A possible role of fluctuating clay-water systems in the production of ordered prebiotic oligomers

Clays and the Origin of Life: The Experiments

There are three groups of scientists dominating the search for the origin of life: the organic chemists (the Soup), the molecular biologists (RNA world), and the inorganic chemists (metabolism and transient-state metal ions), all of which have experimental adjuncts. It is time for Clays and the Origin of Life to have its experimental adjunct. The clay data coming from Mars and carbonaceous chondrites have necessitated a review of the role that clays played in the origin of life on Earth. The data from Mars have suggested that Fe-clays such as nontronite, ferrous saponites, and several other clays were formed on early Mars when it had sufficient water. This raised the question of the possible role that these clays may have played in the origin of life on Mars. This has put clays front and center in the studies on the origin of life not only on Mars but also here on Earth. One of the major questions is: What was the catalytic role of Fe-clays in the origin and development of metabolism here on Earth? First, there is the recent finding of a chiral amino acid (isovaline) that formed on the surface of a clay mineral on several carbonaceous chondrites. This points to the formation of amino acids on the surface of clay minerals on carbonaceous chondrites from simpler molecules, e.g., CO2, NH3, and HCN. Additionally, there is the catalytic role of small organic molecules, such as dicarboxylic acids and amino acids found on carbonaceous chondrites, in the formation of Fe-clays themselves. Amino acids and nucleotides adsorb on clay surfaces on Earth and subsequently polymerize. All of these observations and more must be subjected to strict experimental analysis. This review provides an overview of what has happened and is now happening in the experimental clay world related to the origin of life. The emphasis is on smectite-group clay minerals, such as montmorillonite and nontronite.

Transition metals enhance prebiotic depsipeptide oligomerization reactions involving histidine

Biochemistry exhibits an intense dependence on metals. Here we show that during dry-down reactions, zinc and a few other transition metals increase the yield of long histidine-containing depsipeptides, which contain both ester and amide linkages. Our results suggest that interactions of proto-peptides with metal ions influenced early chemical evolution.

Transition metals enhance prebiotic proto-peptide oligomerization reactions through direct association with histidine.

Potential for the Biodegradation of Atrazine Using Leaf Litter Fungi from a Subtropical Protection Area

The intense use of pesticides in agricultural activities for the last several decades has caused contamination of the ecosystems connected with crop fields. Despite the well-documented occurrence of pesticide biodegradation by microbes, natural attenuation of atrazine (ATZ), and its effects on ecological processes in subtropical forested areas, such as Iguaçu National Park located in Brazil, has been poorly investigated. Subtropical environments sustain a great degree of fungal biodiversity, and the patterns and roles of these organisms should be better understood. This work aimed to evaluate nine ligninolytic-producer fungi isolated from the INP edge to degrade and detoxify ATZ solutions. ATZ degradation and the main metabolites produced, including deisopropylatrazine and deethylatrazine (DEA), were analyzed using dispersive liquid-liquid microextraction followed by gas chromatography-mass spectrometer. Four fungi were able to degrade ATZ to DEA, and the other five showed potential to grow and facilitate ATZ biodegradation. Furthermore, two strains of Fusarium spp. showed an enhanced potential for detoxification according to the Allium cepa (onion) test. Although the isolates produced ligninolytic enzymes, no ligninolytic activity was observed in the biodegradation of ATZ, a feature with ecological significance. In conclusion, Ascomycota fungi from the INP edge can degrade and detoxify ATZ in solution. Increasing the knowledge of biodiversity in subtropical protected areas, such as ecosystem services provided by microbes, enhances ecosystem conservation.

A Possible Prebiotic Ancestry of Porphyrin-Type Protein Cofactors

In previous experiments that simulated conditions on primordial volcanic islands, we demonstrated the abiotic formation of hydrophobic porphyrins. The present study focused on the question whether such porphyrins can be metalated by prebiotically plausible metal ion sources. We used water-insoluble octaethylporphyrin (H2oep) as a model compound. Experiments were conducted in a nitrogen atmosphere under cyclic wet-dry conditions in order to simulate the fluctuating environment in prebiotic rock pools. Wetting-drying proved to be a crucial factor. Significant yields of the metalloporphyrins (20-78% with respect to H2oep) were obtained from the soluble salts MCl2 (M = Mg, Fe, Co, Ni and Cu) in freshwater. Even almost insoluble minerals and rocks metalated the porphyrin. Basalt (an iron source, 11% yield), synthetic jaipurite (CoS, 33%) and synthetic covellite (CuS, 57%) were most efficient. Basalt, magnetite and FeCl2 gave considerably higher yields in artificial seawater than in freshwater. From iron sources, the highest yields, however, were obtained in an acidic medium (hydrochloric acid with an initial pH of 2.1). Under these conditions, iron meteorites also metalated the porphyrin. Acidic conditions were considered because they are known to occur during eruptions on volcanic islands. Octaethylporphyrinatomagnesium(II) did not form in acidic medium and was unstable towards dissolved Fe2+. It is therefore questionable whether magnesium porphyrins, i.e. possible ancestors of chlorophyll, could have accumulated in primordial rock pools. However, abiotically formed ancestors of the modern cofactors heme (Fe), B12 (Co), and F430 (Ni) may have been available to hypothetical protometabolisms and early organisms.

