Adenosine monophosphate forms ordered arrays in multilamellar lipid matrices: insights into assembly of nucleic acid for primitive life

Perspective: Protocells and the Path to Minimal Life

The path to minimal life involves a series of stages that can be understood in terms of incremental, stepwise additions of complexity ranging from simple solutions of organic compounds to systems of encapsulated polymers capable of capturing nutrients and energy to grow and reproduce. This brief review will describe the initial stages that lead to populations of protocells capable of undergoing selection and evolution. The stages incorporate knowledge of chemical and physical properties of organic compounds, self-assembly of membranous compartments, non-enzymatic polymerization of amino acids and nucleotides followed by encapsulation of polymers to produce protocell populations. The results are based on laboratory simulations related to cyclic hydrothermal conditions on the prebiotic Earth. The final portion of the review looks ahead to what remains to be discovered about this process in order to understand the evolutionary path to minimal life.

Membrane Catalyzed Formation of Nucleotide Clusters and Their Role in the Origins of Life: Insights from Molecular Simulations and Lattice Modeling

One of the mysteries in studying the molecular "Origin of Life" is the emergence of RNA and RNA-based life forms, where nonenzymatic polymerization of nucleotides is a crucial hypothesis in formation of large RNA chains. The nonenzymatic polymerization can be mediated by various environmental settings, such as cycles of hydration and dehydration, temperature variations, and proximity to a variety of organizing matrices, such as clay, salt, fatty acids, lipid membrane, and mineral surface. In this work, we explore the influence of different phases of the lipid membrane toward nucleotide organization and polymerization in a simulated prebiotic setting. Our molecular simulations quantify the localization propensity of a mononucleotide, uridine monophosphate (UMP), in distinct membrane settings. We perform all-atom molecular dynamics (MD) simulations to estimate the role of the monophasic and biphasic membranes in modifying the behavior of UMPs localization and their clustering mechanism. Based on the interaction energy of mononucleotides with the membrane and their diffusion profile from our MD calculations, we developed a lattice-based model to explore the thermodynamic limits of the observations made from the MD simulations. The mathematical model substantiates our hypothesis that the lipid layers can act as unique substrates for "catalyzing" polymerization of mononucleotides due to the inherent spatiotemporal heterogeneity and phase change behavior.

Crystallization as a selection force at the polymerization of nucleotides in a prebiotic context

Accumulation and selection of nucleotides is one of the most challenging problems surrounding the origin of the first RNA molecules on our planet. In the current work we propose that guanosine 3',5' cyclic monophosphate could selectively crystallize upon evaporation of an acidic prebiotic pool containing various other nucleotides. The conditions of the evaporative crystallization are fully compatible with the subsequent acid catalyzed polymerization of this cyclic nucleotide reported in earlier studies and may be relevant in a broad range of possible prebiotic environments. Albeit cytidine 3',5' cyclic monophosphate has the ability to selectively accumulate under the same conditions, its crystal structure is not likely to support polymer formation.

Nonenzymatic Template-Directed Primer Extension Using 2'-3' Cyclic Nucleotides Under Wet-Dry Cycles

RNA World Hypothesis is centred around the idea of a period in the early history of life's origin, wherein nonenzymatic oligomerization and replication of RNA resulted in functional ribozymes. Previous studies in this endeavour have demonstrated template-directed primer extension using chemically modified nucleotides and primers. Nonetheless, similar studies that used non-activated nucleotides led to the formation of RNA only with abasic sites. In this study, we report template-directed primer extension with prebiotically relevant cyclic nucleotides, under dehydration-rehydration (DH-RH) cycles occurring at high temperature (90 °C) and alkaline conditions (pH 8). 2'-3' cyclic nucleoside monophosphates (cNMP) resulted in primer extension, while 3'-5' cNMP failed to do so. Intact extension of up to two nucleotide additions was observed with both canonical hydroxy-terminated (OH-primer) and activated amino-terminated (NH2-primer) primers. We demonstrate primer extension reactions using both purine and pyrimidine 2'-3' cNMPs, with higher product yield observed during cAMP additions. Further, the presence of lipid was observed to significantly enhance the extended product in cCMP reactions. In all, our study provides a proof-of-concept for nonenzymatic primer extension of RNA, using intrinsically activated prebiotically relevant cyclic nucleotides as monomers.

The Formation of RNA Pre-Polymers in the Presence of Different Prebiotic Mineral Surfaces Studied by Molecular Dynamics Simulations

We used all-atom Molecular Dynamics (MD) computer simulations to study the formation of pre-polymers between the four nucleotides in RNA (AMP, UMP, CMP, GMP) in the presence of different substrates that could have been present in a prebiotic environment. Pre-polymers are C3'-C5' hydrogen-bonded nucleotides that have been suggested to be the precursors of phosphodiester-bonded RNA polymers. We simulated wet-dry cycles by successively removing water molecules from the simulations, from ~60 to 3 water molecules per nucleotide. The nine substrates in this study include three clay minerals, one mica, one phosphate mineral, one silica, and two metal oxides. The substrates differ in their surface charge and ability to form hydrogen bonds with the nucleotides. From the MD simulations, we quantify the interactions between different nucleotides, and between nucleotides and substrates. For comparison, we included graphite as an inert substrate, which is not charged and cannot form hydrogen bonds. We also simulated the dehydration of a nucleotide-only system, which mimics the drying of small droplets. The number of hydrogen bonds between nucleotides and nucleotides and substrates was found to increase significantly when water molecules were removed from the systems. The largest number of C3'-C5' hydrogen bonds between nucleotides occurred in the graphite and nucleotide-only systems. While the surface of the substrates led to an organization and periodic arrangement of the nucleotides, none of the substrates was found to be a catalyst for pre-polymer formation, neither at full hydration, nor when dehydrated. While confinement and dehydration seem to be the main drivers for hydrogen bond formation, substrate interactions reduced the interactions between nucleotides in all cases. Our findings suggest that small supersaturated water droplets that could have been produced by geysers or springs on the primitive Earth may play an important role in non-enzymatic RNA polymerization.

