Interaction of Aromatic Amines with Iron Oxides: Implications for Prebiotic Chemistry

The interaction of aromatic amines (aniline, p-chloroaniline, p-toludine and p-anisidine) with iron oxides (goethite, akaganeite and hematite) has been studied. Maximum uptake of amines was observed around pH 7. The adsorption data obtained at neutral pH were found to follow Langmuir adsorption. Anisidine was found to be a better adsorbate probably due to its higher basicity. In alkaline medium (pH?>?8), amines reacted on goethite and akaganeite to give colored products. Analysis of the products by GC–MS showed benzoquinone and azobenzene as the reaction products of aniline while p-anisidine afforded a dimer. IR analysis of the amine–iron oxide hydroxide adduct suggests that the surface acidity of iron oxide hydroxides is responsible for the interaction. The present study suggests that iron oxide hydroxides might have played a role in the stabilization of organic molecules through their surface activity and in prebiotic condensation reactions.     

Site-Specific Prebiotic Oligomerization Reactions of Glycine on the Surface of Hectorite

Condensation reactions of the amino acid glycine on the surface of Cu(II)-exchanged hectorite are investigated using the technique of scanning force microscopy. Prebiotic conditions are simulated using alternate wetting and heating cycles. Concentration, immobilization, and subsequent polymerization resulting in glycine oligomers are seen to occur primarily at step edges or faults in the topmost layer. Condensation reactions also occur within tiny micropores or defects in the topmost layer. These reactions are facilitated by the availability of intergallery metal cations at the step edges or pores in the surface region. Received: 19 January 1998 / Accepted: 24 April 1998     

Thermal Wet Decomposition of Prussian Blue: Implications for Prebiotic Chemistry

The complex salt named Prussian Blue, Fe₄[Fe(CN)₆]₃?15 H₂O, can release cyanide at pH>10. From the point of view of the origin of life, this fact is of interest, since the oligomers of HCN, formed in the presence of ammonium or amines, leads to a variety of biomolecules. In this work, for the first time, the thermal wet decomposition of Prussian Blue was studied. To establish the influence of temperature and reaction time on the ability of Prussian Blue to release cyanide and to subsequently generate other compounds, suspensions of Prussian Blue were heated at temperatures from room temperature to 150° at pH 12 in NH₃ environment for several days. The NH₃ wet decomposition of Prussian Blue generated hematite, α‐Fe₂O₃, the soluble complex salt (NH₄)₄[Fe(CN₆)]?1.5 H₂O, and several organic compounds, the nature and yield of which depend on the experimental conditions. Urea, lactic acid, 5,5‐dimethylhydantoin, and several amino acids and carboxylic acids were identified by their trimethylsilyl (TMS) derivatives. HCN, cyanogen (C₂N₂), and formamide (HCONH₂) were detected in the gas phase by GC/MS analysis.     

Degradation of Glycine and Alanine on Irradiated Quartz

Recent researches suggest participation of minerals in the formation of life under primordial conditions. Among all of the minerals, quartz seems to be one of the most probable to take part in such processes. However, an external source of energy is needed, e.g. electric discharge. A device simulating the proposed conditions was designed and was used to simulate prebiotic conditions. Investigation of processes occurring during the stimulation of quartz with electric discharge was studied by means of Ultraviolet–visible (UV–VIS) spectroscopy, in order to monitor the generation kinetics of free radicals. Additionally, infrared spectroscopy was applied to identify chemical reaction products created in a solution of alanine or glycine, in the presence of quartz treated with electric discharge. Formation of increased amounts of free radicals, compared to experiments performed without quartz and/or amino acid, is reported, along with identification of possible degradation products of alanine. No synthetic reactions were observed.     