The Influence of Mineral Matrices on the Thermal Behavior of Glycine

On the Hadean-Early Archean Earth, the first islands must have provided hot and dry environments for abiotically formed organic molecules. The heat sources, mainly volcanism and meteorite impacts, were also available on Mars during the Noachian period. In recent work simulating this scenario, we have shown that neat glycine forms a black, sparingly water-soluble polymer ("thermomelanoid") when dry-heated at 200 °C under pure nitrogen. The present study explores whether relevant minerals and mineral mixtures can change this thermal behavior. Most experiments were conducted at 200 or 250 °C for 2 or 7 days. The mineral matrices used were phyllosilicates (Ca-montmorillonites SAz-1 and STx-1, Na-montmorillonite SAz-1-Na, nontronite NAu-1, kaolinite KGa-1), salts (NaCl, NaCl-KCl, CaCl2, artificial sea salt, gypsum, magnesite), picritic basalt, and three Martian regolith simulants (P-MRS, S-MRS, JSC Mars-1A). The main analytical method employed was high-performance liquid chromatography (HPLC). Glycine intercalated in SAz-1 and SAz-1-Na was well protected against thermomelanoid formation and sublimation at 200 °C: after 2 days, 95 and 79 %, respectively, had either survived unaltered or been transformed into the cyclic dipeptide (DKP) and linear peptides up to Gly6. The glycine survival rate followed the order SAz-1 > SAz-1-Na > STx-1 ≈ NAu-1 > KGa-1. Very good protection was also provided by artificial sea salt (84 % unaltered glycine after 200 °C for 7 days). P-MRS promoted the condensation up to Gly6, consistent with its high phyllosilicate content. The remaining matrices were less effective in preserving glycine as such or as peptides.

Chiral Ceramic Nanoparticles and Peptide Catalysis

The chirality of nanoparticles (NPs) and their assemblies has been investigated predominantly for noble metals and II-VI semiconductors. However, ceramic NPs represent the majority of nanoscale materials in nature. The robustness and other innate properties of ceramics offer technological opportunities in catalysis, biomedical sciences, and optics. Here we report the preparation of chiral ceramic NPs, as represented by tungsten oxide hydrate, WO_3-x·H₂O, dispersed in ethanol. The chirality of the metal oxide core, with an average size of ca. 1.6 nm, is imparted by proline (Pro) and aspartic acid (Asp) ligands via bio-to-nano chirality transfer. The amino acids are attached to the NP surface through C-O-W linkages formed from dissociated carboxyl groups and through amino groups weakly coordinated to the NP surface. Surprisingly, the dominant circular dichroism bands for NPs coated by Pro and Asp are different despite the similarity in the geometry of the NPs; they are positioned at 400-700 nm and 500-1100 nm for Pro- and Asp-modified NPs, respectively. The differences in the spectral positions of the main chiroptical band for the two types of NPs are associated with the molecular binding of the two amino acids to the NP surface; Asp has one additional C-O-W linkage compared to Pro, resulting in stronger distortion of the inorganic crystal lattice and greater intensity of CD bands associated with the chirality of the inorganic core. The chirality of WO_3-x·H₂O atomic structure is confirmed by atomistic molecular dynamics simulations. The proximity of the amino acids to the mineral surface is associated with the catalytic abilities of WO_3-x·H₂O NPs. We found that NPs facilitate formation of peptide bonds, leading to Asp-Asp and Asp-Pro dipeptides. The chiroptical activity, chemical reactivity, and biocompatibility of tungsten oxide create a unique combination of properties relevant to chiral optics, chemical technologies, and biomedicine.

Thermal Condensation of Glycine and Alanine on Metal Ferrite Surface: Primitive Peptide Bond Formation Scenario

The amino acid condensation reaction on a heterogeneous mineral surface has been regarded as one of the important pathways for peptide bond formation. Keeping this in view, we have studied the oligomerization of the simple amino acids, glycine and alanine, on nickel ferrite (NiFe₂O₄), cobalt ferrite (CoFe₂O₄), copper ferrite (CuFe₂O₄), zinc ferrite (ZnFe₂O₄), and manganese ferrite (MnFe₂O₄) nanoparticles surfaces, in the temperature range from 50-120 °C for 1-35 days, without applying any wetting/drying cycles. Among the metal ferrites tested for their catalytic activity, NiFe₂O₄ produced the highest yield of products by oligomerizing glycine to the trimer level and alanine to the dimer level, whereas MnFe₂O₄ was the least efficient catalyst, producing the lowest yield of products, as well as shorter oligomers of amino acids under the same set of experimental conditions. It produced primarily diketopiperazine (Ala) with a trace amount of alanine dimer from alanine condensation, while glycine was oligomerized to the dimer level. The trend in product formation is in accordance with the surface area of the minerals used. A temperature as low as 50 °C can even favor peptide bond formation in the present study, which is important in the sense that the condensation process is highly feasible without any sort of localized heat that may originate from volcanoes or hydrothermal vents. However, at a high temperature of 120 °C, anhydrides of glycine and alanine formation are favored, while the optimum temperature for the highest yield of product formation was found to be 90 °C.