Visualizing RNA polymers produced by hot wet-dry cycling

It is possible that the transition from abiotic systems to life relied on RNA polymers that served as ribozyme-like catalysts and for storing genetic information. The source of such polymers is uncertain, but previous investigations reported that wet-dry cycles simulating prebiotic hot springs provide sufficient energy to drive condensation reactions of mononucleotides to form oligomers and polymers. The aim of the study reported here was to verify this claim and visualize the products prepared from solutions composed of single mononucleotides and 1:1 mixture of two mononucleotides. Therefore, we designed experiments that allowed comparisons of all such mixtures representing six combinations of the four mononucleotides of RNA. We observed irregular stringy patches and crystal strands when wet-dry cycling was performed at room temperature (20 °C). However, when the same solutions were exposed to wet-dry cycles at 80 °C, we observed what appeared to be true polymers. Their thickness was consistent with RNA-like products composed of covalently bonded monomers, while irregular strings and crystal segments of mononucleotides dried or cycled at room temperature were consistent with structures assembled and stabilized by weak hydrogen bonds. In a few instances we observed rings with short polymer attachments. These observations are consistent with previous claims of polymerization during wet-dry cycling. We conclude that RNA-like polymers and rings could have been synthesized non-enzymatically in freshwater hot springs on the prebiotic Earth with sizes sufficient to fold into ribozymes and genetic molecules required for life to begin.

Evolution of Realistic Organic Mixtures for the Origins of Life through Wet–Dry Cycling

One of the challenges in understanding chemical evolution is the large number of starting organics and environments that were plausible on early Earth. Starting with realistic organic mixtures and using chemical analyses that are not biologically biased, understanding the interplay between organic composition and environment can be approached using statistical analysis. In this work, a mixture of 73 organics was cycled through dehydrating conditions five times, considering environmental parameters of pH, salinity, and rehydration solution. Products were analyzed by HPLC, amide and ester assays, and phosphatase and esterase assays. While all environmental factors were found to influence chemical evolution, salinity was found to play a large role in the evolution of these mixtures, with samples diverging at very high sea salt concentrations. This framework should be expanded and formalized to improve our understanding of abiogenesis.

Possible Ribose Synthesis in Carbonaceous Planetesimals

The origin of life might be sparked by the polymerization of the first RNA molecules in Darwinian ponds during wet-dry cycles. The key life-building block ribose was found in carbonaceous chondrites. Its exogenous delivery onto the Hadean Earth could be a crucial step toward the emergence of the RNA world. Here, we investigate the formation of ribose through a simplified version of the formose reaction inside carbonaceous chondrite parent bodies. Following up on our previous studies regarding nucleobases with the same coupled physico-chemical model, we calculate the abundance of ribose within planetesimals of different sizes and heating histories. We perform laboratory experiments using catalysts present in carbonaceous chondrites to infer the yield of ribose among all pentoses (5Cs) forming during the formose reaction. These laboratory yields are used to tune our theoretical model that can only predict the total abundance of 5Cs. We found that the calculated abundances of ribose were similar to the ones measured in carbonaceous chondrites. We discuss the possibilities of chemical decomposition and preservation of ribose and derived constraints on time and location in planetesimals. In conclusion, the aqueous formose reaction might produce most of the ribose in carbonaceous chondrites. Together with our previous studies on nucleobases, we found that life-building blocks of the RNA world could be synthesized inside parent bodies and later delivered onto the early Earth.

Prebiotic Membranes and Micelles Do Not Inhibit Peptide Formation During Dehydration

Cycles of dehydration and rehydration could have enabled formation of peptides and RNA in otherwise unfavorable conditions on the early Earth. Development of the first protocells would have hinged upon colocalization of these biopolymers with fatty acid membranes. Using atomic force microscopy, we find that a prebiotic fatty acid (decanoic acid) forms stacks of membranes after dehydration. Using LC-MS-MS (liquid chromatography-tandem mass spectrometry) with isotope internal standards, we measure the rate of formation of serine dipeptides. We find that dipeptides form during dehydration at moderate temperatures (55 °C) at least as fast in the presence of decanoic acid membranes as in the absence of membranes. Our results are consistent with the hypothesis that protocells could have formed within evaporating environments on the early Earth.

Emergence of ribozyme and tRNA-like structures from mineral-rich muddy pools on prebiotic earth

The RNA world hypothesis, although a viable one regarding the origin of life on earth, has so far failed to provide a compelling explanation for the synthesis of RNA enzymes from free nucleotides via abiotic processes. To tackle this long-standing problem, we develop a realistic model for the onset of the RNA world, using experimentally determined rates for polymerization reactions. We start with minimal assumptions about the initial state that only requires the presence of short oligomers or just free nucleotides and consider the effects of environmental cycling by dividing a day into a dry, semi-wet and wet phases that are distinguished by the nature of reactions they support. Long polymers, with maximum lengths sometimes exceeding 100 nucleotides, spontaneously emerge due to a combination of non-enzymatic, non-templated polymer extension and template-directed primer extension processes. The former helps in increasing the lengths of RNA strands, whereas the later helps in producing complementary copies of the strands. Strands also undergo hydrolysis in a structure-dependent manner that favour breaking of bonds connecting unpaired nucleotides. We identify the most favourable conditions needed for the emergence of ribozyme and tRNA-like structures and double stranded RNA molecules, classify all RNA strands on the basis of their secondary structures and determine their abundance in the population. Our results indicate that under suitable environmental conditions, non-enzymatic processes would have been sufficient to lead to the emergence of a variety of ribozyme-like molecules with complex secondary structures and potential catalytic functions.

