Origin of the RNA world: The fate of nucleobases in warm little ponds

Eta-Earth Revisited II: Deriving a Maximum Number of Earth-Like Habitats in the Galactic Disk

In Lammer et al. (2024), we defined Earth-like habitats (EHs) as rocky exoplanets within the habitable zone of complex life (HZCL) on which Earth-like N2-O2-dominated atmospheres with minor amounts of CO2 can exist, and derived a formulation for estimating the maximum number of EHs in the galaxy given realistic probabilistic requirements that have to be met for an EH to evolve. In this study, we apply this formulation to the galactic disk by considering only requirements that are already scientifically quantifiable. By implementing literature models for star formation rate, initial mass function, and the mass distribution of the Milky Way, we calculate the spatial distribution of disk stars as functions of stellar mass and birth age. For the stellar part of our formulation, we apply existing models for the galactic habitable zone and evaluate the thermal stability of nitrogen-dominated atmospheres with different CO2 mixing ratios inside the HZCL by implementing the newest stellar evolution and upper atmosphere models. For the planetary part, we include the frequency of rocky exoplanets, the availability of surface water and subaerial land, and the potential requirement of hosting a large moon by evaluating their importance and implementing these criteria from minima to maxima values as found in the scientific literature. We also discuss further factors that are not yet scientifically quantifiable but may be requirements for EHs to evolve. Based on such an approach, we find that EHs are relatively rare by obtaining plausible maximum numbers of 2.5 - 2.4 + 71.6 × 10 5 and 0.6 - 0.59 + 27.1 × 10 5 planets that can potentially host N2-O2-dominated atmospheres with maximum CO2 mixing ratios of 10% and 1%, respectively, implying that, on average, a minimum of ∼ 10 3 - 10 6 rocky exoplanets in the HZCL are needed for 1 EH to evolve. The actual number of EHs, however, may be substantially lower than our maximum ranges since several requirements with unknown occurrence rates are not included in our model (e.g., the origin of life, working carbon-silicate and nitrogen cycles); this also implies extraterrestrial intelligence (ETI) to be significantly rarer still. Our results illustrate that not every star can host EHs nor can each rocky exoplanet within the HZCL evolve such that it might be able to host complex animal-like life or even ETIs. The Copernican Principle of Mediocrity therefore cannot be applied to infer that such life will be common in the galaxy.

A Bayesian Analysis of the Probability of the Origin of Life Per Site Conducive to Abiogenesis

The emergence of life from nonlife, or abiogenesis, remains a fundamental question in scientific inquiry. In this article, we investigate the probability of the origin of life (per conducive site) by leveraging insights from Earth's environments. If life originated endogenously on Earth, its existence is indeed endowed with informative value, although the interpretation of the attendant significance hinges critically upon prior assumptions. By adopting a Bayesian framework, for an agnostic prior, we establish a direct connection between the number of potential locations for abiogenesis on Earth and the probability of life's emergence per site. Our findings suggest that constraints on the availability of suitable environments for the origin(s) of life on Earth may offer valuable insights into the probability of abiogenesis and the frequency of life in the universe.

Major evolutionary transitions before cells: A journey from molecules to organisms

Basing on logical assumptions and necessary steps of complexification along biological evolution, we propose here an evolutionary path from molecules to cells presenting four ages and three major transitions. At the first age, the basic biomolecules were formed and become abundant. The first transition happened with the event of a chemical symbiosis between nucleic acids and peptides worlds, which marked the emergence of both life and the process of organic encoding. FUCA, the first living process, was composed of self-replicating RNAs linked to amino acids and capable to catalyze their binding. The second transition, from the age of FUCA to the age of progenotes, involved the duplication and recombination of proto-genomes, leading to specialization in protein production and the exploration of protein to metabolite interactions in the prebiotic soup. Enzymes and metabolic pathways were incorporated into biology from protobiotic reactions that occurred without chemical catalysts, step by step. Then, the fourth age brought origin of organisms and lineages, occurring when specific proteins capable to stackle together facilitated the formation of peptidic capsids. LUCA was constituted as a progenote capable to operate the basic metabolic functions of a cell, but still unable to interact with lipid molecules. We present evidence that the evolution of lipid interaction pathways occurred at least twice, with the development of bacterial-like and archaeal-like membranes. Also, data in literature suggest at least two paths for the emergence of DNA biosynthesis, allowing the stabilization of early life strategies in viruses, archaeas and bacterias. Two billion years later, the eukaryotes arouse, and after 1,5 billion years of evolution, they finally learn how to evolve multicellularity via tissue specialization.

Base-pairing of uracil and 2,6-diaminopurine: from cocrystals to photoreactivity

We show that the non-canonical nucleobase 2,6-diaminopurine (D) spontaneously base pairs with uracil (U) in water and the solid state without the need to be attached to the ribose-phosphate backbone. Depending on the reaction conditions, D and U assemble in thermodynamically stable hydrated and anhydrated D-U base-paired cocrystals. Under UV irradiation, an aqueous solution of D-U base-pair undergoes photochemical degradation, while a pure aqueous solution of U does not. Our simulations suggest that D may trigger the U photodimerization and show that complementary base-pairing modifies the photochemical properties of nucleobases, which might have implications for prebiotic chemistry.

UV Transmission in Prebiotic Environments on Early Earth

Ultraviolet (UV) light is likely to have played important roles in surficial origins of life scenarios, potentially as a productive source of energy and molecular activation, as a selective means to remove unwanted side products, or as a destructive mechanism resulting in loss of molecules/biomolecules over time. The transmission of UV light through prebiotic waters depends upon the chemical constituents of such waters, but constraints on this transmission are limited. Here, we experimentally measure the molar decadic extinction coefficients for a number of small molecules used in various prebiotic synthetic schemes. We find that many small feedstock molecules absorb most at short (∼200 nm) wavelengths, with decreasing UV absorption at longer wavelengths. For comparison, we also measured the nucleobase adenine and found that adenine absorbs significantly more than the simpler molecules often invoked in prebiotic synthesis. Our results enable the calculation of UV photon penetration under varying chemical scenarios and allow further constraints on plausibility and self-consistency of such scenarios. While the precise path that prebiotic chemistry took remains elusive, improved understanding of the UV environment in prebiotically plausible waters can help constrain both the chemistry and the environmental conditions that may allow such chemistry to occur.

