Beating the acetyl coenzyme A-pathway to the origin of life

Analogs of Precambrian microbial communities formed de novo in Caucasian mineral water aquifers

The microbiome of deep continental aquifers is considered the most slowly evolving part of the biosphere. The Yessentukskoye Mineral Water Basin (YMWB), located in the pre-Caucasus region, contains three closely spaced but distinct aquifers, the Upper Cretaceous, the Lower Cretaceous, and the Upper Jurassic, which represent unique objects for subsurface biosphere research due to gas-hydrogeochemical and thermal anomalies of the area. We analyzed the geological and hydrogeochemical parameters of the three aquifers and a recharge area of the YMWB and investigated their microbial communities using metagenomic and cultivation-based approaches within a long-term survey. Correlation analysis of the obtained data revealed stable and highly stratified microbial communities inhabiting four distinct ecosystems. Their structure and the metabolic traits of their prokaryotic populations were similar to those presumed to have dominated the Earth's biosphere during several critical periods of its evolutionary history, that is, the Early Archean, the period of banded iron formations accumulation, and the Great Oxidation Event. Among the YMWB strata, the Upper Jurassic aquifer, supersaturated with CO2, influenced by magmatic activity, and highly enriched with thermophilic autotrophic hydrogenotrophic acetogens, turned out to be the first described modern ecosystem based on the primary production by a process predicted to support the Last Universal Common Ancestor (LUCA). The characterization of the YMWB microbial communities reveals a contemporary model environment of the early stages of Earth's development and thus contributes to the understanding of the evolutionary traits in microbial populations that may have played a critical role in the formation of the modern biosphere.IMPORTANCEContinental subsurface environments are estimated to harbor up to one-fifth of the planet's total biomass, representing the most stable and slowly evolving part of the biosphere. Among the deep subsurface inhabitants, the microbial communities of drinking mineral waters remain the least studied. Our interdisciplinary study of the Yessentukskoye Mineral Water Basin shows how hydrochemical and hydrodynamic factors shape different subsurface ecosystems, whose microbial populations influence the composition of mineral waters. A comprehensive analysis reveals the similarity of these ecosystems to those predicted for the early Earth. The deepest of the studied aquifers is the first described modern ecosystem with the most probable primary producer performing hydrogenotrophic acetogenesis. Thus, our results contribute to the understanding of the genesis of modern drinking water resources and expand the knowledge of the evolutionary traits that may have played a critical role in the formation of the Earth's biosphere.

Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution

The geosphere and the microbial biosphere have co-evolved for ~3.8 Ga, with many lines of evidence suggesting a hydrothermal habitat for life's origin. However, the extent that contemporary thermophiles and their hydrothermal habitats reflect those that likely existed on early Earth remains unknown. To address this knowledge gap, 64 geochemical analytes were measured and 1022 metagenome-assembled-genomes (MAGs) were generated from 34 chemosynthetic high-temperature springs in Yellowstone National Park and analysed alongside 444 MAGs from 35 published metagenomes. We used these data to evaluate co-variation in MAG taxonomy, metabolism, and phylogeny as a function of hot spring geochemistry. We found that cohorts of MAGs and their functions are discretely distributed across pH gradients that reflect different geochemical provinces. Acidic or circumneutral/alkaline springs harbor MAGs that branched later and are enriched in sulfur- and arsenic-based O2-dependent metabolic pathways that are inconsistent with early Earth conditions. In contrast, moderately acidic springs sourced by volcanic gas harbor earlier-branching MAGs that are enriched in anaerobic, gas-dependent metabolisms (e.g. H2, CO2, CH4 metabolism) that have been hypothesized to support early microbial life. Our results provide insight into the influence of redox state in the eco-evolutionary feedbacks between thermophiles and their habitats and suggest moderately acidic springs as early Earth analogs.

Why pyridoxal phosphate could be a functional predecessor of thiamine pyrophosphate and speculations on a primordial metabolism

The account attempts to substantiate the hypothesis that, from an evolutionary perspective, the coenzyme couple pyridoxal phosphate and pyridoxamine phosphate preceded the coenzyme thiamine pyrophosphate and acted as its less efficient chemical analogue in some form of early metabolism. The analysis combines mechanism-based chemical reactivity with biosynthetic arguments and provides evidence that vestiges of "TPP-like reactivity" are still found for PLP today. From these thoughts, conclusions can be drawn about the key elements of a primordial form of metabolism, which includes the citric acid cycle, amino acid biosynthesis and the pentose phosphate pathway.

New Estimates of Nitrogen Fixation on Early Earth

Fixed nitrogen species generated by the early Earth's atmosphere are thought to be critical to the emergence of life and the sustenance of early metabolisms. A previous study estimated nitrogen fixation in the Hadean Earth's N2/CO2-dominated atmosphere; however, that previous study only considered a limited chemical network that produces NOx species (i.e., no HCN formation) via the thermochemical dissociation of N2 and CO2 in lightning flashes, followed by photochemistry. Here, we present an updated model of nitrogen fixation on Hadean Earth. We use the Chemical Equilibrium with Applications (CEA) thermochemical model to estimate lightning-induced NO and HCN formation and an updated version of KINETICS, the 1-D Caltech/JPL photochemical model, to assess the photochemical production of fixed nitrogen species that rain out into the Earth's early ocean. Our updated photochemical model contains hydrocarbon and nitrile chemistry, and we use a Geant4 simulation platform to consider nitrogen fixation stimulated by solar energetic particle deposition throughout the atmosphere. We study the impact of a novel reaction pathway for generating HCN via HCN2, inspired by the experimental results which suggest that reactions with CH radicals (from CH4 photolysis) may facilitate the incorporation of N into the molecular structure of aerosols. When the HCN2 reactions are added, we find that the HCN rainout rate rises by a factor of five in our 1-bar case and is about the same in our 2- and 12-bar cases. Finally, we estimate the equilibrium concentration of fixed nitrogen species under a kinetic steady state in the Hadean ocean, considering loss by hydrothermal vent circulation, photoreduction, and hydrolysis. These results inform our understanding of environments that may have been relevant to the formation of life on Earth, as well as processes that could lead to the emergence of life elsewhere in the universe.

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.

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.

Methane formation driven by light and heat prior to the origin of life and beyond

Methane is a potent greenhouse gas, which likely enabled the evolution of life by keeping the early Earth warm. Here, we demonstrate routes towards abiotic methane and ethane formation under early-earth conditions from methylated sulfur and nitrogen compounds with prebiotic origin. These compounds are demethylated in Fenton reactions governed by ferrous iron and reactive oxygen species (ROS) produced by light and heat in aqueous environments. After the emergence of life, this phenomenon would have greatly intensified in the anoxic Archean by providing methylated sulfur and nitrogen substrates. This ROS-driven Fenton chemistry can occur delocalized from serpentinization across Earth's humid realm and thereby substantially differs from previously suggested methane formation routes that are spatially restricted. Here, we report that Fenton reactions driven by light and heat release methane and ethane and might have shaped the chemical evolution of the atmosphere prior to the origin of life and beyond.

