Prebiotic Earth Research Articles

K+-Selectivity Due to Coordination with a D4d-Symmetric Homochiral Proline Octamer Verified by Mass Spectrometry and Infrared Photodissociation Spectroscopy.

Both phenomena of homochirality and sodium-potassium ion selectivity in cells have been regarded as important issues in the process of the origin of life. However, whether K+/Na+ selectivity was involved in homochirogenesis has never been considered. Herein, we report that a homochiral proline octamer shows high K+-selectivity. Coordination of K+ results in formation of a stable, noncovalent, D4d-symmetric complex, as demonstrated by mass spectrometry, infrared photodissociation spectroscopy, and calculations. A cooperative relationship between an eight-coordinated metal cation and a homochirality-restricted topological hydrogen-bonded proline network is the key for the K+/Na+ selectivity. As the complex comprises merely the basic chiral amino acid, it provides a possible linkage between K+/Na+ selectivity and the origin of chirality on the prebiotic Earth.

Prebiotic Synthesis of ATP: A Terrestrial Volcanism-Dependent Pathway

Adenosine triphosphate (ATP) is a multifunctional small molecule, necessary for all modern Earth life, which must be a component of the last universal common ancestor (LUCA). However, the relatively complex structure of ATP causes doubts about its accessibility on prebiotic Earth. In this paper, based on previous studies on the synthesis of ATP components, a plausible prebiotic pathway yielding this key molecule is constructed, which relies on terrestrial volcanism to provide the required materials and suitable conditions.

Ferrihydrite synthesis in the presence of amino acids and artificial seawater.

Ferrihydrite is widespread in clays, soils, and living organisms and was found on Mars. This iron-mineral could be found on the prebiotic Earth, which also contained simple monomeric amino acids. For prebiotic chemistry, it is important to understand how amino acids have an effect on the process of iron oxide formations. There are three important results in this work: (a) preconcentration of cysteine and aspartic acid, (b) formation of cystine and probably the cysteine peptide occurred during ferrihydrite syntheses, and (c) amino acids have an effect on iron oxide synthesis. For samples containing aspartic acid and cysteine, their presence on the surface or mineral structure can be confirmed by FT-IR spectra. Surface charge analysis showed a relatively high decrease for samples synthesized with cysteine. Scanning electron microscopy did not show marked morphological differences among the samples, except for the seawater sample containing cysteine, which had a lamina-shaped morphology surrounded by circular iron particles, indicating the possible formation of a cysteine structure involving iron oxide particles. The thermogravimetric analysis of the samples indicates that the presence of salts and amino acids in the synthesis of ferrihydrite has an effect on the thermal behavior of the iron oxide/amino acids and modifying the water-loss temperature. The heating of the cysteine samples, synthesized in distilled water and artificial seawater, showed several peaks of degradation of cysteine. In addition, heating of the aspartic acid samples produced the polymerization of this amino acid and peaks of degradation of it. FTIR spectra and XRD patterns did not indicate the precipitation of methionine, 2-aminoisobutyric acid, lysine, or glycine with the iron oxide formations. However, the heating of the glycine, methionine and lysine samples, synthesized in artificial seawater, showed peaks that could be attributed to the degradation of them. Then this could be an indication that these amino acids precipitate with the minerals during the syntheses. Also, the dissolution of these amino acids in artificial seawater prevents the formation of ferrihydrite.

New models of reflection spectra for terrestrial exoplanets: Present and prebiotic Earth orbiting around stars of different spectral types

In order to recognize a habitable exoplanet from future observed spectra, we present new model reflected spectra and geometric albedo for modern and prebiotic (∼3.9 Ga) Earth-like exoplanets orbiting within the habitable zone of stars of spectral types F, G, K and M. We compute this for various atmospheric and surface compositions of the planets. Molecules that are potential biosignatures and act as greenhouse agents are incorporated in our model atmosphere. Various combinations of solid and liquid materials such as ocean, coast, land consisting of trees, grass, sand or rocks determine the surface albedo of the planet. Geometric albedo and model reflected spectra for a set of nine potential habitable planets, including Proxima Centauri b, TRAPPIST-1d, Kepler-1649c and Teegarden’s Star-b, are also presented. We employ the opacity data derived by using the open-source package Exo-Transmit and adopt different atmospheric Temperature–Pressure profiles depending on the properties of the terrestrial exoplanets. The model-reflected spectra are constructed by numerically solving the multiple scattering radiative transfer equations. We verified our model reflected spectra for a few specific cases by comparing with those published by other researchers. We demonstrate that prebiotic Earth-like exoplanets and present Earth-like exoplanets with increased amount of greenhouse gases in their atmospheres scatter more starlight in the optical. We also present the transmission spectra for modern and prebiotic Earth-like exoplanets with cloudy and cloudless atmospheres.

