Prebiotic Experiments Research Articles

Experimental and theoretical studies of the interactions of alanine onto surfaces of olivine and montmorillonite: relevance in astrobiology

Abstract Amino acids have been detected in some meteorites and are readily synthesized in prebiotic experiments. These molecules may have been precursors of oligomers and polymers in the early Earth. These reactions were likely to happen in the protected confined spaces on the porous surface of olivine and in the interlayer nanospace of montmorillonite. This study describes experimental and theoretical research on the sorption of l-alanine onto surfaces of silicate minerals, olivine and montmorillonite. Kinetics of the sorption of this amino acid at different pH media was performed. This sorption has been also studied at atomic scale by means of quantum mechanical calculations finding that this sorption is energetically favourable. These results strongly support the premise that minerals could have actively participated in prebiotic reactions.

Structural characterization of a novel fucosylated trisaccharide prepared from bacterial exopolysaccharides and evaluation of its prebiotic activity

Fucosylated oligosaccharides have promising prospects in various fields. In this study, a fucosylated trisaccharide (GFG) was separated from the acidolysis products of exopolysaccharides from Clavibacter michiganensis M1. Structural characterization demonstrated that GFG consists of glucose, galactose, and fucose, with a molecular weight of 488 Da. Nuclear magnetic resonance analysis showed that it has a different structure than that of 2′-fucosyllactose (2′-FL), even though they have the same monosaccharide composition. In vitro prebiotic experiments were conducted to evaluate the differences in the utilization of three selected carbohydrates by fourteen bacterial strains. In comparison with 2′-FL, GFG could be utilized by more beneficial bacteria, leading to generate more short-chain fatty acids. Moreover, GFG could not promote the proliferation of Escherichia coli. This work describes a novel fucosylated oligosaccharide and its preparation method, and the obtained trisaccharide may serve as a promising candidate for fucosylated human milk oligosaccharides.

Molecular Precursors of the RNA-World in Space: New Nitriles in the G+0.693−0.027 Molecular Cloud

Nitriles play a key role as molecular precursors in prebiotic experiments based on the RNA-world scenario for the origin of life. These chemical compounds could have been partially delivered to the young Earth from extraterrestrial objects, stressing the importance of establishing the reservoir of nitriles in the interstellar medium. We report here the detection towards the molecular cloud G+0.693−0.027 of several nitriles, including cyanic acid (HOCN), and three C4H3N isomers (cyanoallene, CH2CCHCN; propargyl cyanide, HCCCH2CN; and cyanopropyne (CH3CCCN), and the tentative detections of cyanoformaldehyde (HCOCN), and glycolonitrile (HOCH2CN). We have also performed the first interstellar search of cyanoacetaldehyde (HCOCH2CN), which was not detected. Based on the derived molecular abundances of the different nitriles in G+0.693−0.027 and other interstellar sources, we have discussed their formation mechanisms in the ISM. We propose that the observed HOCN abundance in G+0.693−0.027 is mainly due to surface chemistry and subsequent shock-induced desorption, while HCOCN might be mainly formed through gas-phase chemistry. In the case of HOCH2CN, several grain-surface routes from abundant precursors could produce it. The derived abundances of the three C4H3N isomers in G+0.693−0.027 are very similar, and also similar to those previously reported in the dark cold cloud TMC-1. This suggests that the three isomers are likely formed through gas-phase chemistry from common precursors, possibly unsaturated hydrocarbons (CH3CCH and CH2CCH2) that react with the cyanide radical (CN). The rich nitrile feedstock found towards G+0.693−0.027 confirms that interstellar chemistry is able to synthesize in space molecular species that could drive the prebiotic chemistry of the RNA-world.

