Cyanide as a primordial reductant enables a protometabolic reductive glyoxylate pathway

Pinpointing Conditions for a Metabolic Origin of Life: Underlying Mechanisms and the Role of Coenzymes

ConspectusFamously found written on the blackboard of physicist Richard Feynman after his death was the phrase, "What I cannot create, I do not understand." From this perspective, recreating the origin of life in the lab is a necessary condition for achieving a deep theoretical understanding of biology. The "metabolism-first" hypothesis is one of the leading frameworks for the origin of life. A complex self-organized reaction network is thought to have been driven into existence as a chemical path of least resistance to release free energy in the environment that could otherwise not be dissipated, rerouting energy from planetary processes to organic chemistry. To increase in complexity, the reaction network, initially under catalysis provided by its geochemical environment, must have produced organic catalysts that pruned the existing flux through the network or expanded it in new directions. This boot-strapping process would gradually lessen the dependence on the initial catalytic environment and allow the reaction network to persist using catalysts of its own making. Eventually, this process leads to the seemingly inseparable interdependence at the heart of biology between catalysts (coenzymes, enzymes, genes) and the metabolic pathways that synthesize them. Experimentally, the primary challenge is to recreate the conditions where such a network emerged. However, the near infinite number of microenvironments and sources of energy available on the early Earth or elsewhere poses an enormous combinatorial challenge. To constrain the search, our lab has been surveying conditions where the reactions making up the core of some of the most ancient chemolithoautotrophic metabolisms, which consist of only a small number of repeating chemical mechanisms, occur nonenzymatically. To give a fresh viewpoint in the first part of this account, we have organized the results of our search (along with important results from other laboratories) by reaction mechanism, rather than by pathway. We expect that identifying a common set of conditions for each type of reaction mechanism will help pinpoint the conditions for the emergence of a self-organized reaction network resembling core metabolism. Many of the reaction mechanisms were found to occur in a wide variety of nonenzymatic conditions. Others, such as carboxylate phosphorylation and C-C bond formation from CO2, were found to be the most constraining, and thus help narrow the scope of environments where a reaction network could emerge. In the second part of this account, we highlight examples where small molecules produced by metabolism, known as coenzymes, mediate nonenzymatic chemistry of the type needed for the coenzyme's own synthesis or that turn on new reactivity of interest for expanding a hypothetical protometabolic network. These examples often feature cooperativity between small organic coenzymes and metal ions, recapitulating the transition from inorganic to organic catalysis during the origin of life. Overall, the most interesting conditions are those containing a reducing potential equivalent to H2 gas (electrochemical or H2 itself), Fe in both reduced and more oxidized forms (possibly with other metals like Ni) and localized strong electric fields. Environments that satisfy these criteria simultaneously will be of prime interest for reconstructing a metabolic origin of life.

Viscosity Regulation of Chemically Simple Condensates

This study investigates the viscosity and liquid-solid transition behavior of biomolecular condensates formed by polyarginine chains (Rx) of varying lengths and citric acid (CA) derivatives. By condensing Rx chains of various lengths with CA derivatives, we showed that the shorter Rx chains attenuate the high aggregation tendency of the longer chains when condensed with CA. A mixture of different Rx lengths exhibited uniform intracondensate distribution, while its mobility largely depended on the ratio of the longer Rx chain. Our findings demonstrate a simple method to modulate condensate properties by adjusting the composition of scaffold molecules, shedding light on the role of molecular composition in controlling condensate viscosity and transition dynamics. This research contributes to a deeper understanding of biomolecular condensation processes and offers insights into potential strategies for manipulating condensate properties for various applications, including in the fields of synthetic biology and disease therapeutics in the future.

