Prebiotic formation of enantiomeric excess D-amino acids on natural pyrite

D-amino acids, found in excess in a minority of organisms and crucial for marine invertebrates, contrast with the more common L-amino acids in most life forms. The local prebiotic origin of D-amino acid enantiomeric excess in natural systems remains an unsolved conundrum. Herein, we demonstrate the formation of enantiomeric excess (ee) D-amino acids through photocatalytic reductive amination of α-keto acids on natural pyrite. Various amino acids with ee values in the range of 14.5-42.4%, are formed. The wavy arrangement of atoms on the surface of pyrite is speculated to lead to the preferential formation of D-amino acids. This work reveals the intrinsic asymmetric photocatalytic activity of pyrite, which could expand understandings on mechanism of asymmetric catalysis and chirality of inorganic crystals. Furthermore, it provides a plausible pathway for the prebiotic formation of D-amino acids, adding further evidence to the origin of D-amino acids enantiomeric excess in natural systems.

Quantifying Reductive Amination in Nonenzymatic Amino Acid Synthesis

Amino acid biosynthesis initiates with the reductive amination of α-ketoglutarate with ammonia to produce glutamate. However, the other α-keto acids derived from the glyoxylate and Krebs cycles are converted into amino acids by transamination, rather than by reductive amination. Why is only one amino acid synthesized by reductive amination and not the others? To explore this question, we quantified the inherent reactivities of keto acids in nonenzymatic reduction and reductive amination by using BH3 CN- as a model nucleophile. Biological α-keto acids were found to show pronounced nonenzymatic reactivity differences for the formation of amino acids (α-ketoglutarate Collapse

Key Words

• Amino Acids
• Hydride Transfer
• Kinetics
• Metabolism
• Reductive Amination

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MESH Headings

• Amination
• Ammonia/chemistry
• Ketoglutaric Acids/metabolism
• Amino Acids/chemistry
• Keto Acids
• Glutamic Acid/metabolism
• Amines

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Grants

• HORIZON EUROPE European Research Council
• Volkswagen Foundation
• Deutsche Forschungsgemeinschaft

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Affiliation(s)

Robert J. Mayer Institut de Science et d'Ingénierie Supramoléculaires (ISIS)CNRS UMR 7006Université de Strasbourg8 Allée Gaspard Monge67000StrasbourgFrance
Joseph Moran Institut de Science et d'Ingénierie Supramoléculaires (ISIS)CNRS UMR 7006Université de Strasbourg8 Allée Gaspard Monge67000StrasbourgFrance Institut Universitaire de France (IUF)75005ParisFrance

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Prebiotic synthesis of α-amino acids and orotate from α-ketoacids potentiates transition to extant metabolic pathways

The Strecker reaction of aldehydes is the pre-eminent pathway to explain the prebiotic origins of α-amino acids. However, biology employs transamination of α-ketoacids to synthesize amino acids which are then transformed to nucleobases, implying an evolutionary switch-abiotically or biotically-of a prebiotic pathway involving the Strecker reaction into today's biosynthetic pathways. Here we show that α-ketoacids react with cyanide and ammonia sources to form the corresponding α-amino acids through the Bucherer-Bergs pathway. An efficient prebiotic transformation of oxaloacetate to aspartate via N-carbamoyl aspartate enables the simultaneous formation of dihydroorotate, paralleling the biochemical synthesis of orotate as the precursor to pyrimidine nucleobases. Glyoxylate forms both glycine and orotate and reacts with malonate and urea to form aspartate and dihydroorotate. These results, along with the previously demonstrated protometabolic analogues of the Krebs cycle, suggest that there can be a natural emergence of congruent forerunners of biological pathways with the potential for seamless transition from prebiotic chemistry to modern metabolism.

