Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA)

Exploring glycolytic enzymes in disease: potential biomarkers and therapeutic targets in neurodegeneration, cancer and parasitic infections

Glycolysis, present in most organisms, is evolutionarily one of the oldest metabolic pathways. It has great relevance at a physiological level because it is responsible for generating ATP in the cell through the conversion of glucose into pyruvate and reducing nicotinamide adenine dinucleotide (NADH) (that may be fed into the electron chain in the mitochondria to produce additional ATP by oxidative phosphorylation), as well as for producing intermediates that can serve as substrates for other metabolic processes. Glycolysis takes place through 10 consecutive chemical reactions, each of which is catalysed by a specific enzyme. Although energy transduction by glucose metabolism is the main function of this pathway, involvement in virulence, growth, pathogen-host interactions, immunomodulation and adaptation to environmental conditions are other functions attributed to this metabolic pathway. In humans, where glycolysis occurs mainly in the cytosol, the mislocalization of some glycolytic enzymes in various other subcellular locations, as well as alterations in their expression and regulation, has been associated with the development and progression of various diseases. In this review, we describe the role of glycolytic enzymes in the pathogenesis of diseases of clinical interest. In addition, the potential role of these enzymes as targets for drug development and their potential for use as diagnostic and prognostic markers of some pathologies are also discussed.

GTP before ATP: The energy currency at the origin of genes

Life is an exergonic chemical reaction. Many individual reactions in metabolism entail slightly endergonic steps that are coupled to free energy release, typically as ATP hydrolysis, in order to go forward. ATP is almost always supplied by the rotor-stator ATP synthase, which harnesses chemiosmotic ion gradients. Because the ATP synthase is a protein, it arose after the ribosome did. What was the energy currency of metabolism before the origin of the ATP synthase and how (and why) did ATP come to be the universal energy currency? About 27 % of a cell's energy budget is consumed as GTP during translation. The universality of GTP-dependence in ribosome function indicates that GTP was the ancestral energy currency of protein synthesis. The use of GTP in translation and ATP in small molecule synthesis are conserved across all lineages, representing energetic compartments that arose in the last universal common ancestor, LUCA. And what came before GTP? Recent findings indicate that the energy supporting the origin of LUCA's metabolism stemmed from H2-dependent CO2 reduction along routes that strongly resemble the reactions and transition metal catalysts of the acetyl-CoA pathway.

An irreversible thermodynamic model of prebiological dissipative molecular structures inside vacuoles at the surface of the Archean Ocean

A prebiotic model, based in the framework of thermodynamic efficiency loss from small dissipative eukaryote organisms is developed to describe the maximum possible concentration of solar power to be dissipated on topological circular molecules structures encapsulated in lipid-walled vacuoles, which floated in the Archean oceans. By considering previously, the analysis of 71 species examined by covering 18 orders of mass magnitude from the Megapteranovaeangliae to Saccharomyces cerevisiae suggest that in molecular structures of smaller masses than any living being known nowadays, the power dissipation must be directly proportional to the power of the photons of solar origin that impinge them to give rise to the formation of more complex self-assembled molecular structures at the prebiotic stage by a quantum mechanics model of resonant photon wavelength excitation. The analysis of 12 circular molecules (encapsulated in lipid-walled vacuoles) relevant to the evolution of life on planet Earth such as the five nucleobases, and some aromatic molecules as pyrimidine, porphyrin, chlorin, coumarin, xanthine, etc., were carried out. Considering one vacuole of each type of molecule per square meter of the ocean's surface of planet Earth (1.8∗1015 vacuoles), their dissipative operation would require only 10-10 times the matter used by the biomass currently existing on Earth. Relevant numbers (1020-1021) for the annual dissipative cycles corresponding to high energy photo chemical events, which in principle allow the assembling of more complex polymers, were obtained. The previous figures are compatible with some results obtained by followers of the primordial soup theory where under certain suppositions about the Archean chemical kinetical changes on the precursors of RNA and DNA try to justify the formation rate of RNA and DNA components and the emergence of life within a 10-million-year window, 3.5 billion years ago. The physical foundation perspective and the simplicity of the proposed approach suggests that it can serve as a possible template for both, the development of new kind of experiments, and for prebiotic theories that address self-organization occurring inside such vacuoles. Our model provides a new way to conceptualize the self-production of simple cyclic dissipative molecular structures in the Archean period of planet Earth. © 2017 ElsevierInc.Allrightsreserved.

