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

抗微生物药物耐药性是一个迫切的问题，需要通过发现新的抗微生物药物来解决。基因组测序表明，微生物基因组编码了产生多种不同化合物的能力，包括数千种潜在的抗菌剂。然而，其中只有一小部分目前被临床使用，绝大多数仍未表征。一个主要的瓶颈是，化合物生产的遗传机制在正常条件下往往是不活跃的——发现和鉴定抗菌先导通常需要将它们转移到异源宿主物种。然而，典型的宿主候选者在使用从不相关的生物体转移的遗传机制产生新化学物质的能力上是有限的。在这个项目中，我们将利用合成基因组学的力量克服这个障碍。我们将探索放线菌类中一组特别有天赋的抗微生物生产者的基因组的共同设计特征，放线菌类已经进化出高度灵活的代谢，预先适应使用水平获得的生物合成机器生产高水平的各种化合物。我们将利用这些信息和早期尝试的见解来设计抗菌高产菌株，设计一个通用的抗菌宿主基因组，我们将使用de-novo和基于模板的策略的创新组合来合成，利用新兴的基因组合成技术和工作流程自动化的进步。创建一个放线菌衍生的通用合成宿主基因组，它可以以灵活，模块化即插即用的方式产生广泛的新化合物，将极大地扩展我们获得基因组序列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体库的化合物修饰和多样化的后续步骤。同时，项目工作将大大提高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，建立了一个创新的基因组合成工作流程，适用于解决创建合成放线菌基因组的主要技术挑战。这些目标将由曼彻斯特大学、东京工业大学和名古屋大学的研究人员组成的强大互补团队共同实现，他们分别位于英国和日本。我们的团队在计算分析（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）、天然产物研究（确定如何生产和修改抗菌剂）、微流体（用于快速合成基因组部分）、和DNA化学（设计新的DNA合成化学反应）。在项目期间，团队成员将前往英国和日本进行交流，并组织一次国际研讨会，将天然产物和工程生物学界聚集在一起。早期职业研究人员和技术人员是我们团队的重要成员，他们将积极参与项目，这将使他们获得国际经验和独立性，同时通过激烈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.