The origin of life-a review of facts and speculations

Three popular hypotheses attempt to explain the origin of prebiotic molecules: synthesis in a reducing atmosphere, input in meteorites and synthesis on metal sulfides in deep-sea vents. It is not possible to decide which is correct. It is also unclear whether the RNA world was the first biological world or whether some simpler world preceded it.     

Glyoxylate as a Backbone Linkage for a Prebiotic Ancestor of RNA

The origin of the first RNA polymers is central to most current theories for the origin of life. Difficulties associated with the prebiotic formation of RNA have lead to the general consensus that a simpler polymer preceded RNA. However, polymers proposed as possible ancestors to RNA are not much easier to synthesize than RNA itself. One particular problem with the prebiotic synthesis of RNA is the formation of phosphoester bonds in the absence of chemical activation. Here we demonstrate that glyoxylate (the ionized form of glyoxylic acid), a plausible prebiotic molecule, represents a possible ancestor of the phosphate group in modern RNA. Although in low yields (∼ 1%), acetals are formed from glyoxylate and nucleosides under neutral conditions, provided that metal ions are present (e.g., Mg²⁺), and provided that water is removed by evaporation at moderate temperatures (e.g., 65 ^∘C), i.e. under “drying conditions”. Such acetals are termed ga-dinucleotides and possess a linkage that is analogous to the backbone in RNA in both structure and electrostatic charge. Additionally, an energy-minimized model of a gaRNA duplex predicts a helical structure similar to that of A-form RNA. We propose that glyoxylate-acetal linkages would have had certain advantages over phosphate linkages for early self-replicating polymers, but that the distinct functional properties of phosphoester and phosphodiester bonds would have eventually lead to the replacement of glyoxylate by phosphate.     

Lipid-assisted Synthesis of RNA-like Polymers from Mononucleotides

A fundamental problem in research on the origin of life is the process by which polymers capable of catalysis and replication were produced on the early Earth. Here we show that RNA-like polymers can be synthesized non-enzymatically from mononucleotides in lipid environments. The RNA-like polymers were initially identified by nanopore analysis, a technique with single molecule sensitivity. To our knowledge, this is the first such application of a nanopore instrument to detect RNA synthesis under simulated prebiotic conditions. The synthesis of the RNA-like polymers was confirmed by standard methods of enzymatic end labeling followed by gel electrophoresis. Chemical activation of the mononucleotides is not required. Instead, synthesis of phosphodiester bonds is driven by the chemical potential of fluctuating anhydrous and hydrated conditions, with heat providing activation energy during dehydration. In the final hydration step, the RNA-like polymer is encapsulated within lipid vesicles. This process provides a laboratory model of an early stage of evolution toward an RNA World.     

N6-substituted adenine derivatives and RNA primitive catalysts

In our search for primitive RNA catalysts, we noticed that N6-ribosyl-adenine, a compound easily synthesized under presumed prebiotic conditions, has a free imidazole group. We showed that it is, as a catalyst, a potential analogue of histidine. Furthermore, among the chemical groups involved in protein catalysis, the imidazole ring of histidine has no equivalent in the RNA world. We have synthesized aliphatic amino groups containing polymers with adenine rings linked to macromolecules by their 6-amino group. These polymers exhibit pronounced catalytic activities in the hydrolysis of p-nitrophenylacetate. We discuss here the fact that in primitive catalysis the imidazole group could have been replaced by N6-substituted adenine derivatives.     

Native transfer RNA catalyzes Diels-Alder reaction

In this paper we show that transfer ribonucleic acids (tRNAs) catalyze the Diels-Alder cycloaddition reaction. A new DNA oxidative damage product, 6-furfuryladenine (kinetin) or its riboside (diene), was transformed with dimethyl acetylenedicarboxylate or maleic anhydride (dienophile). The reaction proceeds in the presence of tRNA at high pressure but not at ambient condition. If so tRNA in prebiotic conditions (RNA world) had at least two functions: catalytic and a carrier of genetic information. It means that tRNA at high pressure shows catalytic properties and is a true Diels-Alderase.     