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

Famously 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.

Chemical Antiquity in Metabolism

Life is an exergonic chemical reaction. The same was true when the very first cells emerged at life's origin. In order to live, all cells need a source of carbon, energy, and electrons to drive their overall reaction network (metabolism). In most cells, these are separate pathways. There is only one biochemical pathway that serves all three needs simultaneously: the acetyl-CoA pathway of CO2 fixation. In the acetyl-CoA pathway, electrons from H2 reduce CO2 to pyruvate for carbon supply, while methane or acetate synthesis are coupled to energy conservation as ATP. This simplicity and thermodynamic favorability prompted Georg Fuchs and Erhard Stupperich to propose in 1985 that the acetyl-CoA pathway might mark the origin of metabolism, at the same time that Steve Ragsdale and Harland Wood were uncovering catalytic roles for Fe, Co, and Ni in the enzymes of the pathway. Subsequent work has provided strong support for those proposals.In the presence of Fe, Co, and Ni in their native metallic state as catalysts, aqueous H2 and CO2 react specifically to formate, acetate, methane, and pyruvate overnight at 100 °C. These metals (and their alloys) thus replace the function of over 120 enzymes required for the conversion of H2 and CO2 to pyruvate via the pathway and its cofactors, an unprecedented set of findings in the study of biochemical evolution. The reactions require alkaline conditions, which promote hydrogen oxidation by proton removal and are naturally generated in serpentinizing (H2-producing) hydrothermal vents. Serpentinizing hydrothermal vents furthermore produce natural deposits of native Fe, Co, Ni, and their alloys. These are precisely the metals that reduce CO2 with H2 in the laboratory; they are also the metals found at the active sites of enzymes in the acetyl-CoA pathway. Iron, cobalt and nickel are relicts of the environments in which metabolism arose, environments that still harbor ancient methane- and acetate-producing autotrophs today. This convergence indicates bedrock-level antiquity for the acetyl-CoA pathway. In acetogens and methanogens growing on H2 as reductant, the acetyl-CoA pathway requires flavin-based electron bifurcation as a source of reduced ferredoxin (a 4Fe4S cluster-containing protein) in order to function. Recent findings show that H2 can reduce the 4Fe4S clusters of ferredoxin in the presence of native iron, uncovering an evolutionary precursor of flavin-based electron bifurcation and suggesting an origin of FeS-dependent electron transfer in proteins. Traditionally discussed as catalysts in early evolution, the most common function of FeS clusters in metabolism is one-electron transfer, also in radical SAM enzymes, a large and ancient enzyme family. The cofactors and active sites in enzymes of the acetyl-CoA pathway uncover chemical antiquity in metabolism involving metals, methyl groups, methyl transfer reactions, cobamides, pterins, GTP, S-adenosylmethionine, radical SAM enzymes, and carbon-metal bonds. The reaction sequence from H2 and CO2 to pyruvate on naturally deposited native metals is maximally simple. It requires neither nitrogen, sulfur, phosphorus, RNA, ion gradients, nor light. Solid-state metal catalysts tether the origin of metabolism to a H2-producing, serpentinizing hydrothermal vent.

The radical impact of oxygen on prokaryotic evolution-enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third

Molecular oxygen is a stable diradical. All O2-dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O2 started accumulating on Earth 2.4 billion years ago. Its evolutionary impact is traditionally sought in respiration and energy yield. We mapped 365 O2-dependent enzymatic reactions of prokaryotes to phylogenies for the corresponding 792 protein families. The main physiological adaptations imparted by O2-dependent enzymes were not energy conservation, but novel organic substrate oxidations and O2-dependent, hence O2-tolerant, alternative pathways for O2-inhibited reactions. Oxygen-dependent enzymes evolved in ancestrally anaerobic pathways for essential cofactor biosynthesis including NAD+, pyridoxal, thiamine, ubiquinone, cobalamin, heme, and chlorophyll. These innovations allowed prokaryotes to synthesize essential cofactors in O2-containing environments, a prerequisite for the later emergence of aerobic respiratory chains.