Potential Impact of Genetic-Code Mutations on Medicine and Health

The genetic code encoding amino acid sequences in ribosomal translation consists of an alphabet of 61 triplet codons for 20 amino acids and three chain termination signals. Basically the same universal code is employed by all organisms from the Last Universal Common Ancestor (LUCA)-proximal Methanobacter kandleri (Mka) to humans. This universal code, which has remained invariant for all living species, enables the transplantation of protein-coding genes between different species without loss of function, and constrains the chemical diversity of the encoded amino acids. Over the initial decades following the discovery of the code, its invariance coupled with the lack of any information regarding its origin have led to the view that the code might represent an inexplicable ‘frozen accident’ in the history of life. However, with the formulation of the coevolution theory of the genetic code and its multifaceted supporting evidence, this view has become untenable. Instead, the encoded amino acids are known to comprise two different classes: ten Class 1 amino acids available on prebiotic Earth were incorporated into the protocells as they evolved into life forms, while the ten Class 2 amino acids were produced by early life through biosynthesis. Thus, the later entry of the Class 2 amino acids identified them as end products of cellular evolution, which suggests the plausibility of continuing alterations of the encoded amino acids after an eons-long pause. Accordingly, attempts were made by our group to replace Trp by 4-fluroTrp (4FTrp) from the proteome of Bacillus subtilis. The targeted replacement obtained proved the inherent mutability of the code, and this has stimulated the development of a wide range of mutated codes through a variety of approaches. Hundreds of genetic code mutants have now been successfully isolated from microbes to animals, transforming the code from an immutable construct to a highly malleable molecular device. The effects of such new codes on medicine and health range from treatments for a variety of diseases to the alleviation of food crisis arising from the degradation of the environment and devastation due to natural disasters.

Probing the surface environment of large T-type asteroids

Context. The thermal and radiative environments encountered by asteroids have shaped their surface features. Recent observations have focused on asteroids in the main belt and showed indications for ices and organics in the interiors of the asteroids that were likely significant on prebiotic Earth. They stand out in reflectance spectra as darker, redder colours than most colocated asteroids. Aims. We probe the surface environment of large (>80km in diameter) T-type asteroids. This taxonomic type is relatively ill-constrained as an independent group. We discuss their place of origin based on our probing. Methods. We performed spectroscopic observations of two T-type asteroids, (96) Aegle and (570) Kythera, over the L band (2.8–4.0 µm) using the Subaru telescope. The spectra of other T-type asteroids are available in the literature, as are survey datasets. Based on this, we strove to find commonalities and global trends in this group. We also used the archival polarimetric data of the asteroids and meteorite spectra from laboratory experiments to constrain their surface texture and composition. Results. Our targets exhibit red L-band continuum slopes, (0.30±0.04) µm−1 for (96) Aegle and (0.31 ± 0.03) µm−1 for (570) Kythera, that are similar to those of (1) Ceres and 67P/Churyumov-Gerasimenko, and have an OH-absorption feature with band centres <2.8 µm. For (96) Aegle, we find an indication of a shallow N–H band near 3.1 µm and a C–H band of organic materials over 3.4–3.6 µm, whereas no diagnostic bands of water ice and other volatiles exceeding the noise of the data were seen for both asteroids. The large T-type asteroids except for (596) Scheila display spectral shapes similar to those of to our targets. About 50% of large T-type asteroids contain an absorption band near 0.6−0.65 µm that is likely associated with hydrated minerals. For T-type asteroids (except for Jupiter Trojans) of all sizes, we found a weak correlation that the smaller the diameter and the closer to the Sun, the redder the visible (0.5−0.8 µm) slope. Conclusions. The 2.9 µm band depths of large T-type asteroids suggest that they might have experienced aqueous alteration comparable to Ch-type asteroids, but that it was more intense than for most of the main-belt asteroids. The polarimetric phase curve of the T-type asteroids is well described by a particular surface structure. The 0.5−4.0 µm reflectance spectra of large T-type asteroids appear most similar to those of CI chondrites with grain sizes of ~25−35 µm. Taken as a whole, we propose that large T-type asteroids may have been dislodged roughly around 10 au in the early Solar System.

