The origin and early evolution of life on Earth

Gradual evolution of a homo-l-peptide world on homo-d-configured RNA and DNA

Modern life requires the translation of genetic information - encoded by nucleic acids - into proteins, which establishes the essential link between genotype and phenotype. During translation, exclusively l-amino acids are loaded onto transfer RNA molecules (tRNA), which are then connected at the ribosome to give homo-l-proteins. In contrast to the homo-l-configuration of amino acids and proteins, the oligonucleotides involved are all d-configured (deoxy)ribosides. Previously, others and us have shown that if peptide synthesis occurs at homo d-configured oligonucleotides, a pronounced l-amino acid selectivity is observed, which reflects the d-sugar/l-amino acid world that evolved in nature. Here we further explore this astonishing selectivity. We show a peptide-synthesis/recapture-cycle that can lead to a gradual enrichment and hence selection of a homo-l-peptide world. We show that even if peptides with a mixed l/d-stereochemistry are formed, they are not competitive against the homo-l-counterparts. We also demonstrate that this selectivity is not limited to RNA but that peptide synthesis on DNA features the same l-amino acid preference. In total, the data bring us a step closer to an understanding of how homochirality on Earth once evolved.

A Bayesian Analysis of the Probability of the Origin of Life Per Site Conducive to Abiogenesis

The emergence of life from nonlife, or abiogenesis, remains a fundamental question in scientific inquiry. In this article, we investigate the probability of the origin of life (per conducive site) by leveraging insights from Earth's environments. If life originated endogenously on Earth, its existence is indeed endowed with informative value, although the interpretation of the attendant significance hinges critically upon prior assumptions. By adopting a Bayesian framework, for an agnostic prior, we establish a direct connection between the number of potential locations for abiogenesis on Earth and the probability of life's emergence per site. Our findings suggest that constraints on the availability of suitable environments for the origin(s) of life on Earth may offer valuable insights into the probability of abiogenesis and the frequency of life in the universe.

A Fusion-Growth Protocell Model Based on Vesicle Interactions with Pyrite Particles

Protocell models play a pivotal role in the exploration of the origin of life. Vesicles are one type of protocell model that have attracted much attention. Simple single-chain amphiphiles (SACs) and organic small molecules (OSMs) possess primitive relevance and were most likely the building blocks of protocells on the early Earth. OSM@SAC vesicles have been considered to be plausible protocell models. Pyrite (FeS2), a mineral with primitive relevance, is ubiquitous in nature and plays a crucial role in the exploration of the origin of life in the mineral-water interface scenario. "How do protocell models based on OSM@SAC vesicles interact with a mineral-water interface scenario that simulates a primitive Earth environment" remains an unresolved question. Hence, we select primitive relevant sodium monododecyl phosphate (SDP), isopentenol (IPN) and pyrite (FeS2) mineral particles to build a protocell model. The model investigates the basic physical and chemical properties of FeS2 particles and reveals the effects of the size, content and duration of interaction of FeS2 particles on IPN@SDP vesicles. This deepens the understanding of protocell growth mechanisms in scenarios of mineral-water interfaces in primitive Earth environments and provides new information for the exploration of the origin of life.

Information Transmission via Molecular Communication in Astrobiological Environments

The ubiquity of information transmission via molecular communication between cells is comprehensively documented on Earth; this phenomenon might even have played a vital role in the origin(s) and early evolution of life. Motivated by these considerations, a simple model for molecular communication entailing the diffusion of signaling molecules from transmitter to receiver is elucidated. The channel capacity C (maximal rate of information transmission) and an optimistic heuristic estimate of the actual information transmission rate ℐ are derived for this communication system; the two quantities, especially the latter, are demonstrated to be broadly consistent with laboratory experiments and more sophisticated theoretical models. The channel capacity exhibits a potentially weak dependence on environmental parameters, whereas the actual information transmission rate may scale with the intercellular distance d as ℐ ∝ d-4 and could vary substantially across settings. These two variables are roughly calculated for diverse astrobiological environments, ranging from Earth's upper oceans (C ∼ 3.1 × 103 bits/s; ℐ ∼ 4.7 × 10-2 bits/s) and deep sea hydrothermal vents (C ∼ 4.2 × 103 bits/s; ℐ ∼ 1.2 × 10-1 bits/s) to the hydrocarbon lakes and seas of Titan (C ∼ 3.8 × 103 bits/s; ℐ ∼ 2.6 × 10-1 bits/s).

Viruses in astrobiology

Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.

The Dissipative Photochemical Origin of Life: UVC Abiogenesis of Adenine

The non-equilibrium thermodynamics and the photochemical reaction mechanisms are described which may have been involved in the dissipative structuring, proliferation and complexation of the fundamental molecules of life from simpler and more common precursors under the UVC photon flux prevalent at the Earth’s surface at the origin of life. Dissipative structuring of the fundamental molecules is evidenced by their strong and broad wavelength absorption bands in the UVC and rapid radiationless deexcitation. Proliferation arises from the auto- and cross-catalytic nature of the intermediate products. Inherent non-linearity gives rise to numerous stationary states permitting the system to evolve, on amplification of a fluctuation, towards concentration profiles providing generally greater photon dissipation through a thermodynamic selection of dissipative efficacy. An example is given of photochemical dissipative abiogenesis of adenine from the precursor HCN in water solvent within a fatty acid vesicle floating on a hot ocean surface and driven far from equilibrium by the incident UVC light. The kinetic equations for the photochemical reactions with diffusion are resolved under different environmental conditions and the results analyzed within the framework of non-linear Classical Irreversible Thermodynamic theory.

