Optstrain: a Hierarchical Metabolic Pathway Discovery and Design Framework for Microbial Production Systems

In this contribution, we will discuss a hierarchical procedure termed OptStrain aimed at guiding pathway modifications, through pathway additions and deletions, of microbial networks for the overproduction of targeted compounds. A comprehensive database of biotransformations, referred to as the Universal database (with over 5,700 reactions), is compiled and regularly updated by downloading and curating reactions from multiple biopathway database sources. Combinatorial optimization is then employed to elucidate the set(s) of non-native functionalities, extracted from this Universal database, to add to the examined production host for enabling the desired product formation. Subsequently, competing functionalities that divert flux away from the targeted product are identified and removed to ensure higher product yields coupled with growth. The range and utility of OptStrain is demonstrated by addressing two very diffferent product molecules, hydrogen and vanillin, which represent the extreme ends of the product size spectrum.