Significance of Mineral Salts in Prebiotic RNA Synthesis Catalyzed by Montmorillonite

The montmorillonite-catalyzed reactions of the 5′-phosphorimidazolide of adenosine used as a model generated RNA type oligomers. These reactions were found to be dependent on the presence of mineral salts. Whereas montmorillonite (pH 7) produced only dimers and traces of trimer in water, addition of sodium chloride (0.1–2.0 M) enhanced the chain length of oligomers to 10-mers as detected by HPLC. Maximum catalytic activity was observed with sodium chloride at a concentration between 0.8 and 1.2 M. This concentration of sodium chloride resembled its abundance in the ancient oceans (0.9–1.2 M). Magnesium chloride produced a similar effect but its joint action with sodium chloride did not produce any difference in the oligomer chain length. Therefore, Mg²⁺ was not deemed necessary for generating longer oligomers. The effect of monovalent cations upon RNA chain length was: Li⁺ > Na⁺ > K⁺. A similar effect was observed with the anions with enhanced oligomer length in the following order: Cl^? > Br^? > I^?. Thus, the smaller ions facilitated the formation of the longest oligomers. Inorganic salts that tend to salt out organic compounds from water and salts which show salt-in effects had no influence on the oligomerization process indicating that the montmorillonite-catalyzed RNA synthesis is not affected by either of these hydrophobic or hydrophilic interactions. A 2.3-fold decrease in the yield of cyclic dimer was observed upon increasing the sodium chloride concentration from 0.2 to 2.0 M. Inhibition of cyclic dimer formation is vital for increasing the yield of linear dimers and longer oligomers. In summary, sodium chloride is likely to have played an essential role in any clay mineral-catalyzed prebiotic RNA synthesis.     

Arsenic Bioremediation by Biogenic Iron Oxides and Sulfides

Microcosms containing sediment from an aquifer in Cambodia with naturally elevated levels of arsenic in the associated groundwater were used to evaluate the effectiveness of microbially mediated production of iron minerals for in situ As remediation. The microcosms were first incubated without amendments for 28 days, and the release of As and other geogenic chemicals from the sediments into the aqueous phase was monitored. Nitrate or a mixture of sulfate and lactate was then added to stimulate biological Fe(II) oxidation or sulfate reduction, respectively. Without treatment, soluble As concentrations reached 3.9 ± 0.9 μM at the end of the 143-day experiment. However, in the nitrate- and sulfate-plus-lactate-amended microcosms, soluble As levels decreased to 0.01 and 0.41 ± 0.13 μM, respectively, by the end of the experiment. Analyses using a range of biogeochemical and mineralogical tools indicated that sorption onto freshly formed hydrous ferric oxide (HFO) and iron sulfide mineral phases are the likely mechanisms for As removal in the respective treatments. Incorporation of the experimental results into a one-dimensional transport-reaction model suggests that, under conditions representative of the Cambodian aquifer, the in situ precipitation of HFO would be effective in bringing groundwater into compliance with the World Health Organization (WHO) provisional guideline value for As (10 ppb or 0.13 μM), although soluble Mn release accompanying microbial Fe(II) oxidation presents a potential health concern. In contrast, production of biogenic iron sulfide minerals would not remediate the groundwater As concentration below the recommended WHO limit.     

Safety Implications of High-Field MRI: Actuation of Endogenous Magnetic Iron Oxides in the Human Body

Background

Magnetic Resonance Imaging scanners have become ubiquitous in hospitals and high-field systems (greater than 3 Tesla) are becoming increasingly common. In light of recent European Union moves to limit high-field exposure for those working with MRI scanners, we have evaluated the potential for detrimental cellular effects via nanomagnetic actuation of endogenous iron oxides in the body.

Methodology

Theoretical models and experimental data on the composition and magnetic properties of endogenous iron oxides in human tissue were used to analyze the forces on iron oxide particles.

Principal Finding and Conclusions

Results show that, even at 9.4 Tesla, forces on these particles are unlikely to disrupt normal cellular function via nanomagnetic actuation.     

