Pyrophosphate and Irreversibility in Evolution, or why PPi Is Not an Energy Currency and why Nature Chose Triphosphates

Abstract

The possible evolutionary significance of pyrophosphate (PP_i) has been discussed since the early 1960s. Lipmann suggested that PP_i could have been an ancient currency or a possible environmental source of metabolic energy at origins, while Kornberg proposed that PP_i vectorializes metabolism because ubiquitous pyrophosphatases render PP_i forming reactions kinetically irreversible. To test those ideas, we investigated the reactions that consume phosphoanhydride bonds among the 402 reactions of the universal biosynthetic core that generates amino acids, nucleotides, and cofactors from H₂, CO₂, and NH₃. We find that 36% of the core's phosphoanhydride hydrolyzing reactions generate PP_i, while no reactions use PP_i as an energy currency. The polymerization reactions that generate ~80% of cell mass - protein, RNA, and DNA synthesis - all generate PP_i, while none use PP_i as an energy source. In typical prokaryotic cells, aminoacyl tRNA synthetases (AARS) underlie ~80% of PP_i production. We show that the irreversibility of the AARS reaction is a kinetic, not a thermodynamic effect. The data indicate that PP_i is not an ancient energy currency and probably never was. Instead, PP_i hydrolysis is an ancient mechanism that imparts irreversibility, as Kornberg suggested, functioning like a ratchet's pawl to vectorialize the life process toward growth. The two anhydride bonds in nucleoside triphosphates offer ATP-cleaving enzymes an option to impart either thermodynamic control (P_i formation) or kinetic control (PP_i formation) upon reactions. This dual capacity explains why nature chose the triphosphate moiety of ATP as biochemistry's universal energy currency.

Keywords: bioenergetics; chemical evolution; early evolution; energetics; kinetics; metabolism; origin of life; thermodynamics.