A Prebiotic Genetic Nucleotide as an Early Darwinian Ancestor for Pre-RNA Evolution

Prebiotic genetic nucleotides (PGNs) often outcompete canonical alphabets in the formation of nucleotides and subsequent RNA oligomerization under early Earth conditions. This indicates that the early genetic code might have been dominated by pre-RNA that contained PGNs for information transfer and catalysis. Despite this, deciphering pre-RNAs' capacity to acquire function and delineating their evolutionary transition to a canonical RNA World has remained under-researched in the origins of life (OoL) field. We report the synthesis of a prebiotically relevant nucleotide (BaTP) containing the noncanonical nucleobase barbituric acid. We demonstrate the first instance of its enzymatic incorporation into an RNA, using a T7 RNA polymerase. BaTP's incorporation into baby spinach aptamer allowed it to retain its overall secondary structure and function. Finally, we also demonstrate faithful transfer of information from the pre-RNA-containing BaTP to DNA, using a high-fidelity RNA-dependent DNA polymerase, alluding to how selection pressures and complexities could have ensued during the molecular evolution of the early genetic code.

Formation of extraterrestrial peptides and their derivatives

The formation of protein precursors, due to the condensation of atomic carbon under the low-temperature conditions of the molecular phases of the interstellar medium, opens alternative pathways for the origin of life. We perform peptide synthesis under conditions prevailing in space and provide a comprehensive analytic characterization of its products. The application of 13C allowed us to confirm the suggested pathway of peptide formation that proceeds due to the polymerization of aminoketene molecules that are formed in the C + CO + NH3 reaction. Here, we address the question of how the efficiency of peptide production is modified by the presence of water molecules. We demonstrate that although water slightly reduces the efficiency of polymerization of aminoketene, it does not prevent the formation of peptides.

Microfluidics-Based Drying-Wetting Cycles to Investigate Phase Transitions of Small Molecules Solutions

Drying-wetting cycles play a crucial role in the investigation of the origin of life as processes that both concentrate and induce the supramolecular assembly and polymerization of biomolecular building blocks, such as nucleotides and amino acids. Here, we test different microfluidic devices to study the dehydration-hydration cycles of the aqueous solutions of small molecules, and to observe, by optical microscopy, the insurgence of phase transitions driven by self-assembly, exploiting water pervaporation through polydimethylsiloxane (PDMS). As a testbed, we investigate solutions of the chromonic dye Sunset Yellow (SSY), which self-assembles into face-to-face columnar aggregates and produces nematic and columnar liquid crystal (LC) phases as a function of concentration. We show that the LC temperature-concentration phase diagram of SSY can be obtained with a fair agreement with previous reports, that droplet hydration-dehydration can be reversibly controlled and automated, and that the simultaneous incubation of samples with different final water contents, corresponding to different phases, can be implemented. These methods can be further extended to study the assembly of diverse prebiotically relevant small molecules and to characterize their phase transitions.

Different Scenarios for the Origin and the Subsequent Succession of a Hypothetical Microbial Community in the Cloud Layer of Venus

The possible existence of a microbial community in the venusian clouds is one of the most intriguing hypotheses in modern astrobiology. Such a community must be characterized by a high survivability potential under severe environmental conditions, the most extreme of which are very low pH levels and water activity. Considering different scenarios for the origin of life and geological history of our planet, a few of these scenarios are discussed in the context of the origin of hypothetical microbial life within the venusian cloud layer. The existence of liquid water on the surface of ancient Venus is one of the key outstanding questions influencing this possibility. We link the inherent attributes of microbial life as we know it that favor the persistence of life in such an environment and review the possible scenarios of life's origin and its evolution under a strong greenhouse effect and loss of water on Venus. We also propose a roadmap and describe a novel methodological approach for astrobiological research in the framework of future missions to Venus with the intent to reveal whether life exists today on the planet.

Prebiotic Vitamin B3 Synthesis in Carbonaceous Planetesimals

Aqueous chemistry within carbonaceous planetesimals is promising for synthesizing prebiotic organic matter essential to all life. Meteorites derived from these planetesimals delivered these life building blocks to the early Earth, potentially facilitating the origins of life. Here, we studied the formation of vitamin B3 as it is an important precursor of the coenzyme NAD(P)(H), which is essential for the metabolism of all life as we know it. We propose a new reaction mechanism based on known experiments in the literature that explains the synthesis of vitamin B3. It combines the sugar precursors glyceraldehyde or dihydroxyacetone with the amino acids aspartic acid or asparagine in aqueous solution without oxygen or other oxidizing agents. We performed thermochemical equilibrium calculations to test the thermodynamic favorability. The predicted vitamin B3 abundances resulting from this new pathway were compared with measured values in asteroids and meteorites. We conclude that competition for reactants and decomposition by hydrolysis are necessary to explain the prebiotic content of meteorites. In sum, our model fits well into the complex network of chemical pathways active in this environment.

Favorable Environments for the Formation of Ferrocyanide, a Potentially Critical Reagent for Origins of Life

Cyanide and its derivatives play important roles in prebiotic chemistry through a variety of possible mechanisms. In particular, cyanide has been shown to allow for the synthesis of ribonucleotides and amino acids. Although dissolved hydrogen cyanide can be lost as a gas or undergo hydrolysis reactions, cyanide can also potentially be stored and stockpiled as ferrocyanide (Fe(CN)6-4), which is more stable. Furthermore, ferrocyanide aids in some prebiotic synthetic reactions. Here, we investigate the formation rates and yields of ferrocyanide as a function of various environmental parameters, such as the pH, temperature, and concentration. We find that ferrocyanide formation rates and yields are optimal at slightly alkaline conditions (pH 8-9) and moderate temperatures (≈20-30 °C). Given the wide range of possible lake environments likely available on early Earth, our results help to constrain the environmental conditions that would favor cyanide- and ferrocyanide-based prebiotic chemistries. We construct lake box models and find that ferrocyanide may be able to form and reach significant concentrations for prebiotic chemistry on the time scale of years under favorable conditions.

Gas-sensing riboceptors

Understanding how cells sense gases or gaseous solutes is a fundamental question in biology and is pivotal for the evolution of molecular and organismal life. In numerous organisms, gases can diffuse into cells, be transported, generated, and sensed. Controlling gases in the cellular environment is essential to prevent cellular and molecular damage due to interactions with gas-dependent free radicals. Consequently, the mechanisms governing acute gas sensing are evolutionarily conserved and have been experimentally elucidated in various organisms. However, the scientific literature on direct gas sensing is largely based on hemoprotein-based gasoreceptors (or sensors). As RNA-based G-quadruplex (G4) structures can also bind to heme, I propose that some ribozymes can act as gas-sensing riboceptors (ribonucleic acid receptors). Additionally, I present a few other ideas for non-heme metal ion- or metal cluster-based gas-sensing riboceptors. Studying riboceptors can help understand the evolutionary origins of cellular and gasocrine signaling.