On the Prebiotic Role of Iron and Sulfur

Thermodynamic data (Sillén, L. G.: 1966, Arkiv Kemi, 25, 159) indicate that there is little support for the idea that metabolic sulfur cycles were involved in prebiotic and early life processes, since under reducing conditions the equilibrium concentration of sulfur in the primordial seas should have been very low, < 10^–8 M. However, it is suggested that metabolic sulfur cycles may have become important when oxygen evolved, when iron(II) ions disappeared from the seas, and when large amounts of sulfur were released from their iron sulfide sources.     

The Asymmetry of Organic Aerosol Fission and Prebiotic Chemistry

We examine the prebiotic applicability of our recent analysis of the fission of an atmospheric aerosol particle coated with an organic film. The fission is made possible by the free energy change upon compression of the exterior monolayer film on the parent particle, which overcomes the increase in surface area associated with the production of two spherical daughter particles. Asymmetric division into a larger and a smaller particle becomes possible following surfactant film collapse. The size of the airborne parent particle is determined by the balance between aerodynamics and gravity, while the ratio of the radii of the daughters is determined by the compression characteristics of the amphiphilic molecules comprising the parent film. For an Earth atmosphere of one bar surface pressure, the larger and smaller daughters have the sizes of a single-celled bacterium and of a virus respectively. Chemical differentiation between the daughters is possible.     

Prebiotic Chemistry and the Origin of the RNA World

The demonstration that ribosomal peptide synthesis is a ribozyme-catalyzed reaction makes it almost certain that there was once an RNA World. The central problem for origin-of-life studies, therefore, is to understand how a protein-free RNA World became established on the primitive Earth. We first review the literature on the prebiotic synthesis of the nucleotides, the nonenzymatic synthesis and copying of polynucleotides, and the selection of ribozyme catalysts of a kind that might have facilitated polynucleotide replication. This leads to a brief outline of the Molecular Biologists' Dream, an optimistic scenario for the origin of the RNA World. In the second part of the review we point out the many unresolved problems presented by the Molecular Biologists' Dream. This in turn leads to a discussion of genetic systems simpler than RNA that might have “invented” RNA. Finally, we review studies of prebiotic membrane formation.     

Perchlorate Chemistry: Implications for Analysis and Remediation

Since the discovery of perchlorate in the ground and surface waters of several western states, there has been increasing interest in the health effects resulting from chronic exposure to low (parts per billion [ppb]) levels. With this concern has come a need to investigate technologies that might be used to remediate contaminated sites or to treat contaminated water to make it safe for drinking. Possible technologies include physical separation (precipitation, anion exchange, reverse osmosis, and electrodialysis), chemical and electrochemical reduction, and biological or biochemical reduction. A fairly unique combination of chemical and physical properties of perchlorate poses challenges to its analysis and reduction in the environment or in drinking water. The implications of these properties are discussed in terms of remediative or treatment strategies. Recent developments are also covered.     

Dynamin-like MxA GTPase: Structural Insights into Oligomerization and Implications for Antiviral Activity

The interferon-inducible MxA GTPase is a key mediator of cell-autonomous innate immunity against a broad range of viruses such as influenza and bunyaviruses. MxA shares a similar domain structure with the dynamin superfamily of mechanochemical enzymes, including an N-terminal GTPase domain, a central middle domain, and a C-terminal GTPase effector domain. Recently, crystal structures of a GTPase domain dimer of dynamin 1 and of the oligomerized stalk of MxA (built by the middle and GTPase effector domains) were determined. These data provide exciting insights into the architecture and antiviral function of the MxA oligomer. Moreover, the structural knowledge paves the way for the development of novel antiviral drugs against influenza and other highly pathogenic viruses.     

Interactions of Amino Acids and Aminoxazole Derivatives: Cocrystal Formation and Prebiotic Implications Enabled by Computational Analysis

Origins of Life and Evolution of Biospheres - In line with the postulated intermediacy of aminoxazoles derived from small sugars toward the direct assembly of nucleoside precursors, we show here a...     