The Role of Lipid Membranes in Life's Origin

At some point in early evolution, life became cellular. Assuming that this step was required for the origin of life, there would necessarily be a pre-existing source of amphihilic compounds capable of assembling into membranous compartments. It is possible to make informed guesses about the properties of such compounds and the conditions most conducive to their self-assembly into boundary structures. The membranes were likely to incorporate mixtures of hydrocarbon derivatives between 10 and 20 carbons in length with carboxylate or hydroxyl head groups. Such compounds can be synthesized by chemical reactions and small amounts were almost certainly present in the prebiotic environment. Membrane assembly occurs most readily in low ionic strength solutions with minimal content of salt and divalent cations, which suggests that cellular life began in fresh water pools associated with volcanic islands rather than submarine hydrothermal vents.

Selective self-assembly of adenine-silver nanoparticles forms rings resembling the size of cells

Self-assembly has played critical roles in the construction of functional nanomaterials. However, the structure of the macroscale multicomponent materials built by the self-assembly of nanoscale building blocks is hard to predict due to multiple intermolecular interactions of great complexity. Evaporation of solvents is usually an important approach to induce kinetically stable assemblies of building blocks with a large-scale specific arrangement. During such a deweting process, we tried to monitor the possible interactions between silver nanoparticles and nucleobases at a larger scale by epifluorescence microscopy, thanks to the doping of silver nanoparticles with luminescent silver nanodots. ssDNA oligomer-stabilized silver nanoparticles and adenine self-assemble to form ring-like compartments similar to the size of modern cells. However, the silver ions only dismantle the self-assembly of adenine. The rings are thermodynamically stable as the drying process only enrich the nanoparticles-nucleobase mixture to a concentration that activates the self-assembly. The permeable membrane-like edge of the ring is composed of adenine filaments glued together by silver nanoparticles. Interestingly, chemicals are partially confined and accumulated inside the ring, suggesting that this might be used as a microreactor to speed up chemical reactions during a dewetting process.

Formation of activated biomolecules by condensation on mineral surfaces--a comparison of peptide bond formation and phosphate condensation

Many studies have reported condensation reactions of prebiotic molecules, such as the formation of peptide bonds between amino acids, to occur to some degree on mineral surfaces. We have studied several such reactions on the same divided silica. When drying steps are applied, the equilibria of peptide formation from glycine, and polyphosphate formation from monophosphate, are displaced to the right because these reactions are dehydrating condensations, accompanied by the emission of water. In contrast, the equilibrium of AMP dismutation is not significantly favored by drying. The silica surface plays little role (if any) in the thermochemistry of the condensation reactions, but is does play a significant kinetic role by acting as a catalyst, lowering the condensation temperatures with respect to bulk solids. Of course, the surface also catalyzes the inverse hydrolysis reactions.

Alteration of bacterial communities and organic matter in microbial fuel cells (MFCs) supplied with soil and organic fertilizer

The alteration of the organic matter (OM) and the composition of bacterial community in microbial fuel cells (MFCs) supplied with soil (S) and a composted organic fertilizer (A) was examined at the beginning and at the end of 3 weeks of incubation under current-producing as well as no-current-producing conditions. Denaturing gradient gel electrophoresis revealed a significant alteration of the microbial community structure in MFCs generating electricity as compared with no-current-producing MFCs. The genetic diversity of cultivable bacterial communities was assessed by random amplified polymorphic DNA (RAPD) analysis of 106 bacterial isolates obtained by using both generic and elective media. Sequencing of the 16S rRNA genes of the more representative RAPD groups indicated that over 50.4% of the isolates from MFCs fed with S were Proteobacteria, 25.1% Firmicutes, and 24.5% Actinobacteria, whereas in MFCs supplied with A 100% of the dominant species belonged to γ-Proteobacteria. The chemical analysis performed by fractioning the OM and using thermal analysis showed that the amount of total organic carbon contained in the soluble phase of the electrochemically active chambers significantly decreased as compared to the no-current-producing systems, whereas the OM of the solid phase became more humified and aromatic along with electricity generation, suggesting a significant stimulation of a humification process of the OM. These findings demonstrated that electroactive bacteria are commonly present in aerobic organic substrates such as soil or a fertilizer and that MFCs could represent a powerful tool for exploring the mineralization and humification processes of the soil OM.