The RNA dreamtime

Modern cells present no signs of a putative prebiotic RNA world. However, RNA coding is not a sine qua non for the accumulation of catalytic polypeptides. Thus, cellular proteins spontaneously fold into active structures that are resistant to proteolysis. The law of mass action suggests that binding domains are stabilized by specific interactions with their substrates. Random polypeptide synthesis in a prebiotic world has the potential to initially produce only a very small fraction of polypeptides that can fold spontaneously into catalytic domains. However, that fraction can be enriched by proteolytic activities that destroy the unfolded polypeptides and regenerate amino acids that can be recycled into polypeptides. In this open system scenario the stable domains that accumulate and the chemical environment in which they are accumulated are linked through self coding of polypeptide structure. Such open polypeptide systems may have been the precursors to the cellular ribonucleoprotein (RNP) world that evolved subsequently.     

A Model for the Origin of Life through Rearrangements among Prebiotic Phosphodiester Polymers

This model proposes that the origin of life on Earth occurred as a result of a process of alteration of the chemical composition of prebiotic macromolecules. The stability of organic compounds assembled into polymers generally exceeded the stability of the same compounds as free monomers. This difference in stability stimulated accumulation of prebiotic macromolecules. The prebiotic circulation of matter included constant formation and decomposition of polymers. Spontaneous chemical reactions between macromolecules with phosphodiester backbones resulted in a non-Darwinian selection for chemical stability, while formation of strong structures provided an advantage in the struggle for stability. Intermolecular structures between nucleotide-containing polymers were further stabilized by occasional acquisition of complementary nucleotides. Less stable macromolecules provided the source of nucleotides. This process resulted first in the enrichment of nucleotide content in prebiotic polymers, and subsequently in the accumulation of complementary oligonucleotides. Finally, the role of complementary copy molecules changed from the stabilization of the original templates to the de novo production of template-like molecules. I associate this stage with the origin of life in the form of cell-free molecular colonies. Original life acquired ready-to-use substrates from constantly forming prebiotic polymers. Metabolism started to develop when life began to consume more substrates than the prebiotic cycling produced. The developing utilization of non-polymeric compounds stimulated the formation of the first membrane-enveloped cells that held small soluble molecules. Cells “digested” the nucleotide-containing prebiotic macromolecules to nucleotide monomers and switched the mode of replication to the polymerization of nucleotide triphosphates.     

An Interpretive Review of the Origin of Life Research

Life appears to be a natural property of matter, but the problem of its origin only arose after early scientists refuted continuous spontaneous generation. There is no chance of life arising ‘all at once’, we need the standard scientific incremental explanation with large numbers of small steps, an approach used in both physical and evolutionary sciences. The necessity for considering both theoretical and experimental approaches is emphasized. After describing basic principles that are available (including the Darwin-Eigen cycle), the search for origins is considered under four main themes. These are the RNA-world hypothesis; potential intermediates between an RNA-world and a modern world via the evolution of protein synthesis and then of DNA; possible alternatives to an RNA-world; and finally the earliest stages from the simple prebiotic systems to RNA. The triplicase/proto-ribosome theory for the origin of the ribosome is discussed where triples of nucleotides are added to a replicating RNA, with the origin of a triplet code well-before protein synthesis begins. The length of the code is suggested to arise from the early development of a ratchet mechanism that overcomes the problem of continued processivity of an RNA-based RNA-polymerase. It is probable that there were precursor stages to RNA with simpler sugars, or just two nucleotides, but we do not yet know of any better alternatives to RNA that were likely to arise naturally. For prebiotic stages (before RNA) a flow-reactor model is suggested to solve metabolism, energy gradients, and compartmentation simultaneously – thus the intense interest in some form of flow reactor. If an autocatalytic cycle could arise in such a system we would be major steps ahead. The most likely physical conditions for the origin of life require further clarification and it is still unclear whether the origin of life is more of an entropy (information) problem (and therefore high temperatures would be detrimental), rather than a kinetic problem (where high temperatures may be advantageous).     

