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 in each of 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.

微生物代谢可用于生产范围广泛的工业重要化学品。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，以改善微生物宿主以实现工业生产。先前关于改进 TRY 指标的研究已经检验了具有不同生长和生产阶段以提高生产力的功效。然而，这些研究假设了从最大生长到最大生产表型的转变。因此，尚待探索在两阶段过程的每个生长和生产阶段具有中间生长和化学生产的表型。增长率降低对基材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，扫描微生物代谢的表型空间，以确定理想的生长和生产表型目标，以达到最佳 TRY 目标。使用这个框架，与大肠杆菌作为模式生物，我们比较了使用动态途径调节的两阶段过程和使用静态干预策略的单阶段过程，以实现不同的生物过程目标。我们的结果表明，即使在由于化学品生产过程中生长减少而导致底物吸收受限的情况下，在生产阶段中间生长的两阶段过程也总是会产生最佳的 TRY 值。通过分析生产增强策略的通量分布，我们确定了需要扰动以实现大肠杆菌中各种代谢物的生产表型的关键反应和反应子系统. 有趣的是，增加磷酸烯醇丙酮酸和 NADPH 可用性的通量扰动在这些生产表型中得到了丰富。此外，磷酸戊糖途径中的反应作为关键控制节点出现，它们共同作用以增加大肠杆菌中大多数产品的前体的可用性。微生物代谢固有的模块化性质导致需要调节共同的反应和反应子系统，以将微生物从其生长目标改变为产生多种代谢物。由于通量扰动中存在这些常见模式，我们提出了通用生产菌株的可能性。