Protein evolution in two co-occurring types of Symbiodinium: an exploration into the genetic basis of thermal tolerance in Symbiodinium clade D

Background

The symbiosis between reef-building corals and photosynthetic dinoflagellates (Symbiodinium) is an integral part of the coral reef ecosystem, as corals are dependent on Symbiodinium for the majority of their energy needs. However, this partnership is increasingly at risk due to changing climatic conditions. It is thought that functional diversity within Symbiodinium may allow some corals to rapidly adapt to different environments by changing the type of Symbiodinium with which they partner; however, very little is known about the molecular basis of the functional differences among symbiont groups. One group of Symbiodinium that is hypothesized to be important for the future of reefs is clade D, which, in general, seems to provide the coral holobiont (i.e., coral host and associated symbiont community) with elevated thermal tolerance. Using high-throughput sequencing data from field-collected corals we assembled, de novo, draft transcriptomes for Symbiodinium clades C and D. We then explore the functional basis of thermal tolerance in clade D by comparing rates of coding sequence evolution among the four clades of Symbiodinium most commonly found in reef-building corals (A-D).

Results

We are able to highlight a number of genes and functional categories as candidates for involvement in the increased thermal tolerance of clade D. These include a fatty acid desaturase, molecular chaperones and proteins involved in photosynthesis and the thylakoid membrane. We also demonstrate that clades C and D co-occur within most of the sampled colonies of Acropora hyacinthus, suggesting widespread potential for this coral species to acclimatize to changing thermal conditions via ‘shuffling’ the proportions of these two clades from within their current symbiont communities.

Conclusions

Transcriptome-wide analysis confirms that the four main Symbiodinium clades found within corals exhibit extensive evolutionary divergence (18.5-27.3% avg. pairwise nucleotide difference). Despite these evolutionary distinctions, many corals appear to host multiple clades simultaneously, which may allow for rapid acclimatization to changing environmental conditions. This study provides a first step toward understanding the molecular basis of functional differences between Symbiodinium clades by highlighting a number of genes with signatures consistent with positive selection along the thermally tolerant clade D lineage.

DNA barcoding and development of species-specific markers for the identification of tea mosquito bugs (Miridae: Heteroptera) in India

Rapid, accurate, and timely identification of insects as a group is important and challenging worldwide, as they outnumber all other animals in number and diversity. DNA barcoding is a method for the identification of species in a wide range of animal taxa, which uses the 5' region of the mitochondrial cytochrome c oxidase-I (CO-I). Yet another easy, accurate, and economical method of species discrimination is by developing species-specific markers, which produce specific amplicon for the species in question. The method is handy because it is not limited by life stages, sex, polymorphism, and other factors. Herein, we measured the usefulness of CO-I for the species discrimination of mirids in India viz. Helopeltis antonii Signoret, H. thievora Waterhouse, H. bradyi Waterhouse, and Pachypeltis maesarum Kirkaldy in their various life stages. Furthermore, our study showed the utility of species-specific markers in differentiating H. antonii (295) and H. bradyi (514) regardless of their life stages. Analysis of CO-I gene revealed <1% intraspecific divergence for all four species examined, whereas the interspecific distances ranged from 7 to 13%. This study showed that the DNA barcode and species-specific markers will aid the identification of mirids in India and will stand as a decisive tool in formulating integrated pest management (IPM) strategy, quick identification of invasive and cryptic species, haplotypes, biotypes, and other factors, if any.

Theory, modelling and simulation in origins of life studies

Origins of life studies represent an exciting and highly multidisciplinary research field. In this review we focus on the contributions made by theory, modelling and simulation to addressing fundamental issues in the domain and the advances these approaches have helped to make in the field. Theoretical approaches will continue to make a major impact at the "systems chemistry" level based on the analysis of the remarkable properties of nonlinear catalytic chemical reaction networks, which arise due to the auto-catalytic and cross-catalytic nature of so many of the putative processes associated with self-replication and self-reproduction. In this way, we describe inter alia nonlinear kinetic models of RNA replication within a primordial Darwinian soup, the origins of homochirality and homochiral polymerization. We then discuss state-of-the-art computationally-based molecular modelling techniques that are currently being deployed to investigate various scenarios relevant to the origins of life.

Role of metal oxides in chemical evolution: interaction of ribose nucleotides with alumina

Interaction of ribonucleotides--namely, 5'-AMP, 5'-GMP, 5'-CMP, and 5'-UMP--with acidic, neutral, and basic alumina has been studied. Purine nucleotides showed higher adsorption on alumina in comparison with pyrimidine nucleotides under acidic conditions. Adsorption data obtained followed Langmuir adsorption isotherm, and X(m) and K(L) values were calculated. On the basis of infrared spectral studies of ribonucleotides, alumina, and ribonucleotide-alumina adducts, we propose that the nitrogen base and phosphate moiety of the ribonucleotides interact with the positive charge surface of alumina. Results of the present study may indicate the importance of alumina in concentrating organic molecules from dilute aqueous solutions in primeval seas in the course of chemical evolution on Earth.

