Role of amphiphilic compounds in the evolution of membrane structure on the early earth

Naphthalimide-Based Amphiphiles: Synthesis and DFT Studies of the Aggregation and Interaction of a Simplified Model System with Water Molecules

Systems containing amphiphilic/pathic molecules have the tremendous capacity to self-assemble under appropriate conditions to form morphologies with well-defined structural order (systematic arrangement), nanometer-scale dimensions, and unique properties. In this work, the synthesis of novel naphthalimide-based amphiphilic probes that have 1,8-naphthalimide as the fluorescence signal reporting group, octyl as hydrophobic head, and PEG as hydrophilic tail, is described. These designed molecules represent a new class of self-assembling structures with some promising features. The lack of literature data on the use of 1,8-naphthalimides with cyclic and acyclic hydrophilic PEG fragments as self-assembling structures gives us the opportunity to initiate a new field in materials science. The successful synthesis of such structures is fundamental to synthetic chemistry, and computational studies of the aggregation and binding of water molecules shed light on the ability of these new systems to function as membrane water channels. This study not only expands the list of 1,8-naphthalimide derivatives but may also serve as a new platform for the development of membrane additives based on PEG-functionalized naphthalimides.

Self-assembled prebiotic amphiphile-mixture exhibits tunable catalytic properties

Protocellular surface formation via the self-assembly of amphiphiles, and catalysis by simple peptides/proto-RNA are two important pillars in the evolution of protocells. To hunt for prebiotic self-assembly-supported catalytic reactions, we thought that amino-acid-based amphiphiles might play an important role. In this paper, we investigate the formation of histidine-based and serine-based amphiphiles under mild prebiotic conditions from amino acid : fatty alcohol and amino acid : fatty acid mixtures. The histidine-based amphiphiles were able to catalyze hydrolytic reactions at the self-assembled surface (with a rate increase of ∼1000-fold), and the catalytic ability can be tuned by linkage of the fatty carbon part to histidine (N-acylated vs. O-acylated). Moreover, the presence of cationic serine-based amphiphiles on the surface enhances the catalytic efficiency by another ∼2-fold, whereas the presence of anionic aspartic acid-based amphiphiles reduces the catalytic activity. Ester partitioning into the surface, reactivity, and the accumulation of liberated fatty acid explain the substrate selectivity of the catalytic surface, where the hexyl esters were found to be more hydrolytic than other fatty acyl esters. Di-methylation of the -NH₂ of OLH increases the catalytic efficacy by a further ∼2-fold, whereas trimethylation reduces the catalytic ability. The self-assembly, charge-charge repulsion, and the H-bonding to the ester carbonyl are likely to be responsible for the superior (∼2500-fold higher rate than the pre-micellar OLH) catalytic efficiency of O-lauryl dimethyl histidine (OLDMH). Thus, prebiotic amino-acid-based surfaces served as an efficient catalyst that exhibits regulation of catalytic function, substrate selectivity, and further adaptability to perform bio-catalysis.

Finding or Creating a Living Organism? Past and Future Thought Experiments in Astrobiology Applied to Artificial Intelligence

This is a digest of how various researchers in biology and astrobiology have explored questions of what defines living organisms-definitions based on functions or structures observed in organisms, or on systems terms, or on mathematical conceptions like closure, chirality, quantum mechanics and thermodynamics, or on biosemiotics, or on Darwinian evolution-to clarify the field and make it easier for endeavors in artificial intelligence to make progress. Current ideas are described to promote work between astrobiologists and computer scientists, each concerned with living organisms. A four-parameter framework is presented as a scaffold that is later developed into what machines lack to be considered alive: systems, evolution, energy and consciousness, and includes Jagers operators and the idea of dual closure. A novel definition of consciousness is developed which describes mental objects both with and without communicable properties, and this helps to clarify how consciousness in machines may be studied as an emergent process related to choice functions in systems. A perspective on how quantization, acting on nucleic acids, sets up natural limits to system behavior is offered as a partial address to the problem of biogenesis.

The Construction of Biological 'Inter-Identity' as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution

The concept of identity is used both (i) to distinguish a system as a particular material entity that is conserved as such in a given environment (token-identity: i.e., identity as permanence or endurance over time), and (ii) to relate a system with other members of a set (type-identity: i.e., identity as an equivalence relationship). Biological systems are characterized, in a minimal and universal sense, by a highly complex and dynamic, far-from-equilibrium organization of very diverse molecular components and transformation processes (i.e., 'genetically instructed cellular metabolisms') that maintain themselves in constant interaction with their corresponding environments, including other systems of similar nature. More precisely, all living entities depend on a deeply convoluted organization of molecules and processes (a naturalized von Neumann constructor architecture) that subsumes, in the form of current individuals (autonomous cells), a history of ecological and evolutionary interactions (across cell populations). So one can defend, on those grounds, that living beings have an identity of their own from both approximations: (i) and (ii). These transversal and trans-generational dimensions of biological phenomena, which unfold together with the actual process of biogenesis, must be carefully considered in order to understand the intricacies and metabolic robustness of the first living cells, their underlying uniformity (i.e., their common biochemical core) and the eradication of previous -or alternative- forms of complex natural phenomena. Therefore, a comprehensive approach to the origins of life requires conjugating the actual properties of the developing complex individuals (fusing and dividing protocells, at various stages) with other, population-level features, linked to their collective-evolutionary behavior, under much wider and longer-term parameters. On these lines, we will argue that life, in its most basic sense, here on Earth or anywhere else, demands crossing a high complexity threshold and that the concept of 'inter-identity' can help us realize the different aspects involved in the process. The article concludes by pointing out some of the challenges ahead if we are to integrate the corresponding explanatory frameworks, physiological and evolutionary, in the hope that a more general theory of biology is on its way.

