Plausible Prebiotic Conditions Research Articles

Boron as a Hypothetical Participant in the Prebiological Enantiomeric Enrichment.

Boron, as borate (or boric acid), is known as a mediator of the synthesis of ribose, ribonucleosides, and ribonucleotides (precursors of RNA) under plausible prebiotic conditions. With regard to these phenomena, the potential participation of this chemical element (as a constituent of minerals or hydrogels) for the emergence of prebiological homochirality is considered. This hypothesis is based on characteristics of crystalline surfaces as well as solubility of some minerals of boron in water or specific features of hydrogels with ester bonds from reaction of ribonucleosides and borate.

Multivariate Analysis Applied to Microwave-Driven Cyanide Polymerization: A Statistical View of a Complex System

For the first time, chemometrics was applied to the recently reported microwave-driven cyanide polymerization. Fast, easy, robust, low-cost, and green-solvent processes are characteristic of these types of reactions. These economic and environmental benefits, originally inspired by the constraints imposed by plausible prebiotic synthetic conditions, have taken advantage of the development of a new generation of HCN-derived multifunctional materials. HCN-derived polymers present tunable properties by temperature and reaction time. However, the apparently random behavior observed in the evolution of cyanide polymerizations, assisted by microwave radiation over time at different temperatures, leads us to study this highly complex system using multivariate analytical tools to have a proper view of the system. Two components are sufficient to explain between 84 and 98% of the total variance in the data in all principal component analyses. In addition, two components explain more than 91% of the total variance in the data in the case of principal component analysis for categorical data. These consistent statistical results indicate that microwave-driven polymerization is a more robust process than conventional thermal syntheses but also that plausible prebiotic chemistry in alkaline subaerial environments could be more complex than in the aerial part of these systems, presenting a clear example of the "messy chemistry" approach of interest in the research about the origins of life. In addition, the methodology discussed herein could be useful for the data analysis of extraterrestrial samples and for the design of soft materials, in a feedback view between prebiotic chemistry and materials science.

Erythrose and Threose: Carbonyl Migrations, Epimerizations, Aldol, and Oxidative Fragmentation Reactions under Plausible Prebiotic Conditions.

The prebiotic generation of sugars in the context of origins of life studies is of considerable interest. Among the important intramolecular processes of sugars are carbonyl migrations and accompanying epimerizations. Herein we describe the carbonyl migration-epimerization process occurring down the entire carbon chain of chirally pure d-tetroses sugars under mild conditions. Employing chirally pure 1-13 C-erythrose, 4-13 C-erythrose and 1-13 C-threose, we (1) identify all the species formed as the carbonyl migrates down the four-carbon chain and (2) assess the rates associated with the production of each of these species. Competing aldol reactions and oxidative fragmentation processes were also observed. Further observations of self-condensation of glycolaldehyde mainly yielding 2-keto-hexoses (sorbose and tagatose) and tetrulose also provides a basis for understanding the effect of carbonyl migrations on the product distribution in plausible prebiotic scenarios.

Frontispiece: On the Evolutionary History of the Twenty Encoded Amino Acids

Reflections on the origin of life are speculative per se. And fundamental questions such as a) how the 20 proteinogenic amino acids were selected and b) in what temporal sequence they are likely to have appeared on the world stage, open up the possibility of deductively delving far into the darkness of the past. A. Kirschning addresses these questions in the Review article 10.1002/chem.202200407 by focusing on prebiotic and metabolic aspects of amino acids and proteins starting with meteorites, followed by their formation, including peptides, under plausible prebiotic conditions, and the major biosynthetic pathways in the various kingdoms of life. Coenzymes play a key role in the present analysis, with the report opening additional perspectives and facets on the molecular evolution of primary metabolism.

On the Evolutionary History of the Twenty Encoded Amino Acids.

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

Rapid Radiolytic Degradation of Amino Acids in the Martian Shallow Subsurface: Implications for the Search for Extinct Life.

