Analysis of metabolic network disruption in engineered microbial hosts due to enzyme promiscuity

• DOI: 10.1016/j.mec.2021.e00170
• Publication Date: 2021-03-08T03:30:29Z
• Authors: Vladimir Porokhin; Sara A. Amin; Trevor B. Nicks; Venkatesh Endalur...; Nikhil U. Nair; Soha Hassoun
• Keywords: Metabolic Engineering; Metabolic network; Synthetic Biology; Heterologous; Promiscuity

Increasing understanding of metabolic and regulatory networks underlying microbial physiology has enabled creation progressively more complex synthetic biological systems for biochemical, biomedical, agricultural, environmental applications. However, despite best efforts, confounding phenotypes still emerge from unforeseen interplay between parts, the design robust modular remains elusive. Such interactions are difficult to predict when designing may manifest during experimental testing as inefficiencies that need be overcome. Transforming organisms such Escherichia coli into factories is achieved via several engineering strategies, used individually or in combination, with goal maximizing production chosen target compounds. One technique relies on suppressing overexpressing selected genes; another involves introducing heterologous enzymes a host. These modifications steer mass flux towards set desired metabolites but create unexpected interactions. In this work, we develop computational method, termed Metabolic Disruption Workflow (MDFlow), discovering network disruptions arising enzyme promiscuity - ability act wide range molecules structurally similar their native substrates. We apply MDFlow two experimentally verified cases where strains essential genes knocked out rescued by resulting overexpression one other genes. demonstrate how aid cells adapting functions. then evaluate number putative promiscuous reactions can interfere pathways designed 3-hydroxypropionic acid (3-HP) production. Using MDFlow, identify subsequent formation unintended undesirable byproducts not only disruptive host metabolism also intended end-objective high biosynthetic productivity yield. As demonstrate, provides an innovative workflow systematically incompatibilities its engineered due promiscuity.