A Prebiotic Synthesis of Canonical Pyrimidine and Purine Ribonucleotides

Intellectual frameworks to understand complex biochemical systems at the origin of life

Understanding the emergence of complex biochemical systems, such as protein translation, is a great challenge. Although synthetic approaches can provide insight into the potential early stages of life, they do not address the equally important question of why the complex systems of life would have evolved. In particular, the intricacies of the mechanisms governing the transfer of information from nucleic acid sequences to proteins make it difficult to imagine how coded protein synthesis could have emerged from a prebiotic soup. Here we discuss the use of intellectual frameworks in studying the emergence of life. We discuss how one such framework, namely the RNA world theory, has spurred research, and provide an overview of its limitations. We suggest that the emergence of coded protein synthesis could be broken into experimentally tractable problems by treating it as a molecular bricolage-a complex system integrating many different parts, each of which originally evolved for uses unrelated to its modern function-to promote a concrete understanding of its origin.

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.

Abiotic Ribose Synthesis Under Aqueous Environments with Various Chemical Conditions

Ribose is the defining sugar in ribonucleic acid (RNA), which is often proposed to have carried the genetic information and catalyzed the biological reactions of the first life on Earth. Thus, abiological processes that yield ribose under prebiotic conditions have been studied for decades. However, aqueous environments required for the formation of ribose from materials available in quantity under geologically reasonable models, where the ribose formed is not immediately destroyed, remain unclear. This is due in large part to the challenge of analysis of carbohydrates formed under a wide range of aqueous conditions. Thus, the formation of ribose on prebiotic Earth has sometimes been questioned. We investigated the quantitative effects of pH, temperature, cation, and the concentrations of formaldehyde and glycolaldehyde on the synthesis of diverse sugars, including ribose. The results suggest a range of conditions that produce ribose and that ribose could have formed in constrained aquifers on prebiotic Earth.

Origin of life: Drawing the big picture

Trying to provide a broad overview about the origin of life in Earth, the most significant transitions of life before cells are listed and discussed. The current approach emphasizes the symbiotic relationships that emerged with life. We propose a rational, stepwise scenario for the origin of life that starts with the origin of the first biomolecules and steps forward until the origins of the first cells. Along this path, we aim to provide a brief, though comprehensive theoretical model that will consider the following steps: (i) how nucleotides and other biomolecules could be made prebiotically in specific prebiotic refuges; (ii) how the first molecules of RNAs were formed; (iii) how the proto-peptidyl transferase center was built by the concatenation of proto-tRNAs; (iv) how the ribosome and the genetic code could be structured; (v) how progenotes could live and reproduce as "naked" ribonucleoprotein molecules; (vi) how peptides started to bind molecules in the prebiotic soup allowing biochemical pathways to evolve from those bindings; (vii) how genomes got bigger by the symbiotic relationship of progenotes and lateral transference of genetic material; (viii) how the progenote LUCA has been formed by assembling most biochemical routes; (ix) how the first virion capsids probably emerged and evolved; (x) how phospholipid membranes emerged probably twice by the evolution of lipid-binding proteins; (xi) how DNA synthesis have been formed in parallel in Bacteria and Archaea; and, finally, (xii) how DNA-based cells of Bacteria and Archaeabacteria have been constituted. The picture provided is conjectural and present epistemological gaps. Future research will help to advance into the elucidation of gaps and confirmation/refutation of current statements.

Prebiotic Synthesis of ATP: A Terrestrial Volcanism-Dependent Pathway

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

How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active

The modern ribosome catalyzes all coded protein synthesis in extant organisms. It is likely that its core structure is a direct descendant from the ribosome present in the last common ancestor (LCA). Hence, its earliest origins likely predate the LCA and therefore date further back in time. Of special interest is the pseudosymmetrical region (SymR) that lies deep within the large subunit (LSU) where the peptidyl transfer reaction takes place. It was previously proposed that two RNA oligomers, representing the P- and A-regions of extant ribosomes dimerized to create a pore-like structure, which hosted the necessary properties that facilitate peptide bond formation. However, recent experimental studies show that this may not be the case. Instead, several RNA constructs derived exclusively from the P-region were shown to form a homodimer capable of peptide bond synthesis. Of special interest will be the origin issues because the homodimer would have allowed a pre-LCA ribosome that was significantly smaller than previously proposed. For the A-region, the immediate issue will likely be its origin and whether it enhances ribosome performance. Here, we reanalyze the RNA/RNA interaction regions that most likely lead to SymR formation in light of these recent findings. Further, it has been suggested that the ability of these RNA constructs to dimerize and enhance peptide bond formation is sequence-dependent. We have analyzed the implications of sequence variations as parts of functional and nonfunctional constructs.

