Phosphates as Energy Sources to Expand Metabolic Networks

Abstract

Phosphates are essential for modern metabolisms. A recent study reported a phosphate-free metabolic network and suggested that thioesters, rather than phosphates, could alleviate thermodynamic bottlenecks of network expansion. As a result, it was considered that a phosphorus-independent metabolism could exist before the phosphate-based genetic coding system. To explore the origin of phosphorus-dependent metabolism, the present study constructs a protometabolic network that contains phosphates prebiotically available using computational systems biology approaches. It is found that some primitive phosphorylated intermediates could greatly alleviate thermodynamic bottlenecks of network expansion. Moreover, the phosphorus-dependent metabolic network exhibits several ancient features. Taken together, it is concluded that phosphates played a role as important as that of thioesters during the origin and evolution of metabolism. Both phosphorus and sulfur are speculated to be critical to the origin of life.

Plausibility of Early Life in a Relatively Wide Temperature Range: Clues from Simulated Metabolic Network Expansion

“…These functions are also not greatly influenced by the change in temperature (Figure 2B and Figure S1B, and Table S3). When including the reactions without accurate free energy estimation, the scale of the phosphate-dependent network obtained at −25 °C is close to the thermodynamically constrained network constructed in our previous study (360 vs. 338 metabolites) [15]. At this temperature, this network is mainly composed of reactions that participate in glycolysis, the tricarboxylic acid (TCA) cycle, and carbon fixation, which supply the basic carbohydrates and energy to living systems.…”

Subtoxic dose of lithium cobalt oxide nanosheets impacts critical molecular pathways in trout gill epithelial cells

“…Furthermore, LCO NPs have been shown previously to adsorb phosphate in solution. 35,36 As phosphates are a crucial component in metabolism, 53 among many other cellular functions, a depletion of phosphate due to sorption onto the NPs might disrupt metabolic balance and explain the upregulation of metabolic pathways observed here. Additionally, nanomaterials such as gold, 54 platinum, 55 and titanium dioxide 56 have been shown previously to catalyze the oxidation of NADH to NAD + .…”

Nonenzymatic Metabolic Reactions and Life’s Origins

“…It is possible that thioester and polyphosphate-driven chemistries were both required from the outset in order to circumvent thermodynamic bottlenecks. 181 Prebiotic sources of phosphate and prebiotic means of phosphorylation have been the subject of investigation for a long time and have recently been reviewed. [182][183][184] However, studies on non-enzymatic versions of the phosphorylation reactions found in core metabolic pathways remains rare, with a notable exception being the phosphorylation of adenosine, AMP or ADP to ATP.…”