Prebiotic Microreactors: A Synthesis of Purines and Dihydroxy Compounds in Aqueous Aerosol

We report the synthesis of purine bases and other heterocycles and the formation of amino acids, hydroxy acids and dihydroxy compounds by the spark activation of an atmosphere of methane, nitrogen and hydrogen, in the presence of an aqueous aerosol. With the aid of the interface air–water, the organic material obtained shows greater amounts and diversity of molecules with biological interest than the products obtained in the absence of an aerosol. Our results support the suggestion that aerosols may have played a significant role in the prebiotic origin of molecular diversity and evolution.     

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.     

Hydrothermal Circulation of Seawater through Hot Vents and Contribution of Interface Chemistry to Prebiotic Synthesis

Synthesizing oligopeptides from glycine andalanine in a flow reactor, which stimulates constanthydrothermal circulation of seawater through hot vents onthe primitive Earth, demonstrated that an exponential growthof the products is possible. The initial rapid growth of the product is a consequence of using the products formed inone cycle as the starting materials for the cycle of synthesis.     

Asymmetric Spatiotemporal Evolution of Prebiotic Homochirality

The role of asymmetry on the evolution of prebiotic homochirality is investigated in the context of autocatalytic polymerization reaction networks. A model featuring enantiometric cross-inhibition and chiral bias is used to study the diffusion equations controlling the spatiotemporal development of left and right-handed domains. Bounds on the chiral bias are obtained based on present-day constraints on the emergence of life on early Earth. The viability of biasing mechanisms such as weak neutral currents and circularly polarized UV light is discussed. The results can be applied to any hypothetical planetary platform.     

Prebiotic Adenine Revisited: Eutectics and Photochemistry

Recent studies support an earlier suggestion that, if adenine was formed prebiotically on the primitive earth, eutectic freezing of hydrogen cyanide solutions is likely to have been important. Here we revisit the suggestion that the synthesis of adenine may have involved the photochemical conversion of the tetramer of hydrogen cyanide in eutectic solution to 4-amino-5-cyano-imidazole. This would make possible a reaction sequence that does not require the presence of free ammonia. It is further suggested that the reaction of cyanoacetylene with cyanate in eutectic solution to give cytosine might have proceeded in parallel with adenine synthesis.     

Prebiotic Methylation and the Evolution of Methyl Transfer Reactions in Living Cells

An hypothesis is presented for theprebiotic origin of methyl groups and the evolution ofmethyl transfer reactions in living cells. This hypothesis,described in terms of prebiotic and early biotic chemicalevolution, is based on experimental observations in our laband in those of others, and on the mechanisms of enzymaticmethyl transfer reactions that occur in living cells. Ofparticular interest is our demonstration of the reductivemethylation of ethanolamine and glycine in aqueous solutionby excess formaldehyde. These reactions, involving prebioticcompounds and conditions, are mechanistically analogous tothe de novo origin of methyl groups in modern cellsby reduction of methylene tetrahydrofolate. Furthermore,modern cellular methyl transfers from S-adenosylmethionineto amine nitrogen may involve formaldehyde as anintermediate and subsequent reductive methylation, analogousto the prebiotic chemistry observed herein.     

Concentration by Evaporation and the Prebiotic Synthesis of Cytosine

The efficient prebiotic synthesis of cytosine from urea andcyanoacetaldehyde (CA) has recently been claimed to be invalidon the basis of possible side reactions of the starting materials and the inapplicability of prebiotic syntheses usingdrying beach conditions. We therefore have investigated the synthesis of cytosine and uracil from urea and cyanoacetaldehydeat 100 °C under dry-down conditions, and in solution at 4 °C and -20 °C. We find that cytosine isproduced from the low temperature experiments more efficientlythan calculated from the Arrhenius extrapolation from highertemperatures, i.e., 60-120 °C. In addition, we findthat CA dimer is as efficient as the monomer in cytosine synthesis. We also studied whether evaporating very dilutesolutions of nonvolatile organic compounds will concentrateaccording to theory. Solutions as dilute as 10^-4 M concentrate from pure water approximately according to theory.Similar solutions in 0.5 M NaCl have less than theoreticalconcentrations due to absorption, but concentrations neardryness were very high.     

Prebiotic Synthesis of Nucleotides

If an RNA-only world preceded more complex forms oflife, then it is essential that the process wherebythe first nucleotides were made be considered. Presumably there were no enzymes and no templates tofacilitate the synthesis of the first nucleotides soanother form of chemical evolution must have beeninvolved. Answers to problems of this sort weresought vigorously in the 1960s and the early 1970s butmany issues were left unresolved. Progress made inthe last few years has added to this early work andbrings us closer to a satisfactory solution. In thisarticle key results, old and new, and some ideas as tohow further progress is likely to be made are discussed.There are reasons for optimism. Substantial progresshas been made on the synthesis of purines and ribose,phosphorylation and polyphosphorylation. Theoutstanding problems at this juncture relate to thesynthesis of ribose to the exclusion of the otheraldopentoses and to the problem of linking ribose tothe purine bases.     