One Step up the Ladder of Prebiotic Complexity: Formation of Nonrandom Linear Polypeptides from Binary Systems of Amino Acids on Silica

Evidence for the formation of linear oligopeptides with nonrandom sequences from mixtures of amino acids coadsorbed on silica and submitted to a simple thermal activation is presented. The amino acid couples (glutamic acid+leucine) and (aspartic acid+valine) were deposited on a fumed silica and submitted to a single heating step at moderate temperature. The evolution of the systems was characterized by X-ray diffraction, infrared spectroscopy, thermosgravimetric analysis, HPLC, and electrospray ionization mass spectrometry (ESI-MS). Evidence for the formation of amide bonds was found in all systems studied. While the products of single amino acids activation on silica could be considered as evolutionary dead ends, (glutamic acid+leucine) and, at to some extent, (aspartic acid+valine) gave rise to the high yield formation of linear peptides up to the hexamers. Oligopeptides of such length have not been observed before in surface polymerization scenarios (unless the amino acids had been deposited by chemical vapor deposition, which is not realistic in a prebiotic environment). Furthermore, not all possible amino acid sequences were present in the activation products, which is indicative of polymerization selectivity. These results are promising for origins of life studies because they suggest the emergence of nonrandom biopolymers in a simple prebiotic scenario.

When the Surface Matters: Prebiotic Peptide-Bond Formation on the TiO2 (101) Anatase Surface through Periodic DFT-D2 Simulations

The mechanism of the peptide-bond formation between two glycine (Gly) molecules has been investigated by means of PBE-D2* and PBE0-D2* periodic simulations on the TiO₂ (101) anatase surface. This is a process of great relevance both in fundamental prebiotic chemistry, as the reaction univocally belongs to one of the different organizational events that ultimately led to the emergence of life on Earth, as well as from an industrial perspective, since formation of amides is a key reaction for pharmaceutical companies. The efficiency of the surface catalytic sites is demonstrated by comparing the reactions in the gas phase and on the surface. At variance with the uncatalyzed gas-phase reaction, which involves a concerted nucleophilic attack and dehydration step, on the surface these two steps occur along a stepwise mechanism. The presence of surface Lewis and Brönsted sites exerts some catalytic effect by lowering the free energy barrier for the peptide-bond formation by about 6 kcal mol^-1 compared to the gas-phase reaction. Moreover, the co-presence of molecules acting as proton-transfer assistants (i.e., H₂ O and Gly) provide a more significant kinetic energy barrier decrease. The reaction on the surface is also favorable from a thermodynamic standpoint, involving very large and negative reaction energies. This is due to the fact that the anatase surface also acts as a dehydration agent during the condensation reaction, since the outermost coordinatively unsaturated Ti atoms strongly anchor the released water molecules. Our theoretical results provide a comprehensive atomistic interpretation of the experimental results of Martra et al. (Angew. Chem. Int. Ed. 2014, 53, 4671), in which polyglycine formation was obtained by successive feedings of Gly vapor on TiO₂ surfaces in dry conditions and are, therefore, relevant in a prebiotic context envisaging dry and wet cycles occurring, at mineral surfaces, in a small pool.

Phosphorylation, oligomerization and self-assembly in water under potential prebiotic conditions

Prebiotic phosphorylation of (pre)biological substrates under aqueous conditions is a critical step in the origins of life. Previous investigations have had limited success and/or require unique environments that are incompatible with subsequent generation of the corresponding oligomers or higher-order structures. Here, we demonstrate that diamidophosphate (DAP)-a plausible prebiotic agent produced from trimetaphosphate-efficiently (amido)phosphorylates a wide variety of (pre)biological building blocks (nucleosides/tides, amino acids and lipid precursors) under aqueous (solution/paste) conditions, without the need for a condensing agent. Significantly, higher-order structures (oligonucleotides, peptides and liposomes) are formed under the same phosphorylation reaction conditions. This plausible prebiotic phosphorylation process under similar reaction conditions could enable the systems chemistry of the three classes of (pre)biologically relevant molecules and their oligomers, in a single-pot aqueous environment.

Astrobiology: Towards an Understanding of the Emergence of Life in the Universe

Long before the idea of spontaneous generation was incorporated by JeanBaptiste de Lamarck into evolutionary biology to explain the first emergence of life, the possibility that other planets were inhabited had been discussed, sometimes in considerable detail, by scientists and philosophers alike (Lazcano 2001). More often than not, these were speculations that rested on the idea of a uniform universe but with little or no empirical basis. Today our approaches to the issue of life in the Universe have changed dramatically; neither the formation of planets nor the origin of life are seen as the result of inscrutable random events, but rather as natural outcomes of evolutionary events. The interconnection between these two processes is evident: understanding the formation of planets has major implications for our understanding of the early terrestrial environment, and therefore for the origin of living systems.

