Clays as possible catalysts for peptide formation in the prebiotic era

From the point of view of prebiotic synthesis, clays might have performed functions of concentration, catalysis, and protection of molecules.The degrees of polymerization obtained, when amino acid adenylates are added to montmorillonite suspensions in water, are much higher than those obtained by polymerization in the absence of such a clay. In addition, they are of a discrete spectrum, usually multiplies of 6 or 7, and reach values of up to 40 mers. In the absence of clay a continuous spectrum of degrees of polymerization is obtained, and usually up to 4–6 mers only. Copolymerization in the absence of clays yields mostly random copolymers, in their presence mostly block copolymers are obtained.Optical density measurements show that after adsorption has taken place on the clay, stacking of its layers occurs. Polymerization starts only after these stacked layers have been formed. The distances between the layers — as measured by X-rays — increase during polymerization, probably because the resulting polymers settle in their interspace, while the adsorption site of the active monomers is at the edges of the clay.     

Clays as possible catalysts for peptide formation in the prebiotic era.

From the point of view of prebiotic synthesis, clays might have performed functions of concentration, catalysis, and protection of molecules. The degree of polymerization obtained when amino acid adenylates are added to montmorillonite suspensions in water, are much iigher than those obtained by polymerization in the absence of such a clay. In addition, they are of a discrete spectrum, usually multiplies of 6 or 7, and reach values of up to 40 mers. In the absence of clay a continuous spectrum of degrees of polymerization is obtained, and usually up to 4-6 mers only. Copolymerization in the absence of clays yields mostly random copolymers in their presence mostly block copolymers are obtained. Optical density measurements show that after adsorption has taken place on the clay, stacking of its layers occurs. Polymerization starts only after these stacked layers have been formed. The distance between the layers - as measured by X-rays - increase during polymerization, probably because the resulting polymers settle in their interspace, while the adsorption site of the active monomers is at the edges of the clay.     

The possible role of clays in prebiotic peptide synthesis

Hypotheses of macromolecule formations during the prebiotic era are described. The presumed role of minerals and clays in these reactions are: concentration of monomers, proton release by ion exchange whenever the reaction demands it, scattering of the charges of the interacting substances, thus allowing such substances to interact, which in the absence of clays repel each other due to their charges. Because of these reasons the polymerization mechanism in the presence of clays is different from that in their absence. While in the absence of clays only free amino acids or peptides can interact with active amino acid anhydrides, giving thus peptides increased by only one unit, in the presence of clays two molecules of amino acid anhydrides can interact, giving a still active peptide anhydride which can interact with another active peptide. Clays catalyze polymerization only in these cases where the amino acid is small enough to enter between the sheets of the clay. Apparently most of the reactions also occur there and not on the surface of the clay. Copolymerization of different pairs of amino acids proceeds selectively in the presence of clay. The relationship between this selecitvity and prebiotic parent proteins is discussed.     

The polymerization of amino acid adenylates on sodium-montmorillonite with preadsorbed polypeptides

We studied the spontaneous polymerization of amino acid adenylates on Na-montmorillonite in dilute, neutral suspension, after polypeptides were adsorbed on the clay. This led to the unexpected finding that the degrees of polymerization (DP's) of the oligo- and poly-peptides obtained depended on the amounts of polypeptides that were preadsorbed. Plotting average molecular weights obtained against c-spacings of the clay platelet aggregates which widened as a result of polypeptide addition and adsorption before the polymerization, does not permit an obvious explanation of these observations. The best correlation assigns a role to the fractional occupation of the individual intercalation layers of the polypeptides, as the adsorption increases towards a first complete mono-interlayer, then to an incipient and eventually to a complete double layer on to a third interlayer, after which the clay stacking breaks up. Spacings which correspond to an intermediate occupation of any of the three successive interlayers favor amino acids self-addition to polymers. The opposite is true for nearly empty or filled intercalation layers. We hypothesize and describe, how a catalytic activity may derive from c-spacings that offer adsorption sites for the reagent amino acid adenylate within the peripheral recesses of irregularly stacked clay platelets by bringing the anhydride bonds and neutral amino groups into favorable reaction distances. Moderately filled intercalation spaces may also act as sinks for the newly formed oligomers and facilitate the freeing of reaction sites for the occupation by fresh reagent. The c-spacings required for these mechanisms are the result of the intercalation of the preadsorbed polymer, but similar conditions prevail when polymers are adsorbed as they are generated during polymerization.     