Prebiotic experiments simulating hydrothermal vents: Influence of olivine in the decomposition of simple carboxylic acids

Hydrothermal systems have been proposed as keen environments on the early Earth where chemical evolution processes could have occurred. The presence of minerals and a continuous energy flux stand out among the most remarkable conditions in such environments. In this research the decomposition of two organic acids was studied. Ionizing radiation and thermal energy were the sources selected for decomposition tests, as both are naturally present on hydrothermal systems and probably, they were present on early Earth. Radiation could come from unstable elements in minerals, and heat is the most abundant energy source in hydrothermal systems. As minerals play a key role in prebiotic chemistry experiments and are an essential component on hydrothermal environments, the role of olivine in decomposition was tested. Results indicate that both organic acids highly decomposed when irradiated or heated. Radiation is more efficient than heating in decomposing the carboxylic acids and forming other carboxylic acids. Interestingly, the occurrence of olivine affects decomposition on both heated and irradiated samples, as both the rate of decomposition, and the amount and type of products vary compared with experiments without the mineral. The formation of other carboxylic acids was followed in all samples. Succinic, tricarballilic, citric and carboxisuccinic acids were detected in radiolysis experiments of acetic acid. The radiolysis of formic acid produced oxalic and tartronic. The heating of acetic acid solutions formed succinic, tricarballilic, citric and carboxisuccinic acids. However, the heating of formic acids only generated oxalic acid. The presence of olivine affected the amount and type of carboxylic acids formed in radiation and heating experiments. Natural hydrothermal systems are complex environments and many variables are present in them. Our results reinforce the idea that a combination of variables is necessary to better simulate these environments in prebiotic chemistry experiments. All variables could have affected the prebiotic chemical reactions; and hence, the role of hydrothermal systems in prebiotic chemistry could be much more complex that thought.

Study of Ferrocyanide Adsorption onto Different Minerals as Prebiotic Chemistry Assays.

Considered one of the most promising building blocks of life on primitive Earth, cyanide and its complexes are likely to have played an important role in the emergence of life on the planet. Investigation into cyanide on Earth has primarily considered high concentrations, but the cyanide concentration in the oceans of prebiotic Earth was exceptionally low. Thus, Bernal's hypothesis has allowed investigators to work around this problem. We observed, however, that cyanide does not adsorb onto several minerals; therefore, ferrocyanide could be used as a cyanide source when adsorbed onto mineral surfaces to promote the synthesis of molecules of biological significance. When adsorbed onto bentonite, a mineral that has Fe3+ atoms in its interlayers, the formation of Prussian blue analog complexes occurs through endothermic reaction and with increased entropy. The adsorption of ferrocyanide onto kaolinite indicates an exothermic and outer-sphere interaction, which results in degeneracy breakdown for C ≡ N stretch energy into two new bands of FTIR-ATR spectrum. Magnetite, which has iron atoms in its structure, and ferrocyanide interactions have been observed by outer-sphere coordination as well as the formation of Prussian blue analogs, as confirmed by the appearance of a new doublet in the Mössbauer spectra and a broadband close to 750 nm at UV-visible spectroscopy. Magnetite and kaolinite experiments presented relevant results only when performed in seawater, which suggests the importance of seawater composition for prebiotic experiments. These obtained results prove that ferrocyanide interacts with minerals differently according to structure and composition and show that this complex, like the Prussian blue analogs, may have played a crucial role as a source of cyanide on primitive Earth.

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.

A carbonate-rich lake solution to the phosphate problem of the origin of life

Phosphate is central to the origin of life because it is a key component of nucleotides in genetic molecules, phospholipid cell membranes, and energy transfer molecules such as adenosine triphosphate. To incorporate phosphate into biomolecules, prebiotic experiments commonly use molar phosphate concentrations to overcome phosphate's poor reactivity with organics in water. However, phosphate is generally limited to micromolar levels in the environment because it precipitates with calcium as low-solubility apatite minerals. This disparity between laboratory conditions and environmental constraints is an enigma known as "the phosphate problem." Here we show that carbonate-rich lakes are a marked exception to phosphate-poor natural waters. In principle, modern carbonate-rich lakes could accumulate up to ∼0.1 molal phosphate under steady-state conditions of evaporation and stream inflow because calcium is sequestered into carbonate minerals. This prevents the loss of dissolved phosphate to apatite precipitation. Even higher phosphate concentrations (>1 molal) can form during evaporation in the absence of inflows. On the prebiotic Earth, carbonate-rich lakes were likely abundant and phosphate-rich relative to the present day because of the lack of microbial phosphate sinks and enhanced chemical weathering of phosphate minerals under relatively CO2-rich atmospheres. Furthermore, the prevailing CO2 conditions would have buffered phosphate-rich brines to moderate pH (pH 6.5 to 9). The accumulation of phosphate and other prebiotic reagents at concentration and pH levels relevant to experimental prebiotic syntheses of key biomolecules is a compelling reason to consider carbonate-rich lakes as plausible settings for the origin of life.

