Simulated Prebiotic Conditions Research Articles

Interactions Between Iron Sulfide Minerals and Organic Carbon: Implications for Biosignature Preservation and Detection

Microbe-mineral interactions can produce unique composite materials, which can preserve biosignatures. Geological evidence suggests that iron sulfide (Fe-S) minerals are abundant in the subsurface of Mars. On Earth, the formation of Fe-S minerals is driven by sulfate-reducing microorganisms (SRM) that produce reactive sulfide. Moreover, SRM metabolites, as well as intact cells, can influence the morphology, particle size, aggregation, and composition of biogenic Fe-S minerals. In this work, we evaluated how simple and complex organic molecules-hexoses and amino acid/peptide mixtures, respectively-influence the formation of Fe-S minerals (simulated prebiotic conditions), and whether the observed patterns mimic the biological influence of SRM. To this end, organo-mineral aggregates were characterized with X-ray diffraction, scanning electron microscopy, and scanning transmission X-ray microscopy coupled to near-edge X-ray absorption fine structure spectroscopy. Overall, Fe-S minerals were found to have a strong affinity for proteinaceous organic matter. Fe-S minerals precipitated at simulated prebiotic conditions yielded organic carbon distributions that were more homogeneous than treatments with whole SRM cells. In prebiotic experiments, spectroscopy detected potential organic transformations during Fe-S mineral formation, including conversion of hexoses to sugar acids and polymerization of amino acids/peptides into larger peptides/proteins. In addition, prebiotic mineral-carbon assemblages produced nanometer-scaled filamentous aggregated morphologies. On the contrary, in biotic treatments with cells, organic carbon in minerals displayed a more heterogeneous distribution. Notably, "hot spots" of organic carbon and oxygen-containing functional groups, with the size, shape, and composition of microbial cells, were preserved in mineral aggregates. We propose a list of characteristics that could be used to help distinguish biogenic from prebiotic/abiotic Fe-S minerals and help refine the search of extant or extinct microbial life in the martian subsurface.

Irradiation of glyceraldehyde under simulated prebiotic conditions: Study in solid and aqueous state

We investigated the radiolysis of dl-glyceraldehyde in a solid state and in an aqueous solution. The catalytic effect of a clay onto glyceraldehyde was also studied. We carried out the irradiation in a 60Co gamma ray source (Gammabeam 650 PT), with doses up to 360 kGy, at three temperatures (77, 198 and 295 K). For the analysis, we used various spectroscopic and chromatographic analytical methods. The results show that this compound is labile under irradiation and that it forms malondialdehyde, glycolaldehyde and other sugar-like compounds that are important in chemical-evolution studies.

Prebiotic formation of cyclic dipeptides under potentially early Earth conditions

Cyclic dipeptides, also known as 2,5-diketopiperazines (DKPs), represent the simplest peptides that were first completely characterized. DKPs can catalyze the chiral selection of reactions and are considered as peptide precursors. The origin of biochemical chirality and synthesis of peptides remains abstruse problem believed to be essential precondition to origin of life. Therefore, it is reasonable to believe that the DKPs could have played a key role in the origin of life. How the formation of the DKPs through the condensation of unprotected amino acids in simulated prebiotic conditions has been unclear. Herein, it was found that cyclo-Pro-Pro could be formed directly from unprotected proline in the aqueous solution of trimetaphosphate (P3m) under mild condition with the yield up to 97%. Other amino acids were found to form proline-containing DKPs under the same conditions in spite of lower yield. During the formation process of these DKPs, P3m promotes the formation of linear dipeptides in the first step of the mechanism. The above findings are helpful and significant for understanding the formation of DKPs in the process of chemical evolution of life.

Giant vesicles from rehydrated crude mixtures containing unexpected mixtures of amphiphiles formed under plausibly prebiotic conditions.

Giant lipid vesicles resemble compartments of biological cells, mimicking them in their dimension, membrane structure and partly in their membrane composition. The spontanenous appearance of closed membranes composed of bilayers of self-assembling amphiphiles was likely a prerequisite for Darwinian competitive behavior to set in at the molecular level. Such compartments should be dynamic in their membrane composition (evolvable), and sufficiently stable to harbor macromolecules (leak-free), yet semi-permeable for reactive small molecules to get across the membrane (stay away from chemical equilibrium). Here we describe bottom-up experiments simulating prebiotic environments that support the formation of simple amphiphilic molecules capable of self-assembling into vesicular objects on the micrometer scale. Long-chain alkyl phosphates, together with related amphiphilic compounds, were formed under simulated prebiotic phosphorylation conditions by using cyanamide, a recognized prebiotic chemical activator and a precursor for several compound classes. Crude dry material of the thus obtained prebiotic mixtures formed multilamellar giant vesicles once rehydrated at the appropriate pH and in the presence of plausibly prebiotic co-surfactants, as observed by optical microscopy. The size and the shape of lipid aggregates tentatively suggest that prebiotic lipid assemblies could encapsulate peptides or nucleic acids that could be formed under similar chemical prebiotic conditions. The formation of prebiotic amphiphiles was monitored by using TLC, IR, NMR and ESI-MS and UPLC-HRMS. In addition we provide a spectroscopic analysis of cyanamide under simulated prebiotic conditions in the presence of phosphate sources and spectroscopic analysis of O-phosphorylethanolamine as a plausible precursor for phosphoethanolamine lipids.