Twenty Years of "Lipid World": A Fertile Partnership with David Deamer

"The Lipid World" was published in 2001, stemming from a highly effective collaboration with David Deamer during a sabbatical year 20 years ago at the Weizmann Institute of Science in Israel. The present review paper highlights the benefits of this scientific interaction and assesses the impact of the lipid world paper on the present understanding of the possible roles of amphiphiles and their assemblies in the origin of life. The lipid world is defined as a putative stage in the progression towards life's origin, during which diverse amphiphiles or other spontaneously aggregating small molecules could have concurrently played multiple key roles, including compartment formation, the appearance of mutually catalytic networks, molecular information processing, and the rise of collective self-reproduction and compositional inheritance. This review brings back into a broader perspective some key points originally made in the lipid world paper, stressing the distinction between the widely accepted role of lipids in forming compartments and their expanded capacities as delineated above. In the light of recent advancements, we discussed the topical relevance of the lipid worldview as an alternative to broadly accepted scenarios, and the need for further experimental and computer-based validation of the feasibility and implications of the individual attributes of this point of view. Finally, we point to possible avenues for exploring transition paths from small molecule-based noncovalent structures to more complex biopolymer-containing proto-cellular systems.

Primordial sex facilitates the emergence of evolution

Compartments are ubiquitous throughout biology, and they have very likely played a crucial role at the origin of life. Here we assume that a protocell, which is a compartment enclosing functional components, requires N such components in order to be evolvable. We calculate the timescale in which a minimal evolvable protocell is produced. We show that when protocells fuse and share information, the timescales polynomially in N By contrast, in the absence of fusion, the worst-case scenario is exponential in N We discuss the implications of this result for the origin of life and other biological processes.

Preferential Equilibrium Partitioning of Positively Charged Tryptophan into Phosphatidylcholine Bilayer Membranes

The interactions between small molecules and lipid bilayers play a critical role in the function of cellular membranes. Understanding how a small molecule interacts with the lipid bilayer differently based on its charge reveals primordial mechanisms of transport across membranes and assists in the design of drug molecules that can penetrate cells. We have previously reported that tryptophan permeated through a phosphatidylcholine lipid bilayer membrane at a faster rate when it was positively charged (Trp+) than when negatively charged (Trp-), which corresponded to a lower potential of mean force (PMF) barrier determined through simulations. In this report, we demonstrate that Trp+ partitions into the lipid bilayer membrane to a greater degree than Trp- by interacting with the ester linkage of a phosphatidylcholine lipid, where it is stabilized by the electron withdrawing glycerol functional group. These results are in agreement with tryptophan's known role as an anchor for transmembrane proteins, though the tendency for binding of a positively charged tryptophan is surprising. We discuss the implications of our results on the mechanisms of unassisted permeation and penetration of small molecules within and across lipid bilayer membranes based on molecular charge, shape, and molecular interactions within the bilayer structure.

Self-Assembly of Amphiphiles into Vesicles and Fibrils: Investigation of Structure and Dynamics Using Spectroscopy and Microscopy Techniques

Amphiphiles are a class of molecules which are known to assemble into a variety of nanostructures. The understanding and applications of self-assembled systems are based on what has been learned from biology. Among the vast number of self-assemblies, in this article, we have described the formation, characterization, and dynamics of two important biologically inspired assemblies: vesicles and fibrils. Vesicles, which can be classified into several categories depending on the sizes and components, are of great interest due to their potential applications in drug delivery and as nanoscale reactors. The structure and dynamics of vesicles can also mimic the complex geometry of the cell membrane. On the other hand, the self-assembly of proteins, peptides, and even single amino acids leads to a number of degenerative disorders. Thus, a complete understanding of these self-assembled systems is necessary. In this article, we discuss recent work on vesicular aggregates composed of phospholipids, fatty acids, and ionic as well as nonionic surfactants and single amino acid-based fibrils such as phenylalanine and tyrosine. Beside the characterization, we also emphasize the excited-state dynamics inside the aggregates for a proper understanding of the organization, reactivity, and heterogeneity of the aggregates.

The synthesis of mono-alkyl phosphates and their derivatives: an overview of their nature, preparation and use, including synthesis under plausible prebiotic conditions

Nucleic acids, phospholipids and other organic phosphates play central roles in biological pathways.

Carrying pieces of information in organocatalytic bytes: Semiopoiesis-A new theory of life and its origins

Living beings have been classically described as autopoietic machines: chemical systems, which maintain a reproducible steady state by producing their components and boundaries. On the other hand, very simple autopoietic micelles have been produced in laboratory. They consist in micelles able to catalyse the production of their own surfactants. However is very clear that these autopoietic systems are unable to evolve. In this way, these autopoietic micelles cannot be associated to living organisms, which are always linked by evolutionary relationships. Here I claim that living beings are a class of autopoietic systems able to conserve molecular information, a feature denoted by the term semiopoiesis. By defining the molecular information of their products, semiopoietic systems control their interaction with the medium and, by being able to convey molecular information beneficial to the maintenance of the organization to their offspring, semiopoietic systems can evolve by natural selection. Information can be described as a specific state or order assumed among a set of other possible states or orders. Thus, molecular information is the specific order by which the molecular components are ordered, such as the sequence of nucleotides in nucleic acids or of amino acids in proteins. However, molecular information is not limited to copolymers. The atoms in small organic compounds may also present diverse orders, giving rise to isomers. Different isomers can present very distinct chemical and physical properties such that the biophysical-chemical properties of an organic compound are determined by its composition and molecular information i.e. the specific positions in which their atoms are posited. This molecular information can be conserved during reactions catalysed by selective organocatalysts. In this way, organocatalysts appear as plausible candidates to primitive hosts for the genetic information, before the emergence of systems based in biopolymers. The bases of a putative organocatalysts-based evolution are discussed. Finally, I argue that organocatalytic micelles can be designed to produce programmable materials, artificial photosynthesis, self-building materials and artificial life with relevant industrial impact.