Radiolysis of succinic acid and its ammonium salt in aqueous solution: relevance in chemical evolution

This research aims to contribute in determining the stability of ammonium succinate and succinic acid in an oxygen-free aqueous medium and exposed to a high radiation field. Both molecules are readily formed in prebiotic experiments and are essential in chemical evolution processes as starting materials for more complex molecules’ formation. Several products were detected, including some N-containing compounds in the ammonium salt experiments. Their formation can be explained via the attack of water radiolysis products. Abstraction and dimerization reactions were the most important in these systems. The decomposition increased with the irradiation dose, giving rise to biologically compounds relevant for chemical evolution processes.

Prebiotic synthesis of protobiopolymers under alkaline ocean conditions.

Clasically, prebiotic chemistry has focused on the production and identification of simple organic molecules, many of them forming part of "intractable polymers" named tholins. In a previous work, we demonstrated that in experiments using an external energy source and inorganic carbon the aqueous aerosols improved the formation of hydrophilic tholins. Herein, we elucidate the role of pH (from 4 to 12) in prebiotic experiments using saline aqueous aerosols, spark discharges and an atmosphere containing CH(4). At all values of pH, the saline aqueous aerosols increased the production of a significant variety of carboxylic acids that could have been present in a primitive Krebs cycle. Moreover, the study for the first time of hydrophilic tholins by 2-D electrophoresis revealed that these are formed by a set of unexpected heavy polymeric species. The initial alkaline conditions significantly increased both the apparent molecular weight of polymeric species up to 80 kDa and their diversity. We propose the term of protobiopolymers to denote those polymeric species fractionated by 2-D electrophoresis since these are formed by biomolecules present in living systems and show diversity in length as well as in functional groups. Thus, aerosols formed in simulated alkaline ocean conditions could provide an optimal medium for the formation of the primeval materials that could be precursors to the emergence of life.

Ice And The Origin Of Life

Sea ice occurs abundantly at the polar caps of the Earth and, probably, of many other planets. Its static and dynamic properties that may be important for prebiotic and early biotic reactions are described. It concentrates substrates and has many features that are important for catalytical actions. We propose that it provided optimal conditions for the early replication of nucleic acids and the RNA world. We repeated a famous prebiotic experiment, the poly-uridylic acid-instructed synthesis of polyadenylic acid from adenylic acid imidazolides in artificial sea ice, simulating the dynamic variability of real sea ice by cyclic temperature variation. Poly(A) was obtained in high yield and reached nucleotide chain lengths up to 400 containing predominantly 3'--> 5' linkages.

Evaluating experimental artifacts in hydrothermal prebiotic synthesis experiments.

Control experiments with ultra pure deionized water were conducted to evaluate the organic contamination in hydrothermal prebiotic experiments. Different combinations of reaction vessel material, sampling tubing and stirring were tested and the amounts of organic contaminants determined. All tested types of polymer tubing were proven to introduce organic contaminants (formate, acetate and propionate ions) into the reacting solution. Stainless steel has a catalytic effect on the decomposition of formate, consistent with earlier work at high temperatures and pressures.

