Determination of growth-coupling strategies and their underlying principles

• Published in: BMC bioinformatics 2019-08, Vol.20 (1), p.447-447, Article 447
• Main Authors: Alter, Tobias B, Ebert, Birgitta E
• Format: Article
• Language: English
• Subjects: Algorithms; Backup software; Bilevel algorithms; Carbon; Cofactors; Computer applications; Coupling; Dependence; Growth rate; Growth-coupled production; Health facilities construction; Maximization; Metabolic engineering; Metabolic networks; Metabolism; Metabolites; Methods; Microbiological research; Microbiological synthesis; Microorganisms; Model-guided metabolic engineering; Optimality principles; Optimization; Principles; Protons; Stoichiometric modeling; Synthesis; Viability
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-019-2946-7

Metabolic coupling of product synthesis and microbial growth is a prominent approach for maximizing production performance. Growth-coupling (GC) also helps stabilizing target production and allows the selection of superior production strains by adaptive laboratory evolution. To support the implementation of growth-coupling strain designs, we seek to identify biologically relevant, metabolic principles that enforce strong growth-coupling on the basis of reaction knockouts. We adapted an established bilevel programming framework to maximize the minimally guaranteed production rate at a fixed, medium growth rate. Using this revised formulation, we identified various GC intervention strategies for metabolites of the central carbon metabolism, which were examined for GC generating principles under diverse conditions. Curtailing the metabolism to render product formation an essential carbon drain was identified as one major strategy generating strong coupling of metabolic activity and target synthesis. Impeding the balancing of cofactors and protons in the absence of target production was the underlying principle of all other strategies and further increased the GC strength of the aforementioned strategies. Maximizing the minimally guaranteed production rate at a medium growth rate is an attractive principle for the identification of strain designs that couple growth to target metabolite production. Moreover, it allows for controlling the inevitable compromise between growth coupling strength and the retaining of microbial viability. With regard to the corresponding metabolic principles, generating a dependency between the supply of global metabolic cofactors and product synthesis appears to be advantageous in enforcing strong GC for any metabolite. Deriving such strategies manually, is a hard task, due to which we suggest incorporating computational metabolic network analyses in metabolic engineering projects seeking to determine GC strain designs.