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PubMed1984

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.

Acetylcysteine↗
PubMed1990

Could organic matter have been preserved on Mars for 3.5 billion years?

3.5 billion years (byr) ago, when it is thought that Mars and Earth had similar climates, biological evolution on Earth had made considerable progress, such that life was abundant. It is therefore surmised that prior to this time period the advent of chemical evolution and subsequent origin of life occurred on Earth and may have occurred on Mars. Analysis for organic compounds in the soil buried beneath the Martian surface may yield useful information regarding the occurrence of chemical evolution and possibly biological evolution. Calculations based on the stability of amino acids lead to the conclusion that remnants of these compounds, if they existed on Mars 3.5 byr ago, might have been preserved buried beneath the surface oxidizing layer. For example, if phenylalanine, an amino acid of average stability, existed on Mars 3.5 byr ago, then 1.6% would remain buried today, or 25 pg-2.5 ng of C g-1 Martian soil may exist from remnants of meteoritic and cometary bombardment, assuming that 1% of the organics survived impact.

Amino Acids↗
PubMed2005

Was Darwin a creationist?

Throughout the Origin of Species, Darwin contrasts his theory of natural selection with the theory that God independently created each species. This makes it seem as though the Origin offers a scientific alternative to a theological worldview. A few months after the Origin appeared, however, the eminent anatomist Richard Owen published a review that pointed out the theological assumptions of Darwin's theory. Owen worked in the tradition of rational morphology, within which one might suggest that evolution occurs by processes that are continuous with those by which life arises from matter; in contrast, Darwin rested his account of life's origins on the notion that God created one or a few life forms upon which natural selection could act. Owen argued that Darwin's reliance on God to explain the origins of life makes his version of evolution no less supernatural than the special creationist that Darwin criticizes: although Darwin limits God to one or a few acts of creation, he still relies upon God to explain life's existence.

Biological Evolution↗
PubMed2006

Serpentinization and its implications for life on the early Earth and Mars.

Ophiolites, sections of ocean crust tectonically displaced onto land, offer significant potential to support chemolithoautotrophic life through the provision of energy and reducing power during aqueous alteration of their highly reduced mineralogies. There is substantial chemical disequilibrium between the primary olivine and pyroxene mineralogy of these ophiolites and the fluids circulating through them. This disequilibrium represents a potential source of chemical energy that could sustain life. Moreover, E (h)-pH conditions resulting from rock- water interactions in ultrabasic rocks are conducive to important abiotic processes antecedent to the origin of life. Serpentinization--the reaction of olivine- and pyroxene-rich rocks with water--produces magnetite, hydroxide, and serpentine minerals, and liberates molecular hydrogen, a source of energy and electrons that can be readily utilized by a broad array of chemosynthetic organisms. These systems are viewed as important analogs for potential early ecosystems on both Earth and Mars, where highly reducing mineralogy was likely widespread in an undifferentiated crust. Secondary phases precipitated during serpentinization have the capability to preserve organic or mineral biosignatures. We describe the petrology and mineral chemistry of an ophiolite-hosted cold spring in northern California and propose criteria to aid in the identification of serpentinizing terranes on Mars that have the potential to harbor chemosynthetic life.

Earth, Planet↗
PubMed2003

The search for life on Europa: limiting environmental factors, potential habitats, and Earth analogues.