Mass Spectrometric Analysis of Purine Intermediary Metabolism Indicates Cyanide Induces Purine Catabolism in Rabbits

Purines are the building blocks of DNA/RNA, energy substrates, and cofactors. Purine metabolites, including ATP, GTP, NADH, and coenzyme A, are essential molecules in diverse biological processes such as energy metabolism, signal transduction, and enzyme activity. When purine levels increase, excess purines are either recycled to synthesize purine metabolites or catabolized to the end product uric acid. Purine catabolism increases during states of low oxygen tension (hypoxia and ischemia), but this metabolic pathway is incompletely understood in the context of histotoxic hypoxia (i.e., inhibition of oxygen utilization despite normal oxygen tension). In rabbits exposed to cyanide-a classical histotoxic hypoxia agent-we demonstrated significant increases in several concordant metabolites in the purine catabolic pathway (including plasma levels of uric acid, xanthosine, xanthine, hypoxanthine, and inosine) via mass spectrometry-based metabolite profiling. Pharmacological inhibition of the purine catabolic pathway with oxypurinol mitigated the deleterious effects of cyanide on skeletal muscle cytochrome c oxidase redox state, measured by non-invasive diffuse optical spectroscopy. Finally, plasma uric acid levels correlated strongly with those of lactic acid, an established clinical biomarker of cyanide exposure, in addition to a tissue biomarker of cyanide exposure (skeletal muscle cytochrome c oxidase redox state). Cumulatively, these findings not only shed light on the in vivo role(s) of cyanide but also have implications in the field of medical countermeasure (MCM) development.

A prebiotic Krebs cycle analog generates amino acids with H2 and NH3 over nickel

Hydrogen (H2) has powered microbial metabolism for roughly 4 billion years. The recent discovery that it also fuels geochemical analogs of the most ancient biological carbon fixation pathway sheds light on the origin of metabolism. However, it remains unclear whether H2 can sustain more complex nonenzymatic reaction networks. Here, we show that H2 drives the nonenzymatic reductive amination of six biological ketoacids and glyoxylate to give the corresponding amino acids in good yields using ammonium concentrations ranging from 6 to 150 mM. Catalytic amounts of nickel or ground meteorites enable these reactions at 22°C and pH 8. The same conditions promote an H2-dependent ketoacid-forming reductive aldol chemistry that co-occurs with reductive amination, producing a continuous reaction network resembling amino acid synthesis in the metabolic core of ancient microbes. The results support the hypothesis that the earliest biochemical networks could have emerged without enzymes or RNA.

Autocatalytic Selection as a Driver for the Origin of Life

Darwin's theory of evolution by natural selection was revolutionary because it provided a mechanism by which variation could be selected. This mechanism can only operate on living systems and thus cannot be applied to the origin of life. Here, we propose a viable alternative mechanism for prebiotic systems: autocatalytic selection, in which molecules catalyze reactions and processes that lead to increases in their concentration. Crucially, this provides a driver for increases in concentrations of molecules to a level that permits prebiotic metabolism. We show how this can produce high levels of amino acids, sugar phosphates, nucleotides and lipids and then lead on to polymers. Our outline is supported by a set of guidelines to support the identification of the most likely prebiotic routes. Most of the steps in this pathway are already supported by experimental results. These proposals generate a coherent and viable set of pathways that run from established Hadean geochemistry to the beginning of life.

Primitive purine biosynthesis connects ancient geochemistry to modern metabolism

An unresolved question in the origin and evolution of life is whether a continuous path from geochemical precursors to the majority of molecules in the biosphere can be reconstructed from modern-day biochemistry. Here we identified a feasible path by simulating the evolution of biosphere-scale metabolism, using only known biochemical reactions and models of primitive coenzymes. We find that purine synthesis constitutes a bottleneck for metabolic expansion, which can be alleviated by non-autocatalytic phosphoryl coupling agents. Early phases of the expansion are enriched with enzymes that are metal dependent and structurally symmetric, supporting models of early biochemical evolution. This expansion trajectory suggests distinct hypotheses regarding the tempo, mode and timing of metabolic pathway evolution, including a late appearance of methane metabolisms and oxygenic photosynthesis consistent with the geochemical record. The concordance between biological and geological analyses suggests that this trajectory provides a plausible evolutionary history for the vast majority of core biochemistry.

Nitrile biosynthesis in nature: how and why?

Covering: up to the end of 2023Natural nitriles comprise a small set of secondary metabolites which however show intriguing chemical and functional diversity. Various patterns of nitrile biosynthesis can be seen in animals, plants, and microorganisms with the characteristics of both evolutionary divergence and convergence. These specialized compounds play important roles in nitrogen metabolism, chemical defense against herbivores, predators and pathogens, and inter- and/or intraspecies communications. Here we review the naturally occurring nitrile-forming pathways from a biochemical perspective and discuss the biological and ecological functions conferred by diversified nitrile biosyntheses in different organisms. Elucidation of the mechanisms and evolutionary trajectories of nitrile biosynthesis underpins better understandings of nitrile-related biology, chemistry, and ecology and will ultimately benefit the development of desirable nitrile-forming biocatalysts for practical applications.