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.

Ferredoxin reduction by hydrogen with iron functions as an evolutionary precursor of flavin-based electron bifurcation

Autotrophic theories for the origin of metabolism posit that the first cells satisfied their carbon needs from CO2 and were chemolithoautotrophs that obtained their energy and electrons from H2. The acetyl-CoA pathway of CO2 fixation is central to that view because of its antiquity: Among known CO2 fixing pathways it is the only one that is i) exergonic, ii) occurs in both bacteria and archaea, and iii) can be functionally replaced in full by single transition metal catalysts in vitro. In order to operate in cells at a pH close to 7, however, the acetyl-CoA pathway requires complex multi-enzyme systems capable of flavin-based electron bifurcation that reduce low potential ferredoxin-the physiological donor of electrons in the acetyl-CoA pathway-with electrons from H2. How can the acetyl-CoA pathway be primordial if it requires flavin-based electron bifurcation? Here, we show that native iron (Fe0), but not Ni0, Co0, Mo0, NiFe, Ni2Fe, Ni3Fe, or Fe3O4, promotes the H2-dependent reduction of aqueous Clostridium pasteurianum ferredoxin at pH 8.5 or higher within a few hours at 40 °C, providing the physiological function of flavin-based electron bifurcation, but without the help of enzymes or organic redox cofactors. H2-dependent ferredoxin reduction by iron ties primordial ferredoxin reduction and early metabolic evolution to a chemical process in the Earth's crust promoted by solid-state iron, a metal that is still deposited in serpentinizing hydrothermal vents today.

Systems theory, thermodynamics and life: Integrated thinking across ecology, organization and biological evolution

In this paper we explore the relevance and integration of system theory and thermodynamics in terms of the Earth system. It is proposed that together, these fields explain the evolution, organization, functionality and directionality of life on Earth. We begin by summarizing historical and current thinking on the definition of life itself. We then investigate the evidence for a single unit of life. Given that any definition of life and its levels of organization are intertwined, we explore how the Earth system is structured and functions from an energetic perspective, by outlining relevant thermodynamic theory relating to molecular, metabolic, cellular, individual, population, species, ecosystem and biome organization. We next investigate the fundamental relationships between systems theory and thermodynamics in terms of the Earth system, examining the key characteristics of self-assembly, self-organization (including autonomy), emergence, non-linearity, feedback and sub-optimality. Finally, we examine the relevance of systems theory and thermodynamics with reference to two specific aspects: the tempo and directionality of evolution and the directional and predictable process of ecological succession. We discuss the importance of the entropic drive in understanding altruism, multicellularity, mutualistic and antagonistic relationships and how maximum entropy production theory may explain patterns thought to evidence the intermediate disturbance hypothesis.

Reaction thermodynamics as a constraint on piscine steroidogenesis flux distributions

