Microbial metabolism can be harnessed to produce a broad range of industrially important chemicals. Often, three key process variables: Titer, Rate and Yield (TRY) are the target of metabolic engineering efforts to improve microbial hosts toward industrial production. Previous research into improving the TRY metrics have examined the efficacy of having distinct growth and production stages to achieve enhanced productivity. However, these studies assumed a switch from a maximum growth to a maximum production phenotype. Hence, phenotypes with intermediate growth and chemical production for the growth and production stages of two-stage processes are yet to be explored. The impact of reduced growth rates on substrate uptake adds to the need for intelligent choice of operating points while designing two-stage processes. In this work, we develop a computational framework that scans the phenotypic space of microbial metabolism to identify ideal growth and production phenotypic targets, to achieve optimal TRY targets. Using this framework, with Escherichia coli as a model organism, we compare two-stage processes that use dynamic pathway regulation, with one-stage processes that use static intervention strategies, for different bioprocess objectives. Our results indicate that two-stage processes with intermediate growth during the production stage always result in optimal TRY values even in cases where substrate uptake is limited due to reduced growth during chemical production. By analyzing the flux distributions for the production enhancing strategies, we identify key reactions and reaction subsystems that require perturbation to achieve a production phenotype for a wide range of metabolites in E. coli. Interestingly, flux perturbations that increase phosphoenolpyruvate and NADPH availability are enriched among these production phenotypes. Furthermore, reactions in the pentose phosphate pathway emerge as key control nodes that function together to increase the availability of precursors to most products in E. coli. The inherently modular nature of microbial metabolism results in common reactions and reaction subsystems that need to be regulated to modify microbes from their target of growth to the production of a diverse range of metabolites. Due to the presence of these common patterns in the flux perturbations, we propose the possibility of a universal production strain.

中文翻译：

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新型的两步法可优化微生物的化学生产

可以利用微生物的新陈代谢来生产各种工业上重要的化学物质。通常，三个关键的工艺变量：Ť ITER，- [R吃和ÿ ield（TRY）是代谢工程努力的目标，以改善微生物宿主向工业化生产的过程。先前有关改善TRY指标的研究已经检查了具有不同的生长和生产阶段以提高生产率的功效。但是，这些研究假设从最大生长表型向最大生产表型转变。因此，对于两阶段过程的生长和生产阶段，具有中间生长和化学生产的表型尚待探索。降低的增长率对底物吸收的影响增加了在设计两阶段工艺时智能选择操作点的需求。在这项工作中，我们开发了一个计算框架，该框架可以扫描微生物代谢的表型空间，以识别理想的生长和生产表型靶标，达到最佳的TRY目标。使用这个框架，大肠杆菌作为模型生物，我们比较了使用动态途径调节的两阶段过程与使用静态干预策略的一阶段过程，以实现不同的生物过程目标。我们的结果表明，即使在由于化学生产过程中生长减少而导致底物吸收受到限制的情况下，在生产阶段中具有中间生长的两阶段过程始终会产生最佳TRY值。通过分析生产促进策略的通量分布，我们确定了关键的反应和反应子系统，这些反应和反应子系统需要扰动才能实现大肠杆菌中多种代谢物的生产表型。有趣的是，在这些生产表型中，增加了磷酸烯醇丙酮酸和NADPH利用率的通量扰动得到了丰富。此外，戊糖磷酸途径中的反应作为关键控制节点出现，它们一起起作用以增加大肠杆菌中大多数产品的前体可用性。微生物代谢的固有模块化性质导致需要对常见的反应和反应子系统进行调节，以使微生物从其生长目标到产生多种代谢产物的过程中进行修饰。由于通量扰动中存在这些常见模式，我们提出了通用生产应变的可能性。