Catalytic Gels for a Prebiotically Relevant Asymmetric Aldol Reaction in Water: From Organocatalyst Design to Hydrogel Discovery and Back Again

This paper reports an investigation into organocatalytic hydrogels as prebiotically relevant systems. Gels are interesting prebiotic reaction media, combining heterogeneous and homogeneous characteristics with a structurally organized active "solid-like" catalyst separated from the surrounding environment, yet in intimate contact with the solution phase and readily accessible via "liquid-like" diffusion. A simple self-assembling glutamine amide derivative 1 was initially found to catalyze a model aldol reaction between cyclohexanone and 4-nitrobenzaldehyde, but it did not maintain its gel structure during reaction. In this study, it was observed that compound 1 could react directly with the benzaldehyde to form a hydrogel in situ based on Schiff base 2 as a low-molecular-weight gelator (LMWG). This new dynamic gel is a rare example of a two-component self-assembled LMWG hydrogel and was fully characterized. It was demonstrated that glutamine amide 1 could select an optimal aldehyde component and preferentially assemble from mixtures. In the hunt for an organocatalyst, reductive conditions were applied to the Schiff base to yield secondary amine 3, which is also a highly effective hydrogelator at very low loadings with a high degree of nanoscale order. Most importantly, the hydrogel based on 3 catalyzed the prebiotically relevant aldol dimerization of glycolaldehyde to give threose and erythrose. In buffered conditions, this reaction gave excellent conversions, good diastereoselectivity, and some enantioselectivity. Catalysis using the hydrogel of 3 was much better than that using non-assembled 3-demonstrating a clear benefit of self-assembly. The results suggest that hydrogels offer a potential strategy by which prebiotic reactions can be promoted using simple, prebiotically plausible LMWGs that can selectively self-organize from complex mixtures. Such processes may have been of prebiotic importance.

Metals promote sequences of the reverse Krebs cycle

The rTCA cycle (also known as the reverse Krebs cycle) is a central anabolic biochemical pathway whose origins are proposed to trace back to geochemistry, long before the advent of enzymes, RNA or cells, and whose imprint still remains intimately embedded in the structure of core metabolism. If it existed, a primordial version of the rTCA cycle would necessarily have been catalyzed by naturally occurring minerals at the earliest stage of the transition from geochemistry to biochemistry. Here we report non-enzymatic promotion of multiple reactions of the rTCA cycle in consecutive sequence, whereby 6 of its 11 reactions are promoted by Zn²⁺, Cr³⁺ and Fe⁰ in an acidic aqueous solution. Two distinct three-reaction sequences can be achieved under a common set of conditions. Selectivity is observed for reduction reactions producing rTCA cycle intermediates compared to those leading off-cycle. Reductive amination of ketoacids to furnish amino acids is observed under similar conditions. The emerging reaction network supports the feasibility of primitive anabolism in an acidic, metal-rich reducing environment.

Alpha-Oxo Acids Assisted Transformation of FeS to Fe3S4 at Low Temperature: Implications for Abiotic, Biotic, and Prebiotic Mineralization

The mineral greigite (Fe3S4) distributes widely in anoxic marine and lake sedimentary systems, with important implications for magnetostratigraphy and paleomagnetism. In living organisms, magnetotactic bacteria can synthesize greigite grains with regular sizes and morphologies. The cubic Fe3S4 structure also occurs as an integral constituent and active center in a family of iron-sulfur proteins in all life-forms on Earth. This basic biochemistry shared by all organisms implies that the Fe3S4 structure might have evolved in the first protocell. Therefore, greigite is of general interest in geochemistry, geophysics, biomineralogy, and origin-of-life sciences. However, the growth of thermodynamically metastable Fe3S4 crystals often requires strictly defined conditions because both Fe and S show variable valences and it is hard to tune their valence fluctuation. Here, we show that freshly precipitated FeS can be selectively oxidized to form greigite in the presence of α-oxo acids, even at room temperature. Based on a brief overview of the experimental findings, a metal-organic complex intermediate model has been put forward and discussed for the discriminative chemical transformation. The results not only provide a possible pathway for the abiotic formation of greigite in nature but also may help explain the biotic mineralization of greigite in magnetotactic bacteria. Moreover, in the context of prebiotic evolution, along with the synergic evolution between greigite and α-oxo acids, Fe3S4 might have been sequestered by primordial peptides, and the whole finally evolved into the first iron-sulfur protein.

