survival, but we have relatively little understanding of how they control the production of their specialised metabolites. This is important because they only make 10% of their specialised metabolites when we grow them in the laboratory. We know this from sequencing all the DNA in their cells which shows they have the instructions and capacity to make many more, we just don't know how to switch on their production. If we can understand how to do this we can discover new antibiotics that will help us treat drug resistant infections and address the antimicrobial resistance crisis. The biosynthetic pathways for each specialised metabolite are encoded by genes which are clustered together on the chromosome and we call them biosynthetic gene clusters (BGCs). If we can activate all of these BGCs we will be able to discover new antibiotics. Up to 25% of the BGCs in any Streptomyces genome also encode two-component systems which sense environmental signals and respond by altering target gene expression. These systems also interact with biosynthetic enzymes to exert multilevel (transcriptional and post translational) control of antibiotic biosynthesis. We have recently shown that by simply over-producing the two component systems encoded by individual BGCs we can switch on antibiotic production in strains that don't usually have antibiotic activity. This is exciting as it suggests we are switching on some of the 90% of biosynthetic pathways that are usually silent under laboratory conditions and this simple technique could enable us and other researchers around the world to discover new antibiotics and other useful molecules. In this proposal we will characterise all seven of the BGC-encoded two component systems in our model organism Streptomyces formicae to identify the genes they control, the proteins they interact with and the specialised metabolites that are produced when we over-express these two component systems. This will identify new antibiotics and will also give us detailed understanding of the roles of BGC-encoded two-component systems in a single organism. We will then extend this to five other strains we have cultured from diverse environments to see if over-expressing the two component systems encoded in their BGCs activates antibiotic production in these organisms. We will share the data, results and techniques widely through public databases, preprints, publications and on http://actinobase.org, a wiki we set up to share protocols and information for working with actinomycetes. We hope that the outputs from this project will help the global research community to activate antibiotic production in their strains of interest and so accelerate the rate of antibiotic discovery.

我们在人类医学中使用的大多数抗生素都源自土壤细菌和真菌的天然产物。我们将这些天然产物称为“特殊代谢物”，因为它们具有特殊的功能，可以帮助生产生物体在高度竞争的土壤环境中生存，但它们并不是生物体在实验室中生长所必需的。这些分子通常对其他细菌和真菌有毒，但其中一些也可以杀死蠕虫、昆虫甚至植物，许多已被用作药物以及农业中的除草剂和杀虫剂。它们对人类非常有用和有价值。专门代谢物的最大生产者是一种称为链霉菌的细菌，我们用作药物的抗生素中有 55% 是由它产生的。这些细菌对人类生存很重要，但我们对它们如何控制其特殊代谢物的产生知之甚少。这很重要，因为当我们在实验室培养它们时，它们只能产生 10% 的特殊代谢物。我们通过对它们细胞中的所有 DNA 进行测序得知这一点，这表明它们拥有制造更多DNA的指令和能力，但我们只是不知道如何启动它们的生产。如果我们能够了解如何做到这一点，我们就可以发现新的抗生素，这将有助于我们治疗耐药感染并解决抗菌素耐药性危机。每种专门代谢物的生物合成途径由聚集在染色体上的基因编码，我们将其称为生物合成基因簇（BGC）。如果我们能够激活所有这些 BGC，我们将能够发现新的抗生素。任何链霉菌基因组中高达 25% 的 BGC 也编码双组分系统，这些系统可感知环境信号并通过改变靶基因表达来做出反应。这些系统还与生物合成酶相互作用，对抗生素生物合成进行多级（转录和翻译后）控制。我们最近表明，通过简单地过量生产由单个 BGC 编码的两个组成系统，我们可以在通常不具有抗生素活性的菌株中开启抗生素生产。这是令人兴奋的，因为它表明我们正在打开 90% 的生物合成途径中的一些，这些途径在实验室条件下通常是沉默的，这种简单的技术可以使我们和世界各地的其他研究人员发现新的抗生素和其他有用的分子。在本提案中，我们将描述我们的模式生物蚁群链霉菌中所有七个 BGC 编码的两个组件系统，以识别它们控制的基因、它们相互作用的蛋白质以及当我们过度表达这两个组件系统时产生的专门代谢物。这将鉴定新的抗生素，并使我们详细了解 BGC 编码的双组分系统在单一生物体中的作用。然后，我们将把这一方法扩展到我们在不同环境中培养的其他五种菌株，看看过度表达 BGC 中编码的两个组分系统是否会激活这些生物体中的抗生素产生。我们将通过公共数据库、预印本、出版物以及 http://actinobase.org 广泛共享数据、结果和技术，http://actinobase.org 是我们为共享放线菌工作方案和信息而建立的维基百科。我们希望该项目的成果将帮助全球研究界激活其感兴趣菌株的抗生素生产，从而加快抗生素发现的速度。