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.

Life Is Simple-Biologic Complexity Is an Epiphenomenon

Life originated from unicellular organisms by circumventing the Second Law of Thermodynamics using the First Principles of Physiology, namely negentropy, chemiosmosis and homeostatic regulation of calcium and lipids. It is hypothesized that multicellular organisms are merely contrivances or tools, used by unicellular organisms as agents for the acquisition of epigenetic inheritance. The First Principles of Physiology, which initially evolved in unicellular organisms are the exapted constraints that maintain, sustain and perpetuate that process. To ensure fidelity to this mechanism, we must return to the first principles of the unicellular state as the determinants of the primary level of selection pressure during the life cycle. The power of this approach is reflected by examples of its predictive value. This perspective on life is a "game changer", mechanistically rendering transparent many dogmas, teleologies and tautologies that constrain the current descriptive view of Biology.

The Emergence of Physiology and Form: Natural Selection Revisited

Natural Selection describes how species have evolved differentially, but it is descriptive, non-mechanistic. What mechanisms does Nature use to accomplish this feat? One known way in which ancient natural forces affect development, phylogeny and physiology is through gravitational effects that have evolved as mechanotransduction, seen in the lung, kidney and bone, linking as molecular homologies to skin and brain. Tracing the ontogenetic and phylogenetic changes that have facilitated mechanotransduction identifies specific homologous cell-types and functional molecular markers for lung homeostasis that reveal how and why complex physiologic traits have evolved from the unicellular to the multicellular state. Such data are reinforced by their reverse-evolutionary patterns in chronic degenerative diseases. The physiologic responses of model organisms like Dictyostelium and yeast to gravity provide deep comparative molecular phenotypic homologies, revealing mammalian Target of Rapamycin (mTOR) as the final common pathway for vertical integration of vertebrate physiologic evolution; mTOR integrates calcium/lipid epistatic balance as both the proximate and ultimate positive selection pressure for vertebrate physiologic evolution. The commonality of all vertebrate structure-function relationships can be reduced to calcium/lipid homeostatic regulation as the fractal unit of vertebrate physiology, demonstrating the primacy of the unicellular state as the fundament of physiologic evolution.

Prebiotic Lipidic Amphiphiles and Condensing Agents on the Early Earth

It is still uncertain how the first minimal cellular systems evolved to the complexity required for life to begin, but it is obvious that the role of amphiphilic compounds in the origin of life is one of huge relevance. Over the last four decades a number of studies have demonstrated how amphiphilic molecules can be synthesized under plausibly prebiotic conditions. The majority of these experiments also gave evidence for the ability of so formed amphiphiles to assemble in closed membranes of vesicles that, in principle, could have compartmented first biological processes on early Earth, including the emergence of self-replicating systems. For a competitive selection of the best performing molecular replicators to become operative, some kind of bounded units capable of harboring them are indispensable. Without the competition between dynamic populations of different compartments, life itself could not be distinguished from an otherwise disparate array or network of molecular interactions. In this review, we describe experiments that demonstrate how different prebiotically-available building blocks can become precursors of phospholipids that form vesicles. We discuss the experimental conditions that resemble plausibly those of the early Earth (or elsewhere) and consider the analytical methods that were used to characterize synthetic products. Two brief sections focus on phosphorylating agents, catalysts and coupling agents with particular attention given to their geochemical context. In Section 5, we describe how condensing agents such as cyanamide and urea can promote the abiotic synthesis of phospholipids. We conclude the review by reflecting on future studies of phospholipid compartments, particularly, on evolvable chemical systems that include giant vesicles composed of different lipidic amphiphiles.

Cardiolipin signaling mechanisms: collapse of asymmetry and oxidation

SIGNIFICANCE

An ancient anionic phospholipid, cardiolipin (CL), ubiquitously present in prokaryotic and eukaryotic membranes, is essential for several structural and functional purposes.

RECENT ADVANCES

The emerging role of CLs in signaling has become the focus of many studies.

CRITICAL ISSUES

In this work, we describe two major pathways through which mitochondrial CLs may fulfill the signaling functions via utilization of their (i) asymmetric distribution across membranes and translocations, leading to the surface externalization and (ii) ability to undergo oxidation reactions to yield the signature products recognizable by the executionary machinery of cells.

FUTURE DIRECTIONS

We present a concept that CLs and their oxidation/hydrolysis products constitute a rich communication language utilized by mitochondria of eukaryotic cells for diversified regulation of cell physiology and metabolism as well as for inter-cellular interactions.

Once upon a time the cell membranes: 175 years of cell boundary research

All modern cells are bounded by cell membranes best described by the fluid mosaic model. This statement is so widely accepted by biologists that little attention is generally given to the theoretical importance of cell membranes in describing the cell. This has not always been the case. When the Cell Theory was first formulated in the XIX(th) century, almost nothing was known about the cell membranes. It was not until well into the XX(th) century that the existence of the plasma membrane was broadly accepted and, even then, the fluid mosaic model did not prevail until the 1970s. How were the cell boundaries considered between the articulation of the Cell Theory around 1839 and the formulation of the fluid mosaic model that has described the cell membranes since 1972? In this review I will summarize the major historical discoveries and theories that tackled the existence and structure of membranes and I will analyze how these theories impacted the understanding of the cell. Apart from its purely historical relevance, this account can provide a starting point for considering the theoretical significance of membranes to the definition of the cell and could have implications for research on early life.