Comments on `Concentration by Evaporation and the Prebiotic Synthesis of Cytosine'

The claim by Nelson et al. (2001) that the reactionof cyanoacetaldehyde and urea provides `an efficient prebioticsynthesis' of cytosine is disputed. The authors have not dealt withthe important points presented in a criticism of this reaction(Shapiro, 1999): (1) The reactants undergo side reactions with commonnucleophiles that appear to proceed more rapidly than cytosineformation, and (2) No reactions have been described thus far thatwould produce cytosine at a rate sufficient to compensate for itsdecomposition by deamination, and permit accumulation over extendedperiods of time. Instead, Nelson et al. have conducted `drying-down' experiments, inan effort to simulate evaporations on the early Earth, but thedesign of these experiments is flawed. The initial reactantconcentrations are much higher than might be expected in a naturalsetting, and potentially interfering substances such as glycine,cyanide and thiols have been excluded. `Drying beaches and dryinglagoons' have been invoked as sites for such a reaction but noeffort has been made to describe the characteristics of such sitesor to estimate their frequency with reference to the present Earth.In the absence of contradictory data, the conclusion put forward inShapiro (1999) remains valid: `It was quite unlikely that cytosineplayed a role in the origin of life'.     

The Fission Yeast php2 Mutant Displays a Lengthened Chronological Lifespan

The Schizosaccharomyces pombe php2 ⁺ gene encodes a subunit of the CCAAT-binding factor complex. We found that disruption of the php2 ⁺ gene extended the chronological lifespan of the fission yeast. Moreover, the lifespan of the Δphp2 mutant was barely extended under calorie restricted (CR) conditions. Many other phenotypes of the Δphp2 mutant resembled those of wild-type cells grown under CR conditions, suggesting that the Δphp2 mutant might undergo CR. The mutant also showed low respiratory activity concomitant with decreased expression of the cyc1 ⁺ and rip1 ⁺ genes, both of which are involved in mitochondrial electron transport. On the basis of a chromatin immunoprecipitation assay, we determined that Php2 binds to a DNA region upstream of cyc1 ⁺ and rip1 ⁺ in S. pombe. Here we discuss the possible mechanisms by which the chronological lifespan of Δphp2 mutant is extended.     

The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe

The rate at which new mutations arise in the genome is a key factor in the evolution and adaptation of species. Here we describe the rate and spectrum of spontaneous mutations for the fission yeast Schizosaccharomyces pombe, a key model organism with many similarities to higher eukaryotes. We undertook an ∼1700-generation mutation accumulation (MA) experiment with a haploid S. pombe, generating 422 single-base substitutions and 119 insertion-deletion mutations (indels) across the 96 replicates. This equates to a base-substitution mutation rate of 2.00 × 10⁻¹⁰ mutations per site per generation, similar to that reported for the distantly related budding yeast Saccharomyces cerevisiae. However, these two yeast species differ dramatically in their spectrum of base substitutions, the types of indels (S. pombe is more prone to insertions), and the pattern of selection required to counteract a strong AT-biased mutation rate. Overall, our results indicate that GC-biased gene conversion does not play a major role in shaping the nucleotide composition of the S. pombe genome and suggest that the mechanisms of DNA maintenance may have diverged significantly between fission and budding yeasts. Unexpectedly, CpG sites appear to be excessively liable to mutation in both species despite the likely absence of DNA methylation.     

Glyoxylate as a Backbone Linkage for a Prebiotic Ancestor of RNA

The origin of the first RNA polymers is central to most current theories for the origin of life. Difficulties associated with the prebiotic formation of RNA have lead to the general consensus that a simpler polymer preceded RNA. However, polymers proposed as possible ancestors to RNA are not much easier to synthesize than RNA itself. One particular problem with the prebiotic synthesis of RNA is the formation of phosphoester bonds in the absence of chemical activation. Here we demonstrate that glyoxylate (the ionized form of glyoxylic acid), a plausible prebiotic molecule, represents a possible ancestor of the phosphate group in modern RNA. Although in low yields (∼ 1%), acetals are formed from glyoxylate and nucleosides under neutral conditions, provided that metal ions are present (e.g., Mg²⁺), and provided that water is removed by evaporation at moderate temperatures (e.g., 65 ^∘C), i.e. under “drying conditions”. Such acetals are termed ga-dinucleotides and possess a linkage that is analogous to the backbone in RNA in both structure and electrostatic charge. Additionally, an energy-minimized model of a gaRNA duplex predicts a helical structure similar to that of A-form RNA. We propose that glyoxylate-acetal linkages would have had certain advantages over phosphate linkages for early self-replicating polymers, but that the distinct functional properties of phosphoester and phosphodiester bonds would have eventually lead to the replacement of glyoxylate by phosphate.     

