Formation of the thioester, N,S-diacetylcysteine, from acetaldehyde and N,N'diacetylcystine in aqueous solution with ultraviolet light

The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain

This article proposes an evolutionary trajectory for the development of biological energy producing systems. Six main stages of energy producing system evolution are described, from early evolutionary pyrite-pulled mechanism through the Last Universal Common Ancestor (LUCA) to contemporary systems. We define the Last Pure Chemical Entity (LPCE) as the last completely non-enzymatic entity. LPCE could have had some life-like properties, but lacked genetic information carriers, thus showed greater instability and environmental dependence than LUCA. A double bubble model is proposed for compartmentalization and cellularization as a prerequisite to both highly efficient protein synthesis and transmembrane ion-gradient. The article finds that although LUCA predominantly functioned anaerobically, it was a non-exclusive anaerobe, and sulfur dominated metabolism preceded phosphate dominated one.

Evolutionary Aspects of the Oxido-Reductive Network of Methylglyoxal

In the chemoautotrophic theory for the origin of life, offered as an alternative to broth theory, the archaic reductive citric acid cycle operating without enzymes is in the center. The non-enzymatic (methyl)glyoxalase pathway has been suggested to be the anaplerotic route for the reductive citric acid cycle. In the recent years, much has been learned about methylglyoxal, but its importance in the metabolic machinery is still uncovered. If methylglyoxal had been essential participant of the early stage of evolution, then it is a legitimate question whether it might have played a role in the early oxido-reduction network, too. Therefore, an oxido-reduction network of methylglyoxal that might have functioned under ancient circumstances without enzymes was constructed and analyzed by virtue of group contribution method. Taking methylglyoxal as input material, it turned out that the evolutionary value of reactions and biomolecules were not similar. Glycerol, glycerate, and tartonate, the output components, were conserved to different degrees. Although the tartonate route was similarly favorable from energetic point of view, its intermediates are almost not present in extant biochemistry. The presence of two carboxyl or aldehyde groups, or their combination in tricarbons of the constructed network seemed disadvantageous for selection, and the inductive effect, resulting in an asymmetry in electron cloud of chemicals, might have been important. The evolutionary role for cysteine, H₂S, and formaldehyde in the emergence of high-energy bonds in the form of thioesters and in Fe-S cluster formation as well as in imidazole synthesis was shown to bridge the gap between prebiotic chemistry and contemporary biochemistry. Overall, the ideas developed here represent an approach fitting to chemoautotrophic origin of life and implying to the role of methylglyoxal in triose formation. The proposed network is expected to have an impact upon how one may think of prebiological chemical processes on methylglyoxal, too. Finally, along the evolutionary time line, the network functioning without enzymes is situated between the formation of simple organic compounds and primeval cells, being closer to the former and well preceding the last common metabolic ancestor developed after primitive cells emerged.

Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life

This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution-leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other.

Uracil-catalyzed synthesis of acetyl phosphate: a photochemical driver for protometabolism

Progress toward a protometabolism (the earliest energy storage networks) has been severely hindered by a shortage of driver reactions, which could have harnessed solar photons or coupled electron sources/sinks on the primordial Earth. Here, it is reported for the first time that thioacetate can be converted into a known metabolite, acetyl phosphate, by ultraviolet light and in aqueous solution at neutral pH. Of more compelling importance, the synthesis is catalyzed by uracil, which suggests that a genetic component may have also facilitated the emergence of metabolic pathways. The chemistry of acetyl phosphate has been extensively studied, and it is known to be a precursor of phosphate esters, pyrophosphate and possibly longer inorganic chains. Moreover, its bifunctional reactivity (as either an acetyl or phosphoryl donor) would have been integral for the first metabolic cycles.

Prebiotic formation of 'energy-rich' thioesters from glyceraldehyde and N-acetylcysteine

The 'energy-rich' thioester, N-acetyl-S-lactoylcysteine, is formed from low concentrations of glyceraldehyde and N-acetylcysteine under anaerobic conditions at ambient temperature in aqueous solutions of sodium phosphate (pH 7.0). Reactions with 2 mM glyceraldehyde, 2 mM N-acetylcysteine, and 500 mM sodium phosphate (pH 7.0) convert about 3%/day of the glyceraldehyde to lactoyl thioester. The formation of lactoyl thioester in similar reactions with 500 mM imidazole hydrochloride (pH 7.0) is supported by the thiol-dependence of lactate formation, which is 3-fold greater in the presence of thiol (0.11%/day) than in the absence of thiol (0.04%/day). The formation of lactoyl thioester is thought to proceed by the phosphate (or imidazole)-catalyzed dehydration of glyceraldehyde to give pyruvaldehyde, which adds to the thiol to form a hemithioacetal that rearranges to the thioester. A limited amount of a second thioester, N-acetyl-S-glyceroyl-cycsteine, is also formed at the beginning of these reactions. The significance of these reactions to the origin of life is discussed.