Glycine and Diglycine as Possible Catalytic Factors in the Prebiotic Evolution of Peptides

Mutual catalytic effects within the Salt-Induced Peptide Formation (SIPF) Reaction might be one little puzzle piece in the complicated process of the formation of complex peptidic systems and their chemical evolution on the prebiotic earth. The catalytic effects of glycine and diglycine on the formation of dipeptides from mixed amino acid systems in the SIPF Reaction was investigated for systems with leucine, proline, valine and aspartic acid and showed to result in a significant increase of the yield of the majority of the produced dipeptides. The results of the experiments strongly confirm previous theories on the catalytic mechanism and show the ability of the SIPF Reaction to produce a very diverse set of peptide products with relevance to the formation of a biosphere.     

Facilitated Oligomerization of Mycobacterial GroEL: Evidence for Phosphorylation-Mediated Oligomerization

The distinctive feature of the GroES-GroEL chaperonin system in mediating protein folding lies in its ability to exist in a tetradecameric state, form a central cavity, and encapsulate the substrate via the GroES lid. However, recombinant GroELs of Mycobacterium tuberculosis are unable to act as effective molecular chaperones when expressed in Escherichia coli. We demonstrate here that the inability of M. tuberculosis GroEL1 to act as a functional chaperone in E. coli can be alleviated by facilitated oligomerization. The results of directed evolution involving random DNA shuffling of the genes encoding M. tuberculosis GroEL homologues followed by selection for functional entities suggested that the loss of chaperoning ability of the recombinant mycobacterial GroEL1 and GroEL2 in E. coli might be due to their inability to form canonical tetradecamers. This was confirmed by the results of domain-swapping experiments that generated M. tuberculosis-E. coli chimeras bearing mutually exchanged equatorial domains, which revealed that E. coli GroEL loses its chaperonin activity due to alteration of its oligomerization capabilities and vice versa for M. tuberculosis GroEL1. Furthermore, studying the oligomerization status of native GroEL1 from cell lysates of M. tuberculosis revealed that it exists in multiple oligomeric forms, including single-ring and double-ring variants. Immunochemical and mass spectrometric studies of the native M. tuberculosis GroEL1 revealed that the tetradecameric form is phosphorylated on serine-393, while the heptameric form is not, indicating that the switch between the single- and double-ring variants is mediated by phosphorylation.GroEL, an essential chaperonin, is known to form a ring-shaped structure for sequestering substrate proteins from the crowded cellular milieu and is responsible for the occurrence of various cellular processes, such as de novo folding, transport, and macromolecular assembly, within a biologically relevant time scale (7, 26, 48, 53). In Escherichia coli, GroEL, along with its cofactor GroES, assists the folding of about 10 to 30% of cytosolic proteins, among which some are known to be essential for cell viability (15, 26, 27, 31). GroEL was originally identified as the host factor responsible for phage λ and T4 capsid protein assembly and was subsequently shown to be essential for cell viability (17, 20). E. coli groEL is found in an operonic arrangement with groES (groESL), and its expression is regulated by multiple promoter elements.GroEL function has been shown to be a complex interplay between its interaction with and encapsulation of substrate proteins, with concomitant conformational changes induced by ATP binding, hydrolysis, and GroES binding (24, 56, 62). E. coli GroEL exists as a homotetradecamer forming two isologous rings of seven identical subunits each. Crystallographic analyses have delineated the three-domain architecture of GroEL monomers and the GroES-GroEL interactions (4, 63). The central region of the GroEL polypeptide, spanning amino acid residues 191 to 376, constitutes the GroES and substrate polypeptide-binding apical domain. The equatorial ATPase domain spanning two extremities of the GroEL polypeptide, that is, residues 6 to 133 and 409 to 523, is responsible for the ATPase activity and the bulk of intersubunit interactions. The hinge-forming intermediate domain, spanning two regions on the polypeptide, namely, residues 134 to 190 and 377 to 