Genome synthesis of a universal synthetic host for antimicrobial drug production - towards the first deep-engineering of an actinobacterial genome

抗菌素耐药性是一个亟待解决的问题，需要通过发现新的抗菌药来解决。基因组测序表明，微生物基因组编码有能力产生大量不同的化合物，包括数千种潜在的抗菌剂。然而，这些药物中只有一小部分目前正在临床使用，而且绝大多数仍然没有特征性。一个主要的瓶颈是，化合物生产的遗传机制在正常情况下往往不活跃--发现和表征抗菌素线索通常需要将它们转移到异源宿主物种。然而，典型的候选宿主利用从无关生物转移的遗传机制生产新化学物质的能力有限。在这个项目中，我们将利用合成基因组学的力量克服这一障碍。我们将探索放线杆菌类中一组特别有才华的抗菌剂生产者的基因组的共同设计特征，他们已经进化出一种高度灵活的新陈代谢，预先适应了使用水平获得的生物合成机械生产高水平的各种化合物。我们将利用这些信息和从早期设计抗菌高产菌株的尝试中获得的见解，设计一个通用的抗菌宿主基因组，我们将使用从头开始和基于模板的策略的创新组合来合成它，利用新兴的基因组合成技术和工作流自动化方面的进展。创建一个由放线细菌衍生的通用合成宿主基因组，它可以以灵活、模块化的即插即用方式产生广泛的新化合物，这将极大地扩展我们获取基因组序列所揭示的抗菌宝藏的能力。它还将促进使用组合方法创建生物合成途径变异体库的化合物修饰和多样化的后续步骤。同时，该项目工作将极大地增强两个东道国的合成基因组学能力。基因组合成在许多方面仍然不成熟，包括昂贵、劳动密集型和自动化程度不够。在这里，我们汇集了互补的专业知识，以建立一个创新的基因组合成工作流程，适合于解决创建合成放线菌基因组的主要技术挑战。这些目标将由来自英国曼彻斯特大学和东京工业大学以及日本名古屋大学的强大互补的研究团队共同实现。我们的团队在使用新兴技术方面拥有专业知识，包括计算分析(用于重新设计基因组以进行合成)、人工智能/机器学习(将数据转化为基因组设计策略)、自动化(用于创建合成基因组和DNA结构)、天然产品研究(确定抗菌剂是如何生产和修饰的)、微流控(用于快速合成微小体积的基因组部分)和DNA化学(用于设计DNA合成的新化学反应)。在项目期间，所有团队成员将通过互访英国和日本，以及通过组织国际研讨会将天然产品和工程生物界聚集在一起，从而实现密切的互动。早期职业研究人员和技术人员是我们团队的重要成员，他们将积极参与该项目，这将使他们能够获得国际经验和独立性，同时通过密集的交流访问获得新的技术技能。

Antimicrobial resistance is an urgent problem that needs to be tackled by discovering new antimicrobial drugs. Genome sequencing has shown that microbial genomes encode the capability to produce an enormous variety of different chemical compounds, including thousands of potential antimicrobials. However, only a tiny fraction of these is currently being clinically used and the vast majority remains uncharacterised. A major bottleneck is the fact that the genetic machinery for compound production tends to be inactive under normal conditions - discovering and characterising antimicrobial leads usually requires their transfer to a heterologous host species. However, typical host candidates are limited in their ability to produce novel chemicals using the transferred genetic machinery from unrelated organisms. In this project we will overcome this barrier using the powers of synthetic genomics. We will explore the common design features of the genomes of a particularly talented group of antimicrobial producers, in the class Actinobacteria, which have evolved a highly flexible metabolism pre-adapted to the production of high levels of a wide variety of compounds using horizontally acquired biosynthetic machinery. We will use this information and insights from earlier attempts to engineer antimicrobial high-production strains, to design a universal antibacterial host genome, which we will synthesise using an innovative combination of de-novo and template-based strategies, exploiting emerging genome synthesis techniques and advances in workflow automation. Creating an actinobacterial-derived universal synthetic host genome, which can produce a broad range of new chemicals compounds in a flexible, modular plug-and-play manner, will greatly expand our ability to access the antimicrobial treasures revealed by genome sequences. It will also facilitate the subsequent steps of compound modification and diversification using combinatorial approaches to create libraries of biosynthetic pathway variants. At the same time, the project work will greatly enhance the synthetic genomics capabilities in both host countries. Genome synthesis is still immature in many senses including expensive, labour-intensive, and not sufficiently automated. Here, we bring together complementary expertise to establish an innovative genome synthesis workflow suitable for tackling the major technical challenges of creating synthetic actinobacterial genomes.These aims will be realised together by the strongly complementary teams of researchers from the University of Manchester and the Tokyo Institute of Technology and Nagoya University, in the UK and Japan, respectively. Together, our teams have expertise in the use of emerging technology in computational analysis (for redesigning the genome for synthesis), artificial intelligence/machine learning (to turn data into genome design strategies), automation (for creating synthetic genomes and DNA constructs), natural product research (to determine how the antimicrobials are produced and modified), microfluidics (for the rapid synthesis of genome parts in tiny volumes), and DNA chemistry (for designing new chemical reactions of DNA synthesis). Close interactions of all team members will be enabled by exchange visits to both the UK and Japan, during the project, as well as by organising an international symposium to bring together the natural products and engineering biology community.Early career researchers and technicians are important members of our teams and will actively participate to the project, which will allow them to gain international experience and independence, while acquiring novel technical skills through the intense exchange visits.