A possible circular RNA at the origin of life

The increasing volume of sequenced genomes and the recent techniques for performing in vitro molecular evolution have rekindled the interest for questions on the origin of life. Nevertheless, a gap continues to exist between the research on prebiotic chemistry and molecule generation, on one hand, and the study of molecular fossils preserved in genomes, on the other. Here we attempt to fill this gap by using some assumptions about the prebiotic scenario (including a strong stereochemical basis for the genetic code) to determine the RNA sequences more likely to appear and subsist. A set of minimal RNA rings is exhaustively determined; a subset of them is then selected through stability arguments, and a particular ring ("AL ring") is finally singled out as the most likely winner of this prebiotic game. The rings happen to have several structural and statistical properties of modern genes: a repeated AUG codon appears spontaneously (and is thus made available for becoming a start signal), the form AUG/STOP emerges, and frequency patterns resemble those of present genes. The whole set of rings was also compared to a database of tRNAs, considering the conserved positions (located in the free parts of the molecule, essentially the loops); the ring that most closely matched tRNA sequences-and matched, in fact, the consensus of tRNA at all the aligned positions-was AL, the same ring independently selected before. The unselected emergence of gene-like features through two simple selection steps and the close similarity between the finally selected ring and tRNA (including some remarkable features of the resulting alignment) suggest a possible link between the prebiotic world and the first biological molecules, which is amenable for experimental testing. Even if our scenario is partially wrong, the unlikely coincidences should provide useful hints for other efforts.     

How long did it take for life to begin and evolve to cyanobacteria?

There is convincing paleontological evidence showing that stromatolite-building phototactic prokaryotes were already in existence 3.5 × 10⁹ years ago. Late accretion impacts may have killed off life on our planet as late as 3.8 × 10⁹ years ago. This leaves only 300 million years to go from the prebiotic soup to the RNA world and to cyanobacteria. However, 300 million years should be more than sufficient time. All known prebiotic reactions take place in geologically rapid time scales, and very slow prebiotic reactions are not feasible because the intermediate compounds would have been destroyed due to the passage of the entire ocean through deep-sea vents every 10⁷ years or in even less time. Therefore, it is likely that self-replicating systems capable of undergoing Darwinian evolution emerged in a period shorter than the destruction rates of its components (<5 million years). The time for evolution from the first DNA/protein organisms to cyanobacteria is usually thought to be very long. However, the similarities of many enzymatic reactions, together with the analysis of the available sequence data, suggest that a significant number of the components involved in basic biological processes are the result of ancient gene duplication events. Assuming that the rate of gene duplication of ancient prokaryotes was comparable to today's present values, the development of a filamentous cyanobacterial-like genome would require approximately 7 × 10⁶ years—or perhaps much less. Thus, in spite of the many uncertainties involved in the estimates of time for life to arise and evolve to cyanobacteria, we see no compelling reason to assume that this process, from the beginning of the primitive soup to cyanobacteria, took more than 10 million years.Correspondence to: A. Lazcano     

Purine Biosynthetic Intermediate-Containing Ribose-Phosphate Polymers as Evolutionary Precursors to RNA