Search for the most 'primitive' membranes and their reinforcers: a review of the polyprenyl phosphates theory

Terpenoids have an essential function in present-day cellular membranes, either as membrane reinforcers in Eucarya and Bacteria or as principal membrane constituents in Archaea. We have shown that some terpenoids, such as cholesterol and α, ω-dipolar carotenoids reinforce lipid membranes by measuring the water permeability of unilamellar vesicles. It was possible to arrange the known membrane terpenoids in a ‘phylogenetic’ sequence, and a retrograde analysis led us to conceive that single-chain polyprenyl phosphates might have been ‘primitive’ membrane constituents. By using an optical microscopy, we have observed that polyprenyl phosphates containing 15 to 30 C-atoms form giant vesicles in water in a wide pH range. The addition of 10 % molar of some polyprenols to polyprenyl phosphate vesicles have been shown to reduce the water permeability of membranes even more efficiently than the equimolecular addition of cholesterol. A ‘prebiotic’ synthesis of C10 and C15 prenols from C5 monoprenols was achieved in the presence of a montmorillonite clay. Hypothetical pathway from C1 or C2 units to ‘primitive’ membranes and that from ‘primitive’ membranes to archaeal lipids are presented.

Vesicles protect activated acetic acid

Abstract Methyl thioacetate, or activated acetic acid, has been proposed to be central to the origin of life and an important energy currency molecule in early cellular evolution. We have investigated the hydrolysis of methyl thioacetate under various conditions. Its uncatalyzed rate of hydrolysis is about 3 orders of magnitude faster (K=0.00663 s(-1); 100°C, pH 7.5, concentration=0.33 mM) than published rates for its catalyzed production, making it unlikely to accumulate under prebiotic conditions. However, our experiments showed that methyl thioacetate was protected from hydrolysis when inside its own hydrophobic droplets. Further, we found that methyl thioacetate protection from hydrolysis was also possible in droplets of hexane and in the membranes of nonanoic acid vesicles. Thus, the hydrophobic regions of prebiotic vesicles and early cell membranes could have offered a refuge for this energetic molecule, increasing its lifetime in close proximity to the reactions for which it would be needed. This model of early energy storage evokes an additional critical function for the earliest cell membranes.

Keynote Paper — AUTOPOIETIC GENE-ENZYME CYCLES AND THE EMERGENCE OF LIFE

Systems concepts are applied to solve the problem of how early life could have emerged from an initially abiotic organic environment. Proteinoid or lipid microspheres are proposed to have polymerized from a primordial organic soup and to contain various amino acids and several different nucleobases. A self-replicating "basic set" hypercycle consisting of 10 XNA gene strands and 10 enzymes is proposed that utilizes inorganic phosphates as an energy source. The genes would utilize triplet combinations of adenosine and uracil to code for a replicase enzyme, a polymerase enzyme and eight-code translator (synthetase) enzymes. It is shown that there is a high probability that the basic set genes would emerge. Fissioning of the basic set microspheres into a population of microspheres all containing the basic set, could eliminate the problem of a single gene monopolizing use of the replicator enzyme at the expense of the others and greatly enhance the survivability of the replicating population as a whole. A thermodynamic analysis of such a self-replicating system is also presented. It is shown that genetic mutations will, in the long run allow the basic set to evolve to increased diversity, higher rates of enzyme synthesis and greater rates of entropy production. Long-term evolution could have resulted in organisms similar to contemporary bacteria that utilize RNA genes with a four nucleobase codon system.

The origins of cellular life

All life on earth can be naturally classified into cellular life forms and virus-like selfish elements, the latter being fully dependent on the former for their reproduction. Cells are reproducers that not only replicate their genome but also reproduce the cellular organization that depends on semipermeable, energy-transforming membranes and cannot be recovered from the genome alone, under the famous dictum of Rudolf Virchow, Omnis cellula e cellula. In contrast, simple selfish elements are replicators that can complete their life cycles within the host cell starting from genomic RNA or DNA alone. The origin of the cellular organization is the central and perhaps the hardest problem of evolutionary biology. I argue that the origin of cells can be understood only in conjunction with the origin and evolution of selfish genetic elements. A scenario of precellular evolution is presented that involves cohesion of the genomes of the emerging cellular life forms from primordial pools of small genetic elements that eventually segregated into hosts and parasites. I further present a model of the coevolution of primordial membranes and membrane proteins, discuss protocellular and non-cellular models of early evolution, and examine the habitats on the primordial earth that could have been conducive to precellular evolution and the origin of cells.

