Thermodynamics of strecker synthesis in hydrothermal systems

Submarine hydrothermal systems on the early Earth may have been the sites from which life emerged. The potential for Strecker synthesis to produce biomolecules (amino and hydroxy acids) from starting compounds (ketones, aldehydes, HCN and ammonia) in such environments is evaluated quantitatively using thermodynamic data and parameters for the revised Helgeson-Kirkham-Flowers (HKF) equation of state. Although there is an overwhelming thermodynamic drive to form biomolecules by the Strecker synthesis at hydrothermal conditions, the availability and concentration of starting compounds limit the efficiency and productivity of Strecker reactions. Mechanisms for concentrating reactant compounds could help overcome this problem, but other mechanisms for production of biomolecules may have been required to produce the required compounds on the early Earth. Geochemical constraints imposed by hydrothermal systems provide important clues for determining the potential of these and other systems as sites for the emergence of life.     

Lipid Synthesis Under Hydrothermal Conditions by Fischer- Tropsch-Type Reactions

Ever since their discovery in the late 1970's, mid-ocean-ridge hydrothermal systems have received a great deal of attention as a possible site for the origin of life on Earth (and environments analogous to mid-ocean-ridge hydrothermal systems are postulated to have been sites where life could have originated on Mars and elsewhere as well). Because no modern-day terrestrial hydrothermal systems are free from the influence of organic compounds derived from biologic processes, laboratory experiments provide the best opportunity for confirmation of the potential for organic synthesis in hydrothermal systems. Here we report on the formation of lipid compounds during Fischer-Tropsch-type synthesis from aqueous solutions of formic acid or oxalic acid. Optimum synthesis occurs in stainless steel vessels by heating at 175 °C for 2–3 days and produces lipid compounds ranging from C2 to >C35 which consist of n-alkanols, n- alkanoic acids, n-alkenes, n-alkanes and alkanones. The precursor carbon sources used are either formic acid or oxalic acid, which disproportionate to H2, CO2 and probably CO. Both carbon sources yield the same lipid classes with essentially the same ranges of compounds. The synthesis reactions were confirmed by using 13C labeled precursor acids.     

Evidence for organic synthesis in high temperature aqueous media — Facts and prognosis

Hydrothermal systems are common along the active tectonic areas of the earth. Potential sites being studied for organic matter alteration and possible organic synthesis are spreading ridges, off-axis systems, back-arc activity, hot spots, volcanism, and subduction. Organic matter alteration, primarily reductive and generally from immature organic detritus, occurs in these high temperature and rapid fluid flow hydrothermal regimes. Hot circulating water (temperature range — warm to >400 °C) is responsible for these molecular alterations, expuslion and migration. Compounds that are obviously synthesized are minor components because they are generally masked by the pyrolysis products formed from contemporary natural organic precursors. Heterocyclic sulfur compounds have been identified in high temperature zones and hydrothermal petroleums of the Guaymas Basin vent systems. They can be interpreted as being synthesized from formaldehyde and sulfur or HS _x ^– in the hydrothermal fluids.Other products from potential synthesis reactions have not yet been found in the natural systems but are expected based on known industrial processes and inferences from experimental simulation data. Various industrial processes have been reviewed and are of relevance to hydrothermal synthesis of organic compounds. The reactivity of organic compounds in hot water (200–350 °C) has been studied in autoclaves, and supercritical water as a medium for chemistry has also been evaluated. This high temperature aqueous organic chemistry and the strong reducing conditions of the natural systems suggest this as an important route to produce organic compounds on the primitive earth. Thus a better understanding of the potential syntheses of organic compounds in hydrothermal systems will require investigations of the chemistry of condensation, autocatalysis, catalysis and hydrolysis reactions in aqueous mineral buffered systems over a range of temperatures from warm to >400 °C.Presented in part at the International Society for the Study of the Origin of Life Meeting, Barcelona, Spain, July 1993.     

Chemical markers of prebiotic chemistry in hydrothermal systems.