Geochemical influences on nonenzymatic oligomerization of prebiotically relevant cyclic nucleotides

The spontaneous emergence of long RNA molecules on the early Earth, a phenomenon central to the RNA World hypothesis, continues to remain an enigma in the field of origins of life. Few studies have looked at the nonenzymatic oligomerization of cyclic mononucleotides under neutral to alkaline conditions, albeit in fully dehydrated state. In this study, we systematically investigated the oligomerization of cyclic nucleotides under prebiotically relevant conditions, wherein starting reactants were subjected to repeated dehydration-rehydration (DH-RH) regimes. DH-RH conditions, a recurring geological theme that was prevalent on prebiotic Earth, are driven by naturally occurring processes including diurnal cycles and tidal pool activity. These conditions have been shown to facilitate uphill oligomerization reactions. The polymerization of 2'-3' and 3'-5' cyclic nucleotides of a purine (adenosine) and a pyrimidine (cytidine) was investigated. Additionally, the effect of amphiphiles was also evaluated. Furthermore, to discern the effect of "realistic" conditions on this process, the reactions were also performed using a hot spring water sample from a candidate early Earth environment. Our study showed that the oligomerization of cyclic nucleotides under DH-RH conditions resulted in intact informational oligomers. Amphiphiles increased the stability of both the starting monomers and the resultant oligomers in selected reactions. In the hot spring reactions, both the oligomerization of nucleotides and the back hydrolysis of the resultant oligomers were pronounced. Altogether, this study demonstrates how nonenzymatic oligomerization of cyclic nucleotides, under both laboratory-simulated prebiotic conditions and in a candidate early Earth environment, could have resulted in RNA oligomers of a putative RNA World.

NMR analysis of nucleotide π-stacking in prebiotically relevant crowded environment

The prebiotic soup of a putative 'RNA World' would have been replete with a plethora of molecules resulting from complex chemical syntheses and exogeneous delivery. The presence of background molecules could lead to molecular crowding, potentially affecting the course of the reactions facilitated therein. Using NMR spectroscopy, we have analyzed the effect of crowding on the stacking ability of RNA monomers. Our findings corroborate that the purines stack more efficiently than the pyrimidine ribonucleotides. This competence is further enhanced in the presence of a crowding agent. This enhanced stacking could result in greater sequestration of the purine monomers, putting their ready availability for relevant nonenzymatic reactions into question. Thus, this study demonstrates the need for systematic characterization of molecular crowding in the context of prebiotically pertinent processes. Unraveling such phenomena is essential for our understanding of the transition from abiotic to biotic, during the origin of life.

The Hot Spring Hypothesis for an Origin of Life

We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized by cycles of hydration and dehydration to form protocells. Drawing on metaphors from the bootstrapping of a simple computer operating system, we show how protocells cycling through wet, dry, and moist phases will subject polymers to combinatorial selection and draw structural and catalytic functions out of initially random sequences, including structural stabilization, pore formation, and primitive metabolic activity. We propose that protocells aggregating into a hydrogel in the intermediate moist phase of wet-dry cycles represent a primitive progenote system. Progenote populations can undergo selection and distribution, construct niches in new environments, and enable a sharing network effect that can collectively evolve them into the first microbial communities. Laboratory and field experiments testing the first steps of the scenario are summarized. The scenario is then placed in a geological setting on the early Earth to suggest a plausible pathway from life's origin in chemically optimal freshwater hot spring pools to the emergence of microbial communities tolerant to more extreme conditions in dilute lakes and salty conditions in marine environments. A continuity is observed for biogenesis beginning with simple protocell aggregates, through the transitional form of the progenote, to robust microbial mats that leave the fossil imprints of stromatolites so representative in the rock record. A roadmap to future testing of the hypothesis is presented. We compare the oceanic vent with land-based pool scenarios for an origin of life and explore their implications for subsequent evolution to multicellular life such as plants. We conclude by utilizing the hypothesis to posit where life might also have emerged in habitats such as Mars or Saturn's icy moon Enceladus. "To postulate one fortuitously catalyzed reaction, perhaps catalyzed by a metal ion, might be reasonable, but to postulate a suite of them is to appeal to magic." -Leslie Orgel.

Lipid-Assisted Polymerization of Nucleotides

In addition to being one of the proponents of the “Lipid World hypothesis”, David Deamer, together with other colleagues, pioneered studies involving formation of RNA-like oligomers from their ‘non-activated’, prebiotically plausible monomeric moieties. In particular, the pioneering work in this regard was a publication from 2008 in Origins of Life and Evolution of Biospheres, The Journal of the International Astrobiology Society, wherein we described the formation of RNA-like oligomers from nucleoside 5’-monophosphates. In that study, we had simulated a terrestrial geothermal environment, a niche that is thought to have facilitated the prebiotic non-enzymatic synthesis of polynucleotides. We showed that a mixture of lipids and non-activated mononucleotides resulted in the formation of relatively long strands of RNA-like polymers when subjected to repeated cycles of dehydration and rehydration (DH-RH). Since 2008, terrestrial geothermal niches and DH-RH conditions have been explored in the context of several other prebiotic processes. In this article, we review the work that we and other researchers have carried out since then in this line of research, including the development of new apparatus to carry out the simulation of prebiotic terrestrial geothermal environments.

Interaction of the mononucleotide UMP with a fluid phospholipid bilayer

Interaction between mononucleotides and lipid membranes is believed to have played an important role in the origin of life on Earth. Studies on mononucleotide-lipid systems hitherto have focused on the influence of the lipid environment on the organization of the mononucleotide molecules, and the effect of the latter on the confining medium has not been investigated in detail. We have probed the interaction of the mononucleotide, uridine 5'-monophosphate (UMP), and its disodium salt (UMPDSS) with fluid dimyristoylphosphatidylcholine (DMPC) membranes, using small-angle X-ray scattering (SAXS), cryogenic scanning electron microscopy (cryo-SEM) and computer simulations. UMP adsorbs and charges the lipid membrane, resulting in the formation of unilamellar vesicles in dilute solutions. Adsorption of UMP reduces the bilayer thickness of DMPC. UMPDSS has a much weaker effect on interbilayer interactions. These observations are in very good agreement with the results of an all-atom molecular dynamics simulation of these systems. In the presence of counterions, such as Na⁺, UMP forms small aggregates in water, which bind to the bilayer without significantly perturbing it. The phosphate moiety in the lipid headgroup is found to bind to the hydrogens from the sugar ring of UMP, while the choline group tends to bind to the two oxygens from the nucleotide base. These studies provide important insights into lipid-nucleotide interactions and the effect of the nucleotide on lipid membranes.