Cations as Mediators of the Adsorption of Nucleic Acids on Clay Surfaces in Prebiotic Environments

Monovalent ([Na⁺] > 10 mM) and divalent ([Ca²⁺], [Mg²⁺] > 1.0 mM) cations induced the precipitationof nucleic acid molecules. In the presence of clay minerals (montmorillonite and kaolinite), there was adsorption instead of precipitation. The cation concentration needed for adsorption depended on both the valence of the cations and the chemical nature of the nucleic acid molecules. Double-stranded nucleic acids needed higher cation concentrations than single-stranded ones to be adsorbed to the same extent on clay. Divalent cations were more efficient than monovalent ones in mediating adsorption. Adsorption to the clay occurred only when both nucleic acids and cations were present. However, once the complexes were formed, the cations could not be removed from the system by washing, indicating that they are directly involved in the association between nucleic acids and mineral surfaces.These observations indicate that cations take part directly in the formation of nucleic acid-clay complexes, acting as a `bridge' between the negative charges on the mineral surface and those of the phosphate groups of the genetic polymer. The relatively low cation concentrations needed for adsorption and the ubiquitous presence of clay minerals in the environment suggest that the adsorption of nucleic acids on mineral surfaces could have taken place in prebiotic habitats. This may have played an important role in the formation and preservation of nucleic acids and/or their precursor polymers.     

Oligomerization of Thioglutamic Acid: Encapsulated Reactions and Lipid Catalysis

For cellular life to begin on the early Earth, a permeation mechanism would be required to allow polar solutes to enter a membrane-bounded compartment. A second process - internal polymerization of peptides from amino acid – would also be an essential step toward the first compartmented metabolic pathways leading to biosynthesis. Here we report a study of amino acid permeation into lipid vesicles, in which thioglutamic acid penetrated lipid bilayer membranes at rates sufficient to support internal polymerization reactions. We also investigated spontaneous non-enzymatic polymerization reactions of thioglutamic acid to form oligopeptides. We found that oligomers up to 11mers are produced in the reaction mixture, and conclude that certain lipid surfaces can act as catalysts in promoting an oligomerization reaction. These observations are pertinent to understanding processes by which peptide bond synthesis could take place in primitive cellular life on the early Earth. H. H. Zepik and S. Rajamani contributed equally to the paper.     

Polypeptides from the condensation of amino acid adenylates

The adenylates of an amino acid mixture were polymerized in aqueous solution as a model to study amino acid sequence control at an intermediate level above prebiological conditions yet in the absence of highly evolved cellular constraints. As a first step, the homogeneous polymerization was investigated in detail. A mixture of sixteen free amino acids, including C-14 label, was converted to the adenylates using a low 101 molar excess of condensing agent over free amino acid. The adenylates were polymerized in alkaline buffer, or hydrolyzed in acid, and directly analyzed on Sephadex and Dowex columns. A comparison of the polymerized and hydrolyzed samples showed that condensed products were formed during the adenylate synthesis stage. The yield of distinctly polymerized material was small (<5%) and was found to trail the elution of free amino acids on Sephadex. This material may be separated into a small number of distinct bands by electrophoresis, and has an amino acid composition that does not reflect that of the starting mixture.     

Origin, Persistence and Biological Activity of Genetic Material in Prebiotic Habitats

Molecules which store genetic information (i.e. RNA and DNA) are central to all life on Earth. The formation of these complex molecules, and ultimately life, required specific conditions, including the synthesis and concentration of precursors (nucleotides), the joining of these monomers into larger molecules (polynucleotides), their protection in critical conditions (like those probably existing in primeval habitats), and the expression of the biological potential of the informational molecule (its capacity to multiply and evolve). Determining how these steps occurred and how the earliest genetic molecules originated on Earth is a problem that is far from being resolved. Recent observations on the polymerization of nucleotides on clay surfaces and on the resistance of clay-adsorbed nucleic acids to environmental degradation suggest that clay minerals could have acted as a resting place for the formation and preservation of prebiotic genetic molecules, whatever they were, and for the self-organization of the first auto-replicating systems. In the present work, the molecular characteristics and biological activity of different nucleic acids (DNA, RNAs) adsorbed/bound on clay minerals are discussed in the light of their possible role in ancestral environments.     