Rethinking nucleic acids from their origins to their applications

Reviewed are three decades of synthetic biology research in our laboratory that has generated alternatives to standard DNA and RNA as possible informational systems to support Darwinian evolution, and therefore life, and to understand their natural history, on Earth and throughout the cosmos. From this, we have learned that: • the core structure of nucleic acids appears to be a natural outcome of non-biological chemical processes probably in constrained, intermittently irrigated, sub-aerial aquifers on the surfaces of rocky planets like Earth and/or Mars approximately 4.36 ± 0.05 billion years ago; • however, this core is not unique. Synthetic biology has generated many different molecular systems able to support the evolution of molecular information; • these alternatives to standard DNA and RNA support biotechnology, including DNA synthesis, human diagnostics, biomedical research and medicine; • in particular, they support laboratory in vitro evolution (LIVE) with performance to generate catalysts at least 104-105 fold better than standard DNA libraries, enhancing access to receptors and catalysts on demand. Coupling nanostructures to the products of LIVE with expanded DNA offers new approaches for disease therapy; and • nevertheless, a polyelectrolyte structure and size regular building blocks are required for any informational polymer to support Darwinian evolution. These features serve as universal and agnostic biosignatures, useful for seeking life throughout the Solar System. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.

Azoles as Auxiliaries and Intermediates in Prebiotic Nucleoside Synthesis

4,5-Dicyanoimidazole and 2-aminothiazole are azoles that have previously been implicated in prebiotic nucleotide synthesis. The former compound is a byproduct of adenine synthesis, and the latter compound has been shown to be capable of separating C₂ and C₃ sugars via crystallization as their aminals. We now report that the elusive intermediate cyanoacetylene can be captured by 4,5-dicyanoimidazole and accumulated as the crystalline compound N-cyanovinyl-4,5-dicyanoimidazole, thus providing a solution to the problem of concentration of atmospherically formed cyanoacetylene. Importantly, this intermediate is a competent cyanoacetylene surrogate, reacting with ribo-aminooxazoline in formamide to give ribo-anhydrocytidine ─ an intermediate in the divergent synthesis of purine and pyrimidine nucleotides. We also report a prebiotically plausible synthesis of 2-aminothiazole and examine the mechanism of its formation. The utilization of each of these azoles enhances the prebiotic synthesis of ribonucleotides, while their syntheses comport with the cyanosulfidic scenario we have previously described.

Prebiotic chemical refugia: multifaceted scenario for the formation of biomolecules in primitive Earth

The origin of life was a cosmic event happened on primitive Earth. A critical problem to better understand the origins of life in Earth is the search for chemical scenarios on which the basic building blocks of biological molecules could be produced. Classic works in pre-biotic chemistry frequently considered early Earth as an homogeneous atmosphere constituted by chemical elements such as methane (CH₄), ammonia (NH₃), water (H₂O), hydrogen (H₂) and hydrogen sulfide (H₂S). Under that scenario, Stanley Miller was capable to produce amino acids and solved the question about the abiotic origin of proteins. Conversely, the origin of nucleic acids has tricked scientists for decades once nucleotides are complex, though necessary molecules to allow the existence of life. Here we review possible chemical scenarios that allowed not only the formation of nucleotides but also other significant biomolecules. We aim to provide a theoretical solution for the origin of biomolecules at specific sites named "Prebiotic Chemical Refugia." Prebiotic chemical refugium should therefore be understood as a geographic site in prebiotic Earth on which certain chemical elements were accumulated in higher proportion than expected, facilitating the production of basic building blocks for biomolecules. This higher proportion should not be understood as static, but dynamic; once the physicochemical conditions of our planet changed periodically. These different concentration of elements, together with geochemical and astronomical changes along days, synodic months and years provided somewhat periodic changes in temperature, pressure, electromagnetic fields, and conditions of humidity, among other features. Recent and classic works suggesting most likely prebiotic refugia on which the main building blocks for biological molecules might be accumulated are reviewed and discussed.