Mineral Surface Chemistry and Nanoparticle-aggregation Control Membrane Self-Assembly

The self-assembly of lipid bilayer membranes to enclose functional biomolecules, thus defining a “protocell,” was a seminal moment in the emergence of life on Earth and likely occurred at the micro-environment of the mineral-water interface. Mineral-lipid interactions are also relevant in biomedical, industrial and technological processes. Yet, no structure-activity relationships (SARs) have been identified to predict lipid self-assembly at mineral surfaces. Here we examined the influence of minerals on the self-assembly and survival of vesicles composed of single chain amphiphiles as model protocell membranes. The apparent critical vesicle concentration (CVC) increased in the presence of positively-charged nanoparticulate minerals at high loadings (mg/mL) suggesting unfavorable membrane self-assembly in such situations. Above the CVC, initial vesicle formation rates were faster in the presence of minerals. Rates were correlated with the mineral’s isoelectric point (IEP) and reactive surface area. The IEP depends on the crystal structure, chemical composition and surface hydration. Thus, membrane self-assembly showed rational dependence on fundamental mineral properties. Once formed, membrane permeability (integrity) was unaffected by minerals. Suggesting that, protocells could have survived on rock surfaces. These SARs may help predict the formation and survival of protocell membranes on early Earth and other rocky planets, and amphiphile-mineral interactions in diverse other phenomena.

Comets and Life on the Primitive Earth

Comets may have contributed substantial amounts of water, volatiles and organic precursors such as HCN for the synthesis of biochemical compounds on the primitive Earth. This suggestion followed closely the prebiotic synthesis of adenine, purines and amino acids from HCN. Recent studies on the terrestrial heavy noble gases provide evidence that comets are the principal external source of Earth’s volatiles. During the encounter of comet Halley strong jets of CN, C2, C3and NH2were measured from Earth observatories, and by spacecraft mass spectrometry HCN, formaldehyde, adenine and many other organic compounds were detected, except amino acids. Obviously the latter require liquid water for their formation. Therefore upon capture of comets by the Earth, and melting of the frozen water, the synthesis of most biochemical compounds could take place readily. The detection of water, HCN and other organics of cometary origin after the impact of Comet SL-9 with Jupiter demonstrated the capability of survival of these molecules even after catastrophic events. Thus on the Earth HCN could be converted into purines, cyanacetylene, after hydration and condensation with urea, into pyrimidines, and formaldehyde into monosaccharides. In the presence of phosphates, which have been detected in cometary IDPs, nucleotides could also be synthesized. In conclusion, comets probably provided the necessary molecular precursors for the generation of life on the Earth.

Diversity of phosphorus reserves in microorganisms

Phosphorus compounds are indispensable components of the Earth's biomass metabolized by all living organisms. Under excess of phosphorus compounds in the environment, microorganisms accumulate reserve phosphorus compounds that are used under phosphorus limitation. These compounds vary in their structure and also perform structural and regulatory functions in microbial cells. The most common phosphorus reserve in microorganism is inorganic polyphosphates, but in some archae and bacteria insoluble magnesium phosphate plays this role. Some yeasts produce phosphomannan as a phosphorus reserve. This review covers also other topics, i.e. accumulation of phosphorus reserves under nutrient limitation, phosphorus reserves in activated sludge, mycorrhiza, and the role of mineral phosphorus compounds in mammals.

Origination of the Protein Fold Repertoire from Oily Pluripotent Peptides

While the repertoire of protein folds that exists today underlies most of life’s capabilities, our mechanistic picture of protein fold origination is incomplete. This paper discusses a hypothetical mechanism for the emergence of the protein fold repertoire from highly dynamic and collapsed peptides, exemplified by peptides with high oil content or hydrophobicity. These peptides are called pluripotent to emphasize their capacity to evolve into numerous folds transiently available to them. As evidence, the paper will discuss previous simulation work on the superior fold evolvability of oily peptides, trace (“fossil”) evidence within proteomes seen today, and a general relationship between protein dynamism and evolvability. Aside from implications on the origination of protein folds, the hypothesis implies that the vanishing utility of a random peptide in protein origination may be relatively exaggerated, as some random peptides with a certain composition (e.g., oily) may fare better than others. In later sections, the hypothesis is discussed in the context of existing discussions regarding the spontaneous origination of biomolecules.

Atmospheric Prebiotic Chemistry and Organic Hazes

Earth's atmospheric composition at the time of the origin of life is not known, but it has often been suggested that chemical transformation of reactive species in the atmosphere was a significant source of prebiotic organic molecules. Experimental and theoretical studies over the past half century have shown that atmospheric synthesis can yield molecules such as amino acids and nucleobases, but these processes are very sensitive to gas composition and energy source. Abiotic synthesis of organic molecules is more productive in reduced atmospheres, yet the primitive Earth may not have been as reducing as earlier workers assumed, and recent research has reflected this shift in thinking. This work provides a survey of the range of chemical products that can be produced given a set of atmospheric conditions, with a particular focus on recent reports. Intertwined with the discussion of atmospheric synthesis is the consideration of an organic haze layer, which has been suggested as a possible ultraviolet shield on the anoxic early Earth. Since such a haze layer - if formed - would serve as a reservoir for organic molecules, the chemical composition of the aerosol should be closely examined. The results highlighted here show that a variety of products can be formed in mildly reducing or even neutral atmospheres, demonstrating that contributions of atmospheric synthesis to the organic inventory on early Earth should not be discounted. This review intends to bridge current knowledge of the range of possible atmospheric conditions in the prebiotic environment and pathways for synthesis under such conditions by examining the possible products of organic chemistry in the early atmosphere.