White and green rust chimneys accumulate RNA in a ferruginous chemical garden

Mechanisms of nucleic acid accumulation were likely critical to life's emergence in the ferruginous oceans of the early Earth. How exactly prebiotic geological settings accumulated nucleic acids from dilute aqueous solutions, is poorly understood. As a possible solution to this concentration problem, we simulated the conditions of prebiotic low-temperature alkaline hydrothermal vents in co-precipitation experiments to investigate the potential of ferruginous chemical gardens to accumulate nucleic acids via sorption. The injection of an alkaline solution into an artificial ferruginous solution under anoxic conditions (O2  < 0.01% of present atmospheric levels) and at ambient temperatures, caused the precipitation of amakinite ("white rust"), which quickly converted to chloride-containing fougerite ("green rust"). RNA was only extractable from the ferruginous solution in the presence of a phosphate buffer, suggesting RNA in solution was bound to Fe2+ ions. During chimney formation, this iron-bound RNA rapidly accumulated in the white and green rust chimney structure from the surrounding ferruginous solution at the fastest rates in the initial white rust phase and correspondingly slower rates in the following green rust phase. This represents a new mechanism for nucleic acid accumulation in the ferruginous oceans of the early Earth, in addition to wet-dry cycles and may have helped to concentrate RNA in a dilute prebiotic ocean.

Synthesis of prebiotic organics from CO2 by catalysis with meteoritic and volcanic particles

The emergence of prebiotic organics was a mandatory step toward the origin of life. The significance of the exogenous delivery versus the in-situ synthesis from atmospheric gases is still under debate. We experimentally demonstrate that iron-rich meteoritic and volcanic particles activate and catalyse the fixation of CO₂, yielding the key precursors of life-building blocks. This catalysis is robust and produces selectively aldehydes, alcohols, and hydrocarbons, independent of the redox state of the environment. It is facilitated by common minerals and tolerates a broad range of the early planetary conditions (150-300 °C, ≲ 10-50 bar, wet or dry climate). We find that up to 6 × 10⁸ kg/year of prebiotic organics could have been synthesized by this planetary-scale process from the atmospheric CO₂ on Hadean Earth.

Enzymatic Fischer-Tropsch-Type Reactions

The Fischer-Tropsch (FT) process converts a mixture of CO and H2 into liquid hydrocarbons as a major component of the gas-to-liquid technology for the production of synthetic fuels. Contrary to the energy-demanding chemical FT process, the enzymatic FT-type reactions catalyzed by nitrogenase enzymes, their metalloclusters, and synthetic mimics utilize H+ and e- as the reducing equivalents to reduce CO, CO2, and CN- into hydrocarbons under ambient conditions. The C1 chemistry exemplified by these FT-type reactions is underscored by the structural and electronic properties of the nitrogenase-associated metallocenters, and recent studies have pointed to the potential relevance of this reactivity to nitrogenase mechanism, prebiotic chemistry, and biotechnological applications. This review will provide an overview of the features of nitrogenase enzymes and associated metalloclusters, followed by a detailed discussion of the activities of various nitrogenase-derived FT systems and plausible mechanisms of the enzymatic FT reactions, highlighting the versatility of this unique reactivity while providing perspectives onto its mechanistic, evolutionary, and biotechnological implications.

Insights into the formation and evolution of extraterrestrial amino acids from the asteroid Ryugu

All life on Earth contains amino acids and carbonaceous chondrite meteorites have been suggested as their source at the origin of life on Earth. While many meteoritic amino acids are considered indigenous, deciphering the extent of terrestrial contamination remains an issue. The Ryugu asteroid fragments (JAXA Hayabusa2 mission), represent the most uncontaminated primitive extraterrestrial material available. Here, the concentrations of amino acids from two particles from different touchdown sites (TD1 and TD2) are reported. The concentrations show that N,N-dimethylglycine (DMG) is the most abundant amino acid in the TD1 particle, but below detection limit in the other. The TD1 particle mineral components indicate it experienced more aqueous alteration. Furthermore, the relationships between the amino acids and the geochemistry suggest that DMG formed on the Ryugu progenitor body during aqueous alteration. The findings highlight the importance of aqueous chemistry for defining the ultimate concentrations of amino acids in primitive extraterrestrial samples.

Ecological Drivers of Community Cohesion

From protocellular to societal, networks of living systems are complex and multiscale. Discerning the factors that facilitate assembly of these intricate interdependencies using pairwise interactions can be nearly impossible. To facilitate a greater understanding, we developed a mathematical and computational model based on a synthetic four-strain Saccharomyces cerevisiae interdependent system. Specifically, we aimed to provide a greater understanding of how ecological factors influence community dynamics. By leveraging transiently structured ecologies, we were able to drive community cohesion. We show how ecological interventions could reverse or slow the extinction rate of a cohesive community. An interconnected system first needs to persist long enough to be a subject of natural selection. Our emulation of Darwin's "warm little ponds" with an ecology governed by transient compartmentalization provided the necessary persistence. Our results reveal utility across scales of organization, stressing the importance of cyclic processes in major evolutionary transitions, engineering of synthetic microbial consortia, and conservation biology. IMPORTANCE We are facing unprecedented disruption and collapse of ecosystems across the globe. To have any hope of mitigating this phenomenon, a much greater understanding of ecosystem dynamics is required. However, ecosystems are typically composed of highly dynamic networks of individual species. These interactions are further modulated by abiotic and biotic factors that vary temporally and spatially. Thus, ecological dynamics are obfuscated by this complexity. Here, we developed a theoretical model, informed by a synthetic experimental system, of Darwin's "warm little ponds." This cycling four-species system seeks to elucidate the ecological factors that drive or inhibit interaction. We show that these factors could provide an essential tool for avoiding the accelerating ecological collapse. Our study also provides a starting point to develop a more encompassing model to inform conservation efforts.