Prebiotic Glycosylation of Uracil with Electron-Donating Substituents

Following the suggestion that nucleoside analogues having their nucleobases joined to ribose via a carbon-carbon bond might easily arise prebiotically, the glycosylation of uracil carrying electron-donating substituents (Me, OH, OCH3, NH2) at its 5 or 6 positions was investigated. Of these, only 6-aminouracil gave glycosylated products in greater than 50% yield under simulated prebiotic conditions. The reaction provided four products, three of which were purified by preparative HPLC. The structure of the isolated compounds was determined by high-resolution mass spectrometry and NMR spectroscopy. The glycosylation products were, as expected, C-nucleosides, with the sugar having either a pyranose or a furanose structure, with the ratio depending on the precise conditions, implying reversible addition. Interestingly, the 6-aminouracil riboside displays two hydrogen bonding patterns, the "acceptor-donor-acceptor" pattern of uridine itself and (upon 180° rotation) the "acceptor-donor-donor" hydrogen bonding pattern. The second, in an artificially expanded genetic information system, is trivially called "V" and pairs with a purine analogue that presents the complementary "donor-acceptor-acceptor" hydrogen bonding pattern, trivially called "J."

Retraction: Formation of L Amino Acids and D Sugars, and Amplification of their Enantioexcesses in Aqueous Solutions, Under Simulated Prebiotic Conditions

Retraction: Formation of L Amino Acids and D Sugars, and Amplification of their Enantioexcesses in Aqueous Solutions, Under Simulated Prebiotic Conditions

Formation of L Amino Acids and D Sugars, and Amplification of their Enantioexcesses in Aqueous Solutions, Under Simulated Prebiotic Conditions

AbstractThe Murchison meteorite delivered five α‐methyl amino acids to Earth with small excesses of the L enantiomer; later, additional examples were found and such compounds were also found in other meteorites. I describe our work using them under prebiotic conditions to form normal proteinogenic amino acids with an excess of the L enantiomers, and to amplify such excesses to dominant concentration in solution. I also extend this work to show how D sugars, such as D‐ribose, can have been formed and amplified in solution. I also show the high concentration amplifications of D‐nucleosides that can be obtained under credible prebiotic conditions. The simple theory of such amplifications, and corrections resulting from solvation effects, are described along with modern ideas of the source of such α‐methyl amino acids in meteorites.

Lipid-assisted synthesis of RNA-like polymers from mononucleotides.

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

Prebiotic chemistry: chemical evolution of organics on the primitive Earth under simulated prebiotic conditions

A series of prebiotic mixtures of simple molecules, sources of C, H, N, and O, were examined under conditions that may have prevailed during the Hadean eon (4.6-3.8 billion years), namely an oxygen-free atmosphere and a significant UV radiation flux over a large wavelength range due to the absence of an ozone layer. Mixtures contained a C source (methanol, acetone or other ketones), a N source (ammonia or methylamine), and an O source (water) at various molar ratios of C : H : N : O. When subjected to UV light or heated for periods of 7 to 45 days under an argon atmosphere, they yielded a narrow product distribution of a few principal compounds. Different initial conditions produced different distributions. The nature of the products was ascertained by gas chromatographic-mass spectral analysis (GC-MS). UVC irradiation of an aqueous methanol-ammonia-water prebiotic mixture for 14 days under low UV dose (6 x 10(-2) Einstein) produced methylisourea, hexamethylenetetramine (HMT), methyl-HMT and hydroxy-HMT, whereas under high UV dose (45 days; 1.9 x 10(-1) Einstein) yielded only HMT. By contrast, the prebiotic mixture composed of acetone-ammonia-water produced five principal species with acetamide as the major component; thermally the same mixture produced a different product distribution of four principal species. UVC irradiation of the CH(3)CN-NH(3)-H(2)O prebiotic mixture for 7 days gave mostly trimethyl-s-triazine, whereas in the presence of two metal oxides (TiO(2) or Fe(2)O(3)) also produced some HMT; the thermal process yielded only acetamide.

