Designing overall stoichiometric conversions and intervening metabolic reactions

Chowdhury, Anupam; Maranas, Costas D.

doi:10.1038/srep16009

Designing overall stoichiometric conversions and intervening metabolic reactions

Journal Article · Wed Nov 04 00:00:00 EST 2015 · Scientific Reports

DOI:https://doi.org/10.1038/srep16009· OSTI ID:1242041

Chowdhury, Anupam ^[1]; Maranas, Costas D. ^[2]

Pennsylvania State Univ., State College, PA (United States); Pennsylvania State University
Pennsylvania State Univ., State College, PA (United States)

Existing computational tools for de novo metabolic pathway assembly, either based on mixed integer linear programming techniques or graph-search applications, generally only find linear pathways connecting the source to the target metabolite. The overall stoichiometry of conversion along with alternate co-reactant (or co-product) combinations is not part of the pathway design. Therefore, global carbon and energy efficiency is in essence fixed with no opportunities to identify more efficient routes for recycling carbon flux closer to the thermodynamic limit. Here, we introduce a two-stage computational procedure that both identifies the optimum overall stoichiometry (i.e., optStoic) and selects for (non-)native reactions (i.e., minRxn/minFlux) that maximize carbon, energy or price efficiency while satisfying thermodynamic feasibility requirements. Implementation for recent pathway design studies identified non-intuitive designs with improved efficiencies. Specifically, multiple alternatives for non-oxidative glycolysis are generated and non-intuitive ways of co-utilizing carbon dioxide with methanol are revealed for the production of C₂₊ metabolites with higher carbon efficiency.

View Accepted Manuscript (DOE)

Research Organization:: Pennsylvania State Univ., State College, PA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0008091

OSTI ID:: 1242041

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Vol. 5; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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A review of computational tools for design and reconstruction of metabolic pathways

Journal Article · Tue Nov 14 19:00:00 EST 2017 · Synthetic and Systems Biotechnology · OSTI ID:1629793

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