A self-sustaining serpentinization mega-engine feeds the fougerite nanoengines implicated in the emergence of guided metabolism

The demonstration by Ivan Barnes et al. that the serpentinization of fresh Alpine-type ultramafic rocks results in the exhalation of hot alkaline fluids is foundational to the submarine alkaline vent theory (AVT) for life's emergence to its 'improbable' thermodynamic state. In AVT, such alkaline fluids ≤ 150°C, bearing H2 > CH4 > HS--generated and driven convectively by a serpentinizing exothermic mega-engine operating in the ultramafic crust-exhale into the iron-rich, CO2> > > NO3--bearing Hadean ocean to result in hydrothermal precipitate mounds comprising macromolecular ferroferric-carbonate oxyhydroxide and minor sulfide. As the nanocrystalline minerals fougerite/green rust and mackinawite (FeS), they compose the spontaneously precipitated inorganic membranes that keep the highly contrasting solutions apart, thereby maintaining redox and pH disequilibria. They do so in the form of fine chimneys and chemical gardens. The same disequilibria drive the reduction of CO2 to HCOO- or CO, and the oxidation of CH4 to a methyl group-the two products reacting to form acetate in a sequence antedating the 'energy-producing' acetyl coenzyme-A pathway. Fougerite is a 2D-layered mineral in which the hydrous interlayers themselves harbor 2D solutions, in effect constricted to ~ 1D by preferentially directed electron hopping/tunneling, and proton Gröthuss 'bucket-brigading' when subject to charge. As a redox-driven nanoengine or peristaltic pump, fougerite forces the ordered reduction of nitrate to ammonium, the amination of pyruvate and oxalate to alanine and glycine, and their condensation to short peptides. In turn, these peptides have the flexibility to sequester the founding inorganic iron oxyhydroxide, sulfide, and pyrophosphate clusters, to produce metal- and phosphate-dosed organic films and cells. As the feed to the hydrothermal mound fails, the only equivalent sustenance on offer to the first autotrophs is the still mildly serpentinizing upper crust beneath. While the conditions here are very much less bountiful, they do offer the similar feed and disequilibria the survivors are accustomed to. Sometime during this transition, a replicating non-ribosomal guidance system is discovered to provide the rules to take on the incrementally changing surroundings. The details of how these replicating apparatuses emerged are the hard problem, but by doing so the progenote archaea and bacteria could begin to colonize what would become the deep biosphere. Indeed, that the anaerobic nitrate-respiring methanotrophic archaea and the deep-branching Acetothermia presently comprise a portion of that microbiome occupying serpentinizing rocks offers circumstantial support for this notion. However, the inescapable, if jarring conclusion is drawn that, absent fougerite/green rust, there would be no structured channelway to life.

Ambient temperature CO2 fixation to pyruvate and subsequently to citramalate over iron and nickel nanoparticles

The chemical reactions that formed the building blocks of life at origins required catalysts, whereby the nature of those catalysts influenced the type of products that accumulated. Recent investigations have shown that at 100 °C awaruite, a Ni3Fe alloy that naturally occurs in serpentinizing systems, is an efficient catalyst for CO2 conversion to formate, acetate, and pyruvate. These products are identical with the intermediates and products of the acetyl-CoA pathway, the most ancient CO2 fixation pathway and the backbone of carbon metabolism in H2-dependent autotrophic microbes. Here, we show that Ni3Fe nanoparticles prepared via the hard-templating method catalyze the conversion of H2 and CO2 to formate, acetate and pyruvate at 25 °C under 25 bar. Furthermore, the 13C-labeled pyruvate can be further converted to acetate, parapyruvate, and citramalate over Ni, Fe, and Ni3Fe nanoparticles at room temperature within one hour. These findings strongly suggest that awaruite can catalyze both the formation of citramalate, the C5 product of pyruvate condensation with acetyl-CoA in microbial carbon metabolism, from pyruvate and the formation of pyruvate from CO2 at very moderate reaction conditions without organic catalysts. These results align well with theories for an autotrophic origin of microbial metabolism under hydrothermal vent conditions.

Spark of Life: Role of Electrotrophy in the Emergence of Life

The emergence of life has been a subject of intensive research for decades. Different approaches and different environmental "cradles" have been studied, from space to the deep sea. Since the recent discovery of a natural electrical current through deep-sea hydrothermal vents, a new energy source is considered for the transition from inorganic to organic. This energy source (electron donor) is used by modern microorganisms via a new trophic type, called electrotrophy. In this review, we draw a parallel between this metabolism and a new theory for the emergence of life based on this electrical electron flow. Each step of the creation of life is revised in the new light of this prebiotic electrochemical context, going from the evaluation of similar electrical current during the Hadean, the CO₂ electroreduction into a prebiotic primordial soup, the production of proto-membranes, the energetic system inspired of the nitrate reduction, the proton gradient, and the transition to a planktonic proto-cell. Finally, this theory is compared to the two other theories in hydrothermal context to assess its relevance and overcome the limitations of each. Many critical factors that were limiting each theory can be overcome given the effect of electrochemical reactions and the environmental changes produced.

A naturalist perspective of microbiology: Examples from methanogenic archaea

Storytelling has been the primary means of knowledge transfer over human history. The effectiveness and reach of stories are improved when the message is appropriate for the target audience. Oftentimes, the stories that are most well received and recounted are those that have a clear purpose and that are told from a variety of perspectives that touch on the varied interests of the target audience. Whether scientists realize or not, they are accustomed to telling stories of their own scientific discoveries through the preparation of manuscripts, presentations, and lectures. Perhaps less frequently, scientists prepare review articles or book chapters that summarize a body of knowledge on a given subject matter, meant to be more holistic recounts of a body of literature. Yet, by necessity, such summaries are often still narrow in their scope and are told from the perspective of a particular discipline. In other words, interdisciplinary reviews or book chapters tend to be the rarity rather than the norm. Here, we advocate for and highlight the benefits of interdisciplinary perspectives on microbiological subjects.

Generation and Physiology of Hydrogen Sulfide and Reactive Sulfur Species in Bacteria

Sulfur is not only one of the most abundant elements on the Earth, but it is also essential to all living organisms. As life likely began and evolved in a hydrogen sulfide (H₂S)-rich environment, sulfur metabolism represents an early form of energy generation via various reactions in prokaryotes and has driven the sulfur biogeochemical cycle since. It has long been known that H₂S is toxic to cells at high concentrations, but now this gaseous molecule, at the physiological level, is recognized as a signaling molecule and a regulator of critical biological processes. Recently, many metabolites of H₂S, collectively called reactive sulfur species (RSS), have been gradually appreciated as having similar or divergent regulatory roles compared with H₂S in living organisms, especially mammals. In prokaryotes, even in bacteria, investigations into generation and physiology of RSS remain preliminary and an understanding of the relevant biological processes is still in its infancy. Despite this, recent and exciting advances in the fields are many. Here, we discuss abiotic and biotic generation of H₂S/RSS, sulfur-transforming enzymes and their functioning mechanisms, and their physiological roles as well as the sensing and regulation of H₂S/RSS.

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.