Binding of adenine and adenine-related compounds to the clay montmorillonite and the mineral hydroxylapatite

The first living things may have consisted of no more than RNA or RNA-like molecules bound to the surfaces of mineral particles. A key aspect of this theory is that these mineral particles have binding sites for RNA and its prebiotic precursors. The object of this study is to explore the binding properties of two of the best studied minerals, montmorillonite and hydroxylapatite, for possible precursors of RNA. The list of compounds investigated includes purines, pyrimidines, nucleosides, nucleotides, nucleotide coenzymes, diaminomaleonitrile and aminoimidazole carbox-amide. Affinities for hydroxylapatite are dominated by ionic interactions between negatively charged small molecules and positively charged sites in the mineral. Binding to montmorillonite presents a more complex picture. These clay particles have a high affinity for organic ring structures which is augmented if they are positively charged. This binding probably takes place on the negatively charged faces of these sheet-like clay particles. Additional binding sites on the edges of of these sheets have a moderate affinity for negatively charged molecules.Small molecules that bind to these minerals sometimes bind independently to sites on the minerals and sometimes bind cooperatively with favorable interactions between the bound molecules.     

Clays in prebiological chemistry

Summary In this review an attempt is made to highlight the structures and properties of clay that may contribute to a better understanding of the role of clays in chemical evolution. The adsorption of organic molecules on clays has been demonstrated, as has the synthesis of bioorganic monomers in the presence of clays. For instance, amino acids (glycine, aspartic acid, threonine, alanine and others) as well as purines and pyrimidines, have been obtained from CO and NH₃ in the presence of clays at relatively high temperatures (250-325°C). Carbohydrates are also easily derived from formaldehyde at relatively low temperatures (80°C). The oligomerization of biochemical monomers, mediated by clays has also been shown to result in the formation of polymer molecules basic to life. For instance the condensation of amino acyl adenylates at room temperature in the presence of montmorillonite is known to yield polypeptides in discrete ranges of molecular weights with degrees of polymerization up to 56. Clays have also been found to affect the condensation of mononucleotides to oligonucleotides. Although the role of clays in the origin of metabolic pathways has not been demonstrated, it is possible that clays may have played a cooperative role with catalytic peptides in an intermediate stage of prebiological chemistry preceding the emergence of life on this planet.     

The Combination of Salt Induced Peptide Formation Reaction and Clay Catalysis: A Way to Higher Peptides under Primitive Earth Conditions

Two reactions with suggested prebiotic relevance for peptide evolution, the saltinduced peptide formation reaction and the peptide chain elongation/stabilization on clay minerals have been combined in experimental series starting from dipeptides and dipeptide/amino acid mixtures. The results show that both reactions can take place simultaneously in the same reaction environment and that the presence of mineral catalysts favours the formation of higher oligopeptides. These findings lend further support to the relevance of these reactions for peptide evolution on the primitive earth. The detailed effects of the specific clay mineral depend both on the nature of the mineral and the reactants in solution.     

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 are 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.     

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.     

Method for the determination of protein evolution rates by amino acid composition. Evolution rate of actins

A method has been developed to determine the actin evolution rate. The method is based on amino acid composition. The actin evolution rate has been established to be extremely low. Only three or less amino acid changes per hundred amino acid residues have accumulated for a 100 million years. One can explain the conservative nature of actin evolution as a sequence of its unique tightly fitted structure rich in biologically active centres at short distances from each other. The peculiar invariability of polar amino acids leads to a conclusion that some given distribution of charges is necessary for the unique functioning of actin molecules.     

Method for the determination of protein evolution rates by amino acid composition. Evolution rate of actins.

A method has been developed to determine the actin evolution rate. The method is based on amino acid compositon. The actin evolution rate has been established to be extremely low. Only three or less amino acid changes per hundred amino acid residues have accumulated for a 100 million years. One can explain the conservative nature of actin evolution as a sequence of its unique tightly fitted structure rich in biologically active centres at short distances from each other. The peculiar invariability of polar amino acids leads to a conclusion that some given distribution of charges is necessary for the unique functioning of actin molecules.     

Biochemical research on oogenesis: protein synthesis by purified 42S particles from Xenopus laevis and Tinca tinca previtellogenic oocytes

When incubated with ATP and a labeled amino acid, the 42S particles from early oocytes of Xenopus laevis and Tinca tinca incorporate radioactivity into tRNA and into a high molecular mass material which can be identified as protein. This incorporation is totally independent of ribosomes of cytosolic, mitochondrial or bacterial origin. The incorporated amino acids are linked to a broad spectrum of proteins by covalent bonds. Simple treatments such as incubation in buffer or addition of synthetic polyribonucleotides can inhibit the protein-labeling activity of the particles without affecting their tRNA aminoacylation activity. The former activity corresponds either to an amino acid polymerization reaction or to a protein-modifying reaction of a novel type. No involvement of mRNA in this process has been demonstrated. The alleged amino acid polymerization activity of the 42S particles could be a consequence of the conditions provided to aminoacyl tRNA by the tRNA-binding sites of the particles. These conditions are likely to allow the peptidyl transfer reaction to take place, although at a much lower rate than in the ribosome.     