Tuning Material States and Functionalities of G-Quadruplex-Modulated RNA-Peptide Condensates

RNA encodes sequence- and structure-dependent interactions to modulate the assembly and properties of biomolecular condensates. RNA G-quadruplexes (rG4s) formed by guanine-rich sequences can trigger the formation of liquid- or solid-like condensates that are involved in many aberrant phase transitions. However, exactly how rG4 motifs modulate different phase transitions and impart distinct material properties to condensates is unclear. Here, using RNA oligonucleotides and cationic peptides as model systems, we show that RNA-peptide condensates exhibit tunability in material properties over a wide spectrum via interactions arising from rG4 folding/unfolding kinetics. rG4-containing oligonucleotides formed strong pairwise attraction with peptides and tended to form solid-like condensates, while their less-structured non-G4 mutants formed liquid-like droplets. We find that the coupling between rG4 dissociation and RNA-peptide complex coacervation triggers solid-to-liquid transition of condensates prior to the complete unfolding of rG4s. This coupling points to a mechanism that material states of rG4-modulated condensates can be finely tuned from solid-like to liquid-like by the addition of less-structured RNA oligonucleotides, which have weak but dominant binding with peptides. We further show that the tunable material states of condensates can enhance RNA aptamer compartmentalization and RNA cleavage reactions. Our results suggest that condensates with complex properties can emerge from subtle changes in RNA oligonucleotides, contributing ways to treat dysfunctional condensates in diseases and insights into prebiotic compartmentalization.

Ancestral Sequence Reconstruction of the Ribosomal Protein uS8 and Reduction of Amino Acid Usage to a Smaller Alphabet

Understanding the origin and early evolution of proteins is important for unveiling how the RNA world developed into an RNA-protein world. Because the composition of organic molecules in the Earth's primitive environment was plausibly not as diverse as today, the number of different amino acids used in early protein synthesis is likely to be substantially less than the current 20 proteinogenic residues. In this study, we have explored the thermal stability and RNA binding of ancestral variants of the ribosomal protein uS8 constructed from a reduced-alphabet of amino acids. First, we built a phylogenetic tree based on the amino acid sequences of uS8 from multiple extant organisms and used the tree to infer two plausible amino acid sequences corresponding to the last bacterial common ancestor of uS8. Both ancestral proteins were thermally stable and bound to an RNA fragment. By eliminating individual amino acid letters and monitoring thermal stability and RNA binding in the resulting proteins, we reduced the size of the amino acid set constituting one of the ancestral proteins, eventually finding that convergent sequences consisting of 15- or 14-amino acid alphabets still folded into stable structures that bound to the RNA fragment. Furthermore, a simplified variant reconstructed from a 13-amino-acid alphabet retained affinity for the RNA fragment, although it lost conformational stability. Collectively, RNA-binding activity may be achieved with a subset of the current 20 amino acids, raising the possibility of a simpler composition of RNA-binding proteins in the earliest stage of protein evolution.

Industrial Biotechnology Conservation Processes: Similarities with Natural Long-Term Preservation of Biological Organisms

Cryopreservation and lyophilization processes are widely used for conservation purposes in the pharmaceutical, biotechnological, and food industries or in medical transplantation. Such processes deal with extremely low temperatures (e.g., -196 °C) and multiple physical states of water, a universal and essential molecule for many biological lifeforms. This study firstly considers the controlled laboratory/industrial artificial conditions used to favor specific water phase transitions during cellular material cryopreservation and lyophilization under the Swiss progenitor cell transplantation program. Both biotechnological tools are successfully used for the long-term storage of biological samples and products, with reversible quasi-arrest of metabolic activities (e.g., cryogenic storage in liquid nitrogen). Secondly, similarities are outlined between such artificial localized environment modifications and some natural ecological niches known to favor metabolic rate modifications (e.g., cryptobiosis) in biological organisms. Specifically, examples of survival to extreme physical parameters by small multi-cellular animals (e.g., tardigrades) are discussed, opening further considerations about the possibility to reversibly slow or temporarily arrest the metabolic activity rates of defined complex organisms in controlled conditions. Key examples of biological organism adaptation capabilities to extreme environmental parameters finally enabled a discussion about the emergence of early primordial biological lifeforms, from natural biotechnology and evolutionary points of view. Overall, the provided examples/similarities confirm the interest in further transposing natural processes and phenomena to controlled laboratory settings with the ultimate goal of gaining better control and modulation capacities over the metabolic activities of complex biological organisms.

Glycine Peptide Chain Formation in the Gas Phase via Unimolecular Reactions

Peptide chain formation from amino acids such as glycine is a key step in the emergence of life. Unlike their synthesis by living systems, how peptide chains grow under abiotic conditions is an open question given the variety of organic compounds discovered in various astrophysical environments, comets and meteorites. We propose a new abiotic route in the presence of protonated molecular dimers of glycine in a cold gaseous atmosphere without further need for a solid catalytic substrate. The results provide evidence for the preferential formation of mixed protonated dimers of glycine consisting of a dipeptide and a glycine molecule instead of pure protonated glycine dimers. Additional measurements mimicking a cosmic-ray impact in terms of internal excitation show that a single gas-phase collision induces polymerization via dehydration in both the mixed and pure dimer ions. Peptide chain growth is thus demonstrated to occur via a unimolecular gas-phase reaction in an excited cluster ion.

Plausible Sources of Membrane-Forming Fatty Acids on the Early Earth: A Review of the Literature and an Estimation of Amounts

The first cells were plausibly bounded by membranes assembled from fatty acids with at least 8 carbons. Although the presence of fatty acids on the early Earth is widely assumed within the astrobiology community, there is no consensus regarding their origin and abundance. In this Review, we highlight three possible sources of fatty acids: (1) delivery by carbonaceous meteorites, (2) synthesis on metals delivered by impactors, and (3) electrochemical synthesis by spark discharges. We also discuss fatty acid synthesis by UV or particle irradiation, gas-phase ion-molecule reactions, and aqueous redox reactions. We compare estimates for the total mass of fatty acids supplied to Earth by each source during the Hadean eon after an extremely massive asteroid impact that would have reset Earth's fatty acid inventory. We find that synthesis on iron-rich surfaces derived from the massive impactor in contact with an impact-generated reducing atmosphere could have contributed ∼10² times more total mass of fatty acids than subsequent delivery by either carbonaceous meteorites or electrochemical synthesis. Additionally, we estimate that a single carbonaceous meteorite would not deliver a high enough concentration of fatty acids (∼15 mM for decanoic acid) into an existing body of water on the Earth's surface to spontaneously form membranes unless the fatty acids were further concentrated by another mechanism, such as subsequent evaporation of the water. Our estimates rely heavily on various assumptions, leading to significant uncertainties; nevertheless, these estimates provide rough order-of-magnitude comparisons of various sources of fatty acids on the early Earth. We also suggest specific experiments to improve future estimates. Our calculations support the view that fatty acids would have been available on the early Earth. Further investigation is needed to assess the mechanisms by which fatty acids could have been concentrated sufficiently to assemble into membranes during the origin of life.