Heated gas bubbles enrich, crystallize, dry, phosphorylate and encapsulate prebiotic molecules

Non-equilibrium conditions must have been crucial for the assembly of the first informational polymers of early life, by supporting their formation and continuous enrichment in a long-lasting environment. Here, we explore how gas bubbles in water subjected to a thermal gradient, a likely scenario within crustal mafic rocks on the early Earth, drive a complex, continuous enrichment of prebiotic molecules. RNA precursors, monomers, active ribozymes, oligonucleotides and lipids are shown to (1) cycle between dry and wet states, enabling the central step of RNA phosphorylation, (2) accumulate at the gas-water interface to drastically increase ribozymatic activity, (3) condense into hydrogels, (4) form pure crystals and (5) encapsulate into protecting vesicle aggregates that subsequently undergo fission. These effects occur within less than 30 min. The findings unite, in one location, the physical conditions that were crucial for the chemical emergence of biopolymers. They suggest that heated microbubbles could have hosted the first cycles of molecular evolution.

Organization and Compartmentalization by Lipid Membranes Promote Reactions Related to the Origin of Cellular Life

Liquid crystals have certain physical properties that promote chemical reactions which cannot occur in bulk phase media. These properties are displayed, among other molecules, by amphiphilic compounds which assemble into membrane structures then concentrate and organize biologically relevant monomers within their confined spaces. When mixtures of lipids and nucleotides are cycled multiple times between hydrated and anhydrous conditions, the monomers polymerize in the dry phase into oligonucleotides. Upon rehydration, mixtures of the polymers are encapsulated in lipid-bounded compartments called protocells. Reactions in liquid crystalline organizing matrices represent a promising approach for future research on how primitive cells could emerge on the early Earth and other habitable planets.

Progress in synthesizing protocells

IMPACT STATEMENT

Advances in the understanding of the biophysics of membranes, the nonenzymatic and enzymatic polymerization of RNA, and in the design of complex chemical reaction networks have led to a new, integrated way of viewing the shared chemistry needed to sustain life. Although a protocell capable of Darwinian evolution has yet to be built, the seemingly disparate pieces are beginning to fit together. At the very least, better cellular mimics are on the horizon that will likely teach us much about the physicochemical underpinnings of cellular life.

Nonenzymatic Polymerization into Long Linear RNA Templated by Liquid Crystal Self-Assembly

Self-synthesizing materials, in which supramolecular structuring enhances the formation of new molecules that participate to the process, represent an intriguing notion to account for the first appearance of biomolecules in an abiotic Earth. We present here a study of the abiotic formation of interchain phosphodiester bonds in solutions of short RNA oligomers in various states of supramolecular arrangement and their reaction kinetics. We found a spectrum of conditions in which RNA oligomers self-assemble and phase separate into highly concentrated ordered fluid liquid crystal (LC) microdomains. We show that such supramolecular state provides a template guiding their ligation into hundred-bases long chains. The quantitative analysis presented here demonstrates that nucleic acid LC boosts the rate of end-to-end ligation and suppresses the formation of the otherwise dominant cyclic oligomers. These results strengthen the concept of supramolecular ordering as an efficient pathway toward the emergence of the RNA World in the primordial Earth.

Templated replication (or lack thereof) under prebiotically pertinent conditions

Accurate replication of encoded information would have been crucial for the formation and propagation of functional ribozymes during the early evolution of life. Studies aimed at understanding prebiotically pertinent nonenzymatic reactions have predominantly used activated nucleotides. However, the existence of concentrated pools of activated monomers on prebiotic Earth is debatable. In this study, we explored the feasibility of nonenzymatic copying reactions using the more prebiotically relevant 5′-nucleoside monophosphates (5′-NMP). These reactions, involving a 20-mer primer, were performed in the presence of amphiphiles, under volcanic geothermal conditions. Interestingly, the extended primer was not comparable to the expected full length 21-mer product. Our results suggest loss of the nitrogenous base in the extended primer. This phenomenon persisted even after lowering the temperature and when different rehydration solutions were used. We envisage that the loss of the informational moiety on the incoming 5′-NMP, might be occurring during addition of this monomer to the pre-existing oligomer. Significantly, when 5′-ribose monophosphate was used, multiple additions to the aforementioned primer were observed that resulted in hybrid polymers. Such hybrid oligomers could have been important for exploring a vast chemical space of plausible alternate nucleobases, thus having important implications for the origin of primitive informational polymers.

Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson-Crick selectivity

The columnar liquid crystal phases reported here are physical associations of the smallest molecular species to self-assemble into the duplex base-paired stacked columnar double-helical structures of nucleic acids. These assemblies of monomers can provide starting states capable of partitioning appropriate molecules from solution with a high degree of selectivity, acting as pathways for the prebiotic appearance of molecular selection, self-assembly, and, ultimately, of the sequence-directed assembly of polymers.

We demonstrate that nucleic acid (NA) mononucleotide triphosphates (dNTPs and rNTPs), at sufficiently high concentration and low temperature in aqueous solution, can exhibit a phase transition in which chromonic columnar liquid crystal ordering spontaneously appears. Remarkably, this polymer-free state exhibits, in a self-assembly of NA monomers, the key structural elements of biological nucleic acids, including: long-ranged duplex stacking of base pairs, complementarity-dependent partitioning of molecules, and Watson–Crick selectivity, such that, among all solutions of adenosine, cytosine, guanine, and thymine NTPs and their binary mixtures, duplex columnar ordering is most stable in the A-T and C-G combinations.

