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PubMedDate not supplied

Abiotic synthesis of organic compounds under the conditions of submarine hydrothermal systems: a perspective.

Deep-sea hydrothermal systems have been proposed to be likely environments for chemical evolution and the origin of life on Earth. Recently, experiments have, therefore, been carried out in order to test the hypothesis that amino acids can be synthesized under conditions representing hydrothermally altered oceanic crust. The variety of amino acids that have been detected in such experiments corresponds roughly to that reported previously for electric sparking in reducing gas mixtures. The relative yields of the protein amino acids detected are significantly higher than in electric spark discharge experiments, and the overall yields are about an order of magnitude higher. The amino acids are all racemic.

Amino Acids↗

PubMed1992

Oligomerization of ribonucleotides on montmorillonite: reaction of the 5'-phosphorimidazolide of adenosine.

The regiospecific formation of oligomers from unblocked monomers in aqueous solution is one of the central tenets in research on the origins of life on earth. Direct experimental support for this hypothesis has been obtained in studies of the condensation of the 5'-phosphorimidazolide of adenosine (ImpA) with itself and with P1,P2-diadenosine-5',5'-pyrophosphate (AppA) in water in the presence of a montmorillonite clay. Oligomers of up to ten nucleotides in length are formed. Analysis of the trimers, tetramers, and pentamers formed from a 9:1 ImpA:AppA mixture has shown that 85% of the bonds formed are 3',5'-linked and that any 2',5'-linkages present are at the phosphodiester bond next to the 3'-terminus of the oligomers.

Adenosine Monophosphate↗

PubMed2004

Detecting autocatalytic, self-sustaining sets in chemical reaction systems.

The ability of systems of molecular reactions to be simultaneously autocatalylic and sustained by some ambient 'food source' of simple molecules may have been an essential step in the origin of life. In this paper we first describe a polynomial-time algorithm that determines whether any given set of molecules, reactions and catalysations contains a subsystem that is both autocatalytic and able to be sustained from a given subset of the molecules. We also describe some combinatorial properties of this algorithm, and show how it can be used to find irreducible auto-catalysing and sustaining subsystems. In the second part of the paper we use the algorithm to investigate random catalytic networks-in particular, a model described by Kauffman. Using simulations and some analytic techniques we investigate the rate of catalysis that is required for the emergence of autocatalytic and sustaining subsystems.

Algorithms↗

PubMed2003

Photoelectrochemical power, chemical energy and catalytic activity for organic evolution on natural pyrite interfaces.

Natural pyrite (FeS2) has frequently been discussed as a material involved in CO2 fixation in presence of H2S and as a possible catalyst for the origin of life. A straightforward chemical fixation of carbon dioxide as proposed by Wächtershauser could not be verified from thermo-chemical equilibrium calculations by minimizing Gibb's Free Energy in the system C, O, H, S, Fe and appears unlikely due to the experimentally encountered large overpotentials involved in CO2 fixation. However, the hypothesis, by W. R. Edwards, that pyrite in shallow coastal waters may have been involved, can be sustained. In this case, daily available photoelectrochemical power from FeS2/Fe2+/3+ interfaces could have made the difference in combination with electrochemical processes, such as hydrogen insertion, and the solubilization of pyrite by the amino acid cysteine to yield dissolved chemical energy. Periodical changes in energy supply could also have entrained primitive self-organization processes for organic-biological evolution. Natural samples from thirteen ore deposits have been investigated photoelectrochemically. Efficient light-induced current generation has been found with several of these samples so that photoelectrochemical processes generated by pyrite have to be considered as naturally occurring phenomena, which could have been even more pronounced in oxygen deficient environments. Pyrite from the Murgul mine in Turkey of suboceanic volcanic origin was closer examined as a model system to understand the morphology and chemistry of pyrite photoactivity.

Carbon Dioxide↗

PubMed1998

Self-replicating structures: evolution, emergence and computation.

Since von Neumann's seminal work around 1950, computer scientists and others have studied the algorithms needed to support self-replicating systems. Much of this work has focused on abstract logical machines (automata) embedded in two-dimensional cellular spaces. This research was motivated by a desire to understand the basic information-processing principles underlying self-replication, the potential long-term applications of programmable self-replicating machines, and the possibility of gaining insight into biological replication and the origins of life. We view past research as taking three main directions: early complex universal computer-constructors modeled after Turing machines, qualitatively simpler self-replicating loops, and efforts to view self-replication as an emergent phenomenon. We discuss our recent studies in the latter category showing that self-replicating structures can emerge from nonreplicating components, and that genetic algorithms can be applied to program automatically simple but arbitrary structures to replicate. We also describe recent work in which self-replicating structures are successfully programmed to do useful problem solving as they replicate. We conclude by identifying some implications and important research directions for the future.