Investigations of Bifidobacterial Ecology and Oligosaccharide Metabolism in a Three-Stage Compound Continuous Culture System

Background: Several different types of in vitro fermentation systems are currently employed to investigate pro- and prebiotic activities in the human large intestinal microbiota, ranging from simple batch cultures, with or without stirring and pH control, to more complex models involving pH controlled single and multiple-component continuous culture systems. Methods: In this investigation, we used a three-stage continuous culture model to study the activities of colonic bacteria. This fermentation system reproduces several of the nutritional and environmental characteristics of the proximal large intestine (vessel 1) and the distal colon (vessels 2 and 3), and was validated using bacteriological, metabolic and chemical measurements made with intestinal material obtained from different regions of the large bowel. In this paper, we report studies on prospective probiotic effects of Bifidobacterium longum NCFB 2259 in relation to other bacterial populations, production of tyrosine and phenylalanine metabolites, and bacterial synthesis of enzymes involved in the formation of putatively genotoxic metabolites, including ß glucosidase (GS), arylsulphatase (AS), ß-glucuronidase (GN), nitroreductase (NR) and azoreductase (AR). Results: Bacterial activities at two different retention times were studied (31.1 and 68.4 h), which correspond to large intestinal transit times. At R = 31.4 h, significant probiotic effects were observed with respect to reductions in GS and GN, upon adding B. longum. However, despite the fact that this organism does not ferment aromatic amino acids or produce significant amounts of genotoxic enzymes, dysbiotic manifestations occurred in that both NR synthesis and dissimilatory tyrosine metabolism were stimulated. In contrast, at R = 68.4 h, GS formation increased between five and 20-fold, while GN and NR activities increased by a factor of two after adding the bifidobacterium. These data are reviewed in relation to potential health hazards that may be encountered with long-term probiotic administration. In the prebiotic experiments, the three-stage fermentation system was operated at R = 65 h. Oligofructose was added to VI to give an initial concentration of 30 grams per litre, when the system was in steady state, to study its effects on a number of experimental parameters including bifidogenicity, bacterial growth, fermentation product formation and mutagenicity. After addition of the oligosaccharide, a multiplicity of effects were observed in VI, where synthesis of NR and AR, bifidobacterial populations and overall fermentation processes were stimulated, although these influences progressively diminished in V2 and V3. Conclusions: These studies indicate that bacterial metabolism and putative beneficial consequences associated with the breakdown of readily fermentable prebiotics in the large intestine may in some circumstances be spatially and temporally limited to the proximal bowel.

Amino acid cosmogeochemistry

Amino acids are ubiquitous components of living organisms and as a result they are widely distributed on the surface of the Earth. Whereas only 20 amino acids are found in proteins, a much more diverse mixture of amino acids has been detected in carbonaceous meteorites. Amino acids in living organisms consist exclusively of the L-enantiomers, but in meteorites, amino acids with chiral carbons are present as racemic mixtures. Protein amino acids undergo a variety of diagenetic reactions that produce some other amino acids but not the unique amino acids present in meteorites. Nevertheless, trace quantities of meteoritic amino acids may occur on the Earth, either as a result of bolide impact or from the capture of cosmic dust particles. The ensemble of amino acids present on the early Earth before life existed was probably similar to those in prebiotic experiments and meteorites. This generates a question about why the L-amino acids on which life is based were selected.

Template-directed synthesis of oligonucleotides under eutectic conditions.

One of the most important sets of model prebiotic experiments consists of reactions that synthesize complementary oligonucleotides from preformed templates under nonenzymatic conditions. Most of these experiments are conducted at 4 degrees C using 0.01-0.1 M concentrations of activated nucleotide monomer and template (monomer equivalent). In an attempt to extend the conditions under which this type of reaction can occur, we have concentrated the reactants by freezing at -18 degrees C, which is close to the NaCl-H2O eutectic at -21 degrees C. The results from this set of experiments suggest that successful syntheses can occur with poly(C) concentrations as low at 5 x 10(-4) M and 2MeImpG concentrations at 10(-3) M. It was also anticipated that this mechanism might allow the previously unsuccessful poly(A)-directed synthesis of oligo(U)s to occur. However, no template effect was seen with the poly(A) and ImpU system. The failure of these conditions to allow template-directed synthesis of oligo(U)s supports the previously proposed idea that pyrimidines may not have been part of the earliest genetic material. Because of the low concentrations of monomer and template that would be expected from prebiotic syntheses, this lower temperature could be considered a more plausible geologic setting for template-directed synthesis than the standard reaction conditions.