Adsorption and polymerization of amino acids on mineral surfaces: a review

The present paper offers a review of recent (post-1980) work on amino acid adsorption and thermal reactivity on oxide and sulfide minerals. This review is performed in the general frame of evaluating Bernal's hypothesis of prebiotic polymerization in the adsorbed state, but written from a surface scientist's point of view. After a general discussion of the thermodynamics of the problem and exactly what effects surfaces should have to make adsorbed-state polymerization a viable scenario, we examine some practical difficulties in experimental design and their bearing on the conclusions that can be drawn from extant works, including the relevance of the various available characterization techniques. We then present the state of the art concerning the mechanisms of the interactions of amino acids with mineral surfaces, including results from prebiotic chemistry-oriented studies, but also from several different fields of application, and discuss the likely consequences for adsorption selectivities. Finally, we briefly summarize the data concerning thermally activated amide bond formation of adsorbed amino acids without activating agents. The reality of the phenomenon is established beyond any doubt, but our understanding of its mechanism and therefore of its prebiotic potential is very fragmentary. The review concludes with a discussion of future work needed to fill the most conspicuous gaps in our knowledge of amino acids/mineral surfaces systems and their reactivity.

Steps towards the formation of a protocell: the possible role of short peptides

The paper deals with molecular self-organization leading to formation of a protocell. Plausible steps towards a protocell include: polymerization of peptides and oligonucleotides on mineral surfaces; coevolution of peptides and oligonucleotides with formation of collectively autocatalytic sets; self-organization of short peptides into vesicles; entrapment of the peptide/oligonucleotide systems in mixed peptide and simple amphiphile membranes; and formation of functioning protocells with metabolism and cell division. The established propensity of short peptides to self-ordering and to formation of vesicles makes this sequence plausible. We further suggest that evolution of a protocell produced cellular ancestors of viruses as well as ancestors of cellular organisms.

On the chemistry and evolution of the pioneer organism

The theory of a chemo-autotrophic origin of life in a volcanic Iron-Sulfur World postulates the emergence of a pioneer organism within a flow of volcanic exhalations. The pioneer organism is characterized by a composite structure with an inorganic substructure and an organic superstructure. Within the surfaces of the inorganic substructure, iron, cobalt, nickel, and other transition-metal centers with sulfido, carbonyl, cyano, and other ligands are catalytically active, and promote the growth of the organic superstructure through carbon fixation, driven by the reducing potential of the volcanic exhalations. This pioneer organism is reproductive by an autocatalytic feedback effect, whereby some organic products serve as ligands for activating the catalytic metal centres whence they arise. This unitary structure-function relationship of the pioneer organism constitutes the 'Anlage' for two major strands of evolution: enzymatization and cellularization, whereby the upward evolution of life by increase of molecular complexity is grounded ultimately in the transition metal-catalyzed, synthetic redox chemistry of the pioneer organism.

Evidence for geographic isolation and signs of endemism within a protistan morphospecies

The possible existence of endemism among microorganisms resulting from and preserved by geographic isolation is one of the most controversial topics in microbial ecology. We isolated 31 strains of "Spumella-like" flagellates from remote sampling sites from all continents, including Antarctica. These and another 23 isolates from a former study were characterized morphologically and by small-subunit rRNA gene sequence analysis and tested for the maximum temperature tolerance. Only a minority of the Spumella morpho- and phylotypes from the geographically isolated Antarctic continent follow the worldwide trend of a linear correlation between ambient (air) temperature during strain isolation and heat tolerance of the isolates. A high percentage of the Antarctic isolates, but none of the isolates from locations on all other continents, were obligate psychrophilic, although some of the latter were isolated at low ambient temperatures. The drastic deviation of Antarctic representatives of Spumella from the global trend of temperature adaptation of this morphospecies provides strong evidence for geographic transport restriction of a microorganism; i.e., Antarctic protistan communities are less influenced by transport of protists to and from the Antarctic continent than by local adaptation, a subtle form of endemism.

Imidazo[1,2-a]pyrazine-3,6-diones derived from alpha-amino acids: a theoretical mechanistic study of their formation via pyrolysis and silica-catalyzed process

Imidazo[1,2-a]pyrazine-3,6-diones are unusual compounds composed of three alpha-amino acid fragments. These bicyclic amidines (BCAs) form under high temperatures or with the use of strong dehydrating reagents. We gave insight into the mechanisms of BCA formation via gas-phase pyrolytic and silica-catalyzed reactions of glycine (Gly) and alpha-aminoisobutyric acid (AIB) with related diketopiperazines (DKPs), using quantum chemical calculations. The entire process requires four steps: (1) O-acylation of DKP with free or silica-bonded amino acid, (2) acyl transfer from the oxygen to the nitrogen atom, (3) intramolecular condensation of the N-acyl DKP into a cyclol, and (4) elimination of water. To study step (1) at silica surface (modeled by H7Si8O12-OH cluster), we employed two-level ONIOM calculations (AM1:UFF, B3LYP/3-21G:UFF and B3LYP/6-31G(d):UFF); all gas-phase reactions were studied at the AM1, B3LYP/3-21G and B3LYP/6-31G(d) levels. The catalytic effect of silica was observed for both Gly and AIB: the activation energy in the O-acylation at the surface was lower by more than 9 kcal mol(-1) as compared to the gas-phase process. Contrary to the exothermic O-acylation, the gas-phase transfer reaction (step 2) was exothermic in both cases, but more favorable for Gly. The cyclocondensation of N-acylated DKPs into BCAs (steps 3 and 4) is endothermic for Gly and exothermic for AIB.