Early self-reproduction, the emergence of division mechanisms in protocells

Synthetic Biology approaches are proposing model systems and providing experimental evidences that life can arise as spontaneous chemical self-assembly process where the ability to reproduce itself is an essential feature of the living system. The appearance of early cells has required an amphiphilic membrane compartment to confine molecular information against diffusion, and the ability to self-replicate the boundary layer and the genetic information. The initial spontaneous self-replication mechanisms based on thermodynamic instability would have evolved in a prebiotic and later biological catalysis. Early studies demonstrate that fatty acids spontaneously assemble into bilayer membranes, building vesicles able to grow by incorporation of free lipid molecules and divide. Early replication mechanisms may have seen inorganic molecules playing a role as the first catalysts. The emergence of a short ribozyme or short catalytic peptide may have initiated the first prebiotic membrane lipid synthesis required for vesicle growth. The evolution of early catalysts towards the simplest translation machine to deliver proteins from RNA sequences was likely to give early birth to one single enzyme controlling protocell membrane division. The cell replication process assisted by complex enzymes for lipid synthesis is the result of evolved pathways in early cells. Evolution from organic molecules to protocells and early cells, thus from chemistry to biology, may have occurred in and out of the boundary layer. Here we review recent experimental work describing membrane and vesicle division mechanisms based on chemico-physical spontaneous processes, inorganic early catalysis and enzyme based mechanisms controlling early protocell division and finally the feedback from minimal genome studies.

Replication of simulated prebiotic amphiphile vesicles controlled by experimental lipid physicochemical properties

We present a new embodiment of the graded autocatalysis replication domain (GARD) for the growth, replication and evolution of lipid vesicles based on a semi-empirical foundation using experimentally measured kinetic values of selected extant lipid species. Extensive simulations using this formalism elucidated the details of the dependence of the replication and properties of the vesicles on the physicochemical properties and concentrations of the lipids, both in the environment and in the vesicle. As expected, the overall concentration and number of amphiphilic components strongly affect average replication time. Furthermore, variations in acyl chain length and unsaturation of vesicles also influence replication rate, as do the relative concentrations of individual lipid types. Understanding of the dependence of replication rates on physicochemical parameters opens a new direction in the study of prebiotic vesicles and lays the groundwork for future studies involving the competition between lipid vesicles for available amphiphilic monomers.

Spatial model of autocatalytic reactions

Biological cells with all of their surface structure and complex interior stripped away are essentially vesicles--membranes composed of lipid bilayers which form closed sacs. Vesicles are thought to be relevant as models of primitive protocells, and they could have provided the ideal environment for prebiotic reactions to occur. In this paper, we investigate the stochastic dynamics of a set of autocatalytic reactions, within a spatially bounded domain, so as to mimic a primordial cell. The discreteness of the constituents of the autocatalytic reactions gives rise to large sustained oscillations even when the number of constituents is quite large. These oscillations are spatiotemporal in nature, unlike those found in previous studies, which consisted only of temporal oscillations. We speculate that these oscillations may have a role in seeding membrane instabilities which lead to vesicle division. In this way synchronization could be achieved between protocell growth and the reproduction rate of the constituents (the protogenetic material) in simple protocells.

Thermodynamics of vesicle growth and instability

We describe the growth of vesicles, due to the accretion of lipid molecules to their surface, in terms of linear irreversible thermodynamics. Our treatment differs from those previously put forward by consistently including the energy of the membrane in the thermodynamic description. We calculate the critical radius at which the spherical vesicle becomes unstable to a change of shape in terms of the parameters of the model. The analysis is carried out for the case both when the increase in volume is due to the absorption of water and when a solute is also absorbed through the walls of the vesicle.

Stability of model membranes in extreme environments

The first forms of cellular life required a source of amphiphilic compounds capable of assembling into stable boundary structures. Membranes composed of fatty acids have been proposed as model systems of primitive membranes, but their bilayer structure is stable only within a narrow pH range and low ionic strength. They are particularly sensitive to aggregating effects of divalent cations (Mg+2, Ca+2, Fe+2) that would be present in Archaean sea water. Here we report that mixtures of alkyl amines and fatty acids form vesicles at strongly basic and acidic pH ranges which are resistant to the effects of divalent cations up to 0.1 M. Vesicles formed by mixtures of decylamine and decanoic acid (1:1 mole ratio) are relatively permeable to pyranine, a fluorescent anionic dye, but permeability could be reduced by adding 2 mol% of a polycyclic aromatic hydrocarbon such as pyrene. Permeability to the dye was also reduced by increasing the chain length of the amphiphiles. For instance, 1:1 mole ratio mixtures of dodecylamine and dodecanoic acid were able to retain pyranine dye during and following gel filtration. We conclude that primitive cell membranes were likely to be composed of mixtures of amphiphilic and hydrophobic molecules that manifested increased stability over pure fatty acid membranes.

Growth of organic microspherules in sugar-ammonia reactions

Reaction of small sugars of less than four carbons with ammonia in water yielded organic microspherules generally less than ten microns in size. The time course of microspherule growth was examined for the D-erythrose-ammonia reaction that yielded microspherules attached to the glass walls of containers. Measurements were made of the elemental composition and infrared spectrum of the microspherule material. These viscose semi-solid microspherules are viewed as possible containers for prebiotic catalytic processes relevant to the origin of life.