Plausible Sources of Membrane-Forming Fatty Acids on the Early Earth: A Review of the Literature and an Estimation of Amounts

The first cells were plausibly bounded by membranes assembled from fatty acids with at least 8 carbons. Although the presence of fatty acids on the early Earth is widely assumed within the astrobiology community, there is no consensus regarding their origin and abundance. In this Review, we highlight three possible sources of fatty acids: (1) delivery by carbonaceous meteorites, (2) synthesis on metals delivered by impactors, and (3) electrochemical synthesis by spark discharges. We also discuss fatty acid synthesis by UV or particle irradiation, gas-phase ion-molecule reactions, and aqueous redox reactions. We compare estimates for the total mass of fatty acids supplied to Earth by each source during the Hadean eon after an extremely massive asteroid impact that would have reset Earth's fatty acid inventory. We find that synthesis on iron-rich surfaces derived from the massive impactor in contact with an impact-generated reducing atmosphere could have contributed ∼10² times more total mass of fatty acids than subsequent delivery by either carbonaceous meteorites or electrochemical synthesis. Additionally, we estimate that a single carbonaceous meteorite would not deliver a high enough concentration of fatty acids (∼15 mM for decanoic acid) into an existing body of water on the Earth's surface to spontaneously form membranes unless the fatty acids were further concentrated by another mechanism, such as subsequent evaporation of the water. Our estimates rely heavily on various assumptions, leading to significant uncertainties; nevertheless, these estimates provide rough order-of-magnitude comparisons of various sources of fatty acids on the early Earth. We also suggest specific experiments to improve future estimates. Our calculations support the view that fatty acids would have been available on the early Earth. Further investigation is needed to assess the mechanisms by which fatty acids could have been concentrated sufficiently to assemble into membranes during the origin of life.

Technologies Enabling Single-Molecule Super-Resolution Imaging of mRNA

The transient nature of RNA has rendered it one of the more difficult biological targets for imaging. This difficulty stems both from the physical properties of RNA as well as the temporal constraints associated therewith. These concerns are further complicated by the difficulty in imaging endogenous RNA within a cell that has been transfected with a target sequence. These concerns, combined with traditional concerns associated with super-resolution light microscopy has made the imaging of this critical target difficult. Recent advances have provided researchers the tools to image endogenous RNA in live cells at both the cellular and single-molecule level. Here, we review techniques used for labeling and imaging RNA with special emphases on various labeling methods and a virtual 3D super-resolution imaging technique.

Urability: A Property of Planetary Bodies That Can Support an Origin of Life

The concept of habitability is now widely used to describe zones in a solar system in which planets with liquid water can sustain life. Because habitability does not explicitly incorporate the origin of life, this article proposes a new word-urability-which refers to the conditions that allow life to begin. The utility of the word is tested by applying it to combinations of multiple geophysical and geochemical factors that support plausible localized zones that are conducive to the chemical reactions and molecular assembly processes required for the origin of life. The concept of urable worlds, planetary bodies that can sustain an arising of life, is considered for bodies in our own solar system and exoplanets beyond.

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.

Evolution of Realistic Organic Mixtures for the Origins of Life through Wet–Dry Cycling

One of the challenges in understanding chemical evolution is the large number of starting organics and environments that were plausible on early Earth. Starting with realistic organic mixtures and using chemical analyses that are not biologically biased, understanding the interplay between organic composition and environment can be approached using statistical analysis. In this work, a mixture of 73 organics was cycled through dehydrating conditions five times, considering environmental parameters of pH, salinity, and rehydration solution. Products were analyzed by HPLC, amide and ester assays, and phosphatase and esterase assays. While all environmental factors were found to influence chemical evolution, salinity was found to play a large role in the evolution of these mixtures, with samples diverging at very high sea salt concentrations. This framework should be expanded and formalized to improve our understanding of abiogenesis.

Searching for Life, Mindful of Lyfe's Possibilities

We are embarking on a new age of astrobiology, one in which numerous interplanetary missions and telescopes will be designed, built, and launched with the explicit goal of finding evidence for life beyond Earth. Such a profound aim warrants caution and responsibility when interpreting and disseminating results. Scientists must take care not to overstate (or over-imply) confidence in life detection when evidence is lacking, or only incremental advances have been made. Recently, there has been a call for the community to create standards of evidence for the detection and reporting of biosignatures. In this perspective, we wish to highlight a critical but often understated element to the discussion of biosignatures: Life detection studies are deeply entwined with and rely upon our (often preconceived) notions of what life is, the origins of life, and habitability. Where biosignatures are concerned, these three highly related questions are frequently relegated to a low priority, assumed to be already solved or irrelevant to the question of life detection. Therefore, our aim is to bring to the fore how these other major astrobiological frontiers are central to searching for life elsewhere and encourage astrobiologists to embrace the reality that all of these science questions are interrelated and must be furthered together rather than separately. Finally, in an effort to be more inclusive of life as we do not know it, we propose tentative criteria for a more general and expansive characterization of habitability that we call genesity.

RNA World Modeling: A Comparison of Two Complementary Approaches

Simple Summary

Despite years of dedicated research, scientists are still not sure what the first ”living” cell would have looked like. One of the most well-known hypotheses is the RNA world hypothesis, which assumes that, in the beginning, life relied on RNA molecules instead of DNA as information carriers and primitive enzymes. The population of such RNAs is made up of self-replicating molecules (replicases) that could make copies of themselves and parasite molecules that could only be copied by replicases. In this study, we further investigated the interplay between these hypothetical prebiotic RNA species, since it plays a crucial role in generating diversity and complexity in prebiotic molecular evolution. We compared two approaches that are commonly used to investigate such simple prebiotic systems, representing different modeling and observation scales—namely, microscopic and macroscopic. In both cases, we were able to obtain consistent results.

Abstract

The origin of life remains one of the major scientific questions in modern biology. Among many hypotheses aiming to explain how life on Earth started, RNA world is probably the most extensively studied. It assumes that, in the very beginning, RNA molecules served as both enzymes and as genetic information carriers. However, even if this is true, there are many questions that still need to be answered—for example, whether the population of such molecules could achieve stability and retain genetic information for many generations, which is necessary in order for evolution to start. In this paper, we try to answer this question based on the parasite–replicase model (RP model), which divides RNA molecules into enzymes (RNA replicases) capable of catalyzing replication and parasites that do not possess replicase activity but can be replicated by RNA replicases. We describe the aforementioned system using partial differential equations and, based on the analysis of the simulation, surmise general rules governing its evolution. We also compare this approach with one where the RP system is modeled and implemented using a multi-agent modeling technique. We show that approaching the description and analysis of the RP system from different perspectives (microscopic represented by MAS and macroscopic depicted by PDE) provides consistent results. Therefore, applying MAS does not lead to erroneous results and allows us to study more complex situations where many cases are concerned, which would not be possible through the PDE model.