Role of ionizing radiation in chemical evolution studies

The purpose of this paper is to emphasize the role of ionizing radiation in radiation-induced reactions in prebiotic chemistry. The use of ionizing radiation as an energy source is based on its unique qualities. Its specific manner of energy deposition and its abundance in the Earth's crust. As an example of radiation-induced reactions, the radiolysis of malonic acid was investigated. Malonic acid is converted into other carboxylic acids. The results obtained have been correlated with the ready formation of this compound in prebiotic experiments.

Racemization and the origin of optically active organic compounds in living organisms

The organic compounds synthetized in prebiotic experiments are racemic mixtures. A number of proposals have been offered to explain how asymmetric organic compounds formed on the Earth before life arose, with the influence of chiral weak nuclear interactions being the most frequent proposal. This and other proposed asymmetric syntheses give only slight enantiomeric excess and any slight excess will be degraded by racemization. This applies particularly to amino acids where half-lives of 10 5–10 6 years are to be expected at temperatures characteristic of the Earth's surface. Since the generation of chiral molecules could not have been a significant process under geological conditions, the origins of this asymmetry must have occurred at the time of the origin of life or shortly thereafter. It is possible that the compounds in the first living organisms were prochiral rather than chiral; this is unlikely for amino acids, but it is possible for the monomers of RNA-like molecules.

Methane as a chemical dosimeter in prebiotic experiments. I. Electrical Discharges, heat and shock waves

Methane as a chemical dosimeter in prebiotic experiments. I. Electrical Discharges, heat and shock waves

Energy yields in the prebiotic synthesis of hydrogen cyanide and formaldehyde

Prebiotic experiments are usually reported in terms of carbon yields, i.e., the yield of product based on the total carbon in the system. These experiments usually involve a large input of energy and are designed to maximize the yields of product. However, large inputs of energy result in multiple activation of the reactants and products. A more realistic prebiotic experiment is to remove the products of the activation step so they are not exposed a second time to the energy source. This is equivalent to transporting the products synthesized in the primitive atmosphere to the ocean, and thereby protecting them from destruction by atmospheric energy sources. Experiments of this type, using lower inputs of energy, give energy yields (moles of products/joule) which can be used to estimate the relative importance of the different energy sources on the primitive earth. Simulated prebiotic atmospheres containing either CH4, CO or CO2 with N2, H2O and variable amounts of H2 were subjected to a high frequency Tesla coil. Samples of the aqueous phase were taken at various time intervals from 1 hr to 7 days, and the energy yields were obtained by extrapolation to zero time. The samples were analyzed for HCN with the cyanide electrode and for H2CO by chromotropic acid. The spark energy was estimated by calorimetry. The temperature rise in an insulated discharge flask was compared with the temperature rise from a resistance heater in the same flask. These results will be compared with calculated production rates of HCN and H2CO from lightning and a number of photochemical processes on the primitive Earth.

Carbon and energy yields in prebiotic syntheses using atmospheres containing CH4, CO and CO2.

Yields based on carbon are usually reported in prebiotic experiments, while energy yields (moles cal-1) are more useful in estimating the yields of products that would have been obtained from the primitive atmosphere of the earth. Energy yields for the synthesis of HCN and H2CO from a spark discharge were determined for various mixtures of CH4, CO, CO2, H2, H2O, N2 and NH3. The maximum yields of HCN and H2CO from CH4, CO, and CO2 as carbon sources are about 4 X 10(-8) moles cal-1.

Role of succinic acid in chemical evolution

Succinic acid is converted into other carboxylic acids by ionizing radiation. The results obtained have been correlated with the ready formation of this compound in prebiotic experiments. Its role in biological systems may be related to its prebiotic occurrence.