Cellular sentience as the primary source of biological order and evolution

All life is cellular, starting some 4 billion years ago with the emergence of the first cells. In order to survive their early evolution in the face of an extremely challenging environment, the very first cells invented cellular sentience and cognition, allowing them to make relevant decisions to survive through creative adaptations in a continuously running evolutionary narrative. We propose that the success of cellular life has crucially depended on a biological version of Maxwell's demons which permits the extraction of relevant sensory information and energy from the cellular environment, allowing cells to sustain anti-entropic actions. These sensor-effector actions allowed for the creative construction of biological order in the form of diverse organic macromolecules, including crucial polymers such as DNA, RNA, and cytoskeleton. Ordered biopolymers store analogue (structures as templates) and digital (nucleotide sequences of DNA and RNA) information that functioned as a form memory to support the development of organisms and their evolution. Crucially, all cells are formed by the division of previous cells, and their plasma membranes are physically and informationally continuous across evolution since the beginning of cellular life. It is argued that life is supported through life-specific principles which support cellular sentience, distinguishing life from non-life. Biological order, together with cellular cognition and sentience, allow the creative evolution of all living organisms as the authentic authors of evolutionary novelty.

Insights into carbon-fixation pathways through metagonomics in the sediments of deep-sea cold seeps

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior. At present, six pathways of autotrophic carbon fixation have been found: the Calvin cycle, the reductive Acetyl-CoA or Wood-Ljungdahl pathway (rAcCoA), the reductive tricarboxylic acid cycle (rTCA), the 3-hydroxypropionate bicycle (3HP), the 3-hydroxypropionate/4-hydroxybutyrate cycle (3HP/4HB), and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB). Although our knowledge about carbon fixation pathways in the ocean has increased significantly, carbon fixation pathways in the cold seeps are still unknown. In this study, we collected sediment samples from two cold seeps and one trough in the south China sea (SCS), and investigated with metagenomic and metagenome assembled genomes (MAGs). We found that six autotrophic carbon fixation pathways present in the cold seeps and trough with rTCA cycle was the most common pathway, whose genes were particularly high in the cold seeps and increased with sediment depths; the rAcCoA cycle mainly occurred in the cold seep regions, and the abundance of module genes increased with sediment depths. We also elucidated members of chemoautotrophic microorganisms involved in these six carbon-fixation pathways. The rAcCoA, rTCA and DC/4-HB cycles required significantly less energy probably play an important role in the deep-sea environments, especially in the cold seeps. This study provided metabolic insights into the carbon fixation pathways in the cold seeps, and laid the foundation for future detailed study on processes and rates of carbon fixation in the deep-sea ecosystems.

Biome-specific distribution of Ni-containing carbon monoxide dehydrogenases

Ni-containing carbon monoxide dehydrogenase (Ni-CODH) plays an important role in the CO/CO₂-based carbon and energy metabolism of microbiomes. Ni-CODH is classified into distinct phylogenetic clades, A–G, with possibly distinct cellular roles. However, the types of Ni-CODH clade used by organisms in different microbiomes are unknown. Here, we conducted a metagenomic survey of a protein database to determine the relationship between the phylogeny and biome distribution of Ni-CODHs. Clustering and phylogenetic analyses showed that the metagenome assembly-derived Ni-CODH sequences were distributed in ~ 60% Ni-CODH clusters and in all Ni-CODH clades. We also identified a novel Ni-CODH clade, clade H. Biome mapping on the Ni-CODH phylogenetic tree revealed that Ni-CODHs of almost all the clades were found in natural aquatic environmental and engineered samples, whereas those of specific subclades were found only in host-associated samples. These results are comparable with our finding that the diversity in the phylum-level taxonomy of host-associated Ni-CODH owners is statistically different from those of the other biomes. Our findings suggest that while Ni-CODH is a ubiquitous enzyme produced across diverse microbiomes, its distribution in each clade is biased and mainly affected by the distinct composition of microbiomes.

Ancient Metabolisms of a Thermophilic Subseafloor Bacterium

The ancient origins of metabolism may be rooted deep in oceanic crust, and these early metabolisms may have persisted in the habitable thermal anoxic aquifer where conditions remain similar to those when they first appeared. The Wood–Ljungdahl pathway for acetogenesis is a key early biosynthetic pathway with the potential to influence ocean chemistry and productivity, but its contemporary role in oceanic crust is not well established. Here, we describe the genome of a novel acetogen from a thermal suboceanic aquifer olivine biofilm in the basaltic crust of the Juan de Fuca Ridge (JdFR) whose genome suggests it may utilize an ancient chemosynthetic lifestyle. This organism encodes the genes for the complete canonical Wood–Ljungdahl pathway, but is potentially unable to use sulfate and certain organic carbon sources such as lipids and carbohydrates to supplement its energy requirements, unlike other known acetogens. Instead, this organism may use peptides and amino acids for energy or as organic carbon sources. Additionally, genes involved in surface adhesion, the import of metallic cations found in Fe-bearing minerals, and use of molecular hydrogen, a product of serpentinization reactions between water and olivine, are prevalent within the genome. These adaptations are likely a reflection of local environmental micro-niches, where cells are adapted to life in biofilms using ancient chemosynthetic metabolisms dependent on H₂ and iron minerals. Since this organism is phylogenetically distinct from a related acetogenic group of Clostridiales, we propose it as a new species, Candidatus Acetocimmeria pyornia.

Antibiotics adaptation costs alter carbon sequestration strategies of microorganisms in karst river

Karst ecosystems make an important contribution to the global carbon cycle, in which carbon-fixing microorganisms play a vital role. However, the healthy functioning of karst ecosystems is threatened because pollutants easily diffuse and spread through them due to their strong hydraulic connectivity. The microbiome of a karst river contaminated with antibiotics was studied. Through co-occurrence network analysis, six ecological clusters (MOD 1-MOD 6) with different distribution characteristics were determined, of which four were significantly correlated with antibiotics. The carbon fixation pathways in different ecological clusters were varied, and the dominant hydroxypropionate-hydroxybutyrate cycle and reductive acetyl-CoA pathway were negatively and positively correlated with antibiotics, respectively. Long-term antibiotic contamination altered the selection of carbonic anhydrase (CA) encoding genes in some of the CA-producing mineralization microorganisms. The selection of different carbon fixation pathways is a possible strategy for the microbial community to compensate for the adaptation costs associated with the pressure of antibiotics contamination and emergence of antibiotics resistance. Bayesian network analysis revealed that some carbon sequestration functions (such as β-CA and reductive acetyl-CoA pathway) surpassed certain antibiotic resistance genes in the regulation of environmental factors and microbial networks. An ecological cluster (MOD5) that possibly homologous to antibiotic contamination was the final node of the microbial community in karst river, which indicated that ecological clusters were not only selected by antibiotics, but were also regulated by multiple environmental factors in the karst river system. The carbon sequestration pathway was more directly reflected in the abundance of ecological groups than in the influence of CA. This study provides new insights into the feedback effect of karst system on typical pollutants generated from human activities.