The RNA world hypothesis proposes that RNA once functioned as the principal genetic material and biological catalyst. However, RNA is a complex molecule made up of phosphate, ribose, and nucleobase moieties, and its evolution is unclear. Yakhnin has proposed a period of prebiotic chemical evolution prior to the advent of replication and Darwinian evolution, in which macromolecules containing polyols joined by phosphodiester linkages underwent spontaneous transesterification reactions with selection for stability. Although he proposes that the nucleobases were obtained during this stage from less stable macromolecules, the ultimate source of the nucleobases is not addressed. We propose that the purine nucleobases arose in situ from simpler precursors attached to a ribose-phosphate backbone, and that the weaker and less specific intra- and interstrand interactions between these precursors were the forerunners to the base pairing and base stacking interactions of the modern RNA nucleobases. Further, in line with Granick’s hypothesis of biosynthetic pathways recapitulating evolution, we propose that these simpler precursors were the same or similar to intermediates of the modern de novo purine biosynthetic pathway. We propose that successive nucleobase precursors formed progressively stronger interactions that stabilized the ribose-phosphate polymer, and that the increased stability of the parent polymer drove the selection and further chemical evolution of the purine nucleobases. Such interactions may have included hydrogen bonding between ribose hydroxyls, hydrogen bonding between carbonyl oxygens and protonated amine side groups, the intra- and interstrand coordination of metal cations, and the stacking of imidazole rings. Five of the eleven steps of the modern de novo purine biosynthetic pathway have previously been shown to have alternative nonenzymatic syntheses, while a sixth step has also been proposed to occur nonenzymatically, supporting a prebiotic origin for the pathway.     

Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor

Extensive fundamental molecular and biological evolution took place between the prebiotic origins of life and the state of the Last Universal Common Ancestor (LUCA). Considering the evolutionary innovations between these two endpoints from the perspective of environmental adaptation, we explore the hypothesis that LUCA was temporally, spatially, and environmentally distinct from life’s earliest origins in an RNA world. Using this lens, we interpret several molecular biological features as indicating an environmental transition between a cold, radiation-shielded origin of life and a mesophilic, surface-dwelling LUCA. Cellularity provides motility and permits Darwinian evolution by connecting genetic material and its products, and thus establishing heredity and lineage. Considering the importance of compartmentalization and motility, we propose that the early emergence of cellularity is required for environmental dispersal and diversification during these transitions. Early diversification and the emergence of ecology before LUCA could be an important pre-adaptation for life’s persistence on a changing planet.     

Addressing the problems of base pairing and strand cyclization in template-directed synthesis: a case for the utility and necessity of 'molecular midwives' and reversible backbone linkages for the origin of proto-RNA

Nucleic acid synthesis is precisely controlled in living organisms by highly evolved protein enzymes. The remarkable fidelity of information transfer realized between template and product strands is the result of both the spatial selectivity of the polymerase active site for Watson-Crick base pairs at the point of nucleotide coupling and subsequent proof-reading mechanisms. In the absence of naturally derived polymerases, in vitro template-directed synthesis by means of chemically activated mononucleotides has proven remarkably inefficient and error-prone. Nevertheless, the spontaneous emergence of RNA polymers and their protein-free replication is frequently taken as a prerequisite for the hypothetical 'RNA world'. We present two specific difficulties that face the de novo synthesis of RNA-like polymers in a prebiotic (enzyme-free) environment: nucleoside base selection and intramolecular strand cyclization. These two problems are inherent to the assumption that RNA formed de novo from pre-existing, chemically-activated mononucleotides in solution. As a possible resolution to these problems, we present arguments and experimental support for our hypothesis that small molecules (referred to as 'molecular midwives') and alternative backbone linkages (under equilibrium control) facilitated the emergence of the first RNA-like polymers of life.     

The RNA worlds in context

There are two RNA worlds. The first is the primordial RNA world, a hypothetical era when RNA served as both information and function, both genotype and phenotype. The second RNA world is that of today's biological systems, where RNA plays active roles in catalyzing biochemical reactions, in translating mRNA into proteins, in regulating gene expression, and in the constant battle between infectious agents trying to subvert host defense systems and host cells protecting themselves from infection. This second RNA world is not at all hypothetical, and although we do not have all the answers about how it works, we have the tools to continue our interrogation of this world and refine our understanding. The fun comes when we try to use our secure knowledge of the modern RNA world to infer what the primordial RNA world might have looked like.     

Synthesis, characterization and hybridization studies of new nucleo-gamma-peptides based on diaminobutyric acid.