Can Life Begin on Enceladus? A Perspective from Hydrothermal Chemistry

Enceladus is a target of future missions designed to search for existing life or its precursors. Recent flybys of Enceladus by the Cassini probe have confirmed the existence of a long-lived global ocean laced with organic compounds and biologically available nitrogen. This immediately suggests the possibility that life could have begun and may still exist on Enceladus. Here we will compare the properties of two proposed sites for the origin of life on Earth-hydrothermal vents on the ocean floor and hydrothermal volcanic fields at the surface-and ask whether similar conditions could have fostered the origin of life on Enceladus. The answer depends on which of the two sites would be more conducive for the chemical evolution leading to life's origin. A hydrothermal vent origin would allow life to begin in the Enceladus ocean, but if the origin of life requires freshwater hydrothermal pools undergoing wet-dry cycles, the Enceladus ocean could be habitable but lifeless. These arguments also apply directly to Europa and indirectly to early Mars. Key Words: Enceladus-Hydrothermal vents-Hydrothermal fields-Origin of life. Astrobiology 17, 834-839.

Chemical systems, chemical contiguity and the emergence of life

Charting the emergence of living cells from inanimate matter remains an intensely challenging scientific problem. The complexity of the biochemical machinery of cells with its exquisite intricacies hints at cells being the product of a long evolutionary process. Research on the emergence of life has long been focusing on specific, well-defined problems related to one aspect of cellular make-up, such as the formation of membranes or the build-up of information/catalytic apparatus. This approach is being gradually replaced by a more "systemic" approach that privileges processes inherent to complex chemical systems over specific isolated functional apparatuses. We will summarize the recent advances in system chemistry and show that chemical systems in the geochemical context imply a form of chemical contiguity in the syntheses of the various molecules that precede modern biomolecules.

Conjecture and hypothesis: The importance of reality checks

In origins of life research, it is important to understand the difference between conjecture and hypothesis. This commentary explores the difference and recommends alternative hypotheses as a way to advance our understanding of how life can begin on the Earth and other habitable planets. As an example of how this approach can be used, two conditions have been proposed for sites conducive to the origin of life: hydrothermal vents in salty seawater, and fresh water hydrothermal fields associated with volcanic landmasses. These are considered as alternative hypotheses and the accumulating weight of evidence for each site is described and analyzed.

The Role of Lipid Membranes in Life's Origin

At some point in early evolution, life became cellular. Assuming that this step was required for the origin of life, there would necessarily be a pre-existing source of amphihilic compounds capable of assembling into membranous compartments. It is possible to make informed guesses about the properties of such compounds and the conditions most conducive to their self-assembly into boundary structures. The membranes were likely to incorporate mixtures of hydrocarbon derivatives between 10 and 20 carbons in length with carboxylate or hydroxyl head groups. Such compounds can be synthesized by chemical reactions and small amounts were almost certainly present in the prebiotic environment. Membrane assembly occurs most readily in low ionic strength solutions with minimal content of salt and divalent cations, which suggests that cellular life began in fresh water pools associated with volcanic islands rather than submarine hydrothermal vents.

Mobility of a Mononucleotide within a Lipid Matrix: A Neutron Scattering Study

An essential question in studies on the origins of life is how nucleic acids were first synthesized and then incorporated into compartments about 4 billion years ago. A recent discovery is that guided polymerization within organizing matrices could promote a non-enzymatic condensation reaction allowing the formation of RNA-like polymers, followed by encapsulation in lipid membranes. Here, we used neutron scattering and deuterium labelling to investigate 5′-adenosine monophosphate (AMP) molecules captured in a multilamellar phospholipid matrix. The aim of the research was to determine and compare how mononucleotides are captured and differently organized within matrices and multilamellar phospholipid structures and to explore the role of water in organizing the system to determine at which level the system becomes sufficiently anhydrous to lock the AMP molecules into an organized structure and initiate ester bond synthesis. Elastic incoherent neutron scattering experiments were thus employed to investigate the changes of the dynamic properties of AMP induced by embedding the molecules within the lipid matrix. The influence of AMP addition to the lipid membrane organization was determined through diffraction measurement, which also helped us to define the best working Q range for dynamical data analysis with respect to specific hydration. The use of different complementary instruments allowed coverage of a wide time-scale domain, from ns to ps, of atomic mean square fluctuations, providing evidence of a well-defined dependence of the AMP dynamics on the hydration level.

Membranes and the Origin of Life: A Century of Conjecture

Cells are the units of all life today, and are defined by their membranous boundaries. The membranes have multiple functions; the most obvious being that, in the absence of a boundary, the systems of functional macromolecular components of the cytosol would spill into the environment and disperse. Membranes also contain the pigments essential for photosynthesis, electron transport enzymes that pump and maintain proton gradients, the ATP synthase that uses proton gradients to produce energy for the cell, and enzymes that use ATP to maintain ion gradients essential for life. But what about the function of membranes in the first forms of cellular life? Could life have begun in the absence of membranous boundaries? In order to answer that question, this review presents a history of the key research observations that began over a century ago.

Co-operation between Polymerases and Nucleotide Synthetases in the RNA World

It is believed that life passed through an RNA World stage in which replication was sustained by catalytic RNAs (ribozymes). The two most obvious types of ribozymes are a polymerase, which uses a neighbouring strand as a template to make a complementary sequence to the template, and a nucleotide synthetase, which synthesizes monomers for use by the polymerase. When a chemical source of monomers is available, the polymerase can survive on its own. When the chemical supply of monomers is too low, nucleotide production by the synthetase is essential and the two ribozymes can only survive when they are together. Here we consider a computational model to investigate conditions under which coexistence and cooperation of these two types of ribozymes is possible. The model considers six types of strands: the two functional sequences, the complementary strands to these sequences (which are required as templates), and non-functional mutants of the two sequences (which act as parasites). Strands are distributed on a two-dimensional lattice. Polymerases replicate strands on neighbouring sites and synthetases produce monomers that diffuse in the local neighbourhood. We show that coexistence of unlinked polymerases and synthetases is possible in this spatial model under conditions in which neither sequence could survive alone; hence, there is a selective force for increasing complexity. Coexistence is dependent on the relative lengths of the two functional strands, the strand diffusion rate, the monomer diffusion rate, and the rate of deleterious mutations. The sensitivity of this two-ribozyme system suggests that evolution of a system of many types of ribozymes would be difficult in a purely spatial model with unlinked genes. We therefore speculate that linkage of genes onto mini-chromosomes and encapsulation of strands in protocells would have been important fairly early in the history of life as a means of enabling more complex systems to evolve.