Chemical Basis of Carbon Fixation Autotrophic Paleometabolism

Abstract

On the basis of biomimetic, phylometabolic, and thermodynamic analysis of modern CO2 assimilation pathways, a paleophenotypic reconstruction of ancient autotrophic metabolism systems was carried out. As a chemical basis for CO2 fixation paleometabolism, metabolic networks capable of self-reproduction and evolution are considered, and the reversibility of the transformation reactions of its intermediates is the most important factor in self-development of this network. The substances of the C–H–O system, paragenetically associated with hydrocarbons, create a phase space, which is a set of universal intermediates of the autotrophic paleometabolism chemical network. The concept of two strategies for the origin and development of autotrophic carbon fixation paleometabolism in the oxidized (CO2) and reduced (CH4) redox regimes of degassing of the ancient Earth is proposed. It was shown that P, T, and the redox conditions of hydrothermal systems of the early Archean were favorable for the development of primary methanotrophic metabolism.

Nitrogen Fixation at Early Mars

The Mars Science Laboratory (MSL) recently discovered nitrates in Gale Crater (e.g., Stern et al., 2015; Sutter et al., 2017). One possible mechanism for ancient nitrate deposition on Mars is through HNOx formation and rain out in the atmosphere, for which lightning-induced NO is likely the fundamental source. This study investigates nitrogen (N₂) fixation in early Mars' atmosphere, with implications for early Mars' habitability. We consider a 1 bar atmosphere of background CO₂, with abundance of N₂, hydrogen, and methane varied from 1% to 10% to explore a swath of potential early Mars climates. We derive lightning-induced thermochemical equilibrium fluxes of NO and HCN by coupling the lightning-rate parametrization from the study of Romps et al. (2014) with chemical equilibrium with applications, and we use a Geant4 simulation platform to estimate the effect of solar energetic particle events. These fluxes are used as input into KINETICS, the Caltech/JPL coupled photochemistry and transport code, which models the chemistry of 50 species linked by 495 reactions to derive rain-out fluxes of HNOx and HCN. We compute equilibrium concentrations of cyanide and nitrate in a putative northern ocean at early Mars, assuming hydrothermal vent circulation and photoreduction act as the dominant loss mechanisms. We find average oceanic concentrations of ∼0.1-2 nM nitrate and ∼0.01-2 mM cyanide. HCN is critical for protein synthesis at concentrations >0.01 M (e.g., Holm and Neubeck, 2009), and our result is astrobiologically significant if secondary local concentration mechanisms occurred. Nitrates may act as high-potential electron acceptors for early metabolisms, although the minimum concentration required is unknown. Our study derives concentrations that will be useful for future laboratory studies to investigate the habitability at early Mars. The aqueous nitrate concentrations correspond to surface nitrate precipitates of ∼1-8 × 10^-4 wt % that may have formed after the evaporation of surface waters, and these values roughly agree with recent MSL measurements.

Experimental Approaches for Testing the Hypothesis of the Emergence of Life at Submarine Alkaline Vents

Since the pioneering experimental work performed by Urey and Miller around 70 years ago, several experimental works have been developed for approaching the question of the origin of life based on very few well-constructed hypotheses. In recent years, attention has been drawn to the so-called alkaline hydrothermal vents model (AHV model) for the emergence of life. Since the first works, perspectives from complexity sciences, bioenergetics and thermodynamics have been incorporated into the model. Consequently, a high number of experimental works from the model using several tools have been developed. In this review, we present the key concepts that provide a background for the AHV model and then analyze the experimental approaches that were motivated by it. Experimental tools based on hydrothermal reactors, microfluidics and chemical gardens were used for simulating the environments of early AHVs on the Hadean Earth (~4.0 Ga). In addition, it is noteworthy that several works used techniques from electrochemistry to investigate phenomena in the vent-ocean interface for early AHVs. Their results provided important parameters and details that are used for the evaluation of the plausibility of the AHV model, and for the enhancement of it.

Diacerein as a Promising Acyl Donor in Biosynthetic Acetyl-CoA and Glycosyl Esters Mediated by a Multifunctional Maltose O-Acetyltransferase from Escherichia coli

Acetyl-coenzyme A (acetyl-CoA) is an important donor for acetylation modifications of nutritional supplements. The existing enzymatic methods for acetyl-CoA synthesis suffer from cofactor dependence, donor inaccessibility, and biocatalyst instability, leading to its high cost. Hence, a promising alternative is highly desired. Herein, a maltose O-acetyltransferase (MAT) with cofactor independence had been identified as a stable acetyl-CoA-synthesizing biocatalyst in a screen of the Escherichia coli genome. Under the action of MAT, an anthraquinone medicine containing two acetyl groups, diacerein, was screened as an acetyl donor. Saturation mutagenesis at Glu125 was performed to increase the acetyl-CoA-synthesizing capacity of MAT, while decreasing the accompanying hydrolase activities. A mutant MAT-E125F was thus generated and could convert diacerein and CoA into the highest yield of 3892.70 mg/L acetyl-CoA. Moreover, MAT could synthesize puerarin 6″-O-acetate and other glycosyl esters through acetyl-CoA-dependent acetylation or diacerein-based transesterification reaction. To most of the tested glycosides, the transesterification efficiency was higher than that of acetylation. The mutant MAT-E125V acquired the highest conversion of 94.0% to puerarin 6″-O-acetate through transesterification, while MAT-E125N yielded the highest conversion of 68.5% through acetylation. Taking together, the multifunctional MAT displayed a potent acetyl-CoA- and glycosyl ester-synthesizing capacity using diacerein as an acetyl donor.

The "Water Problem"(sic), the Illusory Pond and Life's Submarine Emergence-A Review

The assumption that there was a "water problem" at the emergence of life-that the Hadean Ocean was simply too wet and salty for life to have emerged in it-is here subjected to geological and experimental reality checks. The "warm little pond" that would take the place of the submarine alkaline vent theory (AVT), as recently extolled in the journal Nature, flies in the face of decades of geological, microbiological and evolutionary research and reasoning. To the present author, the evidence refuting the warm little pond scheme is overwhelming given the facts that (i) the early Earth was a water world, (ii) its all-enveloping ocean was never less than 4 km deep, (iii) there were no figurative "Icelands" or "Hawaiis", nor even an "Ontong Java" then because (iv) the solidifying magma ocean beneath was still too mushy to support such salient loadings on the oceanic crust. In place of the supposed warm little pond, we offer a well-protected mineral mound precipitated at a submarine alkaline vent as life's womb: in place of lipid membranes, we suggest peptides; we replace poisonous cyanide with ammonium and hydrazine; instead of deleterious radiation we have the appropriate life-giving redox and pH disequilibria; and in place of messy chemistry we offer the potential for life's emergence from the simplest of geochemically available molecules and ions focused at a submarine alkaline vent in the Hadean-specifically within the nano-confined flexible and redox active interlayer walls of the mixed-valent double layer oxyhydroxide mineral, fougerite/green rust comprising much of that mound.