Possible Ribose Synthesis in Carbonaceous Planetesimals

The origin of life might be sparked by the polymerization of the first RNA molecules in Darwinian ponds during wet-dry cycles. The key life-building block ribose was found in carbonaceous chondrites. Its exogenous delivery onto the Hadean Earth could be a crucial step toward the emergence of the RNA world. Here, we investigate the formation of ribose through a simplified version of the formose reaction inside carbonaceous chondrite parent bodies. Following up on our previous studies regarding nucleobases with the same coupled physico-chemical model, we calculate the abundance of ribose within planetesimals of different sizes and heating histories. We perform laboratory experiments using catalysts present in carbonaceous chondrites to infer the yield of ribose among all pentoses (5Cs) forming during the formose reaction. These laboratory yields are used to tune our theoretical model that can only predict the total abundance of 5Cs. We found that the calculated abundances of ribose were similar to the ones measured in carbonaceous chondrites. We discuss the possibilities of chemical decomposition and preservation of ribose and derived constraints on time and location in planetesimals. In conclusion, the aqueous formose reaction might produce most of the ribose in carbonaceous chondrites. Together with our previous studies on nucleobases, we found that life-building blocks of the RNA world could be synthesized inside parent bodies and later delivered onto the early Earth.

UV Transmission in Natural Waters on Prebiotic Earth

Ultraviolet (UV) light plays a key role in surficial theories of the origin of life, and numerous studies have focused on constraining the atmospheric transmission of UV radiation on early Earth. However, the UV transmission of the natural waters in which origins-of-life chemistry (prebiotic chemistry) is postulated to have occurred is poorly constrained. In this work, we combine laboratory and literature-derived absorption spectra of potential aqueous-phase prebiotic UV absorbers with literature estimates of their concentrations on early Earth to constrain the prebiotic UV environment in marine and terrestrial natural waters, and we consider the implications for prebiotic chemistry. We find that prebiotic freshwaters were largely transparent in the UV, contrary to assumptions in some models of prebiotic chemistry. Some waters, such as high-salinity waters like carbonate lakes, may be deficient in shortwave (≤220 nm) UV flux. More dramatically, ferrous waters can be strongly UV-shielded, particularly if the Fe2+ forms highly UV-absorbent species such as F e C N 6 4 - . Such waters may be compelling venues for UV-averse origin-of-life scenarios but are unfavorable for some UV-dependent prebiotic chemistries. UV light can trigger photochemistry even if attenuated through photochemical transformations of the absorber (e.g., e a q - production from halide irradiation), which may have both constructive and destructive effects for prebiotic syntheses. Prebiotic chemistries that invoke waters that contain such absorbers must self-consistently account for the chemical effects of these transformations. The speciation and abundance of Fe2+ in natural waters on early Earth is a major uncertainty and should be prioritized for further investigation, as it played a major role in UV transmission in prebiotic natural waters.

Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets

The evolutionary origin of the genome remains elusive. Here, I hypothesize that its first iteration, the protogenome, was a multi-ribozyme RNA. It evolved, likely within liposomes (the protocells) forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and was amplified by a polymerase. The protogenome thereby linked, in one molecule, the information required to seed the protometabolism (a combination of RNA-based autocatalytic sets) in newly forming protocells. If this combination of autocatalytic sets was evolutionarily advantageous, the protogenome would have amplified in a population of multiplying protocells. It likely was a quasispecies with redundant information, e.g., multiple copies of one ribozyme. As such, new functionalities could evolve, including a genetic code. Once one or more components of the protometabolism were templated by the protogenome (e.g., when a ribozyme was replaced by a protein enzyme), and/or addiction modules evolved, the protometabolism became dependent on the protogenome. Along with increasing fidelity of the RNA polymerase, the protogenome could grow, e.g., by incorporating additional ribozyme domains. Finally, the protogenome could have evolved into a DNA genome with increased stability and storage capacity. I will provide suggestions for experiments to test some aspects of this hypothesis, such as evaluating the ability of ribozyme RNA polymerases to generate random ligation products and testing the catalytic activity of linked ribozyme domains.

Hot Spring Microbial Community Elemental Composition: Hot Spring and Soil Inputs, and the Transition from Biocumulus to Siliceous Sinter

Hydrothermal systems host microbial communities that include some of the most deeply branching members of the tree of life, and recent work has suggested that terrestrial hot springs may have provided ideal conditions for the origin of life. Hydrothermal microbial communities are a potential source for biosignatures, and the presence of terrestrial hot spring deposits in 3.48 Ga rocks as well as on the surface of Mars lends weight to a need to better understand the preservation of biosignatures in these systems. Although there are general patterns of elemental enrichment in hydrothermal water dependent on physical and geochemical conditions, the elemental composition of bulk hydrothermal microbial communities (here termed biocumulus, including cellular biomass and accumulated non-cellular material) is largely unexplored. However, recent work has suggested both bulk and spatial trace element enrichment as a potential biosignature in hot spring deposits. To elucidate the elemental composition of hot spring biocumulus samples and explore the sources of those elements, we analyzed a suite of 16 elements in hot spring water samples and corresponding biocumulus from 60 hot springs sinter samples, and rock samples from 8 hydrothermal areas across Yellowstone National Park. We combined these data with values reported in literature to assess the patterns of elemental uptake into biocumulus and retention in associated siliceous sinter. Hot spring biocumuli are of biological origin, but organic carbon comprises a minor percentage of the total mass of both thermophilic chemotrophic and phototrophic biocumulus. Instead, the majority of hot spring biocumulus is inorganic material-largely silica-and the distribution of major and trace elements mimics that of surrounding rock and soil rather than the hot spring fluids. Analyses indicate a systematic loss of biologically associated elements during diagenetic transformation of biocumulus to siliceous sinter, suggesting a potential for silica sinter to preserve a trace element biosignature.

Was There Land on the Early Earth?

The presence of exposed land on the early Earth is a prerequisite for a certain type of prebiotic chemical evolution in which the oscillating activity of water, driven by short-term, day–night, and seasonal cycles, facilitates the synthesis of proto-biopolymers. Exposed land is, however, not guaranteed to exist on the early Earth, which is likely to have been drastically different from the modern Earth. This mini-review attempts to provide an up-to-date account on the possibility of exposed land on the early Earth by integrating recent geological and geophysical findings. Owing to the competing effects of the growing ocean and continents in the Hadean, a substantial expanse of the Earth’s surface (∼20% or more) could have been covered by exposed continents in the mid-Hadean. In contrast, exposed land may have been limited to isolated ocean islands in the late Hadean and early Archean. The importance of exposed land during the origins of life remains an open question.