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.

Carbonyl Migration in Uronates Affords a Potential Prebiotic Pathway for Pentose Production

Carbohydrate biosynthesis is fundamental to modern terrestrial biochemistry, but how this collection of metabolic pathways originated remains an open question. Prebiotic sugar synthesis has focused primarily on the formose reaction and Kiliani-Fischer homologation; however, how they can transition to extant biochemical pathways has not been studied. Herein, a nonenzymatic pathway for pentose production with similar chemical transformations as those of the pentose phosphate pathway is demonstrated. Starting from a C6 aldonate, namely, gluconate, nonselective chemical oxidation yields a mixture of 2-oxo-, 4-oxo-, 5-oxo-, and 6-oxo-uronate regioisomers. Regardless at which carbinol the oxidation takes place, carbonyl migration enables β-decarboxylation to yield pentoses. In comparison, the pentose phosphate pathway selectively oxidizes 6-phosphogluconate to afford the 3-oxo-uronate derivative, which undergoes facile subsequent β-decarboxylation and carbonyl migration to afford ribose 5-phosphate. The similarities between these two pathways and the potential implications for prebiotic chemistry and protometabolism are discussed.

Environmental Stability and Its Importance for the Emergence of Darwinian Evolution

The emergence of Darwinian evolution represents a central point in the history of life as we know it. However, it is generally assumed that the environments in which life appeared were hydrothermal environments, with highly variable conditions in terms of pH, temperature or redox levels. Are evolutionary processes favored to appear in such settings, where the target of biological adaptation changes over time? How would the first evolving populations compete with non-evolving populations? Using a numerical model, we explore the effect of environmental variation on the outcome of the competition between evolving and non-evolving populations of protocells. Our study found that, while evolving protocells consistently outcompete non-evolving populations in stable environments, they are outcompeted in variable environments when environmental variations occur on a timescale similar to the average duration of a generation. This is due to the energetic burden represented by adaptation to the wrong environmental conditions. Since the timescale of temperature variation in natural hydrothermal settings overlaps with the average prokaryote generation time, the current work indicates that a solution must have been found by early life to overcome this threshold.

Redox-Controlled Shunts in a Synthetic Chemical Reaction Cycle

Shunts, alternative pathways in chemical reaction networks (CRNs), are ubiquitous in nature, enabling adaptability to external and internal stimuli. We introduce a CRN in which the recovery of Michael-accepting species is driven by oxidation chemistry. Using weak oxidants can enable access to two shunts within this CRN with different kinetics and a reduced number of side reactions compared to the main cycle that is driven by strong oxidants. Furthermore, we introduce a strategy to recycle one of the main products under flow conditions to partially reverse the CRN and control product speciation throughout time. These findings introduce new levels of control over artificial CRNs, driven by redox chemistry, narrowing the gap between synthetic and natural systems.

Regulation and function of the mammalian tricarboxylic acid cycle

The tricarboxylic acid (TCA) cycle, otherwise known as the Krebs cycle, is a central metabolic pathway that performs the essential function of oxidizing nutrients to support cellular bioenergetics. More recently, it has become evident that TCA cycle behavior is dynamic, and products of the TCA cycle can be co-opted in cancer and other pathologic states. In this review, we revisit the TCA cycle, including its potential origins and the history of its discovery. We provide a detailed accounting of the requirements for sustained TCA cycle function and the critical regulatory nodes that can stimulate or constrain TCA cycle activity. We also discuss recent advances in our understanding of the flexibility of TCA cycle wiring and the increasingly appreciated heterogeneity in TCA cycle activity exhibited by mammalian cells. Deeper insight into how the TCA cycle can be differentially regulated and, consequently, configured in different contexts will shed light on how this pathway is primed to meet the requirements of distinct mammalian cell states.