Crystal structure of enoyl-CoA hydratase from Thermus thermophilus HB8

Fatty-acid degradation is an oxidative process that involves four enzymatic steps and is referred to as the β-oxidation pathway. During this process, long-chain acyl-CoAs are broken down into acetyl-CoA, which enters the mitochondrial tricarboxylic acid (TCA) cycle, resulting in the production of energy in the form of ATP. Enoyl-CoA hydratase (ECH) catalyzes the second step of the β-oxidation pathway by the syn addition of water to the double bond between C2 and C3 of a 2-trans-enoyl-CoA, resulting in the formation of a 3-hydroxyacyl CoA. Here, the crystal structure of ECH from Thermus thermophilus HB8 (TtECH) is reported at 2.85 Å resolution. TtECH forms a hexamer as a dimer of trimers, and wide clefts are uniquely formed between the two trimers. Although the overall structure of TtECH is similar to that of a hexameric ECH from Rattus norvegicus (RnECH), there is a significant shift in the positions of the helices and loops around the active-site region, which includes the replacement of a longer α3 helix with a shorter α-helix and 3₁₀-helix in RnECH. Additionally, one of the catalytic residues of RnECH, Glu144 (numbering based on the RnECH enzyme), is replaced by a glycine in TtECH, while the other catalytic residue Glu164, as well as Ala98 and Gly141 that stabilize the enolate intermediate, is conserved. Their putative ligand-binding sites and active-site residue compositions are dissimilar.

Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy)

Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons.

To What Inanimate Matter Are We Most Closely Related and Does the Origin of Life Harbor Meaning?

The question concerning the meaning of life is important, but it immediately confronts the present authors with insurmountable obstacles from a philosophical standpoint, as it would require us to define not only what we hold to be life, but what we hold to be meaning in addition, requiring us to do both in a properly researched context. We unconditionally surrender to that challenge. Instead, we offer a vernacular, armchair approach to life’s origin and meaning, with some layman’s thoughts on the meaning of origins as viewed from the biologist’s standpoint. One can observe that biologists generally approach the concept of biological meaning in the context of evolution. This is the basis for the broad resonance behind Dobzhansky’s appraisal that “Nothing in biology makes sense except in the light of evolution”. Biologists try to understand living things in the historical context of how they arose, without giving much thought to the definition of what life or living things are, which for a biologist is usually not an interesting question in the practical context of daily dealings with organisms. Do humans generally understand life’s meaning in the context of history? If we consider the problem of life’s origin, the question of what constitutes a living thing becomes somewhat more acute for the biologist, though not more answerable, because it is inescapable that there was a time when there were no organisms on Earth, followed by a time when there were, the latter time having persisted in continuity to the present. This raises the question of where, in that transition, chemicals on Earth became alive, requiring, in turn, a set of premises for how life arose in order to conceptualize the problem in relation to organisms we know today, including ourselves, which brings us to the point of this paper: In the same way that cultural narratives for origins always start with a setting, scientific narratives for origins also always start with a setting, a place on Earth or elsewhere where we can imagine what happened for the sake of structuring both the problem and the narrative for its solution. This raises the question of whether scientific origins settings convey meaning to humans in that they suggest to us from what kind of place and what kinds of chemicals we are descended, that is, to which inanimate things we are most closely related.

In situ FTIR study of CO2 reduction on inorganic analogues of carbon monoxide dehydrogenase

The CO₂-to-CO reduction by carbon monoxide dehydrogenase (CODH) with a [NiFe₄S₄] cluster is considered to be the oldest pathway of biological carbon fixation and therefore may have been involved in the origin of life. Although previous studies have investigated CO₂ reduction by Fe and Ni sulfides to identify the prebiotic origin of the [NiFe₄S₄] cluster, the reaction mechanism remains largely elusive. Herein, we applied in situ electrochemical ATR-FTIR spectroscopy to probe the reaction intermediates of greigite (Fe₃S₄) and violarite (FeNi₂S₄). Intermediate species assignable to surface-bound CO₂ and formyl groups were found to be stabilized in the presence of Ni, lending insight into its role in enhancing the multistep CO₂ reduction process.

Primordial bioenergy sources: The two facets of adenosine triphosphate

Life requires energy to exist, to reproduce and to survive. Two major hypotheses have been put forward concerning the source of this energy at the very early stages of life evolution: (i) abiotic organics either brought to Earth by comets and/or meteorites, or produced at its atmosphere, and (ii) mineral surface-dependent bioinorganic catalytic reactions. Considering the latter possibility, I propose that, besides being a precursor of nucleic acids, adenosine triphosphate (ATP), which probably was used very early to improve the fidelity of nucleic acid polymerization, played an essential role in the transition between mineral-bound protocells and their free counterparts. Indeed, phosphorylation by ATP renders carboxylate groups electrophilic enough to react with nucleophiles such as amines, an effect that, thanks to their Lewis acid character, also have dehydrated metal ions on mineral surfaces. Early ATP synthesis for metabolic processes most likely depended on substrate level phosphorylation. However, the exaptation of a hexameric helicase-like ATPase and a transmembrane H⁺ pump (which evolved to counteract the acidity caused by fermentation reactions within the protocell) generated a much more efficient membrane-bound ATP synthase that uses chemiosmosis to make ATP.

Molybdenum Enzymes and How They Support Virulence in Pathogenic Bacteria

Mononuclear molybdoenzymes are highly versatile catalysts that occur in organisms in all domains of life, where they mediate essential cellular functions such as energy generation and detoxification reactions. Molybdoenzymes are particularly abundant in bacteria, where over 50 distinct types of enzymes have been identified to date. In bacterial pathogens, all aspects of molybdoenzyme biology such as molybdate uptake, cofactor biosynthesis, and function of the enzymes themselves, have been shown to affect fitness in the host as well as virulence. Although current studies are mostly focused on a few key pathogens such as Escherichia coli, Salmonella enterica, Campylobacter jejuni, and Mycobacterium tuberculosis, some common themes for the function and adaptation of the molybdoenzymes to pathogen environmental niches are emerging. Firstly, for many of these enzymes, their role is in supporting bacterial energy generation; and the corresponding pathogen fitness and virulence defects appear to arise from a suboptimally poised metabolic network. Secondly, all substrates converted by virulence-relevant bacterial Mo enzymes belong to classes known to be generated in the host either during inflammation or as part of the host signaling network, with some enzyme groups showing adaptation to the increased conversion of such substrates. Lastly, a specific adaptation to bacterial in-host survival is an emerging link between the regulation of molybdoenzyme expression in bacterial pathogens and the presence of immune system-generated reactive oxygen species. The prevalence of molybdoenzymes in key bacterial pathogens including ESKAPE pathogens, paired with the mounting evidence of their central roles in bacterial fitness during infection, suggest that they could be important future drug targets.