A possible route to prebiotic vesicle reproduction

Spherical bounded structures such as those formed by surfactant aggregates (mostly micelles and vesicles), with an inside that is chemically and physically different from the outside medium, can be seen as primitive cell models. As such, they are fundamental structures for the theory of autopoiesis as originally formulated by Varela and Maturana. In particular, since self-reproduction is a very important feature of minimal cellular life, the study of self-reproduction of micelles and vesicles represents a quite challenging bio-mimetic approach. Our laboratory has put much effort in recent years into implementing self-reproduction of vesicles as models for self-reproduction of cellular bounded structures, and this article is a further contribution in this direction. In particular, we deal with the so-called matrix effect of vesicles, related to the fact that when fresh surfactant is added to an aqueous solution containing preformed vesicles of a very narrow size distribution, the newly formed vesicles (instead of being polydisperse, as is usually the case) have dimensions very close to those of the preformed ones. In practice, this corresponds to a mechanism of reproduction of vesicles of the same size. In this article, the matrix effect is re-elaborated in the perspective of the origin of life, and in particular in terms of the prebiotic mechanisms that might permit the growth and reproduction of vesicles. The data are analyzed by dynamic light scattering with a new program that permits the calculation of the number-weighted size distribution. It is shown that, on adding a stoichiometric amount of oleate micelles to preformed oleate vesicles extruded at 50 and 100 nm, the final distribution contains about twice the initial number of particles, centered around 50 and 100 nm. The same holds when oleate is added to preformed phospholipid liposomes. By contrast, when the same amount of oleate is added to an aqueous solution (as a control experiment), a very broad distribution ranging between 20 and 1000 nm is obtained. The data can then be seen as a kind of reproduction of the same size vesicles, and the argument is advanced that this may correspond to a simple prebiotic mechanism of vesicle multiplication in prebiotic times, when only physical forces might be responsible for the basic mechanisms of early protocell growth and division. Preliminary data also show that repeated addition of oleate maintains the same basic initial features, and that surfactants other than oleate also respect the reproductive mode of the matrix effect.

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells

All life is organized as cells. Physical compartmentation from the environment and self-organization of self-contained redox reactions are the most conserved attributes of living things, hence inorganic matter with such attributes would be life's most likely forebear. We propose that life evolved in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide-rich hydrothermal fluid and iron(II)-containing waters of the Hadean ocean floor. The naturally arising, three-dimensional compartmentation observed within fossilized seepage-site metal sulphide precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes found in free-living prokaryotes. The known capability of FeS and NiS to catalyse the synthesis of the acetyl-methylsulphide from carbon monoxide and methylsulphide, constituents of hydrothermal fluid, indicates that pre-biotic syntheses occurred at the inner surfaces of these metal-sulphide-walled compartments, which furthermore restrained reacted products from diffusion into the ocean, providing sufficient concentrations of reactants to forge the transition from geochemistry to biochemistry. The chemistry of what is known as the RNA-world could have taken place within these naturally forming, catalyticwalled compartments to give rise to replicating systems. Sufficient concentrations of precursors to support replication would have been synthesized in situ geochemically and biogeochemically, with FeS (and NiS) centres playing the central catalytic role. The universal ancestor we infer was not a free-living cell, but rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its constituents occurred. The first free-living cells are suggested to have been eubacterial and archaebacterial chemoautotrophs that emerged more than 3.8 Gyr ago from their inorganic confines. We propose that the emergence of these prokaryotic lineages from inorganic confines occurred independently, facilitated by the independent origins of membrane-lipid biosynthesis: isoprenoid ether membranes in the archaebacterial and fatty acid ester membranes in the eubacterial lineage. The eukaryotes, all of which are ancestrally heterotrophs and possess eubacterial lipids, are suggested to have arisen ca. 2 Gyr ago through symbiosis involving an autotrophic archaebacterial host and a heterotrophic eubacterial symbiont, the common ancestor of mitochondria and hydrogenosomes. The attributes shared by all prokaryotes are viewed as inheritances from their confined universal ancestor. The attributes that distinguish eubacteria and archaebacteria, yet are uniform within the groups, are viewed as relics of their phase of differentiation after divergence from the non-free-living universal ancestor and before the origin of the free-living chemoautotrophic lifestyle. The attributes shared by eukaryotes with eubacteria and archaebacteria, respectively, are viewed as inheritances via symbiosis. The attributes unique to eukaryotes are viewed as inventions specific to their lineage. The origin of the eukaryotic endomembrane system and nuclear membrane are suggested to be the fortuitous result of the expression of genes for eubacterial membrane lipid synthesis by an archaebacterial genetic apparatus in a compartment that was not fully prepared to accommodate such compounds, resulting in vesicles of eubacterial lipids that accumulated in the cytosol around their site of synthesis. Under these premises, the most ancient divide in the living world is that between eubacteria and archaebacteria, yet the steepest evolutionary grade is that between prokaryotes and eukaryotes.

The sugar model: catalysis by amines and amino acid products

Ammonia and amines (including amino acids) were shown to catalyze the formation of sugars from formaldehyde and glycolaldehyde, and the subsequent conversion of sugars to carbonylcontaining products under the conditions studied (pH 5.5 and 50 degrees C). Sterically unhindered primary amines were better catalysts than ammonia, secondary amines, and sterically hindered primary amines (i.e. alpha-aminoisobutyric acid). Reactions catalyzed by primary amines initially consumed formaldehyde and glycolaldehyde about 15-20 times faster than an uncatalyzed control reaction. The amine-catalyzed reactions yielded aldotriose (glyceraldehyde), ketotriose (dihydroxyacetone), aldotetroses (erythrose and threose), ketotetrose (erythrulose), pyruvaldehyde, acetaldehyde, glyoxal, pyruvate, glyoxylate, and several unindentified carbonyl products. The concentrations of the carbonyl products, except pyruvate and ketotetrose, initially increased and then declined during the reaction, indicating their ultimate conversion to other products (like larger sugars or pyruvate). The uncatalyzed control reaction yielded no pyruvate or glyoxylate, and only trace amounts of pyruvaldehyde, acetaldehyde and glyoxal. In the presence of 15 mM catalytic primary amine, such as alanine, the rates of triose and pyruvaldehyde of synthesis were about 15-times and 1200-times faster, respectively, than the uncatalyzed reaction. Since previous studies established that alanine is synthesized from glycolaldehyde and formaldehyde via pyruvaldehyde as its direct precursor, the demonstration that the alanine catalyzes the conversion of glycolaldehyde and formaldehyde to pyruvaldehyde indicates that this synthetic pathway is capable of autocatalysis. The relevance of this synthetic process, named the Sugar Model, to the origin of life is discussed.