Borate-guided ribose phosphorylation for prebiotic nucleotide synthesis

Polymers of ribonucleotides (RNAs) are considered to store genetic information and promote biocatalytic reactions for the proto life on chemical evolution. Abiotic synthesis of ribonucleotide was successful in past experiments; nucleoside synthesis occurred first, followed by phosphorylation. These abiotic syntheses are far from biotic reactions and have difficulties as a prebiotic reaction in reacting chemicals in a specific order and purifying intermediates from other molecules in multi-steps of reactions. Another reaction, ribose phosphorylation followed by nucleobase synthesis or nucleobase addition, is close to the biotic reactions of nucleotide synthesis. However, the synthesis of ribose 5′-phosphate under prebiotically plausible conditions remains unclear. Here, we report a high-yield regioselective one-pot synthesis of ribose 5′-phosphate from an aqueous solution containing ribose, phosphate, urea, and borate by simple thermal evaporation. Of note, phosphorylation of ribose before the nucleoside formation differs from the traditional prebiotic nucleotide syntheses and is also consistent with biological nucleotide synthesis. Phosphorylation occurred to the greatest extent in ribose compared to other aldopentoses, only in the presence of borate. Borate is known to improve the stability of ribose preferentially. Geological evidence suggests the presence of borate-rich settings on the early Earth. Therefore, borate-rich evaporitic environments could have facilitated preferential synthesis of ribonucleotide coupled with enhanced stability of ribose on the early Earth.

On the prebiotic selection of nucleotide anomers: A computational study

Present-day known predominance of the β- over the α-anomers in nucleosides and nucleotides emerges from a thermodynamic analysis of their assembly from their components, i.e. bases, sugars, and a phosphate group. Furthermore, the incorporation of uracil into RNA and thymine into DNA rather than the other way around is also predicted from the calculations. An interplay of kinetics and thermodynamics must have driven evolutionary selection of life's building blocks. In this work, based on quantum chemical calculations, we focus on the latter control as a tool for “natural selection”.

Catalytic Synthesis of Polyribonucleic Acid on Prebiotic Rock Glasses

Reported here are experiments that show that ribonucleoside triphosphates are converted to polyribonucleic acid when incubated with rock glasses similar to those likely present 4.3-4.4 billion years ago on the Hadean Earth surface, where they were formed by impacts and volcanism. This polyribonucleic acid averages 100-300 nucleotides in length, with a substantial fraction of 3',-5'-dinucleotide linkages. Chemical analyses, including classical methods that were used to prove the structure of natural RNA, establish a polyribonucleic acid structure for these products. The polyribonucleic acid accumulated and was stable for months, with a synthesis rate of 2 × 10^-3 pmoles of triphosphate polymerized each hour per gram of glass (25°C, pH 7.5). These results suggest that polyribonucleotides were available to Hadean environments if triphosphates were. As many proposals are emerging describing how triphosphates might have been made on the Hadean Earth, the process observed here offers an important missing step in models for the prebiotic synthesis of RNA.

Diamidophosphate (DAP): A Plausible Prebiotic Phosphorylating Reagent with a Chem to BioChem Potential?

Known since the 1890s, diamidophosphate (DAP) has been investigated within the context of its inorganic chemistry. In 1999 - with the demonstration of DAP's potential as a phosphorylating agent of sugars in aqueous medium - began the exciting phase of research about DAP's role as a plausible prebiotic phosphorylating agent. More recently, in the last five years, there has been a steady increase in the publications that have documented the surprising versatility of DAP enabling the emergence of many classes of biomolecules of life, such as nucleic acids, peptides and protocells. Thus, though in its infancy, DAP seems to be uniquely positioned to play a central role in modelling abiotic- to prebiotic-chemical evolution. In this context, there is a need for systematic investigations for: (a) establishing DAP's likely availability on the early Earth, and (b) developing DAP's potential as a tool for use in synthetic and bioorganic chemistry.