Amino acids are fundamental to life as we know them as the monomers of proteins and enzymes. They are also readily synthesized under a variety of plausible prebiotic conditions and are common in carbon-rich meteorites. Thus, they represent a reasonable class of organics to target in the search for prebiotic chemistry or chemical evidence of life on Mars. However, regardless of their origin, amino acids and other organic molecules present in near-surface regolith and rocks on Mars can be degraded by exposure to cosmic rays that can penetrate to a depth of a few meters. We exposed several pure amino acids in dry and hydrated silicate mixtures and in mixtures of silicates with perchlorate salts to gamma radiation at various temperatures and radiation doses representative of the martian near-subsurface. We found that irradiation of amino acids mixed with dry silica powder increased the rate of amino acid radiolysis, with the radiolysis constants of amino acids in silicate mixtures at least a factor of 10 larger compared with the radiolysis constants of amino acids alone. The addition of perchlorate salts to the silicate samples or hydration of silicate samples further accelerated the rate of amino acid destruction during irradiation and increased the radiolysis constants by a factor of ∼1.5. Our results suggest that even low-molecular-weight amino acids could degrade in just ∼20 million years in the top 10 cm of the martian surface regolith and rock, and even faster if the material contains elevated abundances of hydrated silicate minerals or perchlorates. We did not detect evidence of amino acid racemization after gamma radiation exposure of the samples, which indicates that the chirality of some surviving amino acids may still be preserved. Our experimental results suggest serious challenges for the search of ancient amino acids and other potential organic biosignatures in the top 2 m of the martian surface.

Synthesis of Phospholipids Under Plausible Prebiotic Conditions and Analogies with Phospholipid Biochemistry for Origin of Life Studies.

Phospholipids are essential components of biological membranes and are involved in cell signalization, in several enzymatic reactions, and in energy metabolism. In addition, phospholipids represent an evolutionary and non-negligible step in life emergence. Progress in the past decades has led to a deeper understanding of these unique hydrophobic molecules and their most pertinent functions in cell biology. Today, a growing interest in "prebiotic lipidomics" calls for a new assessment of these relevant biomolecules.

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.

Depsipeptide Nucleic Acids: Prebiotic Formation, Oligomerization, and Self-Assembly of a New Proto-Nucleic Acid Candidate.

The mechanism by which informational polymers first formed on the early earth is currently unknown. The RNA world hypothesis implies that RNA oligomers were produced prebiotically, before the emergence of enzymes, but the demonstration of such a process remains challenging. Alternatively, RNA may have been preceded by an earlier ancestral polymer, or proto-RNA, that had a greater propensity for self-assembly than RNA, with the eventual transition to functionally superior RNA being the result of chemical or biological evolution. We report a new class of nucleic acid analog, depsipeptide nucleic acid (DepsiPNA), which displays several properties that are attractive as a candidate for proto-RNA. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these DepsiPNA oligomers are capable of complementary self-assembly and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers on the early earth may have been relatively facile if the constraints of an RNA-first scenario are relaxed.

Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA.

The hypothesis that RNA and DNA are products of chemical and biological evolution has motivated our search for alternative nucleic acids that may have come earlier in the emergence of life-polymers that possess a proclivity for covalent and non-covalent self-assembly not exhibited by RNA. Our investigations have revealed a small set of candidate ancestral nucleobases that self-assemble into hexameric rosettes that stack in water to form long, twisted, rigid supramolecular polymers. These structures exhibit properties that provide robust solutions to long-standing problems that have stymied the search for a prebiotic synthesis of nucleic acids. Moreover, their examination by experimental and computational methods provides insight into the chemical and physical principles that govern a particular class of water-soluble one-dimensional supramolecular polymers. In addition to efficient self-assembly, their lengths and polydispersity are modulated by a wide variety of positively charged, planar compounds; their assembly and disassembly are controlled over an exceedingly narrow pH range; they exhibit spontaneous breaking of symmetry; and homochirality emerges through non-covalent cross-linking during hydrogel formation. Some of these candidate ancestral nucleobases spontaneously form glycosidic bonds with ribose and other sugars, and, most significantly, functionalized forms of these heterocycles form supramolecular structures and covalent polymers under plausibly prebiotic conditions. This Perspective recounts a journey of discovery that continues to reveal attractive answers to questions concerning the origins of life and to uncover the principles that control the structure and properties of water-soluble supramolecular polymers.

An Individual Amino Acid as a Possible Prebiotic Catalyst

AbstractBetter understanding how reactions have been catalyzed in the prebiotic world is important for better realizing how enzymes have evolved. The dominant hypothesis is that the first catalyst was an RNA molecule. It was also assumed that amyloid fibrils, self‐assembled by peptides or proteins, served as the first catalysts. However, debate still exists regarding which process occurred first: the polymerization of RNA or the synthesis of proteins. Here, we show that an individual amino acid, L‐3,4‐dihydroxyphenylalanine (DOPA), can act as a catalyst. This amino acid is the main constituent of mussel adhesion proteins that function in harsh conditions very similar to plausible prebiotic conditions. By tracing the hydrolysis of two compounds, p‐nitrophenylacetate and acetylcholine, we showed that DOPA catalyzes a reaction; we suggest its role as a prebiotic catalyst.