Prokaryotic nucleotide excision repair

Nucleotide excision repair (NER) has allowed bacteria to flourish in many different niches around the globe that inflict harsh environmental damage to their genetic material. NER is remarkable because of its diverse substrate repertoire, which differs greatly in chemical composition and structure. Recent advances in structural biology and single-molecule studies have given great insight into the structure and function of NER components. This ensemble of proteins orchestrates faithful removal of toxic DNA lesions through a multistep process. The damaged nucleotide is recognized by dynamic probing of the DNA structure that is then verified and marked for dual incisions followed by excision of the damage and surrounding nucleotides. The opposite DNA strand serves as a template for repair, which is completed after resynthesis and ligation.

Understanding prebiotic chemistry through the analysis of extraterrestrial amino acids and nucleobases in meteorites

The discoveries of amino acids of extraterrestrial origin in many meteorites over the last 50 years have revolutionized the Astrobiology field. A variety of non-terrestrial amino acids similar to those found in life on Earth have been detected in meteorites. A few amino acids have even been found with chiral excesses, suggesting that meteorites could have contributed to the origin of homochirality in life on Earth. In addition to amino acids, which have been productively studied for years, sugar-like molecules, activated phosphates, and nucleobases have also been determined to be indigenous to numerous meteorites. Because these molecules are essential for life as we know it, and meteorites have been delivering them to the Earth since accretion, it is plausible that the origin(s) of life on Earth were aided by extraterrestrially-synthesized molecules. Understanding the origins of life on Earth guides our search for life elsewhere, helping to answer the question of whether biology is unique to Earth. This tutorial review focuses on meteoritic amino acids and nucleobases, exploring modern analytical methods and possible formation mechanisms. We will also discuss the unique window that meteorites provide into the chemistry that preceded life on Earth, a chemical record we do not have access to on Earth due to geologic recycling of rocks and the pervasiveness of biology across the planet. Finally, we will address the future of meteorite research, including asteroid sample return missions.

Elements of metabolic evolution

Research into the origin of evolution is polarized between a genetics-first approach, with its focus on polymer replication, and a metabolism-first approach that takes aim at chemical reaction cycles. Taking the latter approach, we explored reductive carbon fixation in a volcanic hydrothermal setting, driven by the chemical potential of quenched volcanic fluids for converting volcanic C1 compounds into organic products by transition-metal catalysts. These catalysts are assumed to evolve by accepting ever-new organic products as ligands for enhancing their catalytic power, which in turn enhances the rates of synthetic pathways that give rise to ever-new organic products, with the overall effect of a self-expanding metabolism. We established HCN, CO, and CH(3)SH as carbon nutrients, CO and H(2) as reductants, and iron-group transition metals as catalysts. In one case, we employed the "cyano-system" [Ni(OH)(CN)] with [Ni(CN)(4)](2-) as the dominant nickel-cyano species. This reaction mainly produced α-amino acids and α-hydroxy acids as well as various intermediates and derivatives. An organo-metal-catalyzed mechanism is suggested that mainly builds carbon skeletons by repeated cyano insertions, with minor CO insertions in the presence of CO. The formation of elemental nickel (Ni(0)) points to an active reduced-nickel species. In another case, we employed the mercapto-carbonyl system [Co(2)(CO)(8)]/Ca(OH)(2)/CO for the double-carbonylation of mercaptans. In a "hybrid system", we combined benzyl mercaptan with the cyano system, in which [Ni(OH)(CN)] was the most productive for the double-carbon-fixation reaction. Finally, we demonstrated that the addition of products of the cyano system (Gly, Ala) to the hybrid system increased productivity. These results demonstrate the chemical possibility of metabolic evolution through rate-promotion of one synthetic reaction by the products of another.

Earth's earliest atmospheres

Earth is the one known example of an inhabited planet and to current knowledge the likeliest site of the one known origin of life. Here we discuss the origin of Earth's atmosphere and ocean and some of the environmental conditions of the early Earth as they may relate to the origin of life. A key punctuating event in the narrative is the Moon-forming impact, partly because it made Earth for a short time absolutely uninhabitable, and partly because it sets the boundary conditions for Earth's subsequent evolution. If life began on Earth, as opposed to having migrated here, it would have done so after the Moon-forming impact. What took place before the Moon formed determined the bulk properties of the Earth and probably determined the overall compositions and sizes of its atmospheres and oceans. What took place afterward animated these materials. One interesting consequence of the Moon-forming impact is that the mantle is devolatized, so that the volatiles subsequently fell out in a kind of condensation sequence. This ensures that the volatiles were concentrated toward the surface so that, for example, the oceans were likely salty from the start. We also point out that an atmosphere generated by impact degassing would tend to have a composition reflective of the impacting bodies (rather than the mantle), and these are almost without exception strongly reducing and volatile-rich. A consequence is that, although CO- or methane-rich atmospheres are not necessarily stable as steady states, they are quite likely to have existed as long-lived transients, many times. With CO comes abundant chemical energy in a metastable package, and with methane comes hydrogen cyanide and ammonia as important albeit less abundant gases.