The goal of this chapter is to suggest some organic compounds which may be indicative of prebiotic processes in hydrothermal systems or laboratory simulations of them. While the exact processes which led to the origins of life are not known, studies of life's origins of the past forty years have uncovered a plethora of potential precursor molecules. Some of these same molecules were probably present in hydrothermal systems if chemical processes there had a role in the origins of life. The types of molecules formed in primitive Earth simulation experiments and observed in the interstellar medium, on comets and meteorites will be reviewed in Section 2 of this chapter. Some reactions involving these molecules which may have been important in prebiotic syntheses will be outlined. Since near- to supercritical water is found in hydrothermal systems, its properties and aspects of organic chemistry in supercritical water at high temperature and pressure will be discussed in Section 3. Fischer-Tropsch type (FTT) reactions, which are a potential source of the building blocks of biological molecules in hydrothermal systems, are discussed in Section 4. In the concluding section, Section 5, the possible formation in hydrothermal systems of organic molecules that are believed to have been important for the origins of life is discussed.     

Enhanced Photocatalytic Performance of ZnS for Reversible Amination of α-oxo Acids by Hydrothermal Treatment

To understand how life could have originated on early Earth, it is essential to know what biomolecules and metabolic pathways are shared by extant organisms and what organic compounds and their chemical reaction channels were likely to have been primordially available during the initial phase of the formation of prebiotic metabolism. In a previous study, we demonstrated for the first time the reversible amination of α-oxo acids on the surface of photo-illuminated ZnS. The sulfide mineral is a typical component at the periphery of submarine hydrothermal vents which has been frequently argued as a very attractive venue for the origin of life. In this work, in order to simulate more closely the precipitation environments of ZnS in the vent systems, we treated newly-precipitated ZnS with hydrothermal conditions and found that its photocatalytic power was significantly enhanced because the relative crystallinity of the treated sample was markedly increased with increasing temperature. Since the reported experimental conditions are believed to have been prevalent in shallow-water hydrothermal vents of early Earth and the reversible amination of α-oxo acids is a key metabolic pathway in all extant life forms, the results of this work provide a prototypical model of the prebiotic amino acid redox metabolism. The amino acid dehydrogenase-like chemistry on photo-irradiated ZnS surfaces may advance our understanding of the establishment of archaic non-enzymatic metabolic systems.     

Nucleic Acids Bind to Nanoparticulate iron (II) Monosulphide in Aqueous Solutions

In the hydrothermal FeS-world origin of life scenarios nucleic acids are suggested to bind to iron (II) monosulphide precipitated from the reaction between hydrothermal sulphidic vent solutions and iron-bearing oceanic water. In lower temperature systems, the first precipitate from this process is nanoparticulate, metastable FeSm with a mackinawite structure. Although the interactions between bulk crystalline iron sulphide minerals and nucleic acids have been reported, their reaction with nanoparticulate FeSm has not previously been investigated. We investigated the binding of different nucleic acids, and their constituents, to freshly precipitated, nanoparticulate FeSm. The degree to which the organic molecules interacted with FeSm is chromosomal DNA > RNA > oligomeric DNA > deoxadenosine monophosphate approximately deoxyadenosine approximately adenine. Although we found that FeSm does not fluoresce within the visible spectrum and there is no quantum confinement effect seen in the absorption, the mechanism of linkage of the FeSm to these biomolecules appears to be primarily electrostatic and similar to that found for the attachment of ZnS quantum dots. The results of a preliminary study of similar reactions with nanoparticulate CuS further supported the suggestion that the interaction mechanism was generic for nanoparticulate transition metal sulphides. In terms of the FeS-world hypothesis, the results of this study further support the idea that sulphide minerals precipitated at hydrothermal vents interact with biomolecules and could have assisted in the formation and polymerisation of nucleic acids.     