Algorithms↗

PubMed2006

Hydrothermal reactions of pyruvic acid: synthesis, selection, and self-assembly of amphiphilic molecules.

Selection and self-assembly of organic compounds in aqueous phases must have been a primary process leading to emergent molecular complexity and ultimately to the origin of life. Facile reactions of pyruvic acid under hydrothermal conditions produce a complex mixture of larger organic molecules, some of which are amphiphiles that readily self-assemble into cell-sized vesicular structures. Chemical characterization of major components of this mixture reveals similarities to the suite of organic compounds present in the Murchison carbonaceous chondrite, some of whose molecules also self-assemble into membranous vesicles. Physical properties of the products are thus relevant to understanding the prebiotic emergence of molecular complexity. These results suggest that a robust family of prebiotic reaction pathways produces similar products over a range of geochemical and astrochemical environments.

Catalysis↗

PubMed1985

Template-directed synthesis of novel, nucleic acid-like structures.

In studying the origins of life, it is important to examine reactions of substrate mixtures that could plausibly have accumulated on the primitive earth. Nucleoside diphosphates would probably have been synthesized along with the standard nucleotides under prebiotic conditions. For these reasons, the template-directed reactions of activated derivatives of these diphosphates, alone or mixed with activated nucleotides, were investigated. An activated derivative of deoxyguanosine 3',5'-diphosphate condensed efficiently on a polycytidylate template to give oligonucleotide analogues in which each 3',5'-phosphodiester bond was replaced by a pyrophosphate linkage. Oligomers were formed even in the absence of a template, but much more slowly. Template-directed condensation occurred also with an analogous deoxyadenosine derivative on polyuridylic acid and with an analogous acycloguanosine derivative on polycytidylic acid.

Cytosine↗

PubMed2003

Possible origin of a membrane in the subsurface of the Earth.

A location for the origin of life on Earth could have been an oil/water interface in the warm, subsurface environment of the Earth. The physico-chemical conditions of the subsurface would include elevated, but eventually cooling temperatures, anaerobic conditions, and protection from intense surface radiation. This type of subsurface oil/water environment may have been ideal for the assembly of the first simple membrane(s), where no enzyme catalysis was needed. Once a stable, simple, continuous closed membrane was formed, one central component of the first cell(s) would have been present; a semi-permeable open system that allowed the passage of both matter and energy in and out of the cell. Such an open system could also acquire novel functions, whereas a closed system would be unable to evolve.

Cell Membrane↗

PubMed1995

A plausibly prebiotic synthesis of phosphonic acids.

The insolubility of calcium phosphate in water is a significant stumbling block in the chemistry required for the origin of life. The discovery of alkyl phosphonic acids in the Murchison meteorite suggests the possibility of delivery of these water-soluble, phosphorus-containing molecules by meteorites or comets to the early Earth. This could have provided a supply of organic phosphorus for the earliest stages of chemical evolution; although probably not components of early genetic systems, phosphonic acids may have been precursors to the first nucleic acids. Here we report the synthesis of several phosphonic acids, including the most abundant found in the Murchison meteorite, by ultraviolet irradiation of orthophosphorous acid in the presence of formaldehyde, primary alcohols, or acetone. We argue that similar reactions might explain the presence of phosphonic acids in Murchison, and could also have occurred on the prebiotic Earth.

Chromatography, Gas↗

PubMed1984

The improbability of prebiotic nucleic acid synthesis.

Many accounts of the origin of life assume that the spontaneous synthesis of a self-replicating nucleic acid could take place readily. Serious chemical obstacles exist, however, which make such an event extremely improbable. Prebiotic syntheses of adenine from HCN, of D,L-ribose from adenosine, and of adenosine from adenine and D-ribose have in fact been demonstrated. However these procedures use pure starting materials, afford poor yields, and are run under conditions which are not compatible with one another. Any nucleic acid components which were formed on the primitive earth would tend to hydrolyze by a number of pathways. Their polymerization would be inhibited by the presence of vast numbers of related substances which would react preferentially with them. It appears likely that nucleic acids were not formed by prebiotic routes, but are later products of evolution.

Chemical Phenomena↗

PubMed1996

Chance and necessity in the selection of nucleic acid catalysts.

