Production of tartrates by cyanide-mediated dimerization of glyoxylate: a potential abiotic pathway to the citric acid cycle

The protometabolic nature of prebiotic chemistry

The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.

Low-temperature mineralization of perfluorocarboxylic acids

Per- and polyfluoroalkyl substances (PFAS) are persistent, bioaccumulative pollutants found in water resources at concentrations harmful to human health. Whereas current PFAS destruction strategies use nonselective destruction mechanisms, we found that perfluoroalkyl carboxylic acids (PFCAs) could be mineralized through a sodium hydroxide-mediated defluorination pathway. PFCA decarboxylation in polar aprotic solvents produced reactive perfluoroalkyl ion intermediates that degraded to fluoride ions (78 to ~100%) within 24 hours. The carbon-containing intermediates and products were inconsistent with oft-proposed one-carbon-chain shortening mechanisms, and we instead computationally identified pathways consistent with many experiments. Degradation was also observed for branched perfluoroalkyl ether carboxylic acids and might be extended to degrade other PFAS classes as methods to activate their polar headgroups are identified.

Glyoxylate protects against cyanide toxicity through metabolic modulation

Although cyanide's biological effects are pleiotropic, its most obvious effects are as a metabolic poison. Cyanide potently inhibits cytochrome c oxidase and potentially other metabolic enzymes, thereby unleashing a cascade of metabolic perturbations that are believed to cause lethality. From systematic screens of human metabolites using a zebrafish model of cyanide toxicity, we have identified the TCA-derived small molecule glyoxylate as a potential cyanide countermeasure. Following cyanide exposure, treatment with glyoxylate in both mammalian and non-mammalian animal models confers resistance to cyanide toxicity with greater efficacy and faster kinetics than known cyanide scavengers. Glyoxylate-mediated cyanide resistance is accompanied by rapid pyruvate consumption without an accompanying increase in lactate concentration. Lactate dehydrogenase is required for this effect which distinguishes the mechanism of glyoxylate rescue as distinct from countermeasures based solely on chemical cyanide scavenging. Our metabolic data together support the hypothesis that glyoxylate confers survival at least in part by reversing the cyanide-induced redox imbalances in the cytosol and mitochondria. The data presented herein represent the identification of a potential cyanide countermeasure operating through a novel mechanism of metabolic modulation.

Cyanide as a primordial reductant enables a protometabolic reductive glyoxylate pathway

Investigation of prebiotic metabolic pathways is predominantly based on abiotically replicating the reductive citric acid cycle. While attractive from a parsimony point of view, attempts using metal/mineral-mediated reductions have produced complex mixtures with inefficient and uncontrolled reactions. Here we show that cyanide acts as a mild and efficient reducing agent mediating abiotic transformations of tricarboxylic acid intermediates and derivatives. The hydrolysis of the cyanide adducts followed by their decarboxylation enables the reduction of oxaloacetate to malate and of fumarate to succinate, whereas pyruvate and α-ketoglutarate themselves are not reduced. In the presence of glyoxylate, malonate and malononitrile, alternative pathways emerge that bypass the challenging reductive carboxylation steps to produce metabolic intermediates and compounds found in meteorites. These results suggest a simpler prebiotic forerunner of today's metabolism, involving a reductive glyoxylate pathway without oxaloacetate and α-ketoglutarate-implying that the extant metabolic reductive carboxylation chemistries are an evolutionary invention mediated by complex metalloproteins.