Sources of organic nitrogen at the serpentinite‐hosted Lost City hydrothermal field

The reaction of ultramafic rocks with water during serpentinization at moderate temperatures results in alkaline fluids with high concentrations of reduced chemical compounds such as hydrogen and methane. Such environments provide unique habitats for microbial communities capable of utilizing these reduced compounds in present‐day and, possibly, early Earth environments. However, these systems present challenges to microbial communities as well, particularly due to high fluid pH and possibly the availability of essential nutrients such as nitrogen. Here we investigate the source and cycling of organic nitrogen at an oceanic serpentinizing environment, the Lost City hydrothermal field (30°N, Mid‐Atlantic Ridge). Total hydrolizable amino acid (THAA) concentrations in the fluids range from 736 to 2300 nm and constitute a large fraction of the dissolved organic carbon (2.5–15.1%). The amino acid distributions, and the relative concentrations of these compounds across the hydrothermal field, indicate they most likely derived from chemolithoautotrophic production. Previous studies have identified the presence of numerous nitrogen fixation genes in the fluids and the chimneys. Organic nitrogen in actively venting chimneys has δ¹⁵N values as low as 0.1‰ which is compatible with biological nitrogen fixation. Total hydrolizable amino acids in the chimneys are enriched in ¹³C by 2–7‰ compared to bulk organic matter. The distribution and absolute δ¹³C_THAA values are compatible with a chemolithoautotrophic source, an attribution also supported by molar organic C/N ratios in most active chimneys (4.1–5.5) which are similar to those expected for microbial communities. In total, these data indicate nitrogen is readily available to microbial communities at Lost City.     

Using thermodynamics to obtain geochemical information from genomes

Thermodynamic characterization of the relative stabilities of chemical compounds is a pillar of conceptual models in various fields of geosciences. Analogous models applied to genomes can yield new information about the relationship between genomes and their geochemical environments. In this perspective article, we present a chemical and thermodynamic analysis of prokaryotic lineages that have been the target of previous phylogenomic studies of evolutionary adaptation to varying redox conditions. The thermodynamic model development begins by quantifying the effects of hydrogen activity (aH₂) and temperature on the relative stabilities of organic compounds with different carbon oxidation state. When applied to proteins instead of metabolites, the same techniques can be used to identify combinations of aH₂ and temperature at which reference proteomes for Class I or Class II methanogens are relatively stable. The calculated aH₂ values are compatible with reported measurements for habitats of methanogens ranging from highly reducing submarine hydrothermal systems to less reducing environments including methanogenic sediments. In contrast to the transition between the two classes of methanogenic archaea, that between basal and terrestrial groups of Thaumarchaeota (denoting the origin of ammonia-oxidizing archaea) occurs at a less-reducing redox boundary. These examples reveal the consequences of energy minimization driving evolution and show how geochemical calculations involving biomolecules can be used to quantify and better understand the coevolution of the geosphere and biosphere.     

Geochemical constraints on the origin of organic compounds in hydrothermal systems

It is proposed that abiotic synthesis of organic compounds occurs in metastable states. These states are permitted by kinetic barriers which inhibit the approach to stable equilibrium in the C-H-O-N system. Evidence for metastable equilibrium among organic compounds in sedimentary basins is reviewed, and further evidence is elucidated from hydrous pyrolysis experiments reported in the literature. This analysis shows that at hydrothermal conditions, organic compounds are formed or destroyed primarily through oxidation/reduction reactions, and that the role of temperature is to lower the kinetic barriers to these reactions. These lines of evidence allow the development of a scenario in which abiotic synthesis can occur at hydrothermal conditions through the reduction of CO₂ and N₂. This scenario can be tested quantitatively with distribution of species calculations as functions of temperature, pressure, hydrogen fugacity (fH₂) and initial composition. One example of such a test is given for an early, sudden outgassing of the Earth, in which CO₂, H₂O, and N₂ are transported from the mantle to the atmosphere by hydrothermal solutions. Activities of metastable aqueous organic species which form as a consequence of this process are evaluated at conditions appropriate for seafloor hydrothermal systems, and are found to maximize at about 200 °C and between the oxidation states set by two mineral assemblages common in the oceanic crust.     

