Optimization of nucleotide sugar supply for polysaccharide formation via thermodynamic buffering

Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics

Biological systems operate toward the maximization of their self-maintenance and adaptability. This is achieved through the establishment of robust self-maintaining configurations acting as attractors resistant to external and internal perturbations. Ervin Bauer (1890-1938) was the first who formulated this essential thermodynamic constraint in the operation of biological systems, which he defined as the stable non-equilibrium state. The latter appears as the basic attractor relative to which biological organization is established. The stable non-equilibrium state represents a generalized cell energy status corresponding to efficient spatiotemporal organization of the fluxes of matter and energy and constantly reproducing the conditions of self-maintenance of metabolism and controlling the rates of major metabolic fluxes that follow thermodynamically and kinetically defined computational principles. This state is realized in the autopoietic structures having closed loops of causation based on the operation of biological codes. The principle of thermodynamic buffering determines the conditions for optimization of the fluxes of load and consumption in metabolism establishing the conditions of metabolic stable non-equilibrium. In developing and evolving biological systems, the principle of stable non-equilibrium is transformed into the principle of increasing external work, which is grounded in the hyper-restorative non-equilibrium dynamics. Bauer's concept of the stable non-equilibrium state puts thermodynamics into the frames of the internal biological causality governing self-maintenance and development of living systems. It can be defined as a relational theory of biological thermodynamics since the standard to which it refers represents the actual biological function rather than the abstract state of thermodynamic equilibrium.

Exploring Redox Modulation of Plant UDP-Glucose Pyrophosphorylase

UDP-glucose (UDPG) pyrophosphorylase (UGPase) catalyzes a reversible reaction, producing UDPG, which serves as an essential precursor for hundreds of glycosyltransferases in all organisms. In this study, activities of purified UGPases from sugarcane and barley were found to be reversibly redox modulated in vitro through oxidation by hydrogen peroxide or oxidized glutathione (GSSG) and through reduction by dithiothreitol or glutathione. Generally, while oxidative treatment decreased UGPase activity, a subsequent reduction restored the activity. The oxidized enzyme had increased K_m values with substrates, especially pyrophosphate. The increased K_m values were also observed, regardless of redox status, for UGPase cysteine mutants (Cys102Ser and Cys99Ser for sugarcane and barley UGPases, respectively). However, activities and substrate affinities (K_ms) of sugarcane Cys102Ser mutant, but not barley Cys99Ser, were still prone to redox modulation. The data suggest that plant UGPase is subject to redox control primarily via changes in the redox status of a single cysteine. Other cysteines may also, to some extent, contribute to UGPase redox status, as seen for sugarcane enzymes. The results are discussed with respect to earlier reported details of redox modulation of eukaryotic UGPases and regarding the structure/function properties of these proteins.

Toward understanding the emergence of life: A dual function of the system of nucleotides in the metabolically closed autopoietic organization

General structure of metabolism includes the reproduction of catalysts that govern metabolism. In this structure, the system becomes autopoietic in the sense of Maturana and Varela, and it is closed to efficient causation as defined by Robert Rosen. The autopoietic maintenance and operation of the catalysts takes place via the set of free nucleotides while the synthesis of catalysts occurs via the information encoded by the set of nucleotides arranged in polymers of RNA and DNA. Both energy charge and genetic information use the components of the same pool of nucleoside triphosphates, which is equilibrated by thermodynamic buffering enzymes such as nucleoside diphosphate kinase and adenylate kinase. This occurs in a way that the system becomes internally stable and metabolically closed, which initially could be realized at the level of ribozymes catalyzing basic metabolic reactions as well as own reproduction. The function of ATP, GTP, UTP, and CTP is dual, as these species participate both in the general metabolism as free nucleotides and in the transfer of genetic information via covalent polymerization to nucleic acids. The changes in their pools directly impact both bioenergetic pathways and nucleic acid turnover. Here we outline the concept of metabolic closure of biosystems grounded in the dual function of nucleotide coenzymes that serve both as energetic and informational molecules and through this duality generate the autopoietic performance and the ability for codepoietic evolutionary transformations of living systems starting from the emergence of prebiotic systems.

Magnesium and cell energetics: At the junction of metabolism of adenylate and non-adenylate nucleotides

Free magnesium (Mg²⁺) represents a powerful signal arising from interconversions of adenylates (ATP, ADP and AMP). This is a consequence of the involvement of adenylate kinase (AK) which equilibrates adenylates and uses defined species of Mg-complexed and Mg-free adenylates in both directions of its reaction. However, cells contain also other reversible Mg²⁺-dependent enzymes that equilibrate non-adenylate nucleotides (uridylates, cytidylates and guanylates), i.e. nucleoside monophosphate kinases (NMPKs) and nucleoside diphosphate kinase (NDPK). Here, we propose that AK activity is tightly coupled to activities of NMPK and NDPK, linking adenylate equilibrium to equilibria of other nucleotides, and with [Mg²⁺] controlling the ratios of Mg-chelated and Mg-free nucleotides. This coupling establishes main hubs for adenylate-driven equilibration of non-adenylate nucleotides, with [Mg²⁺] acting as signal arising from all nucleotides rather than adenylates only. Further consequences involve an overall adenylate control of UTP-, GTP- and CTP-dependent pathways and the availability of substrates for RNA and DNA synthesis.