High-resolution spectral models of TRAPPIST-1e seen as a Pale Blue Dot for ELT and JWST observations

ABSTRACT Rocky exoplanets orbiting in the habitable zone (HZ) of nearby M dwarfs provide unique opportunities for characterizing their atmospheres and searching for biosignature gases. TRAPPIST-1e, a temperate Earth-sized exoplanet in the HZ of a nearby M dwarf, is arguably the most favourable target for ground- and space-based atmospheric characterization by the extremely large telescopes (ELTs) and the James Webb Space Telescope. To inform future observations in reflected and emitted lights using these upcoming telescopes, we simulate the high-resolution reflection and emission spectra for TRAPPIST-1e for both modern and prebiotic Earth-like atmospheric compositions. To demonstrate the effects of wavelength-dependent albedo on climate and spectra, we further simulate five albedo scenarios for each atmospheric composition: cloudy modern Earth-like, cloud-free modern Earth-like, cloudy ocean planet, 100 per cent cloudy planet, and wavelength-independent albedo of 0.31. We use the recent Mega-MUSCLES spectral energy distribution of TRAPPIST-1 for our models. We show that the O2 + CH4 and O3 + CH4 biosignature pairs as well as climate indicators (CO2 and H2O) show features in both high-resolution reflection and emission spectra of TRAPPIST-1e that the ELTs can search for. Our high-resolution data base for modern and prebiotic Earth TRAPPIST-1e models with various surface compositions and cloud distributions provides a tool for observers to train retrieval algorithms and plan observation strategies to characterize this potentially habitable world.

Entering the labyrinth: A hypothesis about the emergence of metabolism from protobiotic routes

The occurrence of organized chemical transformations defined as metabolism is one of the most important characteristics of life. Surprisingly though, there is not a consensus about how those transformations were originated in the origin of life. RNA world advocates suggest that biochemical pathways started with ribozymes that were further substituted by enzymes. However, most of the biosynthetic routes of ribozymes described do not overlap with the enzymatic routes, and there is not a clear theory about how this transition happened. An important step to solve this dilemma has been elucidated in the last decade when researchers found that some complex routes of chemical transformations, such as the glycolytic and the citric acid pathways, already existed in prebiotic Earth due to physicochemical forces alone. Defined here as protobiotic pathways, we propose that those metabolic exchanges working without the aiding of any biological catalysts were the ones that guided the origin of metabolism. Under this scenario, some quasi-randomly encoded peptides at the origins of translation systems would be capable to bind metabolites in protobiotic routes. When those bounds facilitated or accelerated the conversion of metabolites along the protobiotic path and the products were beneficial, then natural molecular selection acted to preserve the system. Thus, we propose that the origin of metabolism happened when peptides started to bind metabolites in protobiotic routes without disturbing (and possibly aiding) their chemical transformation paths. This should have been the entry point to the metabolic labyrinth, the key step that allowed peptides to come into the path of chemical transformations and further evolve into the enzymes that coordinate nowadays the biochemical pathways.

Water-Controlled Keto-Enol Tautomerization of a Prebiotic Nucleobase.

Barbituric acid is believed to be a proto-RNA nucleobase that was used for biological information transfer on prebiotic earth before DNA and RNA in their present forms evolved. Nucleobases have various tautomeric forms and the relative stability of these forms is critical to their biological function. It has been shown that barbituric acid has a tri-keto form in the gas phase and an enol form in the solid state. However, its dominant tautomeric form in aqueous medium that is most relevant for biology has been investigated only to a limited extent and the findings are inconclusive. We have used multiple approaches, namely, molecular dynamics, quantum chemistry, NMR, and IR spectroscopy to determine the most stable tautomer of barbituric acid in solution. We find a delicate balance in the stability of the two tautomers, tri-keto and enol, which is tipped toward the enol as the extent of solvation by water increases.