Some Mechanistic Aspects on Fmoc Solid Phase Peptide Synthesis

Peptides are biomolecules that may have several biological activities which makes them important to the environment in which they operate. Sometimes it is necessary for larger amounts of peptides to carry out some studies, like biological tests, NMR structural research or even interaction studies between peptides with other molecules. Expression can be an alternative for that. However, synthesis is specially useful when unnatural modifications or introduction of site specific tags are required. Synthetic peptides have been used for different studies such as cell signaling, development of epitope-specific antibodies, in cell-biology, biomarkers for diseases etc. Many different methodologies for peptide synthesis can be found in the literature. Solid phase peptide synthesis (SPPS) has been largely used and can be an excellent alternative to achieve larger quantities of these biomolecules. In this mini review, we aim to describe the SPPS and explain some of the mechanistic aspects and reagents involved in all phases of the synthesis: the use of resin, the ninhydrin test, some of the protecting groups, coupling reagents for peptide bond formation and the cleavage process.     

The Abiotic Formation of Hydrocarbons from Dissolved CO2 Under Hydrothermal Conditions with Cobalt-Bearing Magnetite

Conversion of CO₂ to organic compounds in hydrothermal systems is important in understanding prebiotic chemical evolution leading to the origin of life. However, organic compounds with carbon number of more than 3 have never been produced from dissolved CO₂ in simulated hydrothermal experiments. In this paper, we report that not only CH₄, C₂H₆ and C₃H₈, but also n-C₄H₁₀ and n-C₅H₁₂ could be produced from dissolved CO₂ and H₂ in the presence of cobalt-bearing magnetite at 300°C and 30 MPa. It is shown that unbranched alkanes in Anderson–Schulz–Flory distribution were the dominant hydrocarbon products produced from dissolved CO₂ catalyzed by cobalt-bearing magnetite under certain hydrothermal conditions. It is proposed that magnetite with other transition metals may act potentially as effective mineral catalysts for abiotic formation of organic compounds from dissolved CO₂ in hydrothermal systems.     

Thermodynamic Potential for the Abiotic Synthesis of Adenine, Cytosine, Guanine, Thymine, Uracil, Ribose, and Deoxyribose in Hydrothermal Systems

The thermodynamic potential for the abiotic synthesis of the five common nucleobases (adenine, cytosine, guanine, thymine, and uracil) and two monosaccharides (ribose and deoxyribose) from formaldehyde and hydrogen cyanide has been quantified under temperature, pressure, and bulk composition conditions that are representative of hydrothermal systems. The activities of the precursor molecules (formaldehyde and hydrogen cyanide) required to evaluate the thermodynamics of biomolecule synthesis were computed using the concentrations of aqueous N₂, CO, CO₂ and H₂ reported in the modern Rainbow hydrothermal system. The concentrations of precursor molecules that can be synthesized are strongly dependent on temperature with larger concentrations prevailing at lower temperatures. Similarly, the thermodynamic drive to synthesize nucleobases, ribose and deoxyribose varies considerably as a function of temperature: all of the biomolecules considered in this study are thermodynamically favored to be synthesized throughout the temperature range from 0°C to between 150°C and 250°C, depending on the biomolecule. Furthermore, activity diagrams have been generated to illustrate that activities in the range of 10⁻²– 10⁻⁶ for nucleobases, ribose and deoxyribose can be in equilibrium with a range of precursor molecule activities at 150°C and 500 bars. The results presented here support the notion that hydrothermal systems could have played a fundamental role in the origin of life, and can be used to plan and constrain experimental investigation of the abiotic synthesis of nucleic-acid related biomolecules.     