While a considerable amount is known of the dynamics of piscine steroidogenesis during reproduction, the influence of thermodynamics constraints on its control has not been studied. In this manuscript, Gibbs free energy change of reactions was calculated for piscine steroidogenesis using the in silico eQuilibrator thermodynamics calculator. The analysis identified cytochrome P450 (cyp450) oxidoreductase reactions to have more negative Gibbs free energy changes relative to hydroxysteroid (HSD) and transferase reactions. In addition, a more favorable Gibbs free energy change was predicted for the Δ5 (cyp450 catalyzed) vs. Δ4 (HSD catalyzed) steroidogenesis branch-point, which converts pregnenolone to 17α-hydroxypregnenolone or progesterone respectively. Comparison of in silico predictions with in vivo experimentally measured flux across the Δ5 vs. Δ4 branch-point showed higher flux through the thermodynamically more favorable Δ5 pathway in reproducing or spawning vs. non-spawning fathead minnows (Pimephales promelas). However, the exposure of fish to endocrine stressors such as hypoxia or the synthetic estrogen 17α-ethinylestradiol (EE2), resulted in increased flux through both Δ5 and Δ4 pathways, indicating an adaptive response to increase steroidogenic redundancy. The correspondence of elevated flux through the Δ5 branch-point in spawning fish indicated the use of a thermodynamically favorable pathway to optimize steroid hormone productions during reproduction. We hypothesize that such selective use of a thermodynamically favorable steroidogenesis pathway may conserve reduced equivalents or transcriptional costs for investment to other biosynthetic or catabolic reactions to support reproduction. If generalizable, such an approach can provide novel insights into the structural principles and regulation of steroidogenesis or other metabolic pathways.

The Moon-Forming Impact and the Autotrophic Origin of Life

The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2 . According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2 , forging a direct line of continuity between Earth's initial CO2 -rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.

Serpentinization as the source of energy, electrons, organics, catalysts, nutrients and pH gradients for the origin of LUCA and life

Serpentinization in hydrothermal vents is central to some autotrophic theories for the origin of life because it generates compartments, reductants, catalysts and gradients. During the process of serpentinization, water circulates through hydrothermal systems in the crust where it oxidizes Fe (II) in ultramafic minerals to generate Fe (III) minerals and H2. Molecular hydrogen can, in turn, serve as a freely diffusible source of electrons for the reduction of CO2 to organic compounds, provided that suitable catalysts are present. Using catalysts that are naturally synthesized in hydrothermal vents during serpentinization H2 reduces CO2 to formate, acetate, pyruvate, and methane. These compounds represent the backbone of microbial carbon and energy metabolism in acetogens and methanogens, strictly anaerobic chemolithoautotrophs that use the acetyl-CoA pathway of CO2 fixation and that inhabit serpentinizing environments today. Serpentinization generates reduced carbon, nitrogen and - as newer findings suggest - reduced phosphorous compounds that were likely conducive to the origins process. In addition, it gives rise to inorganic microcompartments and proton gradients of the right polarity and of sufficient magnitude to support chemiosmotic ATP synthesis by the rotor-stator ATP synthase. This would help to explain why the principle of chemiosmotic energy harnessing is more conserved (older) than the machinery to generate ion gradients via pumping coupled to exergonic chemical reactions, which in the case of acetogens and methanogens involve H2-dependent CO2 reduction. Serpentinizing systems exist in terrestrial and deep ocean environments. On the early Earth they were probably more abundant than today. There is evidence that serpentinization once occurred on Mars and is likely still occurring on Saturn's icy moon Enceladus, providing a perspective on serpentinization as a source of reductants, catalysts and chemical disequilibrium for life on other worlds.

Biophysical Interactions Underpin the Emergence of Information in the Genetic Code

The genetic code conceals a 'code within the codons', which hints at biophysical interactions between amino acids and their cognate nucleotides. Yet, research over decades has failed to corroborate systematic biophysical interactions across the code. Using molecular dynamics simulations and NMR, we have analysed interactions between the 20 standard proteinogenic amino acids and 4 RNA mononucleotides in 3 charge states. Our simulations show that 50% of amino acids bind best with their anticodonic middle base in the -1 charge state common to the backbone of RNA, while 95% of amino acids interact most strongly with at least 1 of their codonic or anticodonic bases. Preference for the cognate anticodonic middle base was greater than 99% of randomised assignments. We verify a selection of our results using NMR, and highlight challenges with both techniques for interrogating large numbers of weak interactions. Finally, we extend our simulations to a range of amino acids and dinucleotides, and corroborate similar preferences for cognate nucleotides. Despite some discrepancies between the predicted patterns and those observed in biology, the existence of weak stereochemical interactions means that random RNA sequences could template non-random peptides. This offers a compelling explanation for the emergence of genetic information in biology.