Hydrogen Drives Part of the Reverse Krebs Cycle under Metal or Meteorite Catalysis

Hydrogen (H₂ ) is a geological source of reducing electrons that is thought to have powered the metabolism of the last universal common ancestor to all extant life, and that is still metabolized by various modern organisms. It has been suggested that H₂ drove a geochemical analogue of some or all of the reverse Krebs cycle at the emergence of the metabolic network, catalyzed by metals, but this has yet to be demonstrated experimentally. Herein, we show that three consecutive steps of the reverse Krebs cycle, converting oxaloacetate into succinate, can be driven without enzymes and in one-pot by H₂ as the reducing agent under mild conditions compatible with biological chemistry. Low catalytic amounts of nickel (10-20 mol %) or platinum group metals (0.1-1 mol %) or even small amounts of ground meteorites were found to promote the reductive chemistry at temperatures between 5 and 60 °C and over a wide pH range, including pH 7. These results lend additional support to the hypothesis that geologically produced hydrogen and metal catalysts could have initiated early metabolic networks.

Prebiotic triose glycolysis promoted by co-catalytic proline and phosphate in neutral water

Proline and phosphate promote a near-quantitative aldol reaction between glycolaldehyde phosphate and formaldehyde at neutral pH in water. Our results demonstrate the important role of general acid-base catalysis in water and underscore the essential role that amino acid catalysis may have played in early evolution of life's core metabolic pathways.

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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On the Evolutionary History of the Twenty Encoded Amino Acids

α-Amino acids are essential molecular constituents of life, twenty of which are privileged because they are encoded by the ribosomal machinery. The question remains open as to why this number and why this 20 in particular, an almost philosophical question that cannot be conclusively resolved. They are closely related to the evolution of the genetic code and whether nucleic acids, amino acids, and peptides appeared simultaneously and were available under prebiotic conditions when the first self-sufficient complex molecular system emerged on Earth. This report focuses on prebiotic and metabolic aspects of amino acids and proteins starting with meteorites, followed by their formation, including peptides, under plausible prebiotic conditions, and the major biosynthetic pathways in the various kingdoms of life. Coenzymes play a key role in the present analysis in that amino acid metabolism is linked to glycolysis and different variants of the tricarboxylic acid cycle (TCA, rTCA, and the incomplete horseshoe version) as well as the biosynthesis of the most important coenzymes. Thus, the report opens additional perspectives and facets on the molecular evolution of primary metabolism.

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.

Frontiers in Prebiotic Chemistry and Early Earth Environments

The Prebiotic Chemistry and Early Earth Environments (PCE₃) Consortium is a community of researchers seeking to understand the origins of life on Earth and in the universe. PCE₃ is one of five Research Coordination Networks (RCNs) within NASA’s Astrobiology Program. Here we report on the inaugural PCE₃ workshop, intended to cross-pollinate, transfer information, promote cooperation, break down disciplinary barriers, identify new directions, and foster collaborations. This workshop, entitled, “Building a New Foundation”, was designed to propagate current knowledge, identify possibilities for multidisciplinary collaboration, and ultimately define paths for future collaborations. Presentations addressed the likely conditions on early Earth in ways that could be incorporated into prebiotic chemistry experiments and conceptual models to improve their plausibility and accuracy. Additionally, the discussions that followed among workshop participants helped to identify within each subdiscipline particularly impactful new research directions. At its core, the foundational knowledge base presented in this workshop should underpin future workshops and enable collaborations that bridge the many disciplines that are part of PCE₃.

A Plausible Prebiotic One-Pot Synthesis of Orotate and Pyruvate Suggestive of Common Protometabolic Pathways

A reaction between two prebiotically plausible building blocks, hydantoin and glyoxylate, generates both the nucleobase orotate, a precursor of biological pyrimidines, and pyruvate, a core metabolite in the citric acid cycle and amino acid biosynthesis. The reaction proceeds in water to provide significant yields of the two widely divergent chemical motifs. Additionally, the reaction of thiohydantoin and glyoxylate produces thioorotate in high yield under neutral aqueous conditions. The use of an open-chain thiohydantoin derivative also enables the potential pre-positioning of a nucleosidic bond prior to the synthesis of an orotate nucleoside. The observation that diverse building blocks of modern metabolism can be produced in a single reaction pot, from common reactants under mild conditions, supports the plausibility of orthogonal chemistries operating at the origins of chemical evolution.