Serine Octamers: Cluster Formation, Reactions, and Implications for Biomolecule Homochirality

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Serine Octamers: Cluster Formation, Reactions, and Implications for Biomolecule Homochirality

The emergence of homochirality continues to be one of the most challenging topics associated with the origin of life. One possible scenario is that aggregates of amino acids might have been involved in a sequence of chemical events that led to chiral biomolecules in self-replicating systems, that is, to homochirogenesis. Serine is the amino acid of principal interest, since it forms "magic-number" ionic clusters composed of eight amino acid units, and the clusters have a remarkable preference for homochirality. These serine octamer clusters (Ser8) can be generated under simulated prebiotic conditions and react selectively with other biomolecules. These observations led to the hypothesis that serine reactions were responsible for the first chiral selection in nature which was then passed through chemical reactions to other amino acids, saccharides, and peptides. This Review evaluates the chemistry of Ser8 clusters and the experimental evidence that supports their possible role in homochirogenesis.

Modeling prebiotic catalysis with nucleic acid-like polymers and its implications for the proposed RNA world

The theory that RNA molecules played a pivotal role in the early evolution of life is now widely accepted. Studies related to this hypothetical “RNA world” include three major areas: the formation of precursors for the first RNA molecules, the polymerization process, and the potential of RNA to catalyze chemical and biochemical reactions. Several chemical and biochemical studies performed under simulated prebiotic conditions support the role of RNA as both genetic as well as catalytic material. However, owing to the lack of credible mechanism for de novo nucleic acid synthesis and the hydrolytic instability of RNA molecules, there has been some serious discussion of whether biopolymers that closely resembled nucleic acid preceded the “RNA world”. In this context, an overview of prebiotic chemistry, the role of mineral surface, and the significance of studies related to RNA-like polymers in the origin of life are presented here.

Phosphorylation of adenosine with trimetaphosphate under simulated prebiotic conditions.

The phosphorylation of adenosine with trimetaphosphate in solution, in solid phase and using wet-dry cycles was carried out and it was found that wet-dry cycles were the most efficient. The catalytic effects of some metal ions on the phosphorylation were also studied and it was discovered that Ni(II) is the most effective. The combination of wet-dry cycles (4 cycles) and catalysis by Ni(II) led to an unprecedented high conversion of adenosine to phosphorylated products (30%) near neutral pH. The main phosphorylated products were 2',3'-cyclic AMP (10.4%) and 5'-ATP (13.0%).

Surface and intergallery catalytic properties of Cu(II)-exchanged hectorite: A scanning force microscope study

Many layered silicate clay minerals such as hectorite readily adsorb or intercalate organic species. Surface or intergallery structural effects, electric fields, or charged particles may then facilitate polymerization or other reactions, resulting in novel inorganic/organic host–guest composite systems. We have studied the interaction of Cu(II)-exchanged hectorite with the polar monomer aniline, nonpolar styrene, and the amino acid glycine. Hectorite is known to readily intercalate aniline into its intergallery regions, where spontaneous polymerization occurs, resulting in nearly two-dimensional sheets of the conducting polymer polyaniline. In addition, aniline vapor is spontaneously polymerized on the surface of Cu(II)-exchanged hectorite, due to the presence of micro-pore sites on the silicate surface where oxidizing Cu2+ cations are available. For the nonpolar styrene molecule, little or no intercalation occurs. Surface polymerization of styrene is observed for long, intense exposures to the monomer in solution. Cu(II)-exchanged hectorite was also exposed to the amino acid glycine and subjected to alternate cycles of heating and wetting. Concentration and condensation of the amino acid into short glycine oligomers was observed. These reactions were seen to occur only at surface step edges and micro-pore sites. Polymerization of biological molecules on the surface of clay minerals under simulated prebiotic conditions may help to explain the emergence of these more complex molecules on the early Earth.

Diffusion of Mn2+ ions into liposomes mediated by phosphatidate and monitored by the activation of an encapsulated enzymatic system

Transbilayer diffusion of Mn2+ ions occurred in liposomes formed from dipalmitoyl-phosphatidylcholine or egg-yolk phosphatidylcholine and egg-yolk phosphatidate (molar ratio 2:1) containing DNA and DNase I within their aqueous compartments. Cation diffusion was demonstrated by the hydrolytic activity of DNase I, activated by the Mn2+ ions that diffused into the vesicles, and this was confirmed by light scattering. Phosphatidate, a cone-shaped lipid which has been synthesized under simulated prebiotic conditions, was necessary for cation diffusion across the liposome membranes. Such liposomes represent a simple precellular system that interchanges cations with the surroundings and provides a microenvironment for enzymatic reactions, as evidenced by the hydrolysis of DNA by DNase I inside these closed lipid compartments.