In the present work, we report the synthesis and the characterization of a new chiral nucleoaminoacid, in which a diaminobutyric moiety is connected to the DNA nucleobase by an amidic bond, and its oligomerization to give the corresponding nucleo-gamma-peptide. The ability of this synthetic polymer to bind complementary DNA was studied in order to explore its possible use in antigene/antisense or diagnostic applications. Our interest in the presented DNA analogue was also supported by the importance of gamma-aminoacid-containing compounds in natural products of biological activity and by the known stability of gamma-peptides to enzymatic degradation. Furthermore, our work could contribute to the study of the role of nucleopeptides as prebiotic material in a PNA world that could successively lead to the actual DNA/RNA/protein world, as recently assumed.     

Detection of Macromolecular Fractions in HCN Polymers Using Electrophoretic and Ultrafiltration Techniques

Elucidating the origin of life involves synthetic as well as analytical challenges. Herein, for the first time, we describe the use of gel electrophoresis and ultrafiltration to fractionate HCN polymers. Since the first prebiotic synthesis of adenine by Oró, HCN polymers have gained much interest in studies on the origins of life due to the identification of biomonomers and related compounds within them. Here, we demonstrate that macromolecular fractions with electrophoretic mobility can also be detected within HCN polymers. The migration of polymers under the influence of an electric field depends not only on their sizes (one‐dimensional electrophoresis) but also their different isoelectric points (two‐dimensional electrophoresis, 2‐DE). The same behaviour was observed for several macromolecular fractions detected in HCN polymers. Macromolecular fractions with apparent molecular weights as high as 250 kDa were detected by tricine‐SDS gel electrophoresis. Cationic macromolecular fractions with apparent molecular weights as high as 140 kDa were also detected by 2‐DE. The HCN polymers synthesized were fractionated by ultrafiltration. As a result, the molecular weight distributions of the macromolecular fractions detected in the HCN polymers directly depended on the synthetic conditions used to produce these polymers. The implications of these results for prebiotic chemistry will be discussed.     

A vestige of a prebiotic bonding machine is functioning within the contemporary ribosome

Based on the presumed capability of a prebiotic pocket-like entity to accommodate substrates whose stereochemistry enables the creation of chemical bonds, it is suggested that a universal symmetrical region identified within all contemporary ribosomes originated from an entity that we term the 'proto-ribosome'. This 'proto-ribosome' could have evolved from an earlier machine that was capable of performing essential tasks in the RNA world, called here the 'pre-proto-ribosome', which was adapted for producing proteins.     

15 Combinatorial chemistry in the prebiotic environment

The pathway leading to the origin of life presumably included a process by which polymers were synthesized abiotically from simpler compounds on the early Earth, then encapsulated to form protocells. Previous studies have reported that mineral surfaces can concentrate and organize activated mononucleotides, thereby promoting their polymerization into RNA-like molecules. However, a plausible prebiotic activation mechanism has not been established, and minerals cannot form cellular compartments. We are exploring ways in which nonactivated mononucleotides can undergo polymerization and encapsulation. We found that small yields of RNA-like molecules are synthesized by a condensation reaction when mixtures of amphiphilic lipids and mononucleotides are exposed to cycles of dehydration and rehydration. The lipids concentrate and organize the monomers within multilamellar liquid-crystalline matrices that self-assemble in the dry state. The chemical potential driving the polymerization reaction is supplied by the anhydrous conditions in which water becomes a leaving group, with heat providing activation energy. Significantly, the polymeric products are encapsulated in trillions of microscopic compartments upon rehydration. Each compartment is unique in its composition and contents, and can be considered to be an experiment in a natural version of combinatorial chemistry that would be ubiquitous in the prebiotic environment. A successful experiment would be a compartment that captured polymers capable of catalyzing their own replication. If this can be reproduced in the laboratory, it would represent a significant step toward understanding the origin of cellular life.