The putative ocean of Europa has focused considerable attention on the potential habitats for life on Europa. By generally clement Earth standards, these Europan habitats are likely to be extreme environments. The objectives of this paper were to examine: (1) the limits for biological activity on Earth with respect to temperature, salinity, acidity, desiccation, radiation, pressure, and time; (2) potential habitats for life on Europa; and (3) Earth analogues and their limitations for Europa. Based on empirical evidence, the limits for biological activity on Earth are: (1) the temperature range is from 253 to 394 K; (2) the salinity range is a(H2O) = 0.6-1.0; (3) the desiccation range is from 60% to 100% relative humidity; (4) the acidity range is from pH 0 to 13; (5) microbes such as Deinococcus are roughly 4,000 times more resistant to ionizing radiation than humans; (6) the range for hydrostatic pressure is from 0 to 1,100 bars; and (7) the maximum time for organisms to survive in the dormant state may be as long as 250 million years. The potential habitats for life on Europa are the ice layer, the brine ocean, and the seafloor environment. The dual stresses of lethal radiation and low temperatures on or near the icy surface of Europa preclude the possibility of biological activity anywhere near the surface. Only at the base of the ice layer could one expect to find the suitable temperatures and liquid water that are necessary for life. An ice layer turnover time of 10 million years is probably rapid enough for preserving in the surface ice layers dormant life forms originating from the ocean. Model simulations demonstrate that hypothetical oceans could exist on Europa that are too cold for biological activity (T < 253 K). These simulations also demonstrate that salinities are high, which would restrict life to extreme halophiles. An acidic ocean (if present) could also potentially limit life. Pressure, per se, is unlikely to directly limit life on Europa. But indirectly, pressure plays an important role in controlling the chemical environments for life. Deep ocean basins such as the Mariana Trench are good analogues for the cold, high-pressure ocean of Europa. Many of the best terrestrial analogues for potential Europan habitats are in the Arctic and Antarctica. The six factors likely to be most important in defining the environments for life on Europa and the focus for future work are liquid water, energy, nutrients, low temperatures, salinity, and high pressures.

Cold Temperature↗
PubMed2005

Origins of DNA replication in the three domains of life.

Replication of DNA is essential for the propagation of life. It is somewhat surprising then that, despite the vital nature of this process, cellular organisms show a great deal of variety in the mechanisms that they employ to ensure appropriate genome duplication. This diversity is manifested along classical evolutionary lines, with distinct combinations of replicon architecture and replication proteins being found in the three domains of life: the Bacteria, the Eukarya and the Archaea. Furthermore, although there are mechanistic parallels, even within a given domain of life, the way origins of replication are defined shows remarkable variation.

Archaea↗
PubMed1985

Trace elements in chemical evolution. II: Synthesis of amino acids under simulated primitive earth conditions in the presence of trace elements.

Electric discharge experiments have been performed in a plausible primitive earth atmosphere consisting of methane, nitrogen, and water over an aqueous phase of an ammonia-ammonium buffer solution. In some experiments, ions of metal elements, calcium, magnesium, zinc, iron and molybdenum were introduced. Gas phase products and amino acids in the liquid phase were analyzed by gas chromatography. With trace metal ions, less organic compounds in the gas phase and larger amounts of amino acids were obtained than without them. The results have shown the possible importance of trace elements in chemical evolution and the origin of life on the earth.

Amino Acids↗
PubMed1984

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.

Acetylcysteine↗
PubMed1986

Did template-directed nucleation precede molecular replication?

It is proposed that mononucleotides incorporated into the surfaces of microcrystals of inorganic phosphates such as hydroxyapatite can act as templates to assemble complementary mononucleotides from solution, and that the phosphate groups of the assembled nucleotides can facilitate nucleation of a second hydroxyapatite crystal. This would provide a mechanism of replication that is subject to natural selection. The possible role of a replicating system of this kind in the origins of life on the earth is discussed.

DNA Replication↗
PubMed2000

Closure in the emergence and evolution of life. Multiple discourses or one?

Evolutionary theory formulated in terms of complex systems dynamics shows interesting convergences with the approaches of developmental systems theory and biosemiotics, especially when applied to the problem of the origin of life. Although starting from difference conceptual assumptions, all three approaches agree on the importance of closure in the form of semipermeable chemical and informational boundaries and a more circumscribed role for DNA.

Communication↗
PubMed1996

Phylogenetic perspective on microbial life in hydrothermal ecosystems, past and present.

Understanding hydrothermal ecosystems, both past and present, requires basic information on the types of organisms present. Traditional methods, which require cultivation of microorganisms, fail to detect many taxa. We have used phylogenetic analyses of small subunit rRNA sequences obtained from microorganisms of a hot spring in Yellowstone National Park to explore the archael (archaebacterial) diversity present. Analysis of these sequences reveals several novel groups of archaea, greatly expanding our conception of the diversity of high temperature microorganisms, and demonstrating that hydrothermal systems harbour a rich variety of life. Many of these groups diverged from the archael line of descent early during evolution, and an understanding of their common properties may assist in inference of the nature of the last common ancestor of all life. The data also show a specific relationship between low-temperature marine archaea and some hot spring archaea, consistent with a thermophilic origin of life. Future use of rRNA-sequence-based techniques in exploration of hydrothermal systems should greatly facilitate study of modern thermophiles and give us insight into the activities of extinct communities as well.