Abiotic Synthesis of Nucleoside 5'-Triphosphates with Nickel Borate and Cyclic Trimetaphosphate (CTMP)

While nucleoside 5'-triphosphates are precursors for RNA in modern biology, the presumed difficulty of making these triphosphates on Hadean Earth has caused many prebiotic researchers to consider other activated species for the prebiotic synthesis of RNA. We report here that nickel(II), in the presence of borate, gives substantial amounts (2-3%) of nucleoside 5'-triphosphates upon evaporative heating in the presence of urea, salts, and cyclic trimetaphosphate (CTMP). Also recovered are nucleoside 5'-diphosphates and nucleoside 5'-monophosphates, both likely arising from 5'-triphosphate intermediates. The total level of 5'-phosphorylation is typically 30%. Borate enhances the regiospecificity of phosphorylation, with increased amounts of other phosphorylated species seen in its absence. Experimentally supported paths are already available to make nucleosides in environments likely to have been present on Hadean Earth soon after a midsized 10²¹ to 10²³ kg impactor, which would also have delivered nickel to the Hadean surface. Further, sources of prebiotic CTMP continue to be proposed. Thus, these results fill in one of the few remaining steps needed to demystify the prebiotic synthesis of RNA and support a continuous model from atmospheric components to oligomeric RNA that is lacking only a mechanism to obtain homochirality in the product RNA.

Chemistry of Abiotic Nucleotide Synthesis

The chemistry of abiotic nucleotide synthesis of RNA and DNA in the context of their prebiotic origins on early earth is a continuing challenge. How did (or how can) the nucleotides form and assemble from the small molecule inventories and under conditions that prevailed on early earth 3.5-4 billion years ago? This review provides a background and up-to-date progress that will allow the reader to judge where the field stands currently and what remains to be achieved. We start with a brief primer on the biological synthesis of nucleotides, followed by an extensive focus on the prebiotic formation of the components of nucleotides-either via the synthesis of ribose and the canonical nucleobases and then joining them together or by building both the conjoined sugar and nucleobase, part-by-part-toward the ultimate goal of forming RNA and DNA by polymerization. The review will emphasize that there are-and will continue to be-many more questions than answers from the synthetic, mechanistic, and analytical perspectives. We wrap up the review with a cautionary note in this context about coming to conclusions as to whether the problem of chemistry of prebiotic nucleotide synthesis has been solved.

Prebiotic Chemistry that Could Not Not Have Happened

We present a direct route by which RNA might have emerged in the Hadean from a fayalite–magnetite mantle, volcanic SO₂ gas, and well-accepted processes that must have created substantial amounts of HCHO and catalytic amounts of glycolaldehyde in the Hadean atmosphere. In chemistry that could not not have happened, these would have generated stable bisulfite addition products that must have rained to the surface, where they unavoidably would have slowly released reactive species that generated higher carbohydrates. The formation of higher carbohydrates is self-limited by bisulfite formation, while borate minerals may have controlled aldol reactions that occurred on any semi-arid surface to capture that precipitation. All of these processes have well-studied laboratory correlates. Further, any semi-arid land with phosphate should have had phosphate anhydrides that, with NH₃, gave carbohydrate derivatives that directly react with nucleobases to form the canonical nucleosides. These are phosphorylated by magnesium borophosphate minerals (e.g., lüneburgite) and/or trimetaphosphate-borate with Ni²⁺ catalysis to give nucleoside 5′-diphosphates, which oligomerize to RNA via a variety of mechanisms. The reduced precursors that are required to form the nucleobases came, in this path-hypothesis, from one or more mid-sized (10²³–10²⁰ kg) impactors that almost certainly arrived after the Moon-forming event. Their iron metal content almost certainly generated ammonia, nucleobase precursors, and other reduced species in the Hadean atmosphere after it transiently placed the atmosphere out of redox equilibrium with the mantle. In addition to the inevitability of steps in this path-hypothesis on a Hadean Earth if it had semi-arid land, these processes may also have occurred on Mars. Adapted from a lecture by the Corresponding Author at the All-Russia Science Festival at the Lomonosov Moscow State University on 12 October 2019, and is an outcome of a three year project supported by the John Templeton Foundation and the NASA Astrobiology program. Dedicated to David Deamer, on the occasion of his 80th Birthday.