Design of a minimal di-nickel hydrogenase peptide

Ancestral metabolic processes involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13-amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe] hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase, two ancient, extant proteins central to metabolism. These experimental results demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth.

Modular structure of complex II: An evolutionary perspective

Succinate dehydrogenases (SDHs) and fumarate reductases (FRDs) catalyse the interconversion of succinate and fumarate, a reaction highly conserved in all domains of life. The current classification of SDH/FRDs is based on the structure of the membrane anchor subunits and their cofactors. It is, however, unknown whether this classification would hold in the context of evolution. In this work, a large-scale comparative genomic analysis of complex II addresses the questions of its taxonomic distribution and phylogeny. Our findings report that for types C, D, and F, structural classification and phylogeny go hand in hand, while for types A, B and E the situation is more complex, highlighting the possibility for their classification into subgroups. Based on these findings, we proposed a revised version of the evolutionary scenario for these enzymes in which a primordial soluble module, corresponding to the cytoplasmatic subunits, would give rise to the current diversity via several independent membrane anchor attachment events.

Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria

Ancestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes mean there is much that is still unknown. Here, we apply proteome-wide 3D structure predictions and comparisons to investigate ancestorial metabolism of ancient bacteria and archaea, to provide information beyond sequence as a bridge to the prebiotic processes. We compare representative bacterial and archaeal strains, which reveal surprisingly similar physiological and metabolic characteristics via microbiological and biophysical experiments. Pairwise comparison of protein structures identify the conserved metabolic modules in bacteria and archaea, despite interference from overly variable sequences. The conserved modules (for example, middle of glycolysis, partial TCA, proton/sulfur respiration, building block biosynthesis) constitute the basic functions that possibly existed in the archaeal-bacterial common ancestor, which are remarkably consistent with the experimentally confirmed protometabolic pathways. These structure-based findings provide a new perspective to reconstructing the ancestral metabolism and understanding its origin, which suggests high-throughput protein 3D structure prediction is a promising approach, deserving broader application in future ancestral exploration.

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.

The limits of metabolic heredity in protocells

The universal core of metabolism could have emerged from thermodynamically favoured prebiotic pathways at the origin of life. Starting with H 2 and CO 2 , the synthesis of amino acids and mixed fatty acids, which self-assemble into protocells, is favoured under warm anoxic conditions. Here, we address whether it is possible for protocells to evolve greater metabolic complexity, through positive feedbacks involving nucleotide catalysis. Using mathematical simulations to model metabolic heredity in protocells, based on branch points in protometabolic flux, we show that nucleotide catalysis can indeed promote protocell growth. This outcome only occurs when nucleotides directly catalyse CO 2 fixation. Strong nucleotide catalysis of other pathways (e.g. fatty acids and amino acids) generally unbalances metabolism and slows down protocell growth, and when there is competition between catalytic functions cell growth collapses. Autocatalysis of nucleotide synthesis can promote growth but only if nucleotides also catalyse CO 2 fixation; autocatalysis alone leads to the accumulation of nucleotides at the expense of CO 2 fixation and protocell growth rate. Our findings offer a new framework for the emergence of greater metabolic complexity, in which nucleotides catalyse broad-spectrum processes such as CO 2 fixation, hydrogenation and phosphorylation important to the emergence of genetic heredity at the origin of life.

A Short Tale of the Origin of Proteins and Ribosome Evolution

Proteins are the workhorses of the cell and have been key players throughout the evolution of all organisms, from the origin of life to the present era. How might life have originated from the prebiotic chemistry of early Earth? This is one of the most intriguing unsolved questions in biology. Currently, however, it is generally accepted that amino acids, the building blocks of proteins, were abiotically available on primitive Earth, which would have made the formation of early peptides in a similar fashion possible. Peptides are likely to have coevolved with ancestral forms of RNA. The ribosome is the most evident product of this coevolution process, a sophisticated nanomachine that performs the synthesis of proteins codified in genomes. In this general review, we explore the evolution of proteins from their peptide origins to their folding and regulation based on the example of superoxide dismutase (SOD1), a key enzyme in oxygen metabolism on modern Earth.