HIV and Messenger RNA (mRNA) Vaccine

Human immunodeficiency virus (HIV) is a part of the lentivirus genus of the retroviridae family that incorporates its genome into the host DNA via a series of complex steps. HIV can be classified into two types, HIV-type 1 (HIV-1) and HIV-type 2 (HIV-2), with HIV-1 being the most common type worldwide. Seventy-six million people have been infected since the start of the pandemic, with a mortality rate of 33 million. Even after 40 years, no cure has been developed for this pandemic. The development of the mRNA vaccine has led to further research for the utilization of mRNA vaccine in HIV, in attempts to create a prophylactic and therapeutic treatment. Although messenger RNA (mRNA) vaccine has been around for many years, it has recently drawn attention due to its role and response in the unforeseen coronavirus pandemic. mRNA vaccine has faced its fair-share of challenges, but it also offers many advantages compared to conventional vaccines such as safety, efficacy, rapid preparation, and versatility. mRNA vaccine has shown promising results and has great potential. In this review, we discuss the types of mRNA vaccine, along with development, delivery, advantages, challenges, and how we are working to overcome these challenges.

The Origin(s) of Cell(s): Pre-Darwinian Evolution from FUCAs to LUCA : To Carl Woese (1928-2012), for his Conceptual Breakthrough of Cellular Evolution

The coming of the Last Universal Cellular Ancestor (LUCA) was the singular watershed event in the making of the biotic world. If the coming of LUCA marked the crossing of the "Darwinian Threshold", then pre-LUCA evolution must have been Pre-Darwinian and at least partly non-Darwinian. But how did Pre-Darwinian evolution before LUCA actually operate? I broaden our understanding of the central mechanism of biological evolution (i.e., variation-selection-inheritance) and then extend this broadened understanding to its natural starting point: the origin(s) of the First Universal Cellular Ancestors (FUCAs) before LUCA. My hypothesis centers upon vesicles' making-and-remaking as variation and competition as selection. More specifically, I argue that vesicles' acquisition and merger, via breaking-and-repacking, proto-endocytosis, proto-endosymbiosis, and other similar processes had been a central force of both variation and selection in the pre-Darwinian epoch. These new perspectives shed important new light upon the origin of FUCAs and their subsequent evolution into LUCA.

Origin of Life on Mars: Suitability and Opportunities

Although the habitability of early Mars is now well established, its suitability for conditions favorable to an independent origin of life (OoL) has been less certain. With continued exploration, evidence has mounted for a widespread diversity of physical and chemical conditions on Mars that mimic those variously hypothesized as settings in which life first arose on Earth. Mars has also provided water, energy sources, CHNOPS elements, critical catalytic transition metal elements, as well as B, Mg, Ca, Na and K, all of which are elements associated with life as we know it. With its highly favorable sulfur abundance and land/ocean ratio, early wet Mars remains a prime candidate for its own OoL, in many respects superior to Earth. The relatively well-preserved ancient surface of planet Mars helps inform the range of possible analogous conditions during the now-obliterated history of early Earth. Continued exploration of Mars also contributes to the understanding of the opportunities for settings enabling an OoL on exoplanets. Favoring geochemical sediment samples for eventual return to Earth will enhance assessments of the likelihood of a Martian OoL.

Non-associative phase separation in an evaporating droplet as a model for prebiotic compartmentalization

The synthetic pathways of life’s building blocks are envisaged to be through a series of complex prebiotic reactions and processes. However, the strategy to compartmentalize and concentrate biopolymers under prebiotic conditions remains elusive. Liquid-liquid phase separation is a mechanism by which membraneless organelles form inside cells, and has been hypothesized as a potential mechanism for prebiotic compartmentalization. Associative phase separation of oppositely charged species has been shown to partition RNA, but the strongly negative charge exhibited by RNA suggests that RNA-polycation interactions could inhibit RNA folding and its functioning inside the coacervates. Here, we present a prebiotically plausible pathway for non-associative phase separation within an evaporating all-aqueous sessile droplet. We quantitatively investigate the kinetic pathway of phase separation triggered by the non-uniform evaporation rate, together with the Marangoni flow-driven hydrodynamics inside the sessile droplet. With the ability to undergo liquid-liquid phase separation, the drying droplets provide a robust mechanism for formation of prebiotic membraneless compartments, as demonstrated by localization and storage of nucleic acids, in vitro transcription, as well as a three-fold enhancement of ribozyme activity. The compartmentalization mechanism illustrated in this model system is feasible on wet organophilic silica-rich surfaces during early molecular evolution.

Prebiotic compartmentalization could prove essential for the evolution of life. Guo et al. show that liquid-liquid separation in an aqueous two-phase system driven by evaporation may already suffice to facilitate chemical processes required for the RNA world hypothesis.

Bringing high spatial resolution to the far-infrared: A giant leap for astrophysics

The far-infrared (FIR) regime is one of the wavelength ranges where no astronomical data with sub-arcsecond spatial resolution exist. None of the medium-term satellite projects like SPICA, Millimetron, or the Origins Space Telescope will resolve this malady. For many research areas, however, information at high spatial and spectral resolution in the FIR, taken from atomic fine-structure lines, from highly excited carbon monoxide (CO), light hydrides, and especially from water lines would open the door for transformative science. A main theme will be to trace the role of water in proto-planetary discs, to observationally advance our understanding of the planet formation process and, intimately related to that, the pathways to habitable planets and the emergence of life. Furthermore, key observations will zoom into the physics and chemistry of the star-formation process in our own Galaxy, as well as in external galaxies. The FIR provides unique tools to investigate in particular the energetics of heating, cooling, and shocks. The velocity-resolved data in these tracers will reveal the detailed dynamics engrained in these processes in a spatially resolved fashion, and will deliver the perfect synergy with ground-based molecular line data for the colder dense gas.

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.

Inosine in Biology and Disease

The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of tRNA anticodons, inosine profoundly modifies codon recognition, while in mRNA, inosines can modify the sequence of the translated polypeptide or modulate the stability, localization, and splicing of transcripts. Inosine is also found in non-coding and exogenous RNAs, where it plays key structural and functional roles. In addition, molecular inosine is an important secondary metabolite in purine metabolism that also acts as a molecular messenger in cell signaling pathways. Here, we review the functional roles of inosine in biology and their connections to human health.

