Pareto Optimality Explanation of the Glycolytic Alternatives in Nature

Scientific Reports
Chiam Yu NgCostas D Maranas

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 consist...Continue Reading

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Citations

May 31, 2020·Proceedings of the National Academy of Sciences of the United States of America·Vishnuvardhan MahamkaliEsteban Marcellin
Sep 22, 2020·Evolutionary Applications·Kenneth J PientaSarah R Amend
Jul 21, 2021·Biochemical Society Transactions·St Elmo WilkenOliver Ebenhöh

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Software Mentioned

Gurobi Optimizer
optStoic
GAMS
Graphviz Python
Component Contribution Python
ChemAxon
Graphviz
- Python
Open Babel 62
Molfile

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