Sites of adsorption of adenine, uracil, and their corresponding derivatives on sodium montmorillonite

Clay minerals are considered important to chemical evolution processes due to their properties, ancient origin, and wide distribution. To extend the knowledge of their role in the prebiotic epoch, the adsorption sites of adenine, adenosine, AMP, ADP, ATP, Poly A, uracil, uridine, UMP, UDP, UTP and Poly U on sodium montmorillonite are investigated. X-ray diffraction, ultraviolet and infrared spectroscopy studies indicate that these molecules distribute into the interlamellar channel and the edge of the clay crystals. Monomers are adsorbed predominantly in the interlamellar channel, whereas polymers adsorb along the crystal edges. Such behavior is discussed mainly in terms of bulk pH, pK(a) of the adsorbate, and Van der Waals interactions.

The adsorption of nucleotides and polynucleotides on montmorillonite clay

The binding of adenine derivatives to Na(+)-montmorillonite increases in the order 5'AMP, 3'-AMP, 5'ADP < adenosine < purine, adenine. With the exception of cytosine, cytosine derivatives bind less strongly than the corresponding adenine derivatives in the order 5'-CMP < cytidine < cytosine. There is little difference in the binding of uracil derivatives and these compounds bind less strongly than the corresponding adenine analogs. It is concluded that the adenine ring in adenine derivatives is protonated by the acidic montmorillonite surface and binding is a consequence of the electrostatic interaction between the protonated base and the negative charges on the surface of the montmorillonite. Different binding trends were observed with Cu(2+)-montmorillonite with AMP binding more strongly than adenosine and UMP binding more strongly than uridine. It is concluded that ligation to the Cu2+ is a major force in the binding of nucleotides to Cu(2+)-montmorillonite and are not readily washed from the clay. Factors contributing to the binding are discussed. Watson-Crick hydrogen bonding of 5'-AMP to poly(U) and 5'GMP to poly(C) was observed when the homopolymers are bound to the surface of the clay. No association of 5'-UMP to poly(U) bound to clay was detected. The possible role of montmorillonite clays in the prebiotic formation of RNA is discussed.

The adsorption and reaction of adenine nucleotides on montmorillonite

The binding of AMP to Zn(2+)-montmorillonite was investigated in the presence of buffers and salts. Good's buffers, piperazine-N,N'-bis(2-ethanesulfonate) [PIPES] and morpholine-N-2-ethanesulfonate [MES], perturbed the exchangeable cations to a lesser extent (only 9% of Zn2+ displaced by 0.2 M buffer) than was observed with imidazole and lutidine buffers or NaCl and KCl salts (up to 80% of Zn2+ displaced). AMP adsorption isotherms measured in the presence of 0.2 M PIPES, MES, or Na2SO4 exhibited normal Langmuir-type behavior. The adsorption coefficient, KL, is 3-fold greater in the presence of HEPES or PIPES than it is in the absence of buffers. Basal spacings measured by X-ray diffraction for Zn(2+)-montmorillonite are 13 and 15 angstroms in the presence of PIPES, while a value of 12.8 angstroms was determined in the absence of PIPES. These data are interpreted in a model in which the adsorption of AMP is mediated by a Zn2+ complex of PIPES in different orientations in the interlamellar region of the montmorillonite. The type of exchangeable cation does not affect the ability of the lattice-bound Fe3+ in the montmorillonite to oxidize diaminomaleonitrile (DAMN). Exchangeable Cu2+ oxidizes DAMN, but exchangeable Fe3+ is nearly ineffective as an oxidant. The addition of DISN to 3'-AMP bound to Zn(2+)-montmorillonite in the presence of 0.2 M PIPES resulted in a higher yield of 2',3'-cAMP than is observed with a comparable concentration of Zn2+, a result which inplicates surface catalysis by the montmorillonite.

Peptides and the origin of life

Considering the state-of-the-art views of the geochemical conditions of the primitive earth, it seems most likely that peptides were produced ahead of all other oligomer precursors of biomolecules. Among all the reactions proposed so far for the formation of peptides under primordial earth conditions, the salt-induced peptide formation reaction in connection with adsorption processes on clay minerals would appear to be the simplest and most universal mechanism known to date. The properties of this reaction greatly favor the formation of biologically relevant peptides within a wide variation of environmental conditions such as temperature, pH, and the presence of inorganic compounds. The reaction-inherent preferences of certain peptide linkages make the argument of 'statistical impossibility' of the evolutionary formation of the 'right' peptides and proteins rather insignificant. Indeed, the fact that these sequences are reflected in the preferential sequences of membrane proteins of archaebacteria and prokaryonta distinctly indicates the relevance of this reaction for chemical peptide evolution. On the basis of these results and the recent findings of self-replicating peptides, some ideas have been developed as to the first steps leading to life on earth.