Peptide-dominated membranes preceding the genetic takeover by RNA: latest thinking on a classic controversy

It is commonly presumed that abiotic membranes were colonized by proteins later on. Yet, hydrophobic peptides could have formed primordial protein-dominated membranes on their own. In a metabolism-first context, "autocatalytically closed" sets of statistical peptides could organize a self-maintaining protometabolism, assisted by an unfolding set of ribotide-related cofactors. Pairwise complementary ribotide cofactors may have formed docking guides for stochastic peptide formation, before replicating RNA emerged from this subset. Tidally recurring wet-drying cycles and an early onset of photosynthetic activities are considered most likely to meet the thermodynamic requirements. Conceivably, the earliest peptide-dominated vesicles were engaged in light harvesting, together with isoprenoid-tethered pigments, rather than providing an external boundary. Early on, the bulk of prebiotic organic matter can have formed a contiguous layer covering the mineral sediment, held in place by colloidal coherence of a hydrogel matrix. This unconventional scenario assumes a late onset of cellular individualization - perhaps from within, resembling endosporogenesis.

On the origin of life in the zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth

BACKGROUND

The complexity of the problem of the origin of life has spawned a large number of possible evolutionary scenarios. Their number, however, can be dramatically reduced by the simultaneous consideration of various bioenergetic, physical, and geological constraints.

RESULTS

This work puts forward an evolutionary scenario that satisfies the known constraints by proposing that life on Earth emerged, powered by UV-rich solar radiation, at photosynthetically active porous edifices made of precipitated zinc sulfide (ZnS) similar to those found around modern deep-sea hydrothermal vents. Under the high pressure of the primeval, carbon dioxide-dominated atmosphere ZnS could precipitate at the surface of the first continents, within reach of solar light. It is suggested that the ZnS surfaces (1) used the solar radiation to drive carbon dioxide reduction, yielding the building blocks for the first biopolymers, (2) served as templates for the synthesis of longer biopolymers from simpler building blocks, and (3) prevented the first biopolymers from photo-dissociation, by absorbing from them the excess radiation. In addition, the UV light may have favoured the selective enrichment of photostable, RNA-like polymers. Falsification tests of this hypothesis are described in the accompanying article (A.Y. Mulkidjanian, M.Y. Galperin, Biology Direct 2009, 4:27).

CONCLUSION

The suggested "Zn world" scenario identifies the geological conditions under which photosynthesizing ZnS edifices of hydrothermal origin could emerge and persist on primordial Earth, includes a mechanism of the transient storage and utilization of solar light for the production of diverse organic compounds, and identifies the driving forces and selective factors that could have promoted the transition from the first simple, photostable polymers to more complex living organisms.

Organics produced by irradiation of frozen and liquid HCN solutions: implications for chemical evolution studies

Hydrogen cyanide (HCN), an important precursor of organic compounds, is widely present in extraterrestrial environments. HCN is also readily synthesized in prebiotic simulation experiments. To gain insight into the radiation chemistry of one of the most important and highly versatile constituents of cometary ices, we examined the behavior of over-irradiated frozen and liquid HCN solutions under ionizing radiation. The samples were exposed to gamma radiation at a dose range from 0 up to 419 kGy. Ultraviolet spectroscopy and gas chromatography were used to follow the process. The analyses confirmed that gamma-ray irradiation of liquid HCN solutions generates several organic products. Many of them are essential to life; we verified the presence of carboxylic acids (some of them members of the Krebs cycle) as well as free amino acids and urea. These are the first studies to reveal the presence of these compounds in experiments performed at low temperatures and bulk irradiation. Organic material was produced even at low temperatures and low radiation doses. This work strongly supports the presumption that, as a parent molecule, HCN played a central essential role in the process of chemical evolution on early Earth, comets, and other extraterrestrial environments.

Cell evolution and the problem of membrane topology

Cells somehow evolved from primordial chemistry and their emergence depended on the co-evolution of the cytoplasm, a genetic system and the cell membrane. It is widely believed that the cytoplasm evolved inside a primordial lipid vesicle, but here I argue that the earliest cytoplasm could have co-evolved to high complexity outside a vesicle on the membrane surface. An invagination of the membrane, aided by an early cytoskeletal system, may have formed the first cells--initially within primordial vesicles.

Getting specificity from simplicity in putative proteins from the prebiotic earth

Can unique protein structures arise from a limited set of amino acids present on the prebiotic earth? To address this question, we have determined the stability and structure of KIA7, a 20-residue polypeptide containing chiefly Lys, Ile, and Ala. NMR methods reveal that KIA7 tetramerizes and folds on the millisecond time scale to adopt a four-helix X-bundle structure with a tightly and specifically packed core. Denaturation studies and hydrogen exchange measurements of KIA7 and several variants demonstrate that ridges-into-grooves packing of Ala and Ile side chains and the packing of a C-terminal aromatic group into the hydrophobic core are sufficient to give rise to a rather stable, well folded protein structure, with no favorable electrostatic interactions or tertiary or quaternary hydrogen bonds. Both modern proteins and RNAs can adopt specific structures, but RNAs do so with a limited "alphabet" of residues and types of stabilizing interactions. The results reported here show that specific, well folded protein structures can also arise from a highly reduced set of stabilizing interactions and amino acids that are thought to have been present on the prebiotic earth.