KEY WORDS

Greigite-Mineralization-α-Oxo acid-Magnetosome-Iron-sulfur protein-Prebiotic evolution.

Sphalerite is a geochemical catalyst for carbon-hydrogen bond activation

Reactions among minerals and organic compounds in hydrothermal systems are critical components of the Earth's deep carbon cycle, provide energy for the deep biosphere, and may have implications for the origins of life. However, there is limited information as to how specific minerals influence the reactivity of organic compounds. Here we demonstrate mineral catalysis of the most fundamental component of an organic reaction: the breaking and making of a covalent bond. In the absence of mineral, hydrothermal reaction of cis- and trans-1,2-dimethylcyclohexane is extremely slow and generates many products. In the presence of sphalerite (ZnS), however, the reaction rate increases dramatically and one major product is formed: the corresponding stereoisomer. Isotope studies show that the sphalerite acts as a highly specific heterogeneous catalyst for activation of a single carbon-hydrogen bond in the dimethylcyclohexanes.

Enhanced photocatalytic performance of ZnS for reversible amination of α-oxo acids by hydrothermal treatment

To understand how life could have originated on early Earth, it is essential to know what biomolecules and metabolic pathways are shared by extant organisms and what organic compounds and their chemical reaction channels were likely to have been primordially available during the initial phase of the formation of prebiotic metabolism. In a previous study, we demonstrated for the first time the reversible amination of α-oxo acids on the surface of photo-illuminated ZnS. The sulfide mineral is a typical component at the periphery of submarine hydrothermal vents which has been frequently argued as a very attractive venue for the origin of life. In this work, in order to simulate more closely the precipitation environments of ZnS in the vent systems, we treated newly-precipitated ZnS with hydrothermal conditions and found that its photocatalytic power was significantly enhanced because the relative crystallinity of the treated sample was markedly increased with increasing temperature. Since the reported experimental conditions are believed to have been prevalent in shallow-water hydrothermal vents of early Earth and the reversible amination of α-oxo acids is a key metabolic pathway in all extant life forms, the results of this work provide a prototypical model of the prebiotic amino acid redox metabolism. The amino acid dehydrogenase-like chemistry on photo-irradiated ZnS surfaces may advance our understanding of the establishment of archaic non-enzymatic metabolic systems.

Genetics first or metabolism first? The formamide clue

Life is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, and carbon). The transmissible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information, of living and non-living. The origin-of-life quest has long been split into several attitudes exemplified by the aphorisms "genetics-first" or "metabolism-first". Recently, the opposition between these approaches has been solved by more unitary theoretical and experimental frames taking into account energetic, evolutionary, proto-metabolic and environmental aspects. Nevertheless, a unitary and simple chemical frame is still needed that could afford both the precursors of the synthetic pathways eventually leading to RNA and to the key components of the central metabolic cycles, possibly connected with the synthesis of fatty acids. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, and were embedded under physical-chemical conditions favourable for the onset of both. The singleness of such a prebiotically productive chemical process would partake of Darwinian advantages over more complex fragmentary chemical systems. The prebiotic chemistry of formamide affords in a single and simple physical-chemical frame nucleic bases, acyclonucleosides, nucleotides, biogenic carboxylic acids, sugars, amino sugars, amino acids and condensing agents. Thus, we suggest the possibility that formamide could have jointly provided the main components for the onset of both (pre)genetic and (pre)metabolic processes. As a note of caution, we discuss the fact that these observations only indicate possible solutions at the level of organic substrates, not at the systemic chemical level.