A synthetic genomics platform for antibiotic discovery

用于抗生素发现的合成基因组学平台

• 批准号: 2746098
• 金额: --
• 依托单位: University of Nottingham
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2022
• 资助国家: 英国
• 起止时间: 2022 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2746098
• 关键词: synthetic; genomics; platform; antibiotic; discovery

Antibiotic resistance is the "slow pandemic". A recent UN report estimates that by 2050 it will be responsible for 10 million deaths a year globally, with an economic impact comparable to the 2008 financial crisis. Development of tools to tackle resistance to antimicrobial compounds is of pressing importance and has been identified as a key objective in the BBSRC's Forward Look for UK Bioscience.Nonribosomal peptides (NRPs) represent a diverse class of secondary metabolites and include many antibiotics and antibiotic precursors. They typically consist of amino acids that are assembled enzymatically and then modified by an array of tailoring enzymes. In this way, a core antibiotic molecule can be modified in many ways, potentially circumventing antibiotic resistance mechanisms. We have shown that NRP antibiotic production can be achieved in yeast using a synthetic biology approach. Yeast has an unparalleled genetic toolbox available, opening up new possibilities for discovering novel NRP-derived antibiotics In this project, the student will establish a synthetic yeast platform for production and screening of novel NRP molecules for antibiotic properties. The bacterial co-culture system established in the rotation project will be used to select a strain that is enhanced for penicillin production through SCRaMbLE genome evolution. This strain will then act as the base NRP-production strain for combinatorial prototyping of tailoring enzyme combinations.Bioinformatics tools will be used to identify candidate tailoring enzyme genes from genomic datasets to be tested in our system. Genes will be cloned into a Golden Gate library with SCRaMbLE-compatible formatting. Libraries of different gene combinations will be introduced to the NRP-production strain and SCRaMbLE will be used to further increase host genome and library diversity. These massively diversified libraries will be co-cultured with bacterial strains with different antibiotic resistance profiles. Survival of the yeast cells in these conditions will be reliant on the inhibition of bacterial growth in a way that evades the respective antibiotic resistance mechanism. Strains surviving the assays will be isolated and fully characterised to identify any novel compounds that act as antibiotics or that inhibit antibiotic resistance mechanisms. This work will establish the feasibility of a synthetic yeast approach to antibiotic discovery and may yield novel antimicrobial compounds. The system could subsequently be expanded to include a wider range of candidate tailoring enzymes and additional NRP molecules. Supervision Team - Benjamin Blount is an expert in synthetic genomics and a member of the International Synthetic Yeast Genome Project. He was part of the first team to successfully engineer NRP antibiotic production into S. cerevisiae yeast and was the first to demonstrate that SCRaMbLE can be used to improve production from engineered pathways, including penicillin. John Heap is an expert in combinatorial approaches to metabolic engineering and the application of synthetic biology techniques to the improvement of strains for biotechnology.

抗生素耐药性是一种“缓慢流行病”。联合国最近的一份报告估计，到2050年，全球每年将有1000万人死亡，其经济影响与2008年金融危机相当。开发解决抗微生物化合物耐药性的工具具有紧迫的重要性，并已被确定为BBSRC的英国生物科学前瞻性研究的关键目标。非核糖体肽（NRP）代表了多种次级代谢产物，包括许多抗生素和抗生素前体。它们通常由酶促组装然后由一系列剪裁酶修饰的氨基酸组成。通过这种方式，核心抗生素分子可以以多种方式进行修饰，从而潜在地规避抗生素耐药性机制。我们已经证明，NRP抗生素的生产可以在酵母中使用合成生物学方法实现。酵母具有无与伦比的遗传工具箱，为发现新型NRP衍生抗生素开辟了新的可能性在这个项目中，学生将建立一个合成酵母平台，用于生产和筛选新型NRP分子的抗生素特性。在轮换项目中建立的细菌共培养系统将用于选择通过SCRaMbLE基因组进化增强青霉素生产的菌株。然后，该菌株将作为基础NRP生产菌株，用于剪裁酶组合的组合原型设计。生物信息学工具将用于在我们的系统中测试的基因组数据集中识别候选剪裁酶基因。将基因克隆到具有SCRaMbLE兼容格式的Golden Gate文库中。不同基因组合的文库将被引入NRP生产菌株，SCRaMbLE将用于进一步增加宿主基因组和文库多样性。这些大规模多样化的文库将与具有不同抗生素抗性谱的细菌菌株共培养。酵母细胞在这些条件下的存活将依赖于以逃避相应抗生素抗性机制的方式抑制细菌生长。将分离在试验中存活的菌株，并对其进行充分表征，以鉴定任何用作抗生素或抑制抗生素耐药性机制的新型化合物。这项工作将建立一个合成酵母方法的抗生素发现的可行性，并可能产生新的抗菌化合物。该系统随后可以扩展到包括更广泛的候选剪裁酶和额外的NRP分子。本杰明·布朗特是合成基因组学专家，也是国际合成酵母基因组计划的成员。他是第一个成功地将NRP抗生素生产改造成S。酿酒酵母，是第一个证明SCRaMbLE可用于提高生产工程途径，包括青霉素。约翰·希普是代谢工程组合方法和合成生物学技术应用于生物技术菌株改良的专家。