On the origins of life’s homochirality: Inducing enantiomeric excess with spin-polarized electrons

Life as we know it is homochiral, but the origins of biological homochirality on early Earth remain elusive. Shallow closed-basin lakes are a plausible prebiotic environment on early Earth, and most are expected to have significant sedimentary magnetite deposits. We hypothesize that ultraviolet (200- to 300-nm) irradiation of magnetite deposits could generate hydrated spin-polarized electrons sufficient to induce enantioselective prebiotic chemistry. Such electrons are potent reducing agents that drive reduction reactions where the spin polarization direction can enantioselectively alter the reaction kinetics. Our estimate of this chiral bias is based on the strong effective spin-orbit coupling observed in the chiral-induced spin selectivity (CISS) effect, as applied to energy differences in reduction reactions for different isomers. In the original CISS experiments, spin-selective electron transmission through a monolayer of double-strand DNA molecules is observed at room temperature-indicating a strong coupling between molecular chirality and electron spin. We propose that the chiral symmetry breaking due to the CISS effect, when applied to reduction chemistry, can induce enantioselective synthesis on the prebiotic Earth and thus facilitate the homochiral assembly of life's building blocks.

Visualizing RNA polymers produced by hot wet-dry cycling

It is possible that the transition from abiotic systems to life relied on RNA polymers that served as ribozyme-like catalysts and for storing genetic information. The source of such polymers is uncertain, but previous investigations reported that wet–dry cycles simulating prebiotic hot springs provide sufficient energy to drive condensation reactions of mononucleotides to form oligomers and polymers. The aim of the study reported here was to verify this claim and visualize the products prepared from solutions composed of single mononucleotides and 1:1 mixture of two mononucleotides. Therefore, we designed experiments that allowed comparisons of all such mixtures representing six combinations of the four mononucleotides of RNA. We observed irregular stringy patches and crystal strands when wet-dry cycling was performed at room temperature (20 °C). However, when the same solutions were exposed to wet–dry cycles at 80 °C, we observed what appeared to be true polymers. Their thickness was consistent with RNA-like products composed of covalently bonded monomers, while irregular strings and crystal segments of mononucleotides dried or cycled at room temperature were consistent with structures assembled and stabilized by weak hydrogen bonds. In a few instances we observed rings with short polymer attachments. These observations are consistent with previous claims of polymerization during wet–dry cycling. We conclude that RNA-like polymers and rings could have been synthesized non-enzymatically in freshwater hot springs on the prebiotic Earth with sizes sufficient to fold into ribozymes and genetic molecules required for life to begin.

The Evolution of Nitric Oxide Function: From Reactivity in the Prebiotic Earth to Examples of Biological Roles and Therapeutic Applications.

Nitric oxide was once considered to be of marginal interest to the biological sciences and medicine; however, there is now wide recognition, but not yet a comprehensive understanding, of its functions and effects. NO is a reactive, toxic free radical with numerous biological targets, especially metal ions. However, NO and its reaction products also play key roles as reductant and oxidant in biological redox processes, in signal transduction, immunity and infection, as well as other roles. Consequently, it can be sensed, metabolized and modified in biological systems. Here, we present a brief overview of the chemistry and biology of NO—in particular, its origins in geological time and in contemporary biology, its toxic consequences and its critical biological functions. Given that NO, with its intrinsic reactivity, appeared in the early Earth’s atmosphere before the evolution of complex lifeforms, we speculate that the potential for toxicity preceded biological function. To examine this hypothesis, we consider the nature of non-biological and biological targets of NO, the evolution of biological mechanisms for NO detoxification, and how living organisms generate this multifunctional gas.

Hydrophobic-cationic peptides modulate RNA polymerase ribozyme activity by accretion

Accretion and the resulting increase in local concentration is a widespread mechanism in biology to enhance biomolecular functions (for example, in liquid-liquid demixing phases). Such macromolecular aggregation phases (e.g., coacervates, amyloids) may also have played a role in the origin of life. Here, we report that a hydrophobic-cationic RNA binding peptide selected by phage display (P43: AKKVWIIMGGS) forms insoluble amyloid-containing aggregates, which reversibly accrete RNA on their surfaces in an RNA-length and Mg2+-concentration dependent manner. The aggregates formed by P43 or its sequence-simplified version (K2V6: KKVVVVVV) inhibited RNA polymerase ribozyme (RPR) activity at 25 mM MgCl2, while enhancing it significantly at 400 mM MgCl2. Our work shows that such hydrophobic-cationic peptide aggregates can reversibly concentrate RNA and enhance the RPR activity, and suggests that they could have aided the emergence and evolution of longer and functional RNAs in the fluctuating environments of the prebiotic earth.