Effects of Magnesium, Pyrophosphate and Phosphonates on Pyrophosphorolytic Reaction of UDP-Glucose Pyrophosphorylase

UDP-glucose pyrophosphorylase (UGPase) carries a freely reversible reaction, using glucose-1-P and UTP to produce UDP-glucose (UDPG) and pyrophosphate (PP_i), with UDPG being essential for glycosylation reactions in all organisms including, e.g., synthesis of sucrose, cellulose and glycoproteins. In the present study, we found that free magnesium (Mg²⁺) had profound effects on the reverse reaction of purified barley UGPase, and was absolutely required for its activity, with an apparent K_m of 0.13 mM. More detailed analyses with varied concentrations of MgPP_i allowed us to conclude that it is the MgPP_i complex which serves as true substrate for UGPase in its reverse reaction, with an apparent K_m of 0.06 mM. Free PP_i was an inhibitor in this reaction. Given the key role of PPi in the UGPase reaction, we have also tested possible effects of phosphonates, which are analogs of PPi and phosphate (P_i). Clodronate and etidronate (PP_i analogs) had little or no effect on UGPase activity, whereas fosetyl-Al (P_i analog), a known fungicide, acted as effective near-competitive inhibitor versus PP_i, with K_i of 0.15 mM. The data are discussed with respect to the role of magnesium in the UGPase reaction and elucidating the use of inhibitors in studies on cellular function of UGPase and related enzymes.

Pyrophosphate as an alternative energy currency in plants

In the conditions of [Mg2+] elevation that occur, in particular, under low oxygen stress and are the consequence of the decrease in [ATP] and increase in [ADP] and [AMP], pyrophosphate (PPi) can function as an alternative energy currency in plant cells. In addition to its production by various metabolic pathways, PPi can be synthesized in the combined reactions of pyruvate, phosphate dikinase (PPDK) and pyruvate kinase (PK) by so-called PK/PPDK substrate cycle, and in the reverse reaction of membrane-bound H+-pyrophosphatase, which uses the energy of electrochemical gradients generated on tonoplast and plasma membrane. The PPi can then be consumed in its active forms of MgPPi and Mg2PPi by PPi-utilizing enzymes, which require an elevated [Mg2+]. This ensures a continuous operation of glycolysis in the conditions of suppressed ATP synthesis, keeping metabolism energy efficient and less dependent on ATP.

Magnesium Signaling in Plants

Free magnesium (Mg2+) is a signal of the adenylate (ATP+ADP+AMP) status in the cells. It results from the equilibrium of adenylate kinase (AK), which uses Mg-chelated and Mg-free adenylates as substrates in both directions of its reaction. The AK-mediated primary control of intracellular [Mg2+] is finely interwoven with the operation of membrane-bound adenylate- and Mg2+-translocators, which in a given compartment control the supply of free adenylates and Mg2+ for the AK-mediated equilibration. As a result, [Mg2+] itself varies both between and within the compartments, depending on their energetic status and environmental clues. Other key nucleotide-utilizing/producing enzymes (e.g., nucleoside diphosphate kinase) may also be involved in fine-tuning of the intracellular [Mg2+]. Changes in [Mg2+] regulate activities of myriads of Mg-utilizing/requiring enzymes, affecting metabolism under both normal and stress conditions, and impacting photosynthetic performance, respiration, phloem loading and other processes. In compartments controlled by AK equilibrium (cytosol, chloroplasts, mitochondria, nucleus), the intracellular [Mg2+] can be calculated from total adenylate contents, based on the dependence of the apparent equilibrium constant of AK on [Mg2+]. Magnesium signaling, reflecting cellular adenylate status, is likely widespread in all eukaryotic and prokaryotic organisms, due simply to the omnipresent nature of AK and to its involvement in adenylate equilibration.

Phosphorylation and acylation transfer reactions: Clues to a dual origin of metabolism

Many theories of the origin of life focus on only one primitive polymer as an archetype of a world paradigm. However, life would have emerged within more complex scenarios where a variety of molecules and diverse polymers interconnected by a few similar chemical reactions. Previous work suggested that the ancestors of all major biopolymers would have arisen from abiotic template independent replication processes. They would have been organized in two closed sets of polymerization cycles: polysaccharides, polyribonucleotides and polyphosphates on one site; and peptides, fatty acids and polyhydroxyalkanoates on the other site. Then, these polymerization reaction cycles integrated into a minimal organization closure. Here, the purpose was to explore which kind of reactions could have supported the chemical networks that led to the early (bio)polymers. As a result, the proposed overview suggests that phosphorylation and acylation transfer reactions would have arisen independently and forged two distinct chemical systems that provided the phosphorylated and carboxylated intermediates used for the synthesis of the corresponding polymers. In this sense, modern metabolism may still reflect its dual nature, probably relying on these two reaction networks from the beginnings.