Porphyrin as an ideal biomarker in the search for extraterrestrial life

A key issue in astrobiological research is identifying target molecules that are unambiguously biological in origin and can be easily detected and recognized. We suggest porphyrin derivatives as an ideal target, because these chromophores are global in distribution and found in virtually all living organisms on Earth, including microorganisms that may approximate the early evolution of life on Earth. We discuss the inherent qualities that make porphyrin ideally suited for astrobiological research and discuss methods for detecting porphyrin molecules in terrestrial sedimentary environments. We present preliminary data to support the use of ToFSIMS as a powerful technique in the identification of porphyrins.

Photocatalysis and the origin of life: synthesis of nucleoside bases from formamide on TiO2(001) single surfaces

We report the conversion of a large fraction of formamide (NH(2)CHO) to high-molecular-weight compounds attributed to nucleoside bases on the surface of a TiO(2) (001) single crystal in ultra-high vacuum conditions. If true, we present previously unreported evidence for making biologically relevant molecules from a C1 compound on any single crystal surface in high vacuum and in dry conditions. An UV light of 3.2 eV was necessary to make the reaction. This UV light excites the semiconductor surface but not directly the adsorbed formamide molecules or the reaction products. There thus is no need to use high energy in the form of photons or electrical discharge to make the carbon-carbon and carbon-nitrogen bonds necessary for life. Consequently, the reaction products may accumulate with time and may not be subject to decomposition by the excitation source. The formation of these molecules, by surface reaction of formamide, is proof that some minerals in the form of oxide semiconductors are active materials for making high-molecular-weight organic molecules that may have acted as precursors for biological compounds required for life in the universe.

Condensation reactions and formation of amides, esters, and nitriles under hydrothermal conditions

Hydrothermal pyrolysis experiments were performed to assess condensation (dehydration) reactions to amide, ester, and nitrile functionalities from lipid precursors. Beside product formation, organic compound alteration and stability were also evaluated. Mixtures of nonadecanoic acid, hexadecanedioic acid, or hexadecanamide with water, ammonium bicarbonate, and oxalic acid were heated at 300 degrees C for 72 h. In addition, mixtures of ammonium bicarbonate and oxalic acid solutions were used to test the abiotic formation of organic nitrogen compounds at the same temperature. The resulting products were condensation compounds such as amides, nitriles, and minor quantities of N-methylalkyl amides, alkanols, and esters. Mixtures of alkyl amide in water or oxalic acid yielded mainly hydrolysis and dehydration products, and with ammonium bicarbonate and oxalic acid the yield of condensation products was enhanced. The synthesis experiments with oxalic acid and ammonium bicarbonate solutions yielded homologous series of alkyl amides, alkyl amines, alkanes, and alkanoic acids, all with no carbon number predominances. These organic nitrogen compounds are stable and survive under the elevated temperatures of hydrothermal fluids.

Noisy clues to the origin of life

The origin of stable self-replicating molecules represents a fundamental obstacle to the origin of life. The low fidelity of primordial replicators places restrictions on the quantity of information encoded in a primitive nucleic acid alphabet. Further difficulties for the origin of life are the role of drift in small primordial populations, reducing the rate of fixation of superior replicators, and the hostile conditions increasing developmental noise. Thus, mutation, noise and drift are three different stochastic effects that are assumed to make the evolution of life improbable. Here we show, to the contrary, how noise present in hostile early environments can increase the probability of faithful replication, by amplifying selection in finite populations. Noise has negative consequences in infinite populations, whereas in finite populations, we observe a synergistic interaction among noise sources. Hence, two factors formerly considered inimical to the origin of life-developmental noise and drift in small populations-can in combination give rise to conditions favourable to robust replication.

Reaction behaviors of glycine under super- and subcritical water conditions

The influence of temperature and pressure on the dimerization and decomposition of glycine under simulated hydrothermal system conditions was studied by injecting a glycine solution into water in the sub- and supercritical state. The experiments at five different temperatures of supplied water--250, 300, 350, 374, and 400 degrees C--were performed at 22.2 and 40.0 MPa. At 350 degrees C, experiments under 15.0-40.0 MPa were conducted. Diglycine, triglycine (trace), diketopiperazine, and an unidentified product with a high molecular mass (433 Da) were the main products of oligomerization. The results show that temperature and pressure influence the extent of dimerization and decomposition of glycine. The maximum of dimers formation was observed at 350 and 375 degrees C at 22.2 and 40.0 MPa, respectively, and coincided with a high rate of glycine decomposition. Glycine, alanine, aspartic acid, as well as other amino acids, were obtained by injecting a mixture of formaldehyde and ammonia. The results support the oligomerization and synthesis of amino acids in a submarine hydrothermal system.

Comets and the formation of biochemical compounds on the primitive Earth--a review

Thirty years ago it was suggested that comets impacting on the primitive Earth may have represented a significant source of terrestrial volatiles, including some important precursors for prebiotic synthesis (Oró, 1961, Nature 190: 389). This possibility is strongly supported not only by models of the collisional history of the early Earth, but also by astronomical evidence that suggests that frequent collisions of comet-like bodies from the circumstellar disk around the star beta Pictoris are taking place. Although a significant fraction of the complex organic compounds that appear to be present in cometary nuclei were probably destroyed during impact, it is argued that cometary collisions with the primitive Earth represented an important source of both free-energy and volatiles, and may have created transient, gaseous environments in which prebiotic synthesis may have taken place.