408, connects the said two domains in the tertiary structure. The conformational changes resulting from ATP binding and hydrolysis at the equatorial domain are coupled to those occurring at the apical domain via this hinge region (4, 63).The usual size limit for the substrate proteins, as shown by both in vitro and in vivo studies, is around 57 kDa, although the cis cavity is reported to theoretically accommodate larger proteins, on the order of 104 kDa (10, 27, 35, 46). Productive in vivo folding of the proteins larger than the usual size limit, such as the 86-kDa maltose binding protein fusion and 82-kDa mitochondrial aconitase, has also been reported (9, 29). Since such large substrates are difficult to accommodate in the central cavity, it has been suggested that their productive folding might occur outside the cis cavity. These studies therefore indicate that the substrate recognition patterns of GroEL may be more diverse than initially thought.Recent genome annotation studies of various bacteria have revealed that a few bacterial genomes possess multiple copies of groEL genes (2, 18, 30). The Mycobacterium tuberculosis genome bears two copies of groEL genes (groELs). One of these, groEL1, is arranged in an operon, with the cognate cochaperonin groES being the first gene, while the second copy, groEL2, exists separately on the genome (13). Recombinant mycobacterial GroELs were shown to possess biochemical features that deviated significantly from the trademark properties of E. coli GroEL. The most striking feature of M. tuberculosis GroELs, however, was their oligomeric state, where contrary to expectations, in vitro they did not form the canonical tetradecameric assembly when purified from E. coli. The proteins instead existed as lower oligomers (dimers) irrespective of the presence or absence of cofactors, such as the cognate GroES or ATP (40, 41). Furthermore, they displayed weak ATPase activities and GroES independence in preventing aggregation of the denatured polypeptides.Evolutionary studies of M. tuberculosis groEL sequences have suggested rapid evolution of the groEL1 gene, yet without turning these into pseudogenes (21). The other hypothesis suggests that M. tuberculosis, being an organism that grows slowly, might require GroEL function that does not utilize ATP rapidly but, rather, with a slow turnover rate. Alternately, additional mechanisms might exist in M. tuberculosis which could mediate regulated oligomerization of M. tuberculosis chaperonins. Such regulation might help in the controlled utilization of ATP in nutrient-deprived M. tuberculosis, as observed for other chaperones, such as small heat shock proteins (23).In the present study, we have exploited the unusual oligomeric status of the recombinant M. tuberculosis GroELs to study the significance of oligomer formation for GroEL''s function as a molecular chaperone. Furthermore, we have explored the possibility of the existence of regulated oligomerization for native M. tuberculosis GroELs in their natural setting. We first show that M. tuberculosis groEL genes are not capable of complementing a conditional allele of E. coli groEL, namely, groEL44. The results of phenotypic and biochemical analyses of GroEL variants obtained by gene shuffling and domain swapping suggest that the impaired chaperoning ability of recombinant M. tuberculosis GroELs is a consequence of their inability to form higher-order oligomers in E. coli and that oligomerization is the prelude to the formation of an active GroEL chaperonin. Further, by immunochemical and mass spectrometric (MS) analysis of native mycobacterial GroELs, we show that M. tuberculosis GroEL1 exists in multiple oligomeric forms, viz., monomeric, dimeric, heptameric (single ring), and tetradecameric (double ring) forms, and that the switch between single-ring and double-ring variants is operated by phosphorylation on a serine residue. These observations suggest that the determinants of oligomerization for M. tuberculosis GroEL1 are distinct from those of its E. coli counterpart and that it does oligomerize in M. tuberculosis (its native environment), whereas it loses its oligomerization capability when expressed in E. coli. It could thus be possible that M. tuberculosis GroEL1 requires a certain native M. tuberculosis protein, probably a eukaryotic-like Ser-Thr protein kinase, to oligomerize properly, though the precise reason cannot be discerned by these observations.     

