Glycolytic strategy as a tradeoff between energy yield and protein cost

Abstract

Contrary to the textbook portrayal of glycolysis as a single pathway conserved across all domains of life, not all sugar-consuming organisms use the canonical Embden-Meyerhoff-Parnass (EMP) glycolytic pathway. Prokaryotic glucose metabolism is particularly diverse, including several alternative glycolytic pathways, the most common of which is the Entner-Doudoroff (ED) pathway. The prevalence of the ED pathway is puzzling as it produces only one ATP per glucose-half as much as the EMP pathway. We argue that the diversity of prokaryotic glucose metabolism may reflect a tradeoff between a pathway's energy (ATP) yield and the amount of enzymatic protein required to catalyze pathway flux. We introduce methods for analyzing pathways in terms of thermodynamics and kinetics and show that the ED pathway is expected to require several-fold less enzymatic protein to achieve the same glucose conversion rate as the EMP pathway. Through genomic analysis, we further show that prokaryotes use different glycolytic pathways depending on their energy supply. Specifically, energy-deprived anaerobes overwhelmingly rely upon the higher ATP yield of the EMP pathway, whereas the ED pathway is common among facultative anaerobes and even more common among aerobes. In addition to demonstrating how protein costs can explain the use of alternative metabolic strategies, this study illustrates a direct connection between an organism's environment and the thermodynamic and biochemical properties of the metabolic pathways it employs.evolution | enzyme cost G lycolysis is the process by which glucose is broken down anaerobically into incompletely oxidized compounds like pyruvate, a process which is usually coupled to the synthesis of ATP. Although the Embden-Meyerhof-Parnas pathway (EMP, often simply "glycolysis") is the nearly ubiquitous glycolytic route among eukaryotes (1, 2), it is not the only game in town. Prokaryotes display impressive diversity in glucose metabolism (2, 3) and natural glycolytic alternatives like the Entner-Doudoroff (ED), and phosphoketolase pathways attest to the fact that there are multiple biologically feasible routes for glucose metabolism (2, 4-8). Natural glycolytic pathways vary in their reaction sequence and in how much ATP they produce per glucose metabolized, ranging from zero to three ATP molecules in most cases (7).The EMP and ED pathways ( Fig. 1 A and B and Fig. S1) are the most common bacterial glycolytic pathways (2, 4, 9), and their general schemes are quite similar: glucose is phosphorylated and then cleaved into two three-carbon units, which are further metabolized to produce ATP (4). In some organisms, these pathways differ slightly in the specific redox cofactors they use (e.g., NAD + vs. NADP + ; Fig. 1B, Fig. S2, and Table S1), but here we focus on the prominent difference in ATP yield. If we take lactate as a representative final product, these two pathways have the same net reaction:and differ primarily in n, the number of ATP produced, and the specific intermediate reaction steps (Fig. 1B, SI T...

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