Prebiotic chemistry in clouds

In the traditional concept for the origin of life as proposed by Oparin and Haldane in the 1920s, prebiotic reactants became slowly concentrated in the primordial oceans and life evolved slowly from a series of highly protracted chemical reactions during the first billion years of Earth's history. However, chemical evolution may not have occurred continuously because planetesimals and asteroids impacted the Earth many times during the first billion years, may have sterilized the Earth, and required the process to start over. A rapid process of chemical evolution may have been required in order that life appeared at or before 3.5 billion years ago. Thus, a setting favoring rapid chemical evolution may be required. A chemical evolution hypothesis set forth by Woese in 1979 accomplished prebiotic reactions rapidly in droplets in giant atmospheric reflux columns. However, in 1985 Scherer raised a number of objections to Woese's hypothesis and concluded that it was not valid. We propose a mechanism for prebiotic chemistry in clouds that satisfies Scherer's concerns regarding the Woese hypothesis and includes advantageous droplet chemistry. Prebiotic reactants were supplied to the atmosphere by comets, meteorites, and interplanetary dust or synthesized in the atmosphere from simple compounds using energy sources such as ultraviolet light, corona discharge, or lightning. These prebiotic monomers would have first encountered moisture in cloud drops and precipitation. We propose that rapid prebiotic chemical evolution was facilitated on the primordial Earth by cycles of condensation and evaporation of cloud drops containing clay condensation nuclei and nonvolatile monomers. For example, amino acids supplied by , or synthesized during entry of, meteorites, comets, and interplanetary dust would have been scavenged by cloud drops containing clay condensation nuclei. Polymerization would have occurred within cloud systems during cycles of condensation, freezing, melting, and evaporation of cloud drops. We suggest that polymerization reactions occurred in the atmosphere as in the Woese hypothesis, but life originated in the ocean as in the Oparin-Haldane hypothesis. The rapidity with which chemical evolution could have occurred within clouds accommodates the time constraints suggested by recent astrophysical theories.

Electrical energy sources for organic synthesis on the early Earth

In 1959, Miller and Urey (Science 130, 245) published their classic compilation of energy sources for indigenous prebiotic organic synthesis on the early Earth. Much contemporary origins of life research continues to employ their original estimates for terrestrial energy dissipation by lightning and coronal discharges, 2 x 10(19) J yr-1 and 6 x 10(19) J yr-1, respectively. However, more recent work in terrestrial lightning and point discharge research suggests that these values are overestimates by factors of about 20 and 120, respectively. Calculated concentrations of amino acids (or other prebiotic organic products) in the early terrestrial oceans due to electrical discharge sources may therefore have been equally overestimated. A review of efficiencies for those experiments that provide good analogues to naturally-occurring lightning and coronal discharges suggests that lightning energy yields for organic synthesis (nmole J-1) are about one order of magnitude higher than those for coronal discharge. Therefore organic production by lightning may be expected to have dominated that due to coronae on early Earth. Limited data available for production of nitric oxide in clouds suggests that coronal emission within clouds, a source of energy heretofore too uncertain to be included in the total coronal energy inventory, is insufficient to change this conclusion. Our recommended values for lightning and coronal discharge dissipation rates on the early Earth are, respectively, 1 x 10(18) J yr-1 and 5 x 10(17) J yr-1.

The origin of life. II: How did it begin?

The problem of how a mixture of chemicals can spontaneously transform themselves into even a simple living organism remains one of the great outstanding challenges to science. Various primordial soup theories have been proposed in which chemical self-organization brings about the required level of complexity. Major conceptual obstacles remain, however, such as the emergence of the genetic code, and the "chicken-and-egg" problem concerning which came first: nucleic acids or proteins. Currently fashionable is the so-called RNA world theory, which casts RNA in the role of both chicken and egg. Other theories assume that protein chemistry and even clay crystal life came before nucleic acids. To be fully successful, a theory of biogenesis has to explain not merely the emergence of molecular replication and chemical complexity, but the crucial information content and information processing capabilities of the living cell.

The possible role of volcanic aquifers in prebiologic genesis of organic compounds and RNA

In a volcanic aquifer, a wide range of physical and chemical conditions are not merely possible, but to be expected: relatively oxidizing and reducing environments both are present; hot and moderate temperatures can be expected; distillation and reflux conditions are probable to allow concentration of reactants, stimulation of reaction and fractionation of isotopes; apatite, hydroxides, clays and sulfide minerals are present to act as chromatographic media for separating compounds, to serve as catalytic surfaces and to provide potential energy sources; supersaturated precipitation of optically active crystals is reasonable, allowing for chromatographic separation of racemic mixtures by the resulting fixed chiral phase; and saturated and unsaturated conditions both are present for promotion of constructive reactions and inhibiting destructive hydrolysis reactions. Because the multitude of physical-chemical environments makes the setting robust with respect to circumventing commonly identified problems in origin-of-life theories, even if objections to details proposed herein are identified, the setting is favorable for devising alternatives. This paper describes a theory for the genesis of organic compounds, including RNA, in the mixing zone of juvenile and meteoric waters above a leaky semi-confined aquifer. Starting with basic reactants for best-guess conditions on Archean Earth, parallel sequences of specific reactions are proposed that culminate with RNA oligonucleotides, key molecules in contemporary life. All proposed reactions, or close analogues, are experimentally confirmed and all are set in plausible Archean conditions. Calculations indicate that the proposed reactions would yield C isotopic compositions that are consistent with observed biologic C.