The 1953 Stanley L. Miller Experiment: Fifty Years of Prebiotic Organic Chemistry

The field of prebiotic chemistry effectively began with a publicationin Science 50 years ago by Stanley L. Miller on the spark discharge synthesis of amino acids and other compounds using a mixture of reduced gases that were thought to represent the components of the atmosphere on the primitive Earth. On the anniversary of this landmark publication, weprovide here an accounting of the events leading to the publication of the paper. We also discuss the historical aspects that lead up to the landmark Miller experiment.     

Prebiotic Chemistry of Phosphonic Acids: Products Derived From Phosphonoacetaldehyde in the Presence of Formaldehyde

Phosphonoacetaldehyde (PAL), a phosphonic acid analogue of glycolaldehyde phosphate, reacts in the presence of formaldehyde under mildly basic conditions to produce several new products. The reaction proceeds in two stages: a fast aldol condensation of formaldehyde with PAL, and a slower reaction to produce products containing two phosphonic acid groups. We report on the derivatization, isolation by means of HPLC and characterization of these compounds. One of the products is of potential interest as a building block for a prebiotic informational polymer.     

Ascorbic Acid Oxidation and DNA Scission Catalyzed by Iron and Copper Chelates

The asorbic acid (AH^?) auto-oxidation rates catalyzed by copper chelates of 1,10-phenanthroline (OP) or by iron chelates of bleomycin (BLM) are only slightly higher than the oxidation rates catalyzed by the metal ions. AH^? oxidation in the presence of DNA is accompanied by degradation of the DNA. The rates of DNA scission by the metal chelates are markedly higher than the rates induced by the free metal ions. AH^? oxidation is slowed down in the presence of DNA which forms ternary complexes with the chelates. The ternary complexes react slowly with AH^? but induce DNA double strand breaks more efficiently than the free metal chelates. With OP, DNA is degraded by the reaction of the ternary complex, DNA-(OP)₂Cu(I), withH₂O₂

AH^? oxidation in the presence of DNA was biphasic, showing a marked rate increase after DNA was cleaved. We suggest that this sigmoidal pattern of the oxidation curves reflects the low initial oxidative activity of the ternary complexes, accelerating as DNA is degraded.

Using O₂^?produced by pulse radiolysis as a reductant, we found that AH^? oxidation with (OP)₂Cu(II) induced more DNA double strand breaks per single strand break than bipyridine-copper.

The site specific DNA damaging reactions indicated by these results are relevant to the mechanism of cytotoxic activities of bleomycin and similar antibiotics or cytotoxic agents.     

Ascorbic Acid Oxidation and DNA Scission Catalyzed by Iron and Copper Chelates

The asorbic acid (AH^-) auto-oxidation rates catalyzed by copper chelates of 1,10-phenanthroline (OP) or by iron chelates of bleomycin (BLM) are only slightly higher than the oxidation rates catalyzed by the metal ions. AH^- oxidation in the presence of DNA is accompanied by degradation of the DNA. The rates of DNA scission by the metal chelates are markedly higher than the rates induced by the free metal ions. AH^- oxidation is slowed down in the presence of DNA which forms ternary complexes with the chelates. The ternary complexes react slowly with AH^- but induce DNA double strand breaks more efficiently than the free metal chelates. With OP, DNA is degraded by the reaction of the ternary complex, DNA-(OP)₂Cu(I), withH₂O₂

AH^- oxidation in the presence of DNA was biphasic, showing a marked rate increase after DNA was cleaved. We suggest that this sigmoidal pattern of the oxidation curves reflects the low initial oxidative activity of the ternary complexes, accelerating as DNA is degraded.

Using O₂^-produced by pulse radiolysis as a reductant, we found that AH^- oxidation with (OP)₂Cu(II) induced more DNA double strand breaks per single strand break than bipyridine-copper.

The site specific DNA damaging reactions indicated by these results are relevant to the mechanism of cytotoxic activities of bleomycin and similar antibiotics or cytotoxic agents.