Microbial metabolism can be harnessed to produce a large library of useful chemicals from renewable resources such as plant biomass. However, it is laborious and expensive to create microbial biocatalysts to produce each new product. To tackle this challenge, we have recently developed modular cell (ModCell) design principles that enable rapid generation of production strains by assembling a modular (chassis) cell with exchangeable production modules to achieve overproduction of target molecules. Previous computational ModCell design methods are limited to analyze small libraries of around 20 products. In this study, we developed a new computational method, named ModCell-HPC, that can design modular cells for large libraries with hundreds of products with a highly-parallel and multi-objective evolutionary algorithm and enable us to elucidate modular design properties. We demonstrated ModCell-HPC to design Escherichia coli modular cells towards a library of 161 endogenous production modules. From these simulations, we identified E. coli modular cells with few genetic manipulations that can produce dozens of molecules in a growth-coupled manner with different types of fermentable sugars. These designs revealed key genetic manipulations at the chassis and module levels to accomplish versatile modular cells, involving not only in the removal of major by-products but also modification of branch points in the central metabolism. We further found that the effect of various sugar degradation on redox metabolism results in lower compatibility between a modular cell and production modules for growth on pentoses than hexoses. To better characterize the degree of compatibility, we developed a method to calculate the minimal set cover, identifying that only three modular cells are all needed to couple with all compatible production modules. By determining the unknown compatibility contribution metric, we further elucidated the design features that allow an existing modular cell to be re-purposed towards production of new molecules. Overall, ModCell-HPC is a useful tool for understanding modularity of biological systems and guiding more efficient and generalizable design of modular cells that help reduce research and development cost in biocatalysis.

可以利用微生物代谢从可再生资源（如植物生物质）中产生大量有用的化学物质。然而，创造微生物生物催化剂来生产每一种新产品既费力又昂贵。为了应对这一挑战，我们最近开发了模块化细胞 (ModCell) 设计原则，通过组装具有可交换生产模块的模块化（底盘）细胞来实现目标分子的过量生产，从而能够快速生成生产菌株。以前的计算 ModCell 设计方法仅限于分析大约 20 个产品的小型库。在这项研究中，我们开发了一种新的计算方法，名为 ModCell-HPC，它可以使用高度并行和多目标进化算法为具有数百种产品的大型库设计模块化单元，并使我们能够阐明模块化设计特性。我们展示了 ModCell-HPC 来设计大肠杆菌模块细胞朝向包含 161 个内源性生产模块的文库。从这些模拟中，我们确定了大肠杆菌具有很少遗传操作的模块化细胞，可以与不同类型的可发酵糖以生长耦合的方式产生数十种分子。这些设计揭示了底盘和模块级别的关键基因操作，以实现多功能模块化细胞，不仅涉及主要副产物的去除，还涉及中央代谢分支点的修改。我们进一步发现，各种糖降解对氧化还原代谢的影响导致模块化细胞与在戊糖上生长的生产模块之间的相容性低于己糖。为了更好地表征兼容性程度，我们开发了一种计算最小集合覆盖的方法，确定只需要三个模块化单元即可与所有兼容的生产模块耦合。通过确定未知的兼容性贡献度量，我们进一步阐明了允许将现有模块化单元重新用于生产新分子的设计特征。总体而言，ModCell-HPC 是一种有用的工具，可用于了解生物系统的模块化并指导模块化细胞的更有效和可推广的设计，有助于降低生物催化的研发成本。