RT Journal Article SR Electronic T1 Phenotypic design choices for enhanced productivity in microbial chemical production processes JF bioRxiv FD Cold Spring Harbor Laboratory SP 803023 DO 10.1101/803023 A1 Kaushik Raj A1 Naveen Venayak A1 Radhakrishnan Mahadevan YR 2019 UL http://biorxiv.org/content/early/2019/10/13/803023.abstract AB 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, the choice of operating points for the growth and production stages of two-stage processes is 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 present a computational framework that scans the phenotypic space of microbial metabolism to identify ideal growth and production phenotypic targets, to achieve optimal TRY values. 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. Our results indicate that two-stage processes with intermediate growth during the production stage always result in the highest productivity. By analyzing the flux distributions for the production enhancing strategies, we identify key reactions and reaction subsystems that need to be downregulated for a wide range of metabolites in E. coli. We also elucidate the importance of flux perturbations that increase phosphoenolpyruvate and NADPH availability among strategies to design production platforms. 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. Due to the presence of these common patterns in the flux perturbations, we propose the possibility of a universal production strain that enhances the production of a large number of metabolites.