Study of Physico-Chemical Interactions during the Production of Silver Citrate Nanocomposites with Hemp Fiber

In the study presented in this paper, the results obtained by producing nanocomposites consisting of a silver citrate thin layer deposited on hemp fiber surfaces are analyzed. Using the pulsed laser deposition (PLD) method applied to a silver target with impurities of nickel and iron, the formation of the silver citrate film is performed in various ways and the results are discussed based on Fourier Transform Infrared (FTIR) and Scanning Electron Microscopy coupled with Energy Dispersive X-ray (SEM-EDX) spectroscopy analyses. A mechanism of the physico-chemical processes that take place based on the FTIR vibrational modes and the elemental composition established by the SEM-EDS analysis is proposed. Inhibition of the fermentation process of Saccharomyces cerevisae is demonstrated for the nanocomposite material of the silver citrate thin layer, obtained by means of the PLD method, on hemp fabric. The usefulness of composite materials of this type can extend from sensors and optoelectronics to the medical fields of analysis and treatment.

Synthetic connectivity, emergence, and self-regeneration in the network of prebiotic chemistry

The challenge of prebiotic chemistry is to trace the syntheses of life’s key building blocks from a handful of primordial substrates. Here we report a forward-synthesis algorithm that generates a full network of prebiotic chemical reactions accessible from these substrates under generally accepted conditions. This network contains both reported and previously unidentified routes to biotic targets, as well as plausible syntheses of abiotic molecules. It also exhibits three forms of nontrivial chemical emergence, as the molecules within the network can act as catalysts of downstream reaction types; form functional chemical systems, including self-regenerating cycles; and produce surfactants relevant to primitive forms of biological compartmentalization. To support these claims, computer-predicted, prebiotic syntheses of several biotic molecules as well as a multistep, self-regenerative cycle of iminodiacetic acid were validated by experiment.

Exploring Metabolic Signature of Protein Energy Wasting in Hemodialysis Patients

End-stage renal disease patients undergoing maintenance hemodialysis (HD) are vulnerable to the protein energy wasting (PEW) syndrome. Identification and diagnosis of PEW relies on clinical processes of judgment dependent on fulfilling multiple criteria drawn from serum biochemistry, weight status, predictive muscle mass, dietary energy and protein intakes. Therefore, we sought to explore the biomarkers’ signature with plasma metabolites of PEW by using ¹H-nuclear magnetic resonance for an untargeted metabolomics approach in the HD population, to understand metabolic alteration of PEW. In this case-controlled study, a total of 53 patients undergoing chronic HD were identified having PEW based on established diagnostic criteria and were age- and sex-matched with non-PEW (n = 53) HD patients. Fasting predialysis plasma samples were analyzed. Partial least square discriminant analysis demonstrated a significant separation between groups for specific metabolic pattern alterations. Further quantitative analysis showed that the level of 3-hydroxybutyrate, acetate, arabinose, maltose, ribose, sucrose and tartrate were significantly increased whilst creatinine was significantly decreased (all p < 0.05) in PEW subjects. Pathway analysis indicated that PEW-related metabolites reflected perturbations in fatty acid mechanism and induction of glyoxylate and dicarboxylate pathway attributed to gluconeogenesis. These results provide preliminary data in understanding metabolic alteration of PEW and corresponding abnormal metabolites that could potentially serve as biomarkers of PEW.

Manifesto for the routine use of NMR for the liquid product analysis of aqueous CO2 reduction: from comprehensive chemical shift data to formaldehyde quantification in water

CO2 reduction research is at a critical turnaround since it has the potential to partially or even substantially fulfil future clean energy needs. CO2-to-CO electrochemical conversion is getting closer from industrial implementation requirements. Efforts are now more and more directed to obtain highly reduced products such as methanol, methane, ethylene, ethanol, etc., most of them being liquids. Gas-phase products (e.g., CO, CH4) are typically detected and quantified by well-defined gas chromatography (GC and GC/MS) protocols. On the other hand, NMR, GC-MS, HPLC have been used for the liquid phase characterization, but no routine technique has yet been established, mainly due to lack of versatility of a single technique. Additionally, except NMR and GC-MS, classical techniques cannot distinguish 13C from 12C products, although it is a mandatory step to assess products origin. Herein, we show the efficiency and applicability of 1H NMR as routine technique for liquid phase products analysis and we address two previous shortcomings. We first established a comprehensive 1H and 13C NMR chemical shifts list for all 12CO2 and 13CO2 reduction products in water ranging from C1 to C3. Then we overcame the difficulty of identifying aqueous formaldehyde intermediate by 1H NMR through an efficient chemical trapping step, along with isotopic signature study. Formaldehyde can be reliably quantified in water with a concentration as low as 50 μM.

