Designing overall stoichiometric conversions and intervening metabolic reactions

Chowdhury, Anupam; Maranas, Costas D.

doi:10.1038/srep16009

Title: 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. ^[1]

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.

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

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0008091

OSTI ID:: 1242041

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

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 36 works

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A Prospective Study on the Fermentation Landscape of Gaseous Substrates to Biorenewables Using Methanosarcina acetivorans Metabolic Model Nazem-Bokaee, Hadi; Maranas, Costas D. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01855	journal	August 2018
Expanding Metabolic Capabilities Using Novel Pathway Designs: Computational Tools and Case Studies Saa, Pedro A.; Cortés, María P.; López, Javiera Biotechnology Journal, Vol. 14, Issue 9 https://doi.org/10.1002/biot.201800734	journal	July 2019
A review of computational tools for design and reconstruction of metabolic pathways Wang, Lin; Dash, Satyakam; Ng, Chiam Yu Synthetic and Systems Biotechnology, Vol. 2, Issue 4 https://doi.org/10.1016/j.synbio.2017.11.002	journal	December 2017

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