Biogenic and synthetic high magnesium calcite – A review

Systematic studies on the Mg distributions, the crystal orientations, the formation mechanisms and the mechanical properties of biogenic high-Mg calcites in different marine organisms were summarized in detail in this review. The high-Mg calcites in the hard tissues of marine organisms mentioned generally own a few common features as follows. Firstly, the Mg distribution is not uniform in most of the minerals. Secondly, high-Mg calcite biominerals are usually composed of nanoparticles that own almost the same crystallographic orientations and thus they behave like single crystals or mesocrystals. Thirdly, the formation of thermodynamically unstable high-Mg calcites in marine organisms under mild conditions is affected by three key factors, that is, the formation of amorphous calcium (magnesium) carbonate precursor, the control of polymorph via biomolecules and the high Mg/Ca ratios in modern sea. Lastly, the existence of Mg ions in the Mg-containing calcite may improve the mechanical properties of biogenic minerals. Furthermore, the key progress in the synthesis of high-Mg calcites in the laboratory based on the formation mechanisms of the biogenic high-Mg calcites was reviewed. Many researchers have realized the synthesis of high-Mg calcites in the laboratory under ambient conditions with the help of intermediate amorphous phase, mixed solvents, organic/inorganic surfaces and soluble additives. Studies on the structural analysis and formation mechanisms of thermodynamically unstable biogenic high-Mg calcite minerals may shed light on the preparation of functional materials with enhanced mechanical properties.     

Connective tissue activation in guinea pig lung fibroblast cultures: Regulatory effects of glucocorticoids

Summary Earlier studies showed that guinea pig lung fibroblasts in cell culture could be “activated” by naturally occurring peptides with a resultant increase in glycolysis and glycosaminoglycan formation. Such connective tissue activation (CTA) in human cell systems (synovial, cartilage, dermal) has proved a useful tool for studying the mechanisms of inflammation and dissecting the efficacy and actions of anti-inflammatory drugs. The present study examined the consequences of treating basal and activated guinea pig lung fibroblasts with glucocorticoids. The data indicate that glucocorticoids minimally suppress glycosaminoglycan (GAG) synthesis in nonactivated cultures. Further, CTA was inhibited to only a minor degree in activated lung fibroblast cultures by steroids, and even markedly supraphysiologic concentrations of glucocorticoids were not notably inhibitory. It was of interest that thiols enhanced suppression of incremental GAG synthesis by some glucocorticoids in activated lung fibroblast cultures. This study was supported by USPHS Grant HL-19685.     

Aspergillus oryzae produces compounds inhibiting cholesterol biosynthesis downstream of dihydrolanosterol

The formation of cholesterol synthesis inhibiting molecules by five different strains of the koji mold Aspergillus oryzae was studied. After growing these strains on a complex liquid medium we found in crude organic phase extracts and specific fractions there from compounds inhibiting cholesterol synthesis in human hepatic T9A4 cells in vitro at enzyme sites downstream of dihydrolanosterol. This was evidenced by using different radioactively labeled precursors, namely acetate, mevalonate, 24,25-dihydro-[24,25-(3)H2]-lanosterol or [3-(3)H]-lathosterol.     

Applications in Biocatalysis of Glycosyl Hydrolases from the Hyperthermophilic Archaeon Sulfolobus solfataricus

Abstract

Carbohydrates serve as structural components and energy sources of cells. More interestingly, however, these biomolecules are involved in a variety of molecular recognition processes in intercellular communication and signal transduction such as cell adhesion, differentiation, development and regulation. For these reasons, great interest has arisen in carbohydrate-based pharmaceuticals and on the development of techniques for the analysis and synthesis of oligosaccharides. In this respect, enzymes involved in carbohydrates hydrolysis and modification are increasingly being utilised for the bioconversion of sugars, for the synthesis of oligosaccharides with potential application, and for the characterisation of carbohydrate compounds of unknown structure.

In this review, the enzymology and the applications of three glycosyl hydrolases from the archaeon Sulfolobus solfataricus are described. In particular, we focus on the enzymological properties of β-glycosidase, an α-xylosidase, and an α-fucosidase; their exploitation in oligosaccharides synthesis will also be discussed.     