What makes plants different? Principles of extracellular matrix function in 'soft' plant tissues

An overview of the biomechanic and morphogenetic function of the plant extracellular matrix (ECM) in its primary state is given. ECMs can play a pivotal role in cellular osmo- and volume-regulation, if they enclose the cell hermetically and constrain hydrostatic pressure evoked by osmotic gradients between the cell and its environment. From an engineering viewpoint, such cell walls turn cells into hydraulic machines, which establishes a crucial functional differences between cell walls and other cellular surface structures. Examples of such hydraulic machineries are discussed. The function of cell walls in the control of pressure, volume, and shape establishes constructional evolutionary constraints, which can explain aspects commonly considered typical of plants (sessility, autotrophy). In plants, 'cell division' by insertion of a new cell wall is a process of internal cytoplasmic differentiation. As such it differs fundamentally from cell separation during cytokinesis in animals, by leaving the coherence of the dividing protoplast basically intact. The resulting symplastic coherence appears more important for plant morphogenesis than histological structure; similar morphologies are realized on the basis of distinct tissue architectures in different plant taxa. The shape of a plant cell is determined by the shape its cell wall attains under multiaxial tensile stress. Consequently, the development of form in plants is achieved by a differential plastic deformation of the complex ECM in response to this multiaxial force (hydrostatic pressure). Current concepts of the regulation of these deformation processes are briefly evaluated.

Homochirality and life

After clarifying the frequently misused term homochirality, the crucial importance of homochirality and chiral purity in the development and maintenance of the essential biopolymers of life--proteins and nucleic acids--is discussed. The harsh and forbidding prebiotic environment during the era of cometary impact after formation of the Earth approximately 4.5 Gyr ago is described, after which the most important abiotic mechanisms proposed historically for the genesis of chiral molecules on the primitive Earth are enumerated. Random and determinate terrestrial mechanisms are each evaluated with regard to the environmental restraints imposed during the impact era, and it is concluded that all such mechanisms would be inapplicable and implausible in the realistic prebiotic environment. To circumvent these limitations, an extended hypothesis is presented describing an extraterrestrial source of homochiral terrestrial molecules. Illustrated in Figure 2, this scenario involves the partial asymmetric photolysis of the racemic constituents of organic mantles on interstellar dust grains by the circularly polarized ultraviolet components of the synchrotron radiation emanating from the neutron star remnants of super-novae. The resulting homochiral constituents with low enanantiomeric excesses (e.e.s) so produced in the organic mantles are subsequently conveyed to Earth either by direct accumulation or, more likely, after coalescence into comets or asteroids, followed by repetitive impingement during the impact era. Finally, the low e.e.s of the extraterrestrial homochiral molecules so introduced are amplified by terrestrial autocatalytic or polymerization mechanisms into a state of chiral purity, then are ultimately concentrated and protected by sequestration in the interiors of spontaneously formed protocellular vesicles--there to await further chemical evolution toward the biomolecules of life. Recent observations of the excess of L-over D-amino acids in the Murchison meteorite are cited as validation for the early stages of the proposed hypothesis.

A fission-fusion origin for life

To develop a comprehensive 'cells-first' approach to the origin of life, we propose that protocells form spontaneously and that the fission and fusion of these protocells drives the dynamics of their evolution. The fitness criterion for this evolution is taken to be the the stability (conservation) of domains in the protocellular membrane as determined by non-covalent molecular associations between the amphiphiles of the membrane and a subset of the macromolecules in the protocell. In the presence of a source of free energy the macromolecular content of the protocell (co-)evolves as the result of (domain-dependent) membrane-catalysed polymerisation of the prebiotic constituents delivered to the protocell by fusion. The metabolism of the cell therefore (co-)evolves on a rugged fitness landscape. We indicate how domain evolution with the same fitness criterion can potentially give rise to coding. Membrane domains may therefore provide the link between protocells and the RNA/DNA-world.

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.

The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front

Here we argue that life emerged on Earth from a redox and pH front at c. 4.2 Ga. This front occurred where hot (c. 150 degrees C), extremely reduced, alkaline, bisulphide-bearing, submarine seepage waters interfaced with the acid, warm (c. 90 degrees C), iron-hearing Hadean ocean. The low pH of the ocean was imparted by the ten bars of CO2 considered to dominate the Hadean atmosphere/hydrosphere. Disequilibrium between the two solutions was maintained by the spontaneous precipitation of a colloidal FeS membrane. Iron monosulphide bubbles comprising this membrane were inflated by the hydrothermal solution upon sulphide mounds at the seepage sites. Our hypothesis is that the FeS membrane, laced with nickel, acted as a semipermeable catalytic boundary between the two fluids, encouraging synthesis of organic anions by hydrogenation and carboxylation of hydrothermal organic primers. The ocean provided carbonate, phosphate, iron, nickel and protons; the hydrothermal solution was the source of ammonia, acetate, HS-, H2 and tungsten, as well as minor concentrations of organic sulphides and perhaps cyanide and acetaldehyde. The mean redox potential (delta Eh) across the membrane, with the energy to drive synthesis, would have approximated to 300 millivolts. The generation of organic anions would have led to an increase in osmotic pressure within the FeS bubbles. Thus osmotic pressure could take over from hydraulic pressure as the driving force for distension, budding and reproduction of the bubbles. Condensation of the organic molecules to polymers, particularly organic sulphides, was driven by pyrophosphate hydrolysis. Regeneration of pyrophosphate from the monophosphate in the membrane was facilitated by protons contributed from the Hadean ocean. This was the first use by a metabolizing system of protonmotive force (driven by natural delta pH) which also would have amounted to c. 300 millivolts. Protonmotive force is the universal energy transduction mechanism of life. Taken together with the redox potential across the membrane, the total electrochemical and chemical energy available for protometabolism amounted to a continuous supply at more than half a volt. The role of the iron sulphide membrane in keeping the two solutions separated was appropriated by the newly synthesized organic sulphide polymers. This organic take-over of the membrane material led to the miniaturization of the metabolizing system. Information systems to govern replication could have developed penecontemporaneously in this same milieu. But iron, sulphur and phosphate, inorganic components of earliest life, continued to be involved in metabolism.