Six 'Must-Have' Minerals for Life's Emergence: Olivine, Pyrrhotite, Bridgmanite, Serpentine, Fougerite and Mackinawite

Life cannot emerge on a planet or moon without the appropriate electrochemical disequilibria and the minerals that mediate energy-dissipative processes. Here, it is argued that four minerals, olivine ([Mg>Fe]2SiO4), bridgmanite ([Mg,Fe]SiO3), serpentine ([Mg,Fe,]2-3Si2O5[OH)]4), and pyrrhotite (Fe(1-x)S), are an essential requirement in planetary bodies to produce such disequilibria and, thereby, life. Yet only two minerals, fougerite ([Fe2+6xFe3+6(x-1)O12H2(7-3x)]2+·[(CO2-)·3H2O]2-) and mackinawite (Fe[Ni]S), are vital-comprising precipitate membranes-as initial "free energy" conductors and converters of such disequilibria, i.e., as the initiators of a CO2-reducing metabolism. The fact that wet and rocky bodies in the solar system much smaller than Earth or Venus do not reach the internal pressure (≥23 GPa) requirements in their mantles sufficient for producing bridgmanite and, therefore, are too reduced to stabilize and emit CO2-the staple of life-may explain the apparent absence or negligible concentrations of that gas on these bodies, and thereby serves as a constraint in the search for extraterrestrial life. The astrobiological challenge then is to search for worlds that (i) are large enough to generate internal pressures such as to produce bridgmanite or (ii) boast electron acceptors, including imported CO2, from extraterrestrial sources in their hydrospheres.

CO2 reduction driven by a pH gradient

All life on Earth is built of organic molecules, so the primordial sources of reduced carbon remain a major open question in studies of the origin of life. A variant of the alkaline-hydrothermal-vent theory for life's emergence suggests that organics could have been produced by the reduction of CO₂ via H₂ oxidation, facilitated by geologically sustained pH gradients. The process would be an abiotic analog-and proposed evolutionary predecessor-of the Wood-Ljungdahl acetyl-CoA pathway of modern archaea and bacteria. The first energetic bottleneck of the pathway involves the endergonic reduction of CO₂ with H₂ to formate (HCOO^-), which has proven elusive in mild abiotic settings. Here we show the reduction of CO₂ with H₂ at room temperature under moderate pressures (1.5 bar), driven by microfluidic pH gradients across inorganic Fe(Ni)S precipitates. Isotopic labeling with ¹³C confirmed formate production. Separately, deuterium (²H) labeling indicated that electron transfer to CO₂ does not occur via direct hydrogenation with H₂ but instead, freshly deposited Fe(Ni)S precipitates appear to facilitate electron transfer in an electrochemical-cell mechanism with two distinct half-reactions. Decreasing the pH gradient significantly, removing H₂, or eliminating the precipitate yielded no detectable product. Our work demonstrates the feasibility of spatially separated yet electrically coupled geochemical reactions as drivers of otherwise endergonic processes. Beyond corroborating the ability of early-Earth alkaline hydrothermal systems to couple carbon reduction to hydrogen oxidation through biologically relevant mechanisms, these results may also be of significance for industrial and environmental applications, where other redox reactions could be facilitated using similarly mild approaches.

Methane, arsenic, selenium and the origins of the DMSO reductase family

Mononuclear molybdoenzymes of the dimethyl sulfoxide reductase (DMSOR) family catalyze a number of reactions essential to the carbon, nitrogen, sulfur, arsenic, and selenium biogeochemical cycles. These enzymes are also ancient, with many lineages likely predating the divergence of the last universal common ancestor into the Bacteria and Archaea domains. We have constructed rooted phylogenies for over 1,550 representatives of the DMSOR family using maximum likelihood methods to investigate the evolution of the arsenic biogeochemical cycle. The phylogenetic analysis provides compelling evidence that formylmethanofuran dehydrogenase B subunits, which catalyze the reduction of CO₂ to formate during hydrogenotrophic methanogenesis, constitutes the most ancient lineage. Our analysis also provides robust support for selenocysteine as the ancestral ligand for the Mo/W atom. Finally, we demonstrate that anaerobic arsenite oxidase and respiratory arsenate reductase catalytic subunits represent a more ancient lineage of DMSORs compared to aerobic arsenite oxidase catalytic subunits, which evolved from the assimilatory nitrate reductase lineage. This provides substantial support for an active arsenic biogeochemical cycle on the anoxic Archean Earth. Our work emphasizes that the use of chalcophilic elements as substrates as well as the Mo/W ligand in DMSORs has indelibly shaped the diversification of these enzymes through deep time.

Older Than Genes: The Acetyl CoA Pathway and Origins

For decades, microbiologists have viewed the acetyl CoA pathway and organisms that use it for H2-dependent carbon and energy metabolism, acetogens and methanogens, as ancient. Classical evidence and newer evidence indicating the antiquity of the acetyl CoA pathway are summarized here. The acetyl CoA pathway requires approximately 10 enzymes, roughly as many organic cofactors, and more than 500 kDa of combined subunit molecular mass to catalyze the conversion of H2 and CO2 to formate, acetate, and pyruvate in acetogens and methanogens. However, a single hydrothermal vent alloy, awaruite (Ni3Fe), can convert H2 and CO2 to formate, acetate, and pyruvate under mild hydrothermal conditions on its own. The chemical reactions of H2 and CO2 to pyruvate thus have a natural tendency to occur without enzymes, given suitable inorganic catalysts. This suggests that the evolution of the enzymatic acetyl CoA pathway was preceded by-and patterned along-a route of naturally occurring exergonic reactions catalyzed by transition metal minerals that could activate H2 and CO2 by chemisorption. The principle of forward (autotrophic) pathway evolution from preexisting non-enzymatic reactions is generalized to the concept of patterned evolution of pathways. In acetogens, exergonic reduction of CO2 by H2 generates acyl phosphates by highly reactive carbonyl groups undergoing attack by inert inorganic phosphate. In that ancient reaction of biochemical energy conservation, the energy behind formation of the acyl phosphate bond resides in the carbonyl, not in phosphate. The antiquity of the acetyl CoA pathway is usually seen in light of CO2 fixation; its role in primordial energy coupling via acyl phosphates and substrate-level phosphorylation is emphasized here.

Co-evolution of primitive methane-cycling ecosystems and early Earth's atmosphere and climate

The history of the Earth has been marked by major ecological transitions, driven by metabolic innovation, that radically reshaped the composition of the oceans and atmosphere. The nature and magnitude of the earliest transitions, hundreds of million years before photosynthesis evolved, remain poorly understood. Using a novel ecosystem-planetary model, we find that pre-photosynthetic methane-cycling microbial ecosystems are much less productive than previously thought. In spite of their low productivity, the evolution of methanogenic metabolisms strongly modifies the atmospheric composition, leading to a warmer but less resilient climate. As the abiotic carbon cycle responds, further metabolic evolution (anaerobic methanotrophy) may feed back to the atmosphere and destabilize the climate, triggering a transient global glaciation. Although early metabolic evolution may cause strong climatic instability, a low CO:CH4 atmospheric ratio emerges as a robust signature of simple methane-cycling ecosystems on a globally reduced planet such as the late Hadean/early Archean Earth.