The Potential of Photochemical Transition Metal Reactions in Prebiotic Organic Synthesis. I. Observed Conversion of Methanol into Ethylene Glycol as Possible Prototype for Sugar Alcohol Formation

Photochemical processes involving redox reactions between metal ions and organic substrates possess the versatile potential for having harnessed solar energy for prebiotic organic synthesis. The present study in our Laboratory has shown that ultraviolet irradiation of transition metal ions such as of Ni, Co, Fe, Cu and Ti dissolved in primary or secondary alcohols causes photoreduction of the metal ions with the concomitant oxidation of the alcohol to aldehyde or ketone. An observed accompaniment of this novel 'light' reaction has been the known 'dark' pinacol reaction, whereby the carbonyl derivative underwent bimolecular coupling to the diol by the photogenerated reduced transition metal reagent. These tandem 'light-dark' processes possess the potential for the stepwise synthesis of dimeric 1,2-diols from simpler alcohols under conditions that might have prevailed on the prebiotic earth. Experiments reported here have demonstrated that such a tandem 'light-dark' conversion of methanol into ethylene glycol, via formaldehyde, does in fact occur, when nickel(II) acetylacetonate solutions in methanol undergo prolonged irradiation at 185-254 nm. Since ethylene glycol can be considered as the simplest sugar alcohol, these findings may provide novel insight into the prebiotic oligomerization of formaldehyde into higher sugar alcohols or even sugars.     

Insight into Actin Organization and Function in Cytokinesis from Analysis of Fission Yeast Mutants

Actin is a key cytoskeletal protein with multiple roles in cellular processes such as polarized growth, cytokinesis, endocytosis, and cell migration. Actin is present in all eukaryotes as highly dynamic filamentous structures, such as linear cables and branched filaments. Detailed investigation of the molecular role of actin in various processes has been hampered due to the multifunctionality of the protein and the lack of alleles defective in specific processes. The actin cytoskeleton of the fission yeast, Schizosaccharomyces pombe, has been extensively characterized and contains structures analogous to those in other cell types. In this study, primarily with the view to uncover actin function in cytokinesis, we generated a large bank of fission yeast actin mutants that affect the organization of distinct actin structures and/or discrete physiological functions of actin. Our screen identified 17 mutants with specific defects in cytokinesis. Some of these cytokinesis mutants helped in dissecting the function of specific actin structures during ring assembly. Further genetic analysis of some of these actin mutants revealed multiple genetic interactions with mutants previously known to affect the actomyosin ring assembly. We also characterize a mutant allele of actin that is suppressed upon overexpression of Cdc8p-tropomyosin, underscoring the utility of this mutant bank. Another 22 mutant alleles, defective in polarized growth and/or other functions of actin obtained from this screen, are also described in this article. This mutant bank should be a valuable resource to study the physiological and biochemical functions of actin.     

Analysis of Evolutionarily Independent Protein-RNA Complexes Yields a Criterion to Evaluate the Relevance of Prebiotic Scenarios

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Fission and the dynamics of genets and ramets in clonal cnidarian populations

Until relatively recently many species of entomostracan crustaceans were thought to have widespread, even cosmopolitan distributions. Evidence now suggests that this is far less the case than thought. However, an exception appears to be provided by the crustaceans of episodically filled waterbodies. Typically these include Anostraca, Notostraca and Conchostraca. The paper considers the distribution of Triops australiensis (Branchiopoda: Notostraca) in Australia. There, it is a frequent inhabitant of episodically filled temporary waters. It is absent from such waters in northern Australia. A biogeoclimatic analysis using the program BIOCLIM indicates that this is because of the absence of suitable localities. BIOCLIM enables the preparation of maps which provide statistical predictions of climates suitable for the survival of a particular taxon. These predictions are based upon the known climate of localities where the taxon in question actually occurs. It is suggested that for the biota of shallow ephemeral waters (such as those typically inhabited by Anostraca, Conchostraca and Notostraca) biogeoclimatic analysis has a powerful predictive value.     

Fission of the bilayer lipid tube

The fusion of two black lipid membranes results in the formation of peculiar bilayer lipid tubes (‘cylindrical’) membranes (Neher, E. (1974) Biochim. Biophys. Acta 373, 328–336 and Melikyan, G.B., Abidor, L.G., Chernomordik, L.V. and Chailakhyan, L.M. (1983) Biochim. Biophys. Acta 730, 395–398). The mechanical stability of such tubes has been investigated experimentally and theoretically. With increasing hydrostatic pressure on the outside of the tube the radius of its middle part decreases. After this radius has reached a critical value, which constitutes 0.55 of the radius of the tube base, there occurs a collapse of the tube and its disintegration into two planar bilayers (fission). Expressions are obtained which relate the transmembrane difference of the hydrostatic pressure, causing the collapse, to the geometrical characteristics of the tube (its length and the radius of its base) and to the tension of the lipid bilayer. A method for measuring the membrane tension is proposed on the basis of the phenomenon considered.     

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.