Thioesters provide a plausible prebiotic path to proto-peptides

It is widely assumed that the condensation of building blocks into oligomers and polymers was important in the origins of life. High activation energies, unfavorable thermodynamics and side reactions are bottlenecks for abiotic peptide formation. All abiotic reactions reported thus far for peptide bond formation via thioester intermediates have relied on high energy molecules, which usually suffer from short half-life in aqueous conditions and therefore require constant replenishment. Here we report plausible prebiotic reactions of mercaptoacids with amino acids that result in the formation of thiodepsipeptides, which contain both peptide and thioester bonds. Thiodepsipeptide formation was achieved under a wide range of pH and temperature by simply drying and heating mercaptoacids with amino acids. Our results offer a robust one-pot prebiotically-plausible pathway for proto-peptide formation. These results support the hypothesis that thiodepsipeptides and thiol-terminated peptides formed readily on prebiotic Earth and were possible contributors to early chemical evolution.

Prebiotic Environments with Mg2+ and Thiophilic Metal Ions Increase the Thermal Stability of Cysteine and Non-cysteine Peptides.

Wet-dry cycles driven by heating to high temperatures are frequently invoked for the prebiotic synthesis of peptides. Similarly, iron-sulfur clusters are often cited as an example of an ancient catalyst that helped prune early chemical systems into metabolic-like pathways. Because extant iron-sulfur clusters are metallocofactors of protein enzymes and nearly ubiquitous across biology, a reasonable hypothesis is that prebiotic iron-sulfur peptides formed on the early Earth. However, iron-sulfur clusters are coordinated by multiple cysteine residues, and the stability of cysteines to the heat steps of wet-dry cycles has not been determined. It, therefore, has remained unclear if the peptides needed to stabilize the formation of iron-sulfur clusters could have formed. If not, then iron-sulfur-dependent activity may have emerged later, when milder, more biological-like peptide synthesis machinery took hold. Here, we report the thermal stability of cysteine-containing peptides. We show that temperatures of 150 °C lead to the rapid degradation of cysteinyl peptides. However, the presence of Mg2+ at environmentally reasonable concentrations leads to significant protection. Thiophilic metal ions also protect against degradation at 150 °C but require concentrations not frequently observed in the environment. Nevertheless, cysteine-containing peptides are stable at lower, prebiotically plausible temperatures in seawater, carbonate lake, and ferrous lake conditions. The data are consistent with the persistence of cysteine-containing peptides on the early Earth in environments rich in metal ions. High concentrations of Mg2+ are common intra- and extra-cellularly, suggesting that the protection afforded by Mg2+ may reflect conditions that were present on the prebiotic Earth.

Thermodynamic and Kinetic Sequence Selection in Enzyme-Free Polymer Self-Assembly inside a Non-equilibrium RNA Reactor.

The RNA world is one of the principal hypotheses to explain the emergence of living systems on the prebiotic Earth. It posits that RNA oligonucleotides acted as both carriers of information as well as catalytic molecules, promoting their own replication. However, it does not explain the origin of the catalytic RNA molecules. How could the transition from a pre-RNA to an RNA world occur? A starting point to answer this question is to analyze the dynamics in sequence space on the lowest level, where mononucleotide and short oligonucleotides come together and collectively evolve into larger molecules. To this end, we study the sequence-dependent self-assembly of polymers from a random initial pool of short building blocks via templated ligation. Templated ligation requires two strands that are hybridized adjacently on a third strand. The thermodynamic stability of such a configuration crucially depends on the sequence context and, therefore, significantly influences the ligation probability. However, the sequence context also has a kinetic effect, since non-complementary nucleotide pairs in the vicinity of the ligation site stall the ligation reaction. These sequence-dependent thermodynamic and kinetic effects are explicitly included in our stochastic model. Using this model, we investigate the system-level dynamics inside a non-equilibrium ‘RNA reactor’ enabling a fast chemical activation of the termini of interacting oligomers. Moreover, the RNA reactor subjects the oligomer pool to periodic temperature changes inducing the reshuffling of the system. The binding stability of strands typically grows with the number of complementary nucleotides forming the hybridization site. While shorter strands unbind spontaneously during the cold phase, larger complexes only disassemble during the temperature peaks. Inside the RNA reactor, strand growth is balanced by cleavage via hydrolysis, such that the oligomer pool eventually reaches a non-equilibrium stationary state characterized by its length and sequence distribution. How do motif-dependent energy and stalling parameters affect the sequence composition of the pool of long strands? As a critical factor for self-enhancing sequence selection, we identify kinetic stalling due to non-complementary base pairs at the ligation site. Kinetic stalling enables cascades of self-amplification that result in a strong reduction of occupied states in sequence space. Moreover, we discuss the significance of the symmetry breaking for the transition from a pre-RNA to an RNA world.