Reactivity of Metabolic Intermediates and Cofactor Stability under Model Early Earth Conditions

Understanding the emergence of metabolic pathways is key to unraveling the factors that promoted the origin of life. One popular view is that protein cofactors acted as catalysts prior to the evolution of the protein enzymes with which they are now associated. We investigated the stability of acetyl coenzyme A (Acetyl Co-A, the group transfer cofactor in citric acid synthesis in the TCA cycle) under early Earth conditions, as well as whether Acetyl Co-A or its small molecule analogs thioacetate or acetate can catalyze the transfer of an acetyl group onto oxaloacetate in the absence of the citrate synthase enzyme. Several different temperatures, pH ranges, and compositions of aqueous environments were tested to simulate the Earth's early ocean and its possible components; the effect of these variables on oxaloacetate and cofactor chemistry were assessed under ambient and anoxic conditions. The cofactors tested are chemically stable under early Earth conditions, but none of the three compounds (Acetyl Co-A, thioacetate, or acetate) promoted synthesis of citric acid from oxaloacetate under the conditions tested. Oxaloacetate reacted with itself and/or decomposed to form a sequence of other products under ambient conditions, and under anoxic conditions was more stable; under ambient conditions the specific chemical pathways observed depended on the environmental conditions such as pH and presence/absence of bicarbonate or salt ions in early Earth ocean simulants. This work demonstrates the stability of these metabolic intermediates under anoxic conditions. However, even though free cofactors may be stable in a geological environmental setting, an enzyme or other mechanism to promote reaction specificity would likely be necessary for at least this particular reaction to proceed.

Theoretical study of formate, tartrate, tartronate, and glycolate production from 6-carbon trioxylate intermediate in the citric acid cycle

Reaction pathways of side products (formate, glycolate, and tartronate) from dihydroxyfumarate (DHF) were theoretically investigated as DHF is an intermediate in the process of producing tartrates and oxalate from glyoxylate of the citric acid cycle. The proposed pathways for each reaction were mapped by density functional theory (DFT) calculations. The transitions states were confirmed by analyzing the vibrational frequency and the intrinsic reaction coordinate (IRC) theory. The corresponding reaction activation energy, enthalpy change, Gibb's free energy change, and rate of reactions were calculated to get a clear picture of the whole reaction pathway. In the whole process, the decarboxylation reaction showed the highest energy barrier of 20-23 kcal/mol. Proton transfer and hydroxylation reactions were almost barrierless. As most of these reactions have very low energy barrier, our findings elucidate the high probability of those reactions under experimental conditions.

Experimental conditions affecting the kinetics of aqueous HCN polymerization as revealed by UV-vis spectroscopy

HCN polymerization is one of the most important and fascinating reactions in prebiotic chemistry, and interest in HCN polymers in the field of materials science is growing. However, little is known about the kinetics of the HCN polymerization process. In the present study, a first approach to the kinetics of two sets of aqueous HCN polymerizations, from NH₄CN and NaCN, at middle temperatures between 4 and 38°C, has been carried out. For each series, the presence of air and salts in the reaction medium has been systematically explored. A previous kinetic analysis was conducted during the conversion of the insoluble black HCN polymers obtained as gel fractions in these precipitation polymerizations for a reaction of one month, where a limit conversion was achieved at the highest polymerization temperature. The kinetic description of the gravimetric data for this complex system shows a clear change in the linear dependence with the polymerization temperature for the reaction from NH₄CN, besides a relevant catalytic effect of ammonium, in comparison with those data obtained from the NaCN series. These results also demonstrated the notable influence of air, oxygen, and the saline medium in HCN polymer formation. Similar conclusions were reached when the sol fractions were monitored by UV-vis spectroscopy, and a Hill type correlation was used to describe the polymerization profiles obtained. This technique was chosen because it provides an easy, prompt and fast method to follow the evolution of the liquid or continuous phase of the process under study.