Non-enzymatic synthesis of the coenzymes, uridine diphosphate glucose and cytidine diphosphate choline, and other phosphorylated metabolic intermediates.

The synthesis of uridine diphosphate glucose (UDPG), cytidine diphosphate choline (CDP-choline), glucose-1-phosphate (G1P) and glucose-6-phosphate (G6P) has been accomplished under simulated prebiotic conditions using urea and cyanamide, two condensing agents considered to have been present on the primitive Earth. The synthesis of UDPG was carried out by reacting G1P and UTP at 70 degrees C for 24 hours in the presence of the condensing agents in an aqueous medium. CDP-choline was obtained under the same conditions by reacting choline phosphate and CTP X G1P and G6P were synthesized from glucose and inorganic phosphate at 70 degrees C for 16 hours. Separation and identification of the reaction products have been performed by paper chromatography, thin layer chromatography, enzymatic analysis and ion pair reverse phase high performance liquid chromatography. These results suggest that metabolic intermediates could have been synthesized on the primitive Earth from simple precursors by means of prebiotic condensing agents.

Some thoughts on the evolutionary basis for the prominent role of ATP and ADP in cellular energy metabolism

The predominance of the adenosine triphosphate/adenosine diphosphate (ATP/ADP) couple in cellular phosphorylation reactions, including those that form the basis for cellular energy metabolism, cannot be explained on thermodynamic grounds since a variety of "high energy phosphate" compounds (including ADP itself) found in the cell would, based on thermodynamic considerations, be at least as effective as ATP in serving as a phosphoryl donor. How then did present-day organisms come to rely on the ATP/ADP couple as the principal mediator of phosphorylation reactions? The early appearance of adenine compounds in the prebiotic environment is suggested by experiments indicating that, relative to other purine or pyridimine compounds, adenine derivatives are preferentially synthesized under simulated prebiotic conditions (Ponnamperuma et al., 1963). In addition to the roles of adenine nucleotides in phosphorylation reactions, other adenine derivatives (e.g. Coenzyme A, flavin adenine dinucleotide, puridine nucleotides) are employed in a variety of metabolic roles. The principal function of the adenine moiety in these latter cases is in the binding of these derivatives to the relevant enzyme. The capability for binding of the adenine moiety appears to have arisen early in evolution and been exploited in a multitude of contexts, a suggestion consistent with observed similarities between the binding sites of several enzymes employing adenine derivatives as substrate. The early availability of suitable adenine compounds in the biosphere and development of complementary binding sites on cellular proteins, coupled with the expected advantages in having a limited number of metabolites as central mediators of endergonic and exergonic metabolism could readily have led to the observed pre-eminence of adenine nucleotides in cellular energy metabolism.(ABSTRACT TRUNCATED AT 250 WORDS)

Encapsulation of macromolecules by lipid vesicles under simulated prebiotic conditions.

Phospholipid vesicles (liposomes) were subjected to dehydration-hydration cycles in the presence of 6-carboxyfluorescein or salmon sperm DNA. We found that the vesicles fused into multilamellar structures during dehydration with solutes trapped between the lamellae. Upon rehydration the lamellae swelled and formed large vesicular structures containing solute. This model can be used to study encapsulation of macromolecules by lipid membranes to form protocellular structures under prebiotic conditions.

Synthesis of uracil and thymine under simulated prebiotic conditions

Evaporation and mild heating of solutions of beta-alanine and urea in the presence of clay minerals leads to the formation of 5,6-dihydrouracil (DHU). Ultraviolet irradiation of DHU in the presence of clay minerals and water vapor leads to the synthesis of uracil. Addition of acetate to this system results in the synthesis of thymine. The entire pathway could plausibly occur in pools subject to cycles of dehydration and rehydration and would result in the formation of significant concentrations of uracil and thymine from indisputably prebiotic materials.

Prebiotic phosphorylation-nucleotide synthesis with apatite

An evaporating-pond model has been utilized for the phosphorylation of nucleosides under simulated prebiotic conditions. The evaporation of dilute solutions of uridine and ammonium oxalate, in contact with apatite and under relatively mild conditions, leads to the synthesis of uridine phosphates. The addition of low concentrations of several condensing agents substantially increases the yield of nucleotide. The nature and concentrations of the materials employed are believed to make this model of prebiotic nucleotide synthesis the first reported to be consistent with geological constraints.