A prebiotic basis for ATP as the universal energy currency

ATP is universally conserved as the principal energy currency in cells, driving metabolism through phosphorylation and condensation reactions. Such deep conservation suggests that ATP arose at an early stage of biochemical evolution. Yet purine synthesis requires 6 phosphorylation steps linked to ATP hydrolysis. This autocatalytic requirement for ATP to synthesize ATP implies the need for an earlier prebiotic ATP equivalent, which could drive protometabolism before purine synthesis. Why this early phosphorylating agent was replaced, and specifically with ATP rather than other nucleoside triphosphates, remains a mystery. Here, we show that the deep conservation of ATP might reflect its prebiotic chemistry in relation to another universally conserved intermediate, acetyl phosphate (AcP), which bridges between thioester and phosphate metabolism by linking acetyl CoA to the substrate-level phosphorylation of ADP. We confirm earlier results showing that AcP can phosphorylate ADP to ATP at nearly 20% yield in water in the presence of Fe3+ ions. We then show that Fe3+ and AcP are surprisingly favoured. A wide range of prebiotically relevant ions and minerals failed to catalyse ADP phosphorylation. From a panel of prebiotic phosphorylating agents, only AcP, and to a lesser extent carbamoyl phosphate, showed any significant phosphorylating potential. Critically, AcP did not phosphorylate any other nucleoside diphosphate. We use these data, reaction kinetics, and molecular dynamic simulations to infer a possible mechanism. Our findings might suggest that the reason ATP is universally conserved across life is that its formation is chemically favoured in aqueous solution under mild prebiotic conditions.

Small-molecule autocatalytic networks are universal metabolic fossils

Life and the genetic code are self-referential and so are autocatalytic networks made of simpler, small molecules. Several origins of life theories postulate autocatalytic chemical networks preceding the primordial genetic code, yet demonstration with biochemical systems is lacking. Here, small-molecule reflexively autocatalytic food-generated networks (RAFs) ranging in size from 3 to 619 reactions were found in all of 6683 prokaryotic metabolic networks searched. The average maximum RAF size is 275 reactions for a rich organic medium and 93 for a medium with a single organic cofactor, NAD. In the rich medium, all universally essential metabolites are produced with the exception of glycerol-1-p (archaeal lipid precursor), phenylalanine, histidine and arginine. The 300 most common reactions, present in at least 2732 RAFs, are mostly involved in amino acid biosynthesis and the metabolism of carbon, 2-oxocarboxylic acid and purines. ATP and NAD are central in generating network complexity, and because ATP is also one of the monomers of RNA, autocatalytic networks producing redox and energy currencies are a strong candidate niche of the origin of a primordial information-processing system. The wide distribution of small-molecule autocatalytic networks indicates that molecular reproduction may be much more prevalent in the Universe than hitherto predicted. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.

Quinolinate Synthase: An Example of the Roles of the Second and Outer Coordination Spheres in Enzyme Catalysis

The activation energy barrier of biochemical reactions is normally lowered by an enzyme catalyst, which directly helps the weakening of the bond(s) to be broken. In many metalloenzymes, this is a first coordination sphere effect. Besides having a direct catalytic action, enzymes can fix their reactive groups and substrates so that they are optimally positioned and also modify the water activity in the system. They can either activate substrates prior to their reaction or bind preactivated substrates, thereby drastically reducing local entropic effects. The latter type is well represented by some bisubstrate reactions, where they have been defined as "entropic traps". These can be described as "second coordination sphere" processes, but enzymes can also control the reactivity beyond this point through local conformational changes belonging to an "outer coordinate sphere" that can be modulated by substrate binding. We have chosen the [4Fe-4S] cluster-dependent enzyme quinolinate synthase to illustrate each one of these processes. In addition, this very old metalloenzyme shows low in vitro substrate binding specificity, atypical reactivity that produces dead-end products, and a unique modulation of its active site volume.