The Impact of Molecular Oxygen on Anion Composition in a Hazy Archean Earth Atmosphere

Atmospheric organic hazes are common in planetary bodies in our solar system and likely exoplanet atmospheres as well. In addition, geochemical data support the existence of an organic haze in the early Earth's atmosphere. Much of what is known about organic haze formation derives from studies of Saturn's moon Titan. It is believed that on Titan ions play an important role in haze formation. It is possible, by using Titan as an analog for the Archean Earth, to consider that an Archean haze could have formed by similar processes. Here, we examine the anion chemistry that occurs during laboratory simulations of early Earth haze formation and measure the composition of gaseous anions as a function of O₂ mixing ratio. Gaseous anion composition and relative abundances are measured by an atmospheric pressure interface time-of-flight mass spectrometer and are compared to previous photochemical haze mass loading measurements. Numerous anions are observed spanning from mass-to-charge ratio 26 to 246, with a majority of the identified anions containing carbon, hydrogen, nitrogen, and/or oxygen. A shift in the anion composition occurs with increasing the precursor O₂ mixing ratio. With 0-20 ppmv O₂ in CH₄/CO₂/N₂ mixtures, ions contain mostly organic nitrogen, with CNO^- being the most intense ion peak. As the precursor O₂ is increased to 200 and 2000 ppmv, inorganic nitrogen ions become the dominant chemical group, with NO₃^- having the most intense ion signal. The clear shift in the ionic composition could be indicative of a modification to the gas-phase chemistry that occurs in the transition from an anoxic atmosphere to an oxygen-containing atmosphere, with potential astrobiological significance.

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.

Anaerobic and hydrogenogenic carbon monoxide-oxidizing prokaryotes: Versatile microbial conversion of a toxic gas into an available energy

Carbon monoxide (CO) is a gas that is toxic to various organisms including humans and even microbes; however, it has low redox potential, which can fuel certain microbes, namely, CO oxidizers. Hydrogenogenic CO oxidizers utilize an energy conservation system via a CO dehydrogenase/energy-converting hydrogenase complex to produce hydrogen gas, a zero emission fuel, by CO oxidation coupled with proton reduction. Biochemical and molecular biological studies using a few model organisms have revealed their enzymatic reactions and transcriptional response mechanisms using CO. Biotechnological studies for CO-dependent hydrogen production have also been carried out with these model organisms. In this chapter, we review recent advances in the studies of these microbes, which reveal their unique and versatile metabolic profiles and provides future perspectives on ecological roles and biotechnological applications. Over the past decade, the number of isolates has doubled (37 isolates in 5 phyla, 20 genera, and 32 species). Some of the recently isolated ones show broad specificity to electron acceptors. Moreover, accumulating genomic information predicts their unique physiologies and reveals their phylogenomic relationships with novel potential hydrogenogenic CO oxidizers. Combined with genomic database surveys, a molecular ecological study has unveiled the wide distribution and low abundance of these microbes. Finally, recent biotechnological applications of hydrogenogenic CO oxidizers have been achieved via diverse approaches (e.g., metabolic engineering and co-cultivation), and the identification of thermophilic facultative anaerobic CO oxidizers will promote industrial applications as oxygen-tolerant biocatalysts for efficient hydrogen production by genomic engineering.

Experimental and Simulation Efforts in the Astrobiological Exploration of Exooceans

The icy satellites of Jupiter and Saturn are perhaps the most promising places in the Solar System regarding habitability. However, the potential habitable environments are hidden underneath km-thick ice shells. The discovery of Enceladus' plume by the Cassini mission has provided vital clues in our understanding of the processes occurring within the interior of exooceans. To interpret these data and to help configure instruments for future missions, controlled laboratory experiments and simulations are needed. This review aims to bring together studies and experimental designs from various scientific fields currently investigating the icy moons, including planetary sciences, chemistry, (micro-)biology, geology, glaciology, etc. This chapter provides an overview of successful in situ, in silico, and in vitro experiments, which explore different regions of interest on icy moons, i.e. a potential plume, surface, icy shell, water and brines, hydrothermal vents, and the rocky core.

Prospecting for life

Books with titles like 'The Call of the Wild' seemed to set a path for a life. Thus, I would be an explorer-a plan that did not work out so well, at least at first. On leaving school I got a job as a 'Works Chemist Improver', testing Ni catalysts for the hydrogenation of phenol to cyclohexanol. Taking night classes I passed enough exams to study geology at Queen Mary College, London. Armed thus I travelled to the Solomon Islands where geology is a 'happening'! Next was Canada to visit a mine sunk into a 1.5 billion year old Pb-Zn orebody precipitated from submarine hot springs. At last I reached the Yukon to prospect for silver. Thence to Ireland researching what I also took to be 'exhalative' (i.e. hot spring-related) Pb-Zn orebodies. While there in 1979, the discovery of 350°C metal-bearing acidic waters issuing from submarine Black Smoker chimneys in the Pacific sent us searching for fossil examples in the Irish mines. However, the chimneys we found were more like chemical gardens than Black Smokers, a finding that made us think about the emergence of life. After all, what better for life's emergence than to have a membrane comprising Fe minerals dosed with Ni in our chimneys to mediate the 'hydrogenation' of CO2-life's job anyway. Indeed, such a membrane would keep redox and pH disequilibria at bay, just like biological membranes. At the same time, my field research among Alpine ophiolites-ocean floor mafic rocks obducted to the Alps-indicated that alkaline waters bearing H2 and CH4 were a result of serpentinization, a process that must have operated in all ocean floors over all time. Thus it was that we could predict the Lost City hydrothermal field 10 years before its discovery in the North Atlantic in the year 2000. Lost City comprises a number of alkaline springs at up to 90°C that produce carbonate and brucite (Mg[OH]2) chimneys. We had surmised that Ni-enriched FeS chimneys would have precipitated at comparable alkaline springs issuing into a metal-rich carbonic ocean on the very early Earth (inducing membrane potentials comparable to those capable of succouring all life, and presumably, sufficient to drive life into being). However, our laboratory precipitates also revealed green rust, thought to be the precursor to the magnetite now comprising the Archaean Banded Iron Formations. We now look upon green rust, also known as fougèrite, as the tangible, base fractal of life.

Carbendazim-resistance associated β2 -tubulin substitutions increase deoxynivalenol biosynthesis by reducing the interaction between β2 -tubulin and IDH3 in Fusarium graminearum

Microtubule is a well-known structural protein participating in cell division, motility and vesicle traffic. In this study, we found that β₂ -tubulin, one of the microtubule components, plays an important role in regulating secondary metabolite deoxynivalenol (DON) biosynthesis in Fusarium graminearum by interacting with isocitrate dehydrogenase subunit 3 (IDH3). We found IDH3 negatively regulate DON biosynthesis by reducing acetyl-CoA accumulation in F. graminearum and DON biosynthesis was stimulated by exogenous acetyl-CoA. In addition, the expression of IDH3 significantly decreased in the carbendazim-resistant mutant nt167 (Fgβ₂ ^F167Y ). Furthermore, we found that carbendazim-resistance associated β₂ -tubulin substitutions reducing the interaction intensity between β₂ -tubulin and IDH3. Interestingly, we demonstrated that β₂ -tubulin inhibitor carbendazim can disrupt the interaction between β₂ -tubulin and IDH3. The decreased interaction intensity between β₂ -tubulin and IDH3 resulted in the decreased expression of IDH3, which can cause the accumulation of acetyl-CoA, precursor of DON biosynthesis in F. graminearum. Thus, we revealed that carbendazim-resistance associated β₂ -tubulin substitutions or carbendazim treatment increases DON biosynthesis by reducing the interaction between β₂ -tubulin and IDH3 in F. graminearum. Taken together, the novel findings give the new perspectives of β₂ -tubulin in regulating secondary metabolism in phytopathogenic fungi.