Trans-acting polymerases are cooperative, because they copy neighbouring strands, and do not copy themselves directly. Inaccurate replication creates parasitic strands that act as templates but not ribozymes. It is known that in spatially distributed models with slow strand diffusion, clusters of cooperating polymerases arise that can survive in the presence of parasites provided that the error rate is less than a maximum limit (the error threshold). In the RNA World, we envisage multiple types of ribozymes working together. We would like to understand how a multi-ribozyme system could evolve from a system with a single type of polymerase ribozyme. As a first step in increasing complexity, we consider a two-ribozyme system in which there is one polymerase and one nucleotide synthetase that produces monomers for use by the polymerase. We are particularly interested to find conditions in which the chemical supply of monomers is too low for the polymerase to survive alone, but the additional monomers created by the synthetase allow the two-ribozyme system to survive where the single-ribozyme system could not. There is then a selective force for increasing the complexity of the system. Here we show that spatial clustering is sufficient to allow cooperation and survival of systems of unlinked ribozymes with different functions. Clusters form in which synthetases form fringes around the polymerases. Survival of the two-ribozyme system depends on several factors. The strand diffusion rate must be slow enough for cooperative clusters to emerge. The replication rate of the polymerase must be comparable to that of the synthetase. The diffusion rate of the monomers must be neither too slow nor too fast. The model considers the most difficult case for cooperation–unlinked genes with no compartments. The sensitivity of the two-ribozyme system that we study here suggests that evolution of a spatial system with multiple unlinked ribozymes would become increasingly more difficult as the number of components increased, and suggests that linkage and protocells would need to evolve relatively early in the history of life.

Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System

Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth. This review will address the question of the possible roles of heterogeneous media and catalysis as drivers for the emergence of RNA-based polymer networks. We will show that this approach to non-enzymatic polymerizations of RNA from monomers and RNA evolution cannot only solve some issues encountered during reactions in bulk aqueous solutions, but may also explain the co-emergence of the various polymers indispensable for life in complex mixtures and their organization into primitive networks.

Meteorites and the RNA World: A Thermodynamic Model of Nucleobase Synthesis within Planetesimals

The possible meteorite parent body origin of Earth's pregenetic nucleobases is substantiated by the guanine (G), adenine (A), and uracil (U) measured in various meteorites. Cytosine (C) and thymine (T), however, are absent in meteorites, making the emergence of an RNA and later RNA/DNA/protein world problematic. We investigated the meteorite parent body (planetesimal) origin of all nucleobases by computationally modeling 18 reactions that potentially contribute to nucleobase formation in such environments. Out of this list, we identified the two most important reactions for each nucleobase and found that these involve small molecules such as HCN, CO, NH₃, and water that ultimately arise from the protoplanetary disks in which planetesimals are built. The primary result of this study is that cytosine is unlikely to persist within meteorite parent bodies due to aqueous deamination. Thymine has a thermodynamically favorable reaction pathway from uracil, formaldehyde, and formic acid but likely did not persist within planetesimals containing H₂O₂ due to an oxidation reaction with this molecule. Finally, while Fischer-Tropsch (FT) synthesis is found to be the dominant source of nucleobases within our model planetesimal, non-catalytic (NC) synthesis may still be significant under certain chemical conditions (e.g., within CR2 parent bodies). We discuss several major consequences of our results for the origin of the RNA world. Key Words: Astrobiology-Cosmochemistry-Meteorites-RNA world-Abiotic organic synthesis. Astrobiology 16, 853-872.

Organization of Nucleotides in Different Environments and the Formation of Pre-Polymers

RNA is a linear polymer of nucleotides linked by a ribose-phosphate backbone. Polymerization of nucleotides occurs in a condensation reaction in which phosphodiester bonds are formed. However, in the absence of enzymes and metabolism there has been no obvious way for RNA-like molecules to be produced and then encapsulated in cellular compartments. We investigated 5′-adenosine monophosphate (AMP) and 5′-uridine monophosphate (UMP) molecules confined in multi-lamellar phospholipid bilayers, nanoscopic films, ammonium chloride salt crystals and Montmorillonite clay, previously proposed to promote polymerization. X-ray diffraction was used to determine whether such conditions imposed a degree of order on the nucleotides. Two nucleotide signals were observed in all matrices, one corresponding to a nearest neighbour distance of 4.6 Å attributed to nucleotides that form a disordered, glassy structure. A second, smaller distance of 3.4 Å agrees well with the distance between stacked base pairs in the RNA backbone, and was assigned to the formation of pre-polymers, i.e., the organization of nucleotides into stacks of about 10 monomers. Such ordering can provide conditions that promote the nonenzymatic polymerization of RNA strands under prebiotic conditions. Experiments were modeled by Monte-Carlo simulations, which provide details of the molecular structure of these pre-polymers.

A Self-Assembled Aggregate Composed of a Fatty Acid Membrane and the Building Blocks of Biological Polymers Provides a First Step in the Emergence of Protocells

We propose that the first step in the origin of cellular life on Earth was the self-assembly of fatty acids with the building blocks of RNA and protein, resulting in a stable aggregate. This scheme provides explanations for the selection and concentration of the prebiotic components of cells; the stabilization and growth of early membranes; the catalysis of biopolymer synthesis; and the co-localization of membranes, RNA and protein. In this article, we review the evidence and rationale for the formation of the proposed aggregate: (i) the well-established phenomenon of self-assembly of fatty acids to form vesicles; (ii) our published evidence that nucleobases and sugars bind to and stabilize such vesicles; and (iii) the reasons why amino acids likely do so as well. We then explain how the conformational constraints and altered chemical environment due to binding of the components to the membrane could facilitate the formation of nucleosides, oligonucleotides and peptides. We conclude by discussing how the resulting oligomers, even if short and random, could have increased vesicle stability and growth more than their building blocks did, and how competition among these vesicles could have led to longer polymers with complex functions.