Computational exploration of the chemical structure space of possible reverse tricarboxylic acid cycle constituents

The reverse tricarboxylic acid (rTCA) cycle has been explored from various standpoints as an idealized primordial metabolic cycle. Its simplicity and apparent ubiquity in diverse organisms across the tree of life have been used to argue for its antiquity and its optimality. In 2000 it was proposed that chemoinformatics approaches support some of these views. Specifically, defined queries of the Beilstein database showed that the molecules of the rTCA are heavily represented in such compound databases. We explore here the chemical structure “space,” e.g. the set of organic compounds which possesses some minimal set of defining characteristics, of the rTCA cycle’s intermediates using an exhaustive structure generation method. The rTCA’s chemical space as defined by the original criteria and explored by our method is some six to seven times larger than originally considered. Acknowledging that each assumption in what is a defining criterion making the rTCA cycle special limits possible generative outcomes, there are many unrealized compounds which fulfill these criteria. That these compounds are unrealized could be due to evolutionary frozen accidents or optimization, though this optimization may also be for systems-level reasons, e.g., the way the pathway and its elements interface with other aspects of metabolism.

Prebiotic alternatives to proteins: structure and function of hyperbranched polyesters

Proteins are responsible multiple biological functions, such as ligand binding, catalysis, and ion channeling. This functionality is enabled by proteins' three-dimensional structures that require long polypeptides. Since plausibly prebiotic synthesis of functional polypeptides has proven challenging in the laboratory, we propose that these functions may have been initially performed by alternative macromolecular constructs, namely hyperbranched polymers (HBPs), during early stages of chemical evolution. HBPs can be straightforwardly synthesized in one-pot processes, possess globular structures determined by their architecture as opposed to folding in proteins, and have documented ligand binding and catalytic properties. Our initial study focuses on glycerol-citric acid HBPs synthesized via moderate heating in the dry state. The polymerization products consisted of a mixture of isomeric structures of varying molar mass as evidenced by NMR, mass spectrometry and size-exclusion chromatography. Addition of divalent cations during polymerization resulted in increased incorporation of citric acid into the HBPs and the possible formation of cation-oligomer complexes. The chelating properties of citric acid govern the makeup of the resulting polymer, turning the polymerization system into a rudimentary smart material.

Uncertainty of prebiotic scenarios: the case of the non-enzymatic reverse tricarboxylic acid cycle

We consider the hypothesis of the primordial nature of the non-enzymatic reverse tricarboxylic acid (rTCA) cycle and describe a modeling approach to quantify the uncertainty of this hypothesis due to the combinatorial aspect of the constituent chemical transformations. Our results suggest that a) rTCA cycle belongs to a degenerate optimum of auto-catalytic cycles, and b) the set of targets for investigations of the origin of the common metabolic core should be significantly extended.

Nonenzymatic template-directed RNA synthesis inside model protocells

Efforts to recreate a prebiotically plausible protocell, in which RNA replication occurs within a fatty acid vesicle, have been stalled by the destabilizing effect of Mg(2+) on fatty acid membranes. Here we report that the presence of citrate protects fatty acid membranes from the disruptive effects of high Mg(2+) ion concentrations while allowing RNA copying to proceed, while also protecting single-stranded RNA from Mg(2+)-catalyzed degradation. This combination of properties has allowed us to demonstrate the chemical copying of RNA templates inside fatty acid vesicles, which in turn allows for an increase in copying efficiency by bathing the vesicles in a continuously refreshed solution of activated nucleotides.