Enzyme-containing liposomes can endogenously produce membrane-constituting lipids

BACKGROUND

'Giant vesicles' are liposomes that have diameters of several micrometers. It is possible to microinject biochemicals into a single vesicle and follow the progress of a chemical reaction in real time by light microscopy. We have previously used this technique to inject phospholipase A2 into giant vesicles; the vesicles disappeared as their components were hydrolyzed. Here we investigate whether the lipid components of a vesicle can be synthesized inside it.

RESULTS

Giant vesicles composed of 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (POPC) and palmitoyl-CoA were prepared in a solution containing sn-glycerol-3-phosphate. Microinjection of the enzyme sn-glycerol-3-phosphate-acyltransferase into the vesicle catalyzes the in situ production of the lipid membrane precursor 1-palmitoyl-sn-glycerol-3-phosphate, which remains incorporated in the membrane. The altered membrane chemistry causes shrinkage of the vesicle and formation of smaller liposomes on the inner surface at the site of injection. Similar transformations were seen when the enzyme was added to the outside of the vesicle.

CONCLUSIONS

We have used the first step of the 'salvage pathway' for synthesis of POPC to demonstrate that it is possible to localize the synthesis of a lipid membrane precursor inside a giant vesicle. In the future it may be possible to combine the necessary enzymes and substrates to carry out the reactions for a complete metabolic pathway within a liposome.

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.

Molecular dynamics studies of simple membrane-water interfaces: structure and functions in the beginnings of cellular life

Molecular dynamics computer simulations of the structure and functions of a simple membrane are performed in order to examine whether membranes provide an environment capable of promoting protobiological evolution. Our model membrane is composed of glycerol 1-monooleate. It is found that the bilayer surface fluctuates in time and space, occasionally creating thinning defects in the membrane. These defects are essential for passive transport of simple ions across membranes because they reduce the Born barrier to this process by approximately 40%. Negative ions are transferred across the bilayer more readily than positive ions due to favorable interactions with the electric field at the membrane-water interface. Passive transport of neutral molecules is, in general, more complex than predicted by the solubility-diffusion model. In particular, molecules which exhibit sufficient hydrophilicity and lipophilicity concentrate near membrane surfaces and experience "interfacial resistance" to transport. The membrane-water interface forms an environment suitable for heterogeneous catalysis. Several possible mechanisms leading to an increase of reaction rates at the interface are discussed. We conclude that vesicles have many properties that make them very good candidates for earliest protocells. Some potentially fruitful directions of experimental and theoretical research on this subject are proposed.

Exobiology, the study of the origin, evolution and distribution of life within the context of cosmic evolution: a review

The primary goal of exobiological research is to reach a better understanding of the processes leading to the origin, evolution and distribution of life on Earth or elsewhere in the universe. In this endeavour, scientists from a wide variety of disciplines are involved, such as astronomy, planetary research, organic chemistry, palaeontology and the various subdisciplines of biology including microbial ecology and molecular biology. Space technology plays an important part by offering the opportunity for exploring our solar system, for collecting extraterrestrial samples, and for utilizing the peculiar environment of space as a tool. Exobiological activities include comparison of the overall pattern of chemical evolution of potential precursors of life, in the interstellar medium, and on the planets and small bodies of our solar system; tracing the history of life on Earth back to its roots; deciphering the environments of the planets in our solar system and of their satellites, throughout their history, with regard to their habitability; searching for other planetary systems in our Galaxy and for signals of extraterrestrial civilizations; testing the impact of space environment on survivability of resistant life forms. This evolutionary approach towards understanding the phenomenon of life in the context of cosmic evolution may eventually contribute to a better understanding of the processes regulating the interactions of life with its environment on Earth.

Permeation of membranes by the neutral form of amino acids and peptides: relevance to the origin of peptide translocation

The flux of amino acids and other nutrient solutes such as phosphate across lipid bilayers (liposomes) is 10(5) slower than facilitated inward transport across biological membranes. This suggest that primitive cells lacking highly evolved transport systems would have difficulty transporting sufficient nutrients for cell growth to occur. There are two possible ways by which early life may have overcome this difficulty: (1) The membranes of the earliest cellular life-forms may have been intrinsically more permeable to solutes; or (2) some transport mechanism may have been available to facilitate transbilayer movement of solutes essential for cell survival and growth prior to the evolution of membrane transport proteins. Translocation of neutral species represents one such mechanism. The neutral forms of amino acids modified by methylation (creating protonated weak bases) permeate membranes up to 10(10) times faster than charged forms. This increased permeability when coupled to a transmembrane pH gradient can result in significantly increased rates of net unidirectional transport. Such pH gradients can be generated in vesicles used to model protocells that preceded and were presumably ancestral to early forms of life. This transport mechanism may still play a role in some protein translocation processes (e.g. for certain signal sequences, toxins and thylakoid proteins) in vivo.