Protein expression in liposomes

Compartmentalization is one of the key steps in the evolution of cellular structures and, so far, only few attempts have been made to model this kind of "compartmentalized chemistry" using liposomes. The present work shows that even such complex reactions as the ribosomal synthesis of polypeptides can be carried out in liposomes. A method is described for incorporating into 1-palmitoyl-2-oleoyl-sn-3-phosphocholine (POPC) liposomes the ribosomal complex together with the other components necessary for protein expression. Synthesis of poly(Phe) in the liposomes is monitored by trichloroacetic acid of the (14)C-labelled products. Control experiments carried out in the absence of one of the ribosomal subunits show by contrast no significant polypeptide expression. This methodology opens up the possibility of using liposomes as minimal cell bioreactors with growing degree of synthetic complexity, which may be relevant for the field of origin of life as well as for biotechnological applications.

Primary sources of phosphorus and phosphates in chemical evolution

In this work we consider the role of phosphorus in chemical evolution from an interdisciplinary approach. First we briefly review the presence of this element in different cosmic sites, such as massive stellar cores, circumstellar and interstellar clouds, meteorites, lunar and Martian samples, interplanetary dust particles, cometary dust and planetary atmospheres. Thus we illustrate the fact that phosphorus seems to be, at the same time, scarce and ubiquitous in the solar system. Afterwards, by comparing the phosphorus content of our planet's main reservoirs with the amount of cometary and meteoritic matter captured by the primitive Earth, we conclude that comets may have provided a primary source for phosphorus compounds of prebiotic interest. Finally, we make a number of proposals aimed to gain observational supporting evidence to the above conclusion and other suggestions made in the article.

The first living systems: a bioenergetic perspective

The first systems of molecules having the properties of the living state presumably self-assembled from a mixture of organic compounds available on the prebiotic Earth. To carry out the polymer synthesis characteristic of all forms of life, such systems would require one or more sources of energy to activate monomers to be incorporated into polymers. Possible sources of energy for this process include heat, light energy, chemical energy, and ionic potentials across membranes. These energy sources are explored here, with a particular focus on mechanisms by which self-assembled molecular aggregates could capture the energy and use it to form chemical bonds in polymers. Based on available evidence, a reasonable conjecture is that membranous vesicles were present on the prebiotic Earth and that systems of replicating and catalytic macromolecules could become encapsulated in the vesicles. In the laboratory, this can be modeled by encapsulated polymerases prepared as liposomes. By an appropriate choice of lipids, the permeability properties of the liposomes can be adjusted so that ionic substrates permeate at a sufficient rate to provide a source of monomers for the enzymes, with the result that nucleic acids accumulate in the vesicles. Despite this progress, there is still no clear mechanism by which the free energy of light, ion gradients, or redox potential can be coupled to polymer bond formation in a protocellular structure.

Origin of biochemical organization

The problems of the origin of life and biochemical evolution are analyzed in the context of the biochemical organization concept proposed earlier by the authors. The traditional view according to which the evolution of biological systems occurred from lower levels to systems of higher levels is criticized. It is suggested that the formation of the cell and biological systems of lower levels (subcellular structures, supramolecular structures, biomacromolecules) occurred in a coordinated manner. The liposome and inorganic hypotheses of the origin of life are discussed. Regosome model based on ideas of Nussinov and Mekler which combines advantages of the liposome and inorganic hypotheses has been adopted and modernized. It is suggested that the initial metabolism of protocells based itself on C2-C3-compounds. Autodevelopment of catalytic systems of protocells is discussed.

Polymerase chain reaction in liposomes

BACKGROUND

Compartmentalization of biochemical reactions within a spherically closed bilayer is an important step in the molecular evolution of cells. Liposomes are the most suitable structures to model this kind of chemistry. We have used the polymerase chain reaction (PCR) to demonstrate that complex biochemical reactions such as DNA replication can be carried out inside these compartments.

RESULTS

We describe the first example of DNA amplification by the PCR occurring inside liposomes composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), or of a mixture of POPC and phosphatidylserine. We show that these liposomes are stable even under the high temperature conditions used for PCR. Although only a very small fraction of liposomes contains all eight different reagents together, a significant amount of DNA is produced which can be observed by polyacrylamide gel electrophoresis.

CONCLUSIONS

This work shows that it is possible to carry out complex biochemical reactions within liposomes, which may be germane to the question of the origin of living cells. We have established the parameters and conditions that are critical for carrying out this complex reaction within the liposome compartment.

On the levels of enzymatic substrate specificity: implications for the early evolution of metabolic pathways

The most frequently invoked explanation for the origin of metabolic pathways is the retrograde evolution hypothesis. In contrast, according to the so-called "patchwork" theory, metabolism evolved by the recruitment of relatively inefficient small enzymes of broad specificity that could react with a wide range of chemically related substrates. In this paper it is argued that both sequence comparisons and experimental results on enzyme substrate specificity support the patchwork assembly theory. The available evidence supports previous suggestions that gene duplication events followed by a gradual neoDarwinian accumulation of mutations and other minute genetic changes lead to the narrowing and modification of enzyme function in at least some primordial metabolic pathways.