Pareto Optimality Explanation of the Glycolytic Alternatives in Nature
Abstract
The Entner-Doudoroff (ED) and Embden-Meyerhof-Parnas (EMP) glycolytic pathways are largely conserved across glycolytic species in nature. Is this a coincidence, convergent evolution or there exists a driving force towards either of the two pathway designs? We addressed this question by first employing a variant of the optStoic algorithm to exhaustively identify over 11,916 possible routes between glucose and pyruvate at different pre-determined stoichiometric yields of ATP. Subsequently, we analyzed the thermodynamic feasibility of all the pathways at physiological metabolite concentrations and quantified the protein cost of the feasible solutions. Pareto optimality analysis between energy efficiency and protein cost reveals that the naturally evolved ED and EMP pathways are indeed among the most protein cost-efficient pathways in their respective ATP yield categories and remain thermodynamically feasible across a wide range of ATP/ADP ratios and pathway intermediate metabolite concentration ranges. In contrast, pathways with higher ATP yield (>2) while feasible, are bound within stringent and often extreme operability ranges of cofactor and intermediate metabolite concentrations. The preponderance of EMP and ED is thus consistent with not only optimally balancing energy yield vs. enzyme cost but also with ensuring operability for wide metabolite concentration ranges and ATP/ADP ratios.
- Authors:
-
- Pennsylvania State Univ., University Park, PA (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
- OSTI Identifier:
- 1624453
- Grant/Contract Number:
- AC05-00OR22725; EEC-0813570
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; science & technology; computational models; computer modelling; metabolic pathways
Citation Formats
Ng, Chiam Yu, Wang, Lin, Chowdhury, Anupam, and Maranas, Costas D. Pareto Optimality Explanation of the Glycolytic Alternatives in Nature. United States: N. p., 2019.
Web. doi:10.1038/s41598-019-38836-9.
Ng, Chiam Yu, Wang, Lin, Chowdhury, Anupam, & Maranas, Costas D. Pareto Optimality Explanation of the Glycolytic Alternatives in Nature. United States. https://doi.org/10.1038/s41598-019-38836-9
Ng, Chiam Yu, Wang, Lin, Chowdhury, Anupam, and Maranas, Costas D. Fri .
"Pareto Optimality Explanation of the Glycolytic Alternatives in Nature". United States. https://doi.org/10.1038/s41598-019-38836-9. https://www.osti.gov/servlets/purl/1624453.
@article{osti_1624453,
title = {Pareto Optimality Explanation of the Glycolytic Alternatives in Nature},
author = {Ng, Chiam Yu and Wang, Lin and Chowdhury, Anupam and Maranas, Costas D.},
abstractNote = {The Entner-Doudoroff (ED) and Embden-Meyerhof-Parnas (EMP) glycolytic pathways are largely conserved across glycolytic species in nature. Is this a coincidence, convergent evolution or there exists a driving force towards either of the two pathway designs? We addressed this question by first employing a variant of the optStoic algorithm to exhaustively identify over 11,916 possible routes between glucose and pyruvate at different pre-determined stoichiometric yields of ATP. Subsequently, we analyzed the thermodynamic feasibility of all the pathways at physiological metabolite concentrations and quantified the protein cost of the feasible solutions. Pareto optimality analysis between energy efficiency and protein cost reveals that the naturally evolved ED and EMP pathways are indeed among the most protein cost-efficient pathways in their respective ATP yield categories and remain thermodynamically feasible across a wide range of ATP/ADP ratios and pathway intermediate metabolite concentration ranges. In contrast, pathways with higher ATP yield (>2) while feasible, are bound within stringent and often extreme operability ranges of cofactor and intermediate metabolite concentrations. The preponderance of EMP and ED is thus consistent with not only optimally balancing energy yield vs. enzyme cost but also with ensuring operability for wide metabolite concentration ranges and ATP/ADP ratios.},
doi = {10.1038/s41598-019-38836-9},
journal = {Scientific Reports},
number = 1,
volume = 9,
place = {United States},
year = {Fri Feb 22 00:00:00 EST 2019},
month = {Fri Feb 22 00:00:00 EST 2019}
}
Web of Science
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