Methylofuran is a prosthetic group of the formyltransferase/hydrolase complex and shuttles one-carbon units between two active sites

Methylotrophs play a crucial role in the global carbon cycle as they oxidize reduced one-carbon compounds such as methanol or methane to CO₂. The step-wise conversion of these substrates generally takes place while the one-carbon units are bound to diffusible carrier molecules. However, our crystal structure of the formyltransferase/hydrolase complex from Methylorubrum extorquens demonstrates that the one-carbon carrier methylofuran tightly binds to the enzyme via its extended and branched polyglutamate chain. A swinging motion of the coenzyme then shuttles one-carbon units between the two active sites of the enzyme complex over a distance of 50 Å. The structure further highlights how the bacterial formate generation system relates to the archaeal CO₂ fixation system.

Methylotrophy, the ability of microorganisms to grow on reduced one-carbon substrates such as methane or methanol, is a feature of various bacterial species. The prevailing oxidation pathway depends on tetrahydromethanopterin (H₄MPT) and methylofuran (MYFR), an analog of methanofuran from methanogenic archaea. Formyltransferase/hydrolase complex (Fhc) generates formate from formyl-H₄MPT in two consecutive reactions where MYFR acts as a carrier of one-carbon units. Recently, we chemically characterized MYFR from the model methylotroph Methylorubrum extorquens and identified an unusually long polyglutamate side chain of up to 24 glutamates. Here, we report on the crystal structure of Fhc to investigate the function of the polyglutamate side chain in MYFR and the relatedness of the enzyme complex with the orthologous enzymes in archaea. We identified MYFR as a prosthetic group that is tightly, but noncovalently, bound to Fhc. Surprisingly, the structure of Fhc together with MYFR revealed that the polyglutamate side chain of MYFR is branched and contains glutamates with amide bonds at both their α- and γ-carboxyl groups. This negatively charged and branched polyglutamate side chain interacts with a cluster of conserved positively charged residues of Fhc, allowing for strong interactions. The MYFR binding site is located equidistantly from the active site of the formyltransferase (FhcD) and metallo-hydrolase (FhcA). The polyglutamate serves therefore an additional function as a swinging linker to shuttle the one-carbon carrying amine between the two active sites, thereby likely increasing overall catalysis while decreasing the need for high intracellular MYFR concentrations.

Fougerite: the not so simple progenitor of the first cells

We here review the extraordinary mineralogical properties of green rusts and their naturally occurring form, fougerite, and discuss the pertinence of these properties within the alkaline hydrothermal vent (AHV) hypothesis for life's emergence. We put forward an extended version of the AHV scenario which enhances the conformity between extant life and its earliest progenitor by extensively making use of fougerite's mechanistic and catalytic particularities.

Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea

Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.

Methane metabolism by some lineages of Archaea contributes to the cycling of carbon on Earth. Here, the authors show high diversity of methyl-coenzyme M reductase (Mcr), a key enzyme associated with archaeal methane/alkane metabolism, in hot spring Archaea, and investigate their ecological roles and evolution.

Carbon fixation and energy metabolisms of a subseafloor olivine biofilm

Earth's largest aquifer ecosystem resides in igneous oceanic crust, where chemosynthesis and water-rock reactions provide the carbon and energy that support an active deep biosphere. The Calvin Cycle is the predominant carbon fixation pathway in cool, oxic, crust; however, the energy and carbon metabolisms in the deep thermal basaltic aquifer are poorly understood. Anaerobic carbon fixation pathways such as the Wood-Ljungdahl pathway, which uses hydrogen (H₂) and CO₂, may be common in thermal aquifers since water-rock reactions can produce H₂ in hydrothermal environments and bicarbonate is abundant in seawater. To test this, we reconstructed the metabolisms of eleven bacterial and archaeal metagenome-assembled genomes from an olivine biofilm obtained from a Juan de Fuca Ridge basaltic aquifer. We found that the dominant carbon fixation pathway was the Wood-Ljungdahl pathway, which was present in seven of the eight bacterial genomes. Anaerobic respiration appears to be driven by sulfate reduction, and one bacterial genome contained a complete nitrogen fixation pathway. This study reveals the potential pathways for carbon and energy flux in the deep anoxic thermal aquifer ecosystem, and suggests that ancient H₂-based chemolithoautotrophy, which once dominated Earth's early biosphere, may thus remain one of the dominant metabolisms in the suboceanic aquifer today.

Microfluidic Reactors for Carbon Fixation under Ambient-Pressure Alkaline-Hydrothermal-Vent Conditions

The alkaline-hydrothermal-vent theory for the origin of life predicts the spontaneous reduction of CO₂, dissolved in acidic ocean waters, with H₂ from the alkaline vent effluent. This reaction would be catalyzed by Fe(Ni)S clusters precipitated at the interface, which effectively separate the two fluids into an electrochemical cell. Using microfluidic reactors, we set out to test this concept. We produced thin, long Fe(Ni)S precipitates of less than 10 µm thickness. Mixing simplified analogs of the acidic-ocean and alkaline-vent fluids, we then tested for the reduction of CO₂. We were unable to detect reduced carbon products under a number of conditions. As all of our reactions were performed at atmospheric pressure, the lack of reduced carbon products may simply be attributable to the low concentration of hydrogen in our system, suggesting that high-pressure reactors may be a necessity.

Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases

Anaerobic Ni-containing carbon-monoxide dehydrogenases (Ni-CODHs) catalyze the reversible conversion between carbon monoxide and carbon dioxide as multi-enzyme complexes responsible for carbon fixation and energy conservation in anaerobic microbes. However, few biochemically characterized model enzymes exist, with most Ni-CODHs remaining functionally unknown. Here, we performed phylogenetic and structure-based Ni-CODH classification using an expanded dataset comprised of 1942 non-redundant Ni-CODHs from 1375 Ni-CODH-encoding genomes across 36 phyla. Ni-CODHs were divided into seven clades, including a novel clade. Further classification into 24 structural groups based on sequence analysis combined with structural prediction revealed diverse structural motifs for metal cluster formation and catalysis, including novel structural motifs potentially capable of forming metal clusters or binding metal ions, indicating Ni-CODH diversity and plasticity. Phylogenetic analysis illustrated that the metal clusters responsible for intermolecular electron transfer were drastically altered during evolution. Additionally, we identified novel putative Ni-CODH-associated proteins from genomic contexts other than the Wood–Ljungdahl pathway and energy converting hydrogenase system proteins. Network analysis among the structural groups of Ni-CODHs, their associated proteins and taxonomies revealed previously unrecognized gene clusters for Ni-CODHs, including uncharacterized structural groups with putative metal transporters, oxidoreductases, or transcription factors. These results suggested diversification of Ni-CODH structures adapting to their associated proteins across microbial genomes.