Behavior of amino acids when volatilized in the presence of silica gel and pulverized basaltic lava

To evaluate the types of amino acid thermal transformations caused by silicate materials, we studied the volatilization products of Aib, L-Ala, L-Val and L-Leu under temperatures of up to 270 degrees C in the presence of silica gel as a model catalyst and pulverized basaltic lava samples. It was found that silica gel catalyzes nearly quantitative condensation of amino acids, where piperazinediones are the major products, whereas lava samples have much lower catalytic efficiency. In addition bicyclic and tricyclic amidines and several products of their subsequent thermal decomposition have been identified using the coupled technique of GC-FTIR-MS and HPLC-PB-MS, with auxiliary computer simulation of IR spectra and NMR spectroscopy. The decomposition is due to dehydrogenation, elimination of the alkyl substituents and dehydration as well as cleavage of the bicyclic ring system. The imidazole ring appears to be more resistant to thermal decomposition as compared to the pyperazine moiety, giving rise to the formation of different substituted imidazolones. The amidines were found to hydrolyze under treatment with concentrated HCl, releasing the starting amino acids and thus behaving as amino acid anhydrides. The thermal transformations cause significant racemization of amino acid residues. Based on our observations, the formation of amidine-type products is suggested to be rather common in the high-temperature experiments on amino acid condensation.

Emergence of template-and-sequence-directed (TSD) syntheses: I. A bio-geochemical model

A biogeochemical model for the evolution of template-and-sequence-directed (TSD) syntheses of biological templates (proto-RNAs) and catalysts (peptides) is described. A fluctuating environment characterized by hydrating (cool) and dehydrating (warm) phases with cycles of consecutive organic reactions, as well as a constant supply of the polymeric building blocks is assumed. The scenario starts with the catalyzed formation of a primordial population of small random peptides, based on the relatively-ineffective mineral catalysts. The resulting peptides initiate a catalytic takeover process, during which the catalytic functions are gradually taken over by peptides. The evolution of TSD peptides is based on a combination of Lahav's (1991) co-evolution and Moller and Janssen's (1990) specific recognition sites hypotheses. During the emergence of TSD systems the fraction of TSD peptides and proto-RNA constituents rises from almost insignificance to dominance in a TSD Reactions Takeover. The TSD system is characterized by autocatalysis, positive feedback loops and a primordial genetic code. The model is the basis for a computer program (Part II of present series).

The effect of smectite composition on the catalysis of peptide bond formation

Clay-catalyzed glycine and diglycine oligomerizations were performed as drying/wetting cycles at 80 degrees C. Two trioctahedral smectites (hectorite and saponite), three pure montmorillonites, a ferruginous smectite, an Fe(II)-rich smectite, and three smectites containing goethite admixture were used as catalysts. Highest peptide bond formation was found with trioctahedral smectites. About 7% of glycine was converted to diglycine and diketopiperazine on hectorite after 7 days. In the case of dioctahedral smectites, highest yields were achieved using clays with a negative-layer charge localized in the octahedral sheets (up to 2% of converted glycine after 7 days). The presence of Fe(II) in clay is reflected in a higher efficiency in catalyzing amino acid dimerization (about 3.5% of converted glycine after 7 days). The possible significance of the results for prebiotic chemistry is discussed.

A review of conditions affecting the radiolysis due to 40K on nucleic acid bases and their derivatives adsorbed on clay minerals: implications in prebiotic chemistry

This paper describes the possible effects of ionizing radiation arising from long-lived soluble radionuclides within clays, in particular 40K, at the epoch of the emergence of life on Earth. The free dispersion of soluble radionuclides constitutes an effective in situ irradiation mechanism that might have acted upon adsorbed nucleic bases and their derivatives on clays, inducing chemical changes on these organic molecules. Several types of well documented reactions for radiolysis of nucleic acid bases and their derivatives are known, even at low doses (i.e., 0.1 Gy). For example, estimates with a dose rate calculated from 40K from deep sea clays at 3.8 Ga ago, indicates that over a period of 1000 years the amount of organic material transformated is 1.8 X 10(-7) moles/kg-clay. Although ionizing radiation may also induce synthetic reactions with prebiological interest, all in all these considerations indicate that nucleic acid bases and their derivatives adsorbed on clays were exposed for long periods to degradation conditions. Such situation promotes decomposition of organic molecules rather than protection of them and enhancement of farther polymerization, as it has been usually taken for granted.

Peptide nucleic acid (PNA): a model structure for the primordial genetic material?

It is proposed that the primordial genetic material could have been peptide nucleic acids, i.e., DNA analogues having a peptide backbone. PNA monomers based on the amino acid, alpha, gamma-diaminobutyric acid or ornithine are suggested as compounds that could have been formed in the prebiotic soup. Finally, the possibility of a PNA/RNA world is presented, in which PNA constitutes the stable genetic material, while RNA which may be polymerized using the PNA as template accounts for enzymatic activities including PNA replication.