In Tom Stoppard's famous play [Rosencrantz and Guildenstern are Dead], the ill-fated heroes toss a coin 101 times. The first 100 times they do so the coin lands heads up. The chance of this happening is approximately 1 in 10(30), a sequence of events so rare that one might argue that it could only happen in such a delightful fiction. Similarly rare events, however, may underlie the origins of biological catalysis. What is the probability that an RNA, DNA, or protein molecule of a given random sequence will display a particular catalytic activity? The answer to this question determines whether a collection of such sequences, such as might result from prebiotic chemistry on the early earth, is extremely likely or unlikely to contain catalytically active molecules, and hence whether the origin of life itself is a virtually inevitable consequence of chemical laws or merely a bizarre fluke. The fact that a priori estimates of this probability, given by otherwise informed chemists and biologists, ranged from 10(-5) to 10(-50), inspired us to begin to address the question experimentally. As it turns out, the chance that a given random sequence RNA molecule will be able to catalyze an RNA polymerase-like phosphoryl transfer reaction is close to 1 in 10(13), rare enough, to be sure, but nevertheless in a range that is comfortably accessible by experiment. It is the purpose of this Account to describe the recent advances in combinatorial biochemistry that have made it possible for us to explore the abundance and diversity of catalysts existing in nucleic acid sequence space.

Base Sequence↗

PubMed2003

Spatial models of prebiotic evolution: soup before pizza?

The problem of information integration and resistance to the invasion of parasitic mutants in prebiotic replicator systems is a notorious issue of research on the origin of life. Almost all theoretical studies published so far have demonstrated that some kind of spatial structure is indispensable for the persistence and/or the parasite resistance of any feasible replicator system. Based on a detailed critical survey of spatial models on prebiotic information integration, we suggest a possible scenario for replicator system evolution leading to the emergence of the first protocells capable of independent life. We show that even the spatial versions of the hypercycle model are vulnerable to selfish parasites in heterogeneous habitats. Contrary, the metabolic system remains persistent and coexistent with its parasites both on heterogeneous surfaces and in chaotically mixing flowing media. Persistent metabolic parasites can be converted to metabolic cooperators, or they can gradually obtain replicase activity. Our simulations show that, once replicase activity emerged, a gradual and simultaneous evolutionary improvement of replicase functionality (speed and fidelity) and template efficiency is possible only on a surface that constrains the mobility of macromolecule replicators. Based on the results of the models reviewed, we suggest that open chaotic flows ('soup') and surface dynamics ('pizza') both played key roles in the sequence of evolutionary events ultimately concluding in the appearance of the first living cell on Earth.

Animals↗

PubMed2005

The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure.

The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precursors of modern life both stored information and acted as catalysts. For the first time among extensive studies on ribozymes, we have investigated the influence of hydrostatic pressure on the hairpin ribozyme catalytic activity. High pressures are of interest when studying life under extreme conditions and may help to understand the behavior of macromolecules at the origins of life. Kinetic studies of the hairpin ribozyme self-cleavage were performed under high hydrostatic pressure. The activation volume of the reaction (34 +/- 5 ml/mol) calculated from these experiments is of the same order of magnitude as those of common protein enzymes, and reflects an important compaction of the RNA molecule during catalysis, associated to a water release. Kinetic studies were also carried out under osmotic pressure and confirmed this interpretation and the involvement of water movements (78 +/- 4 water molecules per RNA molecule). Taken together, these results are consistent with structural studies indicating that loops A and B of the ribozyme come into close contact during the formation of the transition state. While validating baro-biochemistry as an efficient tool for investigating dynamics at work during RNA catalysis, these results provide a complementary view of ribozyme catalytic mechanisms.

Base Sequence↗

PubMedDate not supplied

Self-description and the origin of the genetic code.

The genetic code presents an important conceptual challenge within the broader context of the origin of life. Translation of genetic information captures a fundamental property of living systems, i.e. the ability of decoding proteins (e.g. aminoacyl-tRNA synthetases) to reproduce themselves from self-contained RNA/DNA descriptors. Silvano Colombano and I, as graduate students with Howard Pattee in the 1970s, focused on achieving this closure of self-description and self-reproduction in the genetic code. Simulation and analysis of competitive models that allowed alternate code assignments, exploring initial conditions, arbitrary descriptor-catalyst relationships, and degree of non-linearity, indicated that these dynamical systems undergo bifurcations, transforming initial ambiguous stable states to unstable states. New, stable, steady states, progressively closer to a code, became available as the descriptor parameters were varied. The efficiency of utilization of raw materials for the production of a coding family of catalysts is proposed as a selection criterion that drives such systems towards a coded state.

Amino Acyl-tRNA Synthetases↗

PubMed2001

The RNA/protein symmetry hypothesis: experimental support for reverse translation of primitive proteins.