Prebiotically Plausible Organocatalysts Enabling a Selective Photoredox α-Alkylation of Aldehydes on the Early Earth.

Organocatalysis is a powerful approach to extend and (enantio‐) selectively modify molecular structures. Adapting this concept to the Early Earth scenario offers a promising solution to explain their evolution into a complex homochiral world. Herein, we present a class of imidazolidine‐4‐thione organocatalysts, easily accessible from simple molecules available on an Early Earth under highly plausible prebiotic reaction conditions. These imidazolidine‐4‐thiones are readily formed from mixtures of aldehydes or ketones in presence of ammonia, cyanides and hydrogen sulfide in high selectivity and distinct preference for individual compounds of the resulting catalyst library. These organocatalysts enable the enantioselective α‐alkylation of aldehydes under prebiotic conditions and show activities that correlate with the selectivity of their formation. Furthermore, the crystallization of single catalysts as conglomerates opens the pathway for symmetry breaking.

Synthesis of ribonucleotides from the corresponding ribonucleosides under plausible prebiotic conditions within self-assembled supramolecular structures

Abiotic synthesis of ribonucleotides, mainly at the 5′ position, from the corresponding ribonucleosides within guanosine:borate hydrogels in the temperature range of 70–90 °C, using urea and a phosphate source (K2HPO4 or hydroxyapatite).

The Oligomerization of Glucose Under Plausible Prebiotic Conditions.

The prebiotic origin of polysaccharides, the largest class of biopolymers by mass in extant biology, has seldom been investigated experimentally. Herein, we report on the acid-catalyzed condensation of aqueous solutions of glucose, a model monosaccharide, under plausible prebiotic conditions employing a wet-dry (night-day) protocol with 0.01M HCl at 50°C. This protocol leads to the formation of oligosaccharides containing up to eight monomeric units identified by high resolution mass spectrometry. The regio- and stereochemistry of the oligomeric acetal linkages, as well as the quantitative analysis of glucose conversion, are elucidated by combining 1H, 13C and 2D NMR spectroscopy. Ten out of eleven possible acetal linkages, including α- and β- anomers, have been identified with the α- and β- 1,6-acetals being the dominant linkages observed. In addition, the acid-catalyzed oligomerization of several glucose disaccharides such as cellobiose, maltose, and gentiobiose are presented along with an accompanying comparison with the corresponding oligomerization of glucose.

A Stark Contrast to Modern Earth: Phosphate Mineral Transformation and Nucleoside Phosphorylation in an Iron‐ and Cyanide‐Rich Early Earth Scenario

AbstractOrganophosphates were likely an important class of prebiotic molecules. However, their presence on the early Earth is strongly debated because the low availability of phosphate, which is generally assumed to have been sequestered in insoluble calcium and iron minerals, is widely viewed as a major barrier to organophosphate generation. Herein, we demonstrate that cyanide (an essential prebiotic precursor) and urea‐based solvents could promote nucleoside phosphorylation by transforming insoluble phosphate minerals in a “warm little pond” scenario into more soluble and reactive species. Our results suggest that cyanide and its derivatives (metal cyanide complexes, urea, ammonium formate, and formamide) were key reagents for the participation of phosphorus in chemical evolution. These results allow us to propose a holistic scenario in which an evaporitic environment could concentrate abiotically formed organics and transform the underlying minerals, allowing significant organic phosphorylation under plausible prebiotic conditions.

Nitrogen heterocycles form peptide nucleic acid precursors in complex prebiotic mixtures

The ability to store information is believed to have been crucial for the origin and evolution of life; however, little is known about the genetic polymers relevant to abiogenesis. Nitrogen heterocycles (N-heterocycles) are plausible components of such polymers as they may have been readily available on early Earth and are the means by which the extant genetic macromolecules RNA and DNA store information. Here, we report the reactivity of numerous N-heterocycles in highly complex mixtures, which were generated using a Miller-Urey spark discharge apparatus with either a reducing or neutral atmosphere, to investigate how N-heterocycles are modified under plausible prebiotic conditions. High throughput mass spectrometry was used to identify N-heterocycle adducts. Additionally, tandem mass spectrometry and nuclear magnetic resonance spectroscopy were used to elucidate reaction pathways for select reactions. Remarkably, we found that the majority of N-heterocycles, including the canonical nucleobases, gain short carbonyl side chains in our complex mixtures via a Strecker-like synthesis or Michael addition. These types of N-heterocycle adducts are subunits of the proposed RNA precursor, peptide nucleic acids (PNAs). The ease with which these carbonylated heterocycles form under both reducing and neutral atmospheres is suggestive that PNAs could be prebiotically feasible on early Earth.