Archaea↗
PubMed2000

Filamentous microfossils in a 3,235-million-year-old volcanogenic massive sulphide deposit.

The record of Archaean microfossils is sparse. Of the few bona fide fossil assemblages, most are from shallow-water settings, and they are typically associated with laminated, stromatolitic sedimentary rocks. Microfossils from deep-sea hydrothermal systems have not been reported in Precambrian rocks (> 544 million years old), although thermophilic microbes are ubiquitous in modern sea-floor hydrothermal settings, and apparently have the most ancient lineages. Here, I report the discovery of pyritic filaments, the probable fossil remains of thread-like microorganisms, in a 3,235-million-year-old deep-sea volcanogenic massive sulphide deposit from the Pilbara Craton of Australia. From their mode of occurrence, the micro-organisms were probably thermophilic chemotropic prokaryotes, which inhabited sub-sea-floor hydrothermal environments. They represent the first fossil evidence for microbial life in a Precambrian submarine thermal spring system, and extend the known range of submarine hydrothermal biota by more than 2,700 million years. Such environments may have hosted the first living systems on Earth, consistent with proposals for a thermophilic origin of life.

Archaea↗
PubMed1997

Energy from redox disproportionation of sugar carbon drives biotic and abiotic synthesis.

To identify the energy source that drives the biosynthesis of amino acids, lipids, and nucleotides from glucose, we calculated the free energy change due to redox disproportionation of the substrate carbon of (1) 26-carbon fermentation reactions and (2) the biosynthesis of amino acids and lipids of E. coli from glucose. The free energy (cal/mmol of carbon) of these reactions was plotted as a function of the degree of redox disproportionation of carbon (disproportionative electron transfers (mmol)/mmol of carbon). The zero intercept and proportionality between energy yield and degree of redox disporportionation exhibited by this plot demonstrate that redox disproportionation is the principal energy source of these redox reactions (slope of linear fit = -10.4 cal/mmol of disproportionative electron transfers). The energy and disproportionation values of E. coli amino acid and lipid biosynthesis from glucose lie near this linear curve fit with redox disproportionation accounting for 84% and 96% (and ATP only 6% and 1%) of the total energy of amino acid and lipid biosynthesis, respectively. These observations establish that redox disproportionation of carbon, and not ATP, is the primary energy source driving amino acid and lipid biosynthesis from glucose. In contrast, we found that nucleotide biosynthesis involves very little redox disproportionation, and consequently depends almost entirely on ATP for energy. The function of sugar redox disproportionation as the major source of free energy for the biosynthesis of amino acids and lipids suggests that sugar disproportionation played a central role in the origin of metabolism, and probably the origin of life.

Amino Acids↗
PubMed2001

The sugar model: catalytic flow reactor dynamics of pyruvaldehyde synthesis from triose catalyzed by poly-l-lysine contained in a dialyzer.

The formation of pyruvaldehyde from triose sugars was catalyzed by poly-l-lysine contained in a small dialyzer with a 100 molecular weight cut off (100 MWCO) suspended in a much larger triose substrate reservoir at pH 5.5 and 40 degrees C. The polylysine confined in the dialyzer functioned as a catalytic flow reactor that constantly brought in triose from the substrate reservoir by diffusion to offset the drop in triose concentration within the reactor caused by its conversion to pyruvaldehyde. The catalytic polylysine solution (400 mM, 0.35 mL) within the dialyzer generated pyruvaldehyde with a synthetic intensity (rate/volume) that was 3400 times greater than that of the triose substrate solution (12 mM, 120 mL) outside the dialyzer. Under the given conditions the final yield of pyruvaldehyde was greater than twice the weight of the polylysine catalyst. During the reaction the polylysine catalyst was poisoned presumably by reaction of its amino groups with aldehyde reactants and products. Similar results were obtained using a dialyzer with a 500 MWCO. The dialyzer method of catalyst containment was selected because it provides a simple and easily manipulated experimental system for studying the dynamics and evolutionary development of confined autocatalytic processes related to the origin of life under anaerobic conditions.

Catalysis↗
PubMed2004

Sulphate metabolism among thermophiles and hyperthermophiles in natural aquatic systems.