Investigations on the mechanism of the salt-induced peptide formation

The applicability of the salt-induced peptide formation in aqueous solution--the simplest model so far for peptide synthesis under primitive earth conditions--is demonstrated for valine as another amino acid, and the formation of mixed peptides in systems containing glycine, alanine and valine is investigated. The dominant dipeptides formed are Gly-Gly, Gly-Ala and Gly-Val, at longer reaction times sequence inversion produces Ala-Gly and, considerably slower, Val-Gly. Ala-Ala is also produced and the relative amounts of the diastereomers prove the high conservation of optical purity of the original amino acids over a considerable time. The results lead to some further conclusions about the reaction mechanism and the possible dominance of peptide sequences in primordial dipeptides.

Prebiotic co-evolution of self-replication and translation or RNA world?

A prebiotic scenario is proposed, based on the recent "domain hypothesis" model (Lahav, 1989, J. molec. Evol. 29, 475-479), suggested for domain propagation of RNA-like molecules in a fluctuating environment. The same system is suggested now not only for the evolution of ribozymes, but also for the evolution of directed peptide synthesis, as follows: Short, self-structured strands (termed prebioectons), each possessing a templatable domain which is chargeable by an amino acid, are the predecessors of tRNA (proto-tRNA). Complementary domains are formed on these prebioectons during an environmental cycle such as wetting-drying, followed by their dissociation from their template domain and ligation, to form the predecessor of mRNA (proto-mRNA). The evolution of directed peptide synthesis is suggested to be based on the ability of the charged prebioectons to attach preferentially to their complementary domains on the proto-mRNA. Two stages of this process are envisioned, namely: (a) Template-directed, random peptide synthesis taking place when non-specifically-charged prebioectons are sequentially attached each to its complementary domain on the proto-mRNA, followed by peptide bond formation. (b) Template-and-sequence-directed peptide synthesis, which can be realized after the "invention" of a catalytic molecule capable of specifically charging a proto-tRNA by an amino acid; this is the crucial evolutionary stage, where a crude genetic code becomes functional. Gradually, catalytic peptides and ribozymes are selected for their functions and evolve, while being encoded in the primitive "memory" of the emerging system. Thus, rather than the RNA monopoly postulated by the RNA World hypothesis, an early co-evolution of primitive enzymes and ribozymes is suggested.(ABSTRACT TRUNCATED AT 250 WORDS)

Growth of peptide chains on silica in absence of amino acid access from without

Changes in IR spectra during thermal treatment of chemisorption products of glycine and valine vapours on dehydrated silica surfaces have been studied. Peptide products were formed from these chemisorbed species. A scheme of peptide chain growth on the silica surface is suggested based on the idea of ester type "activated intermediates".

Exon-intron-like pattern of the first propagating molecule?

A biogeochemical scenario is proposed, according to which prebiotic self-replication of RNA-like molecules evolved gradually from domain propagation to entire strand replication. The hypothetical replicating entities that formed an evolutionary continuity in time, the prebioectons, were characterized by self-structuring, and started their evolution from strands possessing one or more templatable domains. The inherent self-structuring implies a very early coevolution of the replicating molecules with prebiotic peptides, in line with the cassette model of Cedergren and Grosjean (1987). The proposed approach can be partially tested in the laboratory.

The biogeochemical cycle of the adsorbed template. II: Selective adsorption of mononucleotides on adsorbed polynucleotide templates

Experimental results are presented for the verification of the specific interaction step of the 'adsorbed template' biogeochemical cycle, a simple model for a primitive prebiotic replication system. The experimental system consisted of gypsum as the mineral to which an oligonucleotide template attaches (Poly-C or Poly-U) and 5'-AMP, 5'-GMP, 5'-CMP and 5'-UMP as the interacting biomonomers. When Poly-C or Poly-U were used as adsorbed templates, 5'-GMP and 5'-AMP, respectively were observed to be the most strongly adsorbed species. Moreover, there exists a direct quantitative relationship between the quantity of cytidine or uracil residues in the adsorbed state and the amount of the complementary mononucleotide that is attached to it. NaCl added to the system in order to create conditions of high ionic strength seems to enhance the selectivity of the adsorption of the monmucleotides to these adsorbed templates.

Theoretical investigation of the role of clay edges in prebiotic peptide bond formation. II. Structures and thermodynamics of the activated complex species

Amino acid activation by anhydride formation in model tetrahedral silicate and aluminate sites in clays and neutral phosphates have been studied by semi-empirical molecular orbital calculations. The results have been compared to previous ab initio studies on the reactant species and were found to be in good agreement. The geometries of all species were totally optimized and heats of formation obtained. Relative heats of formation of the anhydrides indicate the extent of anhydride formation to be A1 greater than Si greater than P which is the same order as the stability of hydrolysis. The relative efficacy of the anhydrides in promoting peptide bond formation has been evaluated using both thermodynamic and chemical reactivity criteria. Heats of reaction for model reactions were calculated from calculated enthalpies of formation of the products and reactants. The electrophilicity of the carbonyl carbon and the nucleophilicity of the oxygen were specifically used as indicators of chemical reactivity towards dipeptide formation by the activated amino acids. Our results indicate that if the reaction mechanism is dominated by the nucleophilic character of the oxygen, tetrahedral A1 sites should be more active than Si, and if the electrophilic character dominates, the order would be reversed.