Making Molecules with Clay: Layered Double Hydroxides, Pentopyranose Nucleic Acids and the Origin of Life.

A mixture of sugar diphosphates is produced in reactions between small aldehyde phosphates catalysed by layered double hydroxide (LDH) clays under plausibly prebiotic conditions. A subset of these, pentose diphosphates, constitute the backbone subunits of nucleic acids capable of base pairing, which is not the case for the other products of these LDH-catalysed reactions. Not only that, but to date no other polymer found capable of base pairing—and therefore information transfer—has a backbone for which its monomer subunits have a plausible prebiotic synthesis, including the ribose-5-phosphate backbone subunit of RNA. Pentose diphosphates comprise the backbone monomers of pentopyranose nucleic acids, some of the strongest base pairing systems so far discovered. We have previously proposed that the first base pairing interactions were between purine nucleobase precursors, and that these were weaker and less specific than standard purine-pyrimidine interactions. We now propose that the inherently stronger pairing of pentopyranose nucleic acids would have compensated for these weaker interactions, and produced an informational polymer capable of undergoing nonenzymatic replication. LDH clays might also have catalysed the synthesis of the purine nucleobase precursors, and the polymerization of pentopyranose nucleotide monomers into oligonucleotides, as well as the formation of the first lipid bilayers.

A one-pot, water compatible synthesis of pyrimidine nucleobases under plausible prebiotic conditions.

Herein, we report a new prebiotically plausible pathway towards a pyrimidine nucleobase in continuous manner. The route involves simultaneous methylation and carbamoylation of cyanoacetylene-derived α,β-unsaturated thioamide with N-methyl-N-nitrosourea (MNU) in aqueous media. This provides S-methylpyrimidinone in one-pot, which can be converted into a variety of 4-substituted pyrimidine nucleobases including cytosine and uracil.

PH-Driven RNA Strand Separation under Prebiotically Plausible Conditions

Replication of nucleic acids in the absence of genetically encoded enzymes represents a critical process for the emergence of cellular life. Repeated separation of complementary RNA strands is required to achieve multiple cycles of chemical replication, yet thermal denaturation under plausible prebiotic conditions is impaired by the high temperatures required to separate long RNA strands and by concurrent degradation pathways, the latter accelerated by divalent metal ions. Here we show how the melting temperature of oligoribonucleotide duplexes can be tuned by changes in pH, enabling the separation of RNA strands at moderate temperatures. At the same time, the risk of phosphodiester bond cleavage is reduced under the acid denaturation conditions herein described, both in the presence and in the absence of divalent metal ions. Through a combination of ultraviolet and circular dichroism thermal studies and gel electrophoresis, we demonstrate the relevance of geological pH oscillations in the context of the RNA strand separation problem. Our results reveal new insights in the field of prebiotic chemistry, supporting plausible geochemical scenarios in which non-enzymatic RNA replication might have taken place.

Synthesis of RNA Nucleotides in Plausible Prebiotic Conditions from ab Initio Computer Simulations

Understanding the mechanism of spontaneous formation of ribonucleotides under realistic prebiotic conditions is a key open issue of origins-of-life research. In cells, de novo and salvage nucleotide enzymatic synthesis combines 5-phospho-α-d-ribose-1-diphosphate (α-PRPP) and nucleobases. Interestingly, these reactants are also known as prebiotically plausible compounds. Combining ab initio molecular dynamics simulations with recently developed reaction exploration and enhanced sampling methods, we show that nucleobases and α-PRPP should spontaneously combine, under mild hydrothermal conditions, with an exothermic reaction and a facile mechanism, forming both purine and pyrimidine ribonucleotides. Surprisingly, this mechanism is very similar to the biological one and yields ribonucleotides with the same anomeric carbon chirality as in biological systems. Mass spectrometry experiments performed on solutions of adenine and PRPP in similar conditions support the formation of AMP. These results suggest that natural selection might have optimized, through enzymes, a pre-existing ribonucleotide formation mechanism, carrying it forward to modern life forms.