Selection of Amino Acid Chirality Induced by Cyclic Dipeptide Synthesis in Plausible Prebiotic Conditions

The biological system uses L-amino acids (L-AAs) to construct peptides. The selection of AA chirality in the prebiotic Earth still remains a mystery. Here we report the intrinsic mechanism of AA chiral selection in the formation of prebiotic proline-containing cyclic dipeptide (DKPs). The DKPs were synthesized by equal amounts of L-AA and D-AA with L-Pro that exhibited a clear preference for D-AA as opposed to L-AA. And surprisingly, the L-AA was preferred over D-AA in the mirror-image system with D-Pro. These results indicate that prebiotic DKPs synthesis has a certain selectivity for AA chirality preceded the biological enzymatic catalysis.

Primordial mimicry induces morphological change in Escherichia coli

The morphology of primitive cells has been the subject of extensive research. A spherical form was commonly presumed in prebiotic studies but lacked experimental evidence in living cells. Whether and how the shape of living cells changed are unclear. Here we exposed the rod-shaped bacterium Escherichia coli to a resource utilization regime mimicking a primordial environment. Oleate was given as an easy-to-use model prebiotic nutrient, as fatty acid vesicles were likely present on the prebiotic Earth and might have been used as an energy resource. Six evolutionary lineages were generated under glucose-free but oleic acid vesicle (OAV)-rich conditions. Intriguingly, fitness increase was commonly associated with the morphological change from rod to sphere and the decreases in both the size and the area-to-volume ratio of the cell. The changed cell shape was conserved in either OAVs or glucose, regardless of the trade-offs in carbon utilization and protein abundance. Highly differentiated mutations present in the genome revealed two distinct strategies of adaption to OAV-rich conditions, i.e., either directly targeting the cell wall or not. The change in cell morphology of Escherichia coli for adapting to fatty acid availability supports the assumption of the primitive spherical form.

The primary photo-dissociation dynamics of lactic acid: decarboxylation as CO2 and CO2˙.

We study the primary photolysis dynamics of lactic acid induced by excitation at λ = 200 nm with the aim of elucidating how simple aqueous carboxyl acids react to the deep ultraviolet exposure on the prebiotic Earth. UV-IR transient absorption spectroscopy shows a photolysis quantum yield of Φ(100 ps) = 100 ± 5%. The primary products are CO2, CO2˙- and their counter products CH3CHOH˙ and CH3CHOH-. DFT calculations suggest that the dissociation takes place from the strongly acidic nπ* excited state. Dehydroxylation of lactic acid is not observed.

Prebiotic Membranes and Micelles Do Not Inhibit Peptide Formation During Dehydration.

Cycles of dehydration and rehydration could have enabled formation of peptides and RNA in otherwise unfavorable conditions on the early Earth. Development of the first protocells would have hinged upon colocalization of these biopolymers with fatty acid membranes. Using atomic force microscopy, we find that a prebiotic fatty acid (decanoic acid) forms stacks of membranes after dehydration. Using LC-MS-MS (liquid chromatography-tandem mass spectrometry) with isotope internal standards, we measure the rate of formation of serine dipeptides. We find that dipeptides form during dehydration at moderate temperatures (55 °C) at least as fast in the presence of decanoic acid membranes as in the absence of membranes. Our results are consistent with the hypothesis that protocells could have formed within evaporating environments on the early Earth.