Although the "RNA-world" theory, or the RNA-first theory is renowned for a promising theory of biogenesis, it is also possible that both RNAs and proteins have coevolved forming a stable metabolic complex from the very beginning. I investigated this possibility assuming that the genetic information flowed symmetrically in the era of the origin of life, i.e. the primitive translation machinery worked in both directions (from RNA to protein and from protein to RNA). According to this RNA/protein symmetry theory, the genetic information would have come from existing cellular proteins via reverse translation. This process would have been completed in a short period of time without searching an enormous RNA sequence space. Furthermore, reverse translation would have ensured biological continuity; proteins that were essential for cellular metabolism would have been utilized in the same way as before the protein sequence information would have been transferred into the RNA sequences. I also propose a possible mechanism for the process of reverse translation. The reverse translation would proceed in the 3' to 5' direction using a set of at least 20 reverse transfer RNAs (rtRNAs) that can recognize their specific amino acid residue and carry their corresponding codon. A source of genetic information would be a primary sequence of a protein molecule. Several basic steps of reverse translation were demonstrated using rtRNA(Arg).

3' Untranslated Regions↗

PubMed1987

Binding of DNA hairpins to an assembler-strand as part of a primordial translation device.

A crucial event in the process leading to the origin of life is the emergence of a simple translation device. To approach experimental realization of this device the binding ability of short DNA hairpins to complementary oligonucleotides fixed on a solid support was investigated. The binding is achieved by base pairing between the loop nucleotides of the hairpins containing different numbers of adenosine residues and oligothymidylates covalently linked to cellulose. The loop has to consist of at least five nucleotides to achieve binding. The exact number of established base pairs was determined in two ways. First, the elution temperatures of hairpins and those of oligoadenylates which had the length of the loop were compared. Secondly, the architecture of the loop was analyzed by means of the single-strand-specific nuclease from mung bean acting as structural probe. Only n-2 of n loop nucleotides of a hairpin are able to form base pairs. Therefore, a strong evidence for the formation of a triplet of base pairs between primeval tRNA and mRNA sufficient to stabilize the complex enzyme-free is given.

Base Sequence↗

PubMed2005

Ammonia formation by the reduction of nitrite/nitrate by FeS: ammonia formation under acidic conditions.

One issue for the origin of life under a non-reducing atmosphere is the availability of the reduced nitrogen necessary for amino acids, nucleic acids, etc. One possible source of this nitrogen is the formation of ammonia from the reduction of nitrates and nitrites produced by the shock heating of the atmosphere and subsequent chemistry. Ferrous ions will reduce these species to ammonium, but not under acidic conditions. We wish to report results on the reduction of nitrite and nitrate by another source of iron (II), ferrous sulfide, FeS. FeS reduces nitrite to ammonia at lower pHs than the corresponding reduction by aqueous Fe+ 2. The reduction follows a first order decay, in nitrite concentration, with a half-life of about 150 min (room temperature, CO2, pH 6.25). The highest product yield of ammonia measured was 53%. Under CO2, the product yield decreases from pH 5.0 to pH 6.9. The increasing concentration of bicarbonate, at higher pH, interferes with the reaction. Comparing experiments under N2 CO2 shows the interference of bicarbonate. The reaction proceeds well in the presence of such species as chloride, sulfate, and phosphate, though the yield drops significantly with phosphate. FeS also reduces nitrate and, unlike with Fe+ 2, the reduction shows more reproducibility. Again, the product yield decreases with increasing pH, from 7% at pH 4.7 to 0% at pH 6.9. It appears that nitrate is much more sensitive to the presence of added species, perhaps not competing as well for binding sites on the FeS surface. This may be the cause of the lack of reproducibility of nitrate reduction by Fe+ 2 (which also can be sensitive to binding by certain species).

Ammonia↗

PubMed2002

In silico simulations reveal that replicators with limited dispersal evolve towards higher efficiency and fidelity.

The emergence of functional replicases, acting quickly and with high accuracy, was crucial to the origin of life. Although where the first RNA molecules came from is still unknown, it is nevertheless assumed that catalytic RNA enzymes (ribozymes) with replicase function emerged at some early stage of evolution. The fidelity of copying is especially important because the mutation load limits the length of replicating templates that can be maintained by natural selection. An increase in template length is disadvantageous for a fixed digit copying fidelity, however, longer molecules are expected to be better replicases. An iteration for longer molecules with better replicase function has been suggested and analysed mathematically. Here we show that more efficient replicases can spread, provided they are adsorbed to a prebiotic mineral surface. A cellular automaton simulation reveals that copying fidelity, replicase speed and template efficiency all increase with evolution, despite the presence of molecular parasites, essentially because of reciprocal atruism ('within-species mutualism') on the surface, thus making a gradual improvement of replicase function more plausible.

Adsorption↗