Subcompartmentalization and Pseudo-Division of Model Protocells

Membrane enclosed intracellular compartments have been exclusively associated with the eukaryotes, represented by the highly compartmentalized last eukaryotic common ancestor. Recent evidence showing the presence of membranous compartments with specific functions in archaea and bacteria makes it conceivable that the last universal common ancestor and its hypothetical precursor, the protocell, may have exhibited compartmentalization. To the authors' knowledge, there are no experimental studies yet that have tested this hypothesis. They report on an autonomous subcompartmentalization mechanism for protocells which results in the transformation of initial subcompartments to daughter protocells. The process is solely determined by the fundamental materials properties and interfacial events, and does not require biological machinery or chemical energy supply. In the light of the authors' findings, it is proposed that similar events may have taken place under early Earth conditions, leading to the development of compartmentalized cells and potentially, primitive division.

Elements for the Origin of Life on Land: A Deep-Time Perspective from the Pilbara Craton of Western Australia

For decades, deep sea hydrothermal vents have been a preferred setting for the Origin of Life, but "The Water Problem" as relates to polymerization of organic molecules, together with a propensity to dilute critical prebiotic elements as well as a number of other crucial factors, suggests that a terrestrial hot spring field with the capacity for wet-dry cycling and element concentration may represent a more likely candidate. Here, we investigate a 3.5 billion-year-old, anoxic hot spring setting from the Pilbara Craton (Australia) and show that its hydrothermal veins and compositionally varied pools and springs concentrated all of the essential elements required for prebiotic chemistry (including B, Zn, Mn, and K, in addition to C, H, N, O, P, and S). Temporal variability (seasonal to decadal), together with the known propensity of hot springs for wet-dry cycling and information exchange, would lead to innovation pools with peaks of fitness for developing molecules. An inference from the chemical complexity of the Pilbara analogue is that life could perhaps get started quickly on planets with volcanoes, silicate rocks, an exposed land surface, and water, ingredients that should form the backbone in the search for life in the Universe.

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.

AFM Images of Viroid-Sized Rings That Self-Assemble from Mononucleotides through Wet-Dry Cycling: Implications for the Origin of Life

It is possible that early 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. The aim of the study reported here was to visualize the products by atomic force microscopy. In addition to globular oligomers, ring-like structures ranging from 10–200 nm in diameter, with an average around 30–40 nm, were abundant, particularly when nucleotides capable of base pairing were present. The thickness of the rings was consistent with single stranded products, but some had thicknesses indicating base pair stacking. Others had more complex structures in the form of short polymer attachments and pairing of rings. These observations suggest the possibility that base-pairing may promote polymerization during wet–dry cycling followed by solvation of the rings. We conclude that RNA-like rings and structures could have been synthesized non-enzymatically on the prebiotic Earth, with sizes sufficient to fold into ribozymes and genetic molecules required for life to begin.

Macrobiont: Cradle for the Origin of Life and Creation of a Biosphere

Although the cellular microorganism is the fundamental unit of biology, the origin of life (OoL) itself is unlikely to have occurred in a microscale environment. The macrobiont (MB) is the macro-scale setting where life originated. Guided by the methodologies of Systems Analysis, we focus on subaerial ponds of scale 3 to 300 m diameter. Within such ponds, there can be substantial heterogeneity, on the vertical, horizontal, and temporal scales, which enable multi-pot prebiotic chemical evolution. Pond size-sensitivities for several figures of merit are mathematically formulated, leading to the expectation that the optimum pond size for the OoL is intermediate, but biased toward smaller sizes. Sensitivities include relative access to nutrients, energy sources, and catalysts, as sourced from geological, atmospheric, hydrospheric, and astronomical contributors. Foreshores, especially with mudcracks, are identified as a favorable component for the success of the macrobiont. To bridge the gap between inanimate matter and a planetary-scale biosphere, five stages of evolution within the macrobiont are hypothesized: prebiotic chemistry → molecular replicator → protocell → macrobiont cell → colonizer cell. Comparison of ponds with other macrobionts, including hydrothermal and meteorite settings, allows a conclusion that more than one possible macrobiont locale could enable an OoL.

Liquid Crystal Peptide/DNA Coacervates in the Context of Prebiotic Molecular Evolution

Liquid–liquid phase separation (LLPS) phenomena are ubiquitous in biological systems, as various cellular LLPS structures control important biological processes. Due to their ease of in vitro assembly into membraneless compartments and their presence within modern cells, LLPS systems have been postulated to be one potential form that the first cells on Earth took on. Recently, liquid crystal (LC)-coacervate droplets assembled from aqueous solutions of short double-stranded DNA (s-dsDNA) and poly-L-lysine (PLL) have been reported. Such LC-coacervates conjugate the advantages of an associative LLPS with the relevant long-range ordering and fluidity properties typical of LC, which reflect and propagate the physico-chemical properties of their molecular constituents. Here, we investigate the structure, assembly, and function of DNA LC-coacervates in the context of prebiotic molecular evolution and the emergence of functional protocells on early Earth. We observe through polarization microscopy that LC-coacervate systems can be dynamically assembled and disassembled based on prebiotically available environmental factors including temperature, salinity, and dehydration/rehydration cycles. Based on these observations, we discuss how LC-coacervates can in principle provide selective pressures effecting and sustaining chemical evolution within partially ordered compartments. Finally, we speculate about the potential for LC-coacervates to perform various biologically relevant properties, such as segregation and concentration of biomolecules, catalysis, and scaffolding, potentially providing additional structural complexity, such as linearization of nucleic acids and peptides within the LC ordered matrix, that could have promoted more efficient polymerization. While there are still a number of remaining open questions regarding coacervates, as protocell models, including how modern biologies acquired such membraneless organelles, further elucidation of the structure and function of different LLPS systems in the context of origins of life and prebiotic chemistry could provide new insights for understanding new pathways of molecular evolution possibly leading to the emergence of the first cells on Earth.

Rapid Growth and Fusion of Protocells in Surface-Adhered Membrane Networks

Elevated temperatures might have promoted the nucleation, growth, and replication of protocells on the early Earth. Recent reports have shown evidence that moderately high temperatures not only permit protocell assembly at the origin of life, but can have actively supported it. Here, the fast nucleation and growth of vesicular compartments from autonomously formed lipid networks on solid surfaces, induced by a moderate increase in temperature, are shown. Branches of the networks, initially consisting of self-assembled interconnected nanotubes, rapidly swell into microcompartments which can spontaneously encapsulate RNA fragments. The increase in temperature further causes fusion of adjacent network-connected compartments, resulting in the redistribution of the RNA. The experimental observations and the mathematical model indicate that the presence of nanotubular interconnections between protocells facilitates the fusion process.