Dry/Wet Cycling and the Thermodynamics and Kinetics of Prebiotic Polymer Synthesis

The endoergic nature of protein and nucleic acid assembly in aqueous media presents two questions that are fundamental to the understanding of life’s origins: (i) how did the polymers arise in an aqueous prebiotic world; and (ii) once formed in some manner, how were they sufficiently persistent to engage in further chemistry. We propose here a quantitative resolution of these issues that evolved from recent accounts in which RNA-like polymers were produced in evaporation/rehydration cycles. The equilibrium N_m + N_n ↔ N_m+n + H₂O is endoergic by about 3.3 kcal/mol for polynucleotide formation, and the system thus lies far to the left in the starting solutions. Kinetic simulations of the evaporation showed that simple Le Châtelier’s principle shifts were insufficient, but the introduction of oligomer-stabilizing factors of 5–10 kcal/mol both moved the process to the right and respectively boosted and retarded the elongation and hydrolysis rates. Molecular crowding and excluded volume effects in present-day cells yield stabilizing factors of that order, and we argue here that the crowded conditions in the evaporites generate similar effects. Oligomer formation is thus energetically preferred in those settings, but the process is thwarted in each evaporation step as diffusion becomes rate limiting. Rehydration dissipates disordered oligomer clusters in the evaporites, however, and subsequent dry/wet cycling accordingly “ratchets up” the system to an ultimate population of kinetically trappedthermodynamically preferred biopolymers.

The Effect of Limited Diffusion and Wet-Dry Cycling on Reversible Polymerization Reactions: Implications for Prebiotic Synthesis of Nucleic Acids

A long-standing problem for the origins of life is that polymerization of many biopolymers, including nucleic acids and peptides, is thermodynamically unfavourable in aqueous solution. If bond making and breaking is reversible, monomers and very short oligomers predominate. Recent experiments have shown that wetting and drying cycles can overcome this problem and drive the formation of longer polymers. In the dry phase, bond formation is favourable, but diffusion is restricted, and bonds only form between monomers that are initially close together. In the wet phase, some of the bonds are hydrolyzed. However, repositioning of the molecules allows new bonds to form in the next dry phase, leading to an increase in mean polymer length. Here, we consider a simple theoretical model that explains the effect of cycling. There is an equilibrium length distribution with a high mean length that could be achieved if diffusion occurred freely in the dry phase. This equilibrium is inaccessible without diffusion. A single dry cycle without diffusion leads to mean lengths much shorter than this. Repeated cycling leads to a significant increase in polymerization relative to a single cycle. In the most favourable case, cycling leads to the same equilibrium length distribution as would be achieved if free diffusion were possible in the dry phase. These results support the RNA World scenario by explaining a potential route to synthesis of long RNAs; however, they also imply that cycling would be beneficial to the synthesis of other kinds of polymers, including peptides, where bond formation involves a condensation reaction.

A Field Trip to the Archaean in Search of Darwin's Warm Little Pond

Charles Darwin’s original intuition that life began in a “warm little pond” has for the last three decades been eclipsed by a focus on marine hydrothermal vents as a venue for abiogenesis. However, thermodynamic barriers to polymerization of key molecular building blocks and the difficulty of forming stable membranous compartments in seawater suggest that Darwin’s original insight should be reconsidered. I will introduce the terrestrial origin of life hypothesis, which combines field observations and laboratory results to provide a novel and testable model in which life begins as protocells assembling in inland fresh water hydrothermal fields. Hydrothermal fields are associated with volcanic landmasses resembling Hawaii and Iceland today and could plausibly have existed on similar land masses rising out of Earth’s first oceans. I will report on a field trip to the living and ancient stromatolite fossil localities of Western Australia, which provided key insights into how life may have emerged in Archaean, fluctuating fresh water hydrothermal pools, geological evidence for which has recently been discovered. Laboratory experimentation and fieldwork are providing mounting evidence that such sites have properties that are conducive to polymerization reactions and generation of membrane-bounded protocells. I will build on the previously developed coupled phases scenario, unifying the chemical and geological frameworks and proposing that a hydrogel of stable, communally supported protocells will emerge as a candidate Woese progenote, the distant common ancestor of microbial communities so abundant in the earliest fossil record.

Hydrothermal Conditions and the Origin of Cellular Life

The conditions and properties of hydrothermal vents and hydrothermal fields are compared in terms of their ability to support processes related to the origin of life. The two sites can be considered as alternative hypotheses, and from this comparison we propose a series of experimental tests to distinguish between them, focusing on those that involve concentration of solutes, self-assembly of membranous compartments, and synthesis of polymers. Key Word: Hydrothermal systems.

A decisive step toward the origin of life

Several hypotheses exist regarding how life emerged from the abiotic world, the most popular of which is the 'RNA World' hypothesis. Recent advances describe nonenzymatic polymerization of mononucleotides in a phospholipid liquid crystalline matrix, suggesting that a 'Lipid World' might have preceded the RNA World.

Hydrothermal Systems of Kamchatka are Models of the Prebiotic Environment

The composition of organic matter and fluctuations of thermodynamic parameters were investigated in the hydrothermal systems of the Kamchatka peninsula in the context of the origin of life. Organics were analyzed by gas-chromatography/mass spectrometry, and 111 organic compounds belonging to 14 homologous series (aromatic hydrocarbons, alkanes and isoalkanes, halogenated aromatic hydrocarbons, carboxylic acids, esters, etc.) were found in hot springs inhabited by Archaeal and Bacterial thermophiles. The organics detected in the sterile condensate of water-steam mixture taken from deep boreholes (temperature 108-175 °C) consisted of 69 compounds of 11 homologous series, with aromatic hydrocarbons and alkanes being prevalent. The organic material included important prebiotic components such as nitrogen-containing compounds and lipid precursors. A separate organic phase (oil) was discovered in the Uzon Caldera. A biogenic origin is supported by the presence of sterane and hopane biomarkers and the δ(13)C value of the bulk oil; its age determined by (14)C measurements was 1030 ± 40 years. Multilevel fluctuations of thermodynamic parameters proposed to be required for the origin of life were determined in the Mutnovsky and Pauzhetsky hydrothermal systems. The low-frequency component of the hydrothermal fluid pressure varied by up to 2 bars over periods of hours to days, while mid-frequency variations had regular micro-oscillations with periods of about 20 min; the high-frequency component displayed sharp changes of pressure and microfluctuations with periods less than 5 min. The correlation coefficient between pressure and temperature ranges from 0.89 to 0.99 (average 0.96). The natural regimes of pressure and temperature fluctuations in Kamchatka hydrothermal systems can guide future experiments on prebiotic chemistry under oscillating conditions.