Nonenzymatic formation of "energy-rich" lactoyl and glyceroyl thioesters from glyceraldehyde and a thiol

The "energy-rich" thioester, N-acetyl-S-lactoylcysteine, is formed under anaerobic conditions from glyceraldehyde and N-acetylcysteine at ambient temperature in aqueous solutions of sodium phosphate (pH 7.0). The conversion of glyceraldehyde to lactoyl thioester occurs at a rate of about 0.4%/day in reactions with 10 mM glyceraldehyde, 10 mM thiol, and 500 mM sodium phosphate (pH 7.0). Thioester formation proceeds at an estimated efficiency of 76%, since a similar reaction with 12.5 mM thiol yields 50.7% lactate at 6 months from only 66.5% of the glyceraldehyde (or its isomer, dihydroxyacetone). The formation of lactoyl thioester most likely occurs by the phosphate-catalyzed dehydration of glyceraldehyde to give pyruvaldehyde, which combines with thiol to form a hemithioacetal that rearranges to the thioester. A second energy-rich thioester, N-acetyl-S-glyceroylcysteine, is also produced from glyceraldehyde when these reactions are carried out in the presence of oxygen and to a limited extent in the absence of oxygen. In the presence of oxygen the formation of glyceroyl thioester continues until the thiol disappears completely by oxidation. The significance of these reactions to the energetics of the origin of life is discussed.

Thiol-catalyzed formation of lactate and glycerate from glyceraldehyde

The formation of lactate from glyceraldehyde is catalyzed by the thiol, N-acetylcysteine, at ambient temperature in aqueous sodium phosphate (pH 7.0). The rate of lactate formation is more rapid at higher concentrations of sodium phosphate and is essentially the same in the presence and absence of oxygen. The formation of lactate is efficient, but proceeds slowly with an 8.8% yield of lactate after 16 days from 10 mM glyceraldehyde in the presence of 12.5 mM N-acetylcysteine and 500 mM sodium phosphate (pH 7.0). The formation of glycerate from glyceraldehyde, that occurs in the presence of oxygen and to a small extent when oxygen has been removed, is also catalyzed by the thiol, N-acetylcysteine, under the same conditions. The dramatic increase in the rate of glycerate formation that is brought about by the thiol, N-acetylcysteine, is accompanied by an equally dramatic decrease in the rates of production of glycolate and formate. Presumably, the thiol-dependent formation of lactate and glycerate occurs via their respective thioesters. The significance of these reactions to molecular evolution is discussed.

Formation of pyrophosphate on hydroxyapatite with thioesters as condensing agents

"Energy-rich" thioesters are shown to act as condensing agents in the formation of pyrophosphate on hydroxyapatite in the presence of water at ambient temperature. The yield of pyrophosphate based on thioester ranges from 2.5% to 11.4% and depends upon the pH and concentration of reactants. Reaction of 0.130 M hydroxyapatite suspended in a solution of 0.08 M sodium phosphate and 0.20 M imidazole hydrochloride (pH 7.0) with 0.10 M N,S-diacetylcysteamine for 6 days gives the highest yield of pyrophosphate (11.4%). Pyrophosphate formation requires the presence of hydroxyapatite, sodium phosphate and the thioester, N,S-diacetylcysteamine. The related thioester, N,S-diacetylcysteine, also yields pyrophosphate in reactions on hydroxyapatite.

Formation of pyrophosphate, tripolyphosphate, and phosphorylimidazole with the thioester, n, s-diacetyl-cysteamine, as the condensing agent

Reaction of 0.20M orthophosphate with 0.20M N,S-diacetylcysteamine in 0.40M imidazole at pH 7.0 or 8.0 under drying conditions at 50 degree C for 6 days yields pyrophosphate and tripolyphosphate in the presence and absence of 0.10M divalent metal ion. The efficiency of utilization of N,S-diacetylcysteamine in the formation of pyrophosphate linkages ranges from 3 - 8% under the above conditions. The thioester, N,S-diacetylcysteamine, and imidazole are required for phosphoanhydride formation. Reaction of 0.40M orthophosphate with 0.20M N,S-diacetylcysteamine in 0.40M orthophosphate with 0.20M N,S-diacetylcysteamine in 0.40M imidazole at ambient temperature for 6 days yields phosphorylimidazole in the absence or presence of 0.50M MgCl2. Phosphorylimidazole and pyrophosphate are formed in the presence of 0.05M CaCl2; pyrophosphate and tripolyphosphate are formed with 0.15M CaCl2. The efficiency of utilization of N,S-diacetylcysteamine in the formation of pyrophosphate linkages is roughly 7% at 6 days of reaction with 0.15M CaCl2. The thioester, N,S-diacetylcysteamine and imidazole are required for the formation of phosphoanhydrides. The significance of these reactions to molecular evolution is discussed.