The Role of Submarine Hydrothermal Systems in the Synthesis of Amino Acids

There is little consensus regarding the plausibility of organic synthesis in submarine hydrothermal systems (SHSs) and its possible relevance to the origin of life. The primary reason for the persistence of this debate is that most experimental high temperature and high-pressure organic synthesis studies have neglected important geochemical constraints with respect to source material composition. We report here the results of experiments exploring the potential for amino acid synthesis at high temperature from synthetic seawater solutions of varying composition. The synthesis of amino acids was examined as a function of temperature, heating time, starting material composition and concentration. Using very favorable reactant conditions (high concentrations of reactive, reduced species), small amounts of a limited set of amino acids are generated at moderate temperature conditions (∼125–175°C) over short heating times of a few days, but even these products are significantly decomposed after exposure times of approximately 1 week. The high concentration dependence observed for these synthetic reactions are demonstrated by the fact that a 10-fold drop in concentration results in orders of magnitude lower yields of amino acids. There may be other synthetic mechanisms not studied herein that merit investigation, but the results are likely to be similar. We conclude that although amino acids can be generated from simple likely environmentally available precursors under SHS conditions, the equilibrium at high temperatures characteristic of SHSs favors net amino acid degradation rather than synthesis, and that synthesis at lower temperatures may be more favorable.     

Biomolecular Self-assembly and its Relevance in Silica Biomineralization

Biomineralization, which means the formation of inorganic materials by biological processes, currently finds increasing research interest. It involves the synthesis of calcium-based minerals such as bones and teeth in vertebrates, and of shells. Silica biomineralization occurs, for example, in diatoms and silica sponges. Usually, biominerals are made up of amorphous compounds or small microcrystalline domains embedded into an amorphous matrix. Nevertheless, they exhibit very regular shapes and, as in the case of diatoms, intricate nanopatterns of amazing beauty. It is, therefore, commonly assumed that biominerals are formed under the structure-directing influence of templates. However, single molecules are by far too small to direct the formation of the observed shapes and patterns. Instead, supramolecular aggregates are shown to be involved in the formation of templating superstructures relevant in biomineralization. Specific biomolecules were identified in both diatoms and silica sponges, which elegantly combine two indispensable functions: on the one hand, the molecules are capable of inducing silica precipitation from precursor compounds. On the other hand, these molecules are capable of self-assembling into larger, structure-directing template aggregates. Such molecules are the silaffins in the case of diatoms and the silicateins in sponges. Long-chain polyamines of similar composition have meanwhile been discovered in both organisms. The present review is especially devoted to the discussion of the self-assembly behavior of these molecules. Physico-chemical studies on a model compound, poly(allylamine), are discussed in detail in order to elucidate the nature of the interactions responsible for self-assembly of long-chain polyamines and the parameters controlling this process. Numerous biomimetic silica synthesis experiments are discussed and evaluated with respect to the observations made on the aforementioned "natural" biomolecules.     

Yarrowia lipolytica and pollutants: Interactions and applications

Yarrowia lipolytica is a dimorphic, non-pathogenic, ascomycetous yeast species with distinctive physiological features and biochemical characteristics that are significant in environment-related matters. Strains naturally present in soils, sea water, sediments and waste waters have inherent abilities to degrade hydrocarbons such as alkanes (short and medium chain) and aromatic compounds (biphenyl and dibenzofuran). With the application of slow release fertilizers, design of immobilization techniques and development of microbial consortia, scale-up studies and in situ applications have been possible. In general, hydrocarbon uptake in this yeast is mediated by attachment to large droplets (via hydrophobic cell surfaces) or is aided by surfactants and emulsifiers. Subsequently, the internalized hydrocarbons are degraded by relevant enzymes innately present in the yeast. Some wild-type or recombinant strains also detoxify nitroaromatic (2,4,6-trinitrotoluene), halogenated (chlorinated and brominated hydrocarbons) and organophosphate (methyl parathion) compounds. The yeast can tolerate some metals and detoxify them via different biomolecules. The biomass (unmodified, in combination with sludge, magnetically-modified and in the biofilm form) has been employed in the biosorption of hexavalent chromium ions from aqueous solutions. Yeast cells have also been applied in protocols related to nanoparticle synthesis. The treatment of oily and solid wastes with this yeast reduces chemical oxygen demand or value-added products (single cell oil, single cell protein, surfactants, organic acids and polyalcohols) are obtained. On account of all these features, the microorganism has established a place for itself and is of considerable value in environment-related applications.