A central theory of biology

The history of physiologic cellular-molecular interrelationships can be traced all the way back to the unicellular state by following the pathway formed by lipids ubiquitously accommodating calcium homeostasis, and its consequent adaptive effects on oxygen uptake by cells, tissues and organs. As a result, a cohesive, mechanistically integrated view of physiology can be formulated by recognizing the continuum comprising conception, development, physiologic homeostasis and death mediated by soluble growth factor signaling. Seeing such seemingly disparate processes as embryogenesis, chronic disease and dying as the gain and subsequent loss of cell-cell signaling provides a novel perspective for physiology and medicine. It is emblematic of the self-organizing, self-referential nature of life, starting from its origins. Such organizing principles obviate the pitfalls of teleologic evolution, conversely providing a way of resolving such seeming dichotomies as holism and reductionism, genotype and phenotype, emergence and contingence, proximate and ultimate causation in evolution, cells and organisms. The proposed approach is scale-free and predictive, offering a Central Theory of Biology.

Coupled phases and combinatorial selection in fluctuating hydrothermal pools: a scenario to guide experimental approaches to the origin of cellular life

Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution in dehydrated films on mineral surfaces followed by encapsulation and combinatorial selection in a hydrated bulk phase. The dehydrated phase can consist of concentrated eutectic mixtures or multilamellar liquid crystalline matrices. Both conditions organize and concentrate potential monomers and thereby promote polymerization reactions that are driven by reduced water activity in the dehydrated phase. In the case of multilamellar lipid matrices, polymers that have been synthesized are captured in lipid vesicles upon rehydration to produce a variety of molecular systems. Each vesicle represents a protocell, an “experiment” in a natural version of combinatorial chemistry. Two kinds of selective processes can then occur. The first is a physical process in which relatively stable molecular systems will be preferentially selected. The second is a chemical process in which rare combinations of encapsulated polymers form systems capable of capturing energy and nutrients to undergo growth by catalyzed polymerization. Given continued cycling over extended time spans, such combinatorial processes will give rise to molecular systems having the fundamental properties of life.

Characterization of RNA-Like Oligomers from Lipid-Assisted Nonenzymatic Synthesis: Implications for Origin of Informational Molecules on Early Earth

Prebiotic polymerization had to be a nonenzymatic, chemically driven process. These processes would have been particularly favored in scenarios which push reaction regimes far from equilibrium. Dehydration-rehydration (DH-RH) cycles are one such regime thought to have been prevalent on prebiotic Earth in niches like volcanic geothermal pools. The present study defines the optimum DH-RH reaction conditions for lipid-assisted polymerization of nucleotides. The resultant products were characterized to understand their chemical makeup. Primarily, our study demonstrates that the resultant RNA-like oligomers have abasic sites, which means these oligomers lack information-carrying capability because of losing most of their bases during the reaction process. This results from low pH and high temperature conditions, which, importantly, also allows the formation of sugar-phosphate oligomers when ribose 5'-monophosphates are used as the starting monomers instead. Formation of such oligomers would have permitted sampling of a large variety of bases on a preformed polymer backbone, resulting in “prebiotic phosphodiester polymers” prior to the emergence of modern RNA-like molecules. This suggests that primitive genetic polymers could have utilized bases that conferred greater N-glycosyl bond stability, a feature crucial for information propagation in low pH and high temperature regimes of early Earth.

Synergism and mutualism in non-enzymatic RNA polymerization

The link between non-enzymatic RNA polymerization and RNA self-replication is a key step towards the "RNA world" and still far from being solved, despite extensive research. Clay minerals, lipids and, more recently, peptides were found to catalyze the non-enzymatic synthesis of RNA oligomers. Herein, a review of the main models for the formation of the first RNA polymers is presented in such a way as to emphasize the cooperation between life's building blocks in their emergence and evolution. A logical outcome of the previous results is a combination of these models, in which RNA polymerization might have been catalyzed cooperatively by clays, lipids and peptides in one multi-component prebiotic soup. The resulting RNAs and oligopeptides might have mutualistically evolved towards functional RNAs and catalytic peptides, preceding the first RNA replication, thus supporting an RNA-peptide world. The investigation of such a system is a formidable challenge, given its complexity deriving from a tremendously large number of reactants and innumerable products. A rudimentary experimental design is outlined, which could be used in an initial attempt to study a quaternary component system.

Generation of oligonucleotides under hydrothermal conditions by non-enzymatic polymerization

We previously reported that 5'-mononucleotides organized within a multilamellar lipid matrix can produce oligomers in the anhydrous phase of hydration-dehydration (HD) cycles. However, hydrolysis of oligomers can occur during hydration, and it is important to better understand the steady state in which ester bond synthesis is balanced by hydrolysis. In order to study condensation products of mononucleotides and hydrolysis of their polymers, we established a simulation of HD cycles that would occur on the early Earth when volcanic land masses emerged from the ocean over 4 billion years ago. At this stage on early Earth, precipitation produced hydrothermal fields characterized by small aqueous pools undergoing evaporation and refilling at elevated temperatures. Here, we confirm that under these conditions, the chemical potential made available by cycles of hydration and dehydration is sufficient to drive synthesis of ester bonds. If 5'-mononucleotides are in solution at millimolar concentrations, then oligomers resembling RNA are synthesized and exist in a steady state with their monomers. Furthermore, if the mononucleotides can form complementary base pairs, then some of the products have properties suggesting that secondary structures are present, including duplex species stabilized by hydrogen bonds.