Synthesis and hydrolysis of a phenylalanyl adenylate pentacoordinated phosphorane

Amino acid-nucleotide conjugates have important biological functions and therapeutic applications. For example, aminoacyl adenylates are key intermediates in aminoacyl tRNA synthetase reactions. They may also be involved in the prebiotic synthesis of polypeptides. Finally, various amino acid carbomethoxy aryl phosphoramidates of nucleotide prodrugs may be activated through a mechanism involving a pentacoordinated phosphorane intermediates. In order to understand better the chemistry of these compounds, a phenylalanyl adenylate pentacoodinated phosphorane has been synthesized in 72% yield and its decomposition in aqueous solution studied. Hydrolysis gave 2('),3(')-O-isopropylidene adenosine 5(')-monophosphate, 2('),3(')-O-isopropylidene adenosine, and phenylalanine. The results provide model chemistry for the enzymatic degradation mechanism of antiviral aryl amino acid phosphodiester amidates in cells, which leads to their activation.     

The Level and Landscape of Optimization in the Origin of the Genetic Code

We consider a model of the origin of genetic code organization incorporating the biosynthetic relationships between amino acids and their physicochemical properties. We study the behavior of the genetic code in the set of codes subject both to biosynthetic constraints and to the constraint that the biosynthetic classes of amino acids must occupy only their own codon domain, as observed in the genetic code. Therefore, this set contains the smallest number of elements ever analyzed in similar studies. Under these conditions and if, as predicted by physicochemical postulates, the amino acid properties played a fundamental role in genetic code organization, it can be expected that the code must display an extremely high level of optimization. This prediction is not supported by our analysis, which indicates, for instance, a minimization percentage of only 80%. These observations can therefore be more easily explained by the coevolution theory of genetic code origin, which postulates a role that is important but not fundamental for the amino acid properties in the structuring of the code. We have also investigated the shape of the optimization landscape that might have arisen during genetic code origin. Here, too, the results seem to favor the coevolution theory because, for instance, the fact that only a few amino acid exchanges would have been sufficient to transform the genetic code (which is not a local minimum) into a much better optimized code, and that such exchanges did not actually take place, seems to suggest that, for instance, the reduction of translation errors was not the main adaptive theme structuring the genetic code.     

Origin of the genetic code: A physical-chemical model of primitive codon assignments

Selective compartmentalization of amino acids and nucleotides according to their polarities is proposed as a physical-chemical model for the origin of the genetic code. Assumptions made in this hypothesis are: (1) an oil-slick covered the surface of the primitive ocean, constituents of which formed association colloids or micelles at the water-oil-air interfaces; (2) depending on the polarity of the media, these aggregates possessed hydrophilic and hydrophobic interiors where selective uptake of amino acids and nucleic acid constituents could take place; and 93) condensation and polymerization in the micellar phase were enhanced. According to the chromatographically observed polarities, for example, lysine and uridylate fall into the hydrophilic compartment, and phenylalanine and adenylate are enriched in the hydrophobic environment. These components could eventually be condensed to form a charged adaptor loop with an anticodon which is complementary to the presently valid codon. Only two groups of amino acids, hydrophilic and hydrophobic, were recognized by the primitive translation mechanism. Implications of this hypothesis for the further development of the genetic code is discussed. The catalytic power of micelles have been substantiated by successful synthesis of nucleotides under relatively mild conditions using thiophosphates as high energy phosphates.     

Small molecule interactions were central to the origin of life

Many scientists believe life began with the spontaneous formation of a replicator. This idea has been supported by "prebiotic" syntheses carried out by chemists using modern apparatus and purified reagents. The probability that such reactions would take place spontaneously on the early Earth is minute. These points are illustrated here by considering the often cited oligomerization of activated RNA components by clay minerals. A more likely alternative for the origin of life is one in which a collection of small organic molecules multiply their numbers through catalyzed reaction cycles, driven by a flow of available free energy. Although a number of possible systems of this type have been discussed, no experimental demonstration has been made. The inclusion of a "driver" reaction, directly coupled to the energy source, may lead to a solution.