Although controversial, the idea that hydrothermal systems may have been the site for prebiotic synthesis of organic molecules and origin of life is widely supported. For the nascent life to survive, it must have had some sort of metabolic mechanism for generating energy. However, little is known of the specific metabolic pathways utilized by the early life forms or the effect of high temperatures on their activity. Recent research on natural high temperature aquatic environments, though limited because of difficult field logistics and experimental problems, is revolutionizing our understanding of possible energy-generating redox pathways, such as sulphate reduction. An abridged review of research on thermophilic sulphate reduction is presented here. Because of a complex interplay between microbiological and geochemical entities involved, and the uncertainties that modern hydrothermal systems are proxy for biogeochemical conditions on early Earth, great caution is required for interpretation and extrapolation of data from these studies to primordial times. Furthermore, a general lack of integrated geological and microbiological studies towards a common understanding of origin and sustenance of life on Earth is starkly evident from this review.

Earth, Planet↗
PubMed2026

The proteomic origin of the genetic code.

INTRODUCTION: The origin and evolution of the genetic code is a central problem in molecular biology. Classical models have emphasized stereochemistry, frozen accidents, or adaptive optimization, often treating proteins as passive products of preexisting codes. More recent views instead portray the code as a dynamic, coevolving system shaped by reciprocal interactions among amino acids, RNA, and early catalysts. AREAS COVERED: Here, I review efforts of phylogeny reconstruction of the history of tRNA, protein structural domains, and dipeptide sequences in proteomes. These complementary approaches allow exploration of the entry of amino acids and codons into the code, and the transition from an operational RNA code in the tRNA acceptor arm to the canonical code in the anticodon loop. Evidence for ancestral synthetase enzymes with dual functions in aminoacylation and peptide-bond formation, as well as early bidirectional (sense-antisense) coding reflected in dipeptide-antidipeptide emergence is also discussed. EXPERT OPINION: The genetic code is best viewed as a proteome-driven, evolvable system in which early peptides actively shaped coding rules by stabilizing structure, expanding chemical diversity, and enhancing catalysis. This perspective connects origin-of-life studies with modern efforts of code expansion, translational engineering, and peptide-based therapeutics, highlighting the impact of the code's proteomic origin.

Genetic Code↗
PubMed2002

The protein folds as platonic forms: new support for the pre-Darwinian conception of evolution by natural law.

Before the Darwinian revolution many biologists considered organic forms to be determined by natural law like atoms or crystals and therefore necessary, intrinsic and immutable features of the world order, which will occur throughout the cosmos wherever there is life. The search for the natural determinants of organic form-the celebrated "Laws of Form"-was seen as one of the major tasks of biology. After Darwin, this Platonic conception of form was abandoned and natural selection, not natural law, was increasingly seen to be the main, if not the exclusive, determinant of organic form. However, in the case of one class of very important organic forms-the basic protein folds-advances in protein chemistry since the early 1970s have revealed that they represent a finite set of natural forms, determined by a number of generative constructional rules, like those which govern the formation of atoms or crystals, in which functional adaptations are clearly secondary modifications of primary "givens of physics." The folds are evidently determined by natural law, not natural selection, and are "lawful forms" in the Platonic and pre-Darwinian sense of the word, which are bound to occur everywhere in the universe where the same 20 amino acids are used for their construction. We argue that this is a major discovery which has many important implications regarding the origin of proteins, the origin of life and the fundamental nature of organic form. We speculate that it is unlikely that the folds will prove to be the only case in nature where a set of complex organic forms is determined by natural law, and suggest that natural law may have played a far greater role in the origin and evolution of life than is currently assumed.

Evolution, Molecular↗
PubMed2006

From Never Born Proteins to Minimal Living Cells: two projects in synthetic biology.

The Never Born Proteins (NBPs) and the Minimal Cell projects are two currently developed research lines belonging to the field of synthetic biology. The first deals with the investigation of structural and functional properties of de novo proteins with random sequences, selected and isolated using phage display methods. The minimal cell is the simplest cellular construct which displays living properties, such as self-maintenance, self-reproduction and evolvability. The semi-synthetic approach to minimal cells involves the use of extant genes and proteins in order to build a supramolecular construct based on lipid vesicles. Results and outlooks on these two research lines are shortly discussed, mainly focusing on their relevance to the origin of life studies.

Cell Membrane↗