Thermally driven fission of protocells

We propose a simple mechanism for the self-replication of protocells. Our main hypothesis is that the amphiphilic molecules composing the membrane bilayer are synthesized inside the protocell through exothermic chemical reactions. The slow increase of the inner temperature forces the hottest molecules to move from the inner leaflet to the outer leaflet of the bilayer. Because of this outward translocation flow, the outer leaflet grows faster than the inner leaflet. This differential growth increases the mean curvature and amplifies any local shrinking of the protocell until it splits in two. The proposed model, based on mere laws of physics, is a step in the study of the origin of life, as well as a clue for a better understanding of cell proliferation in cancer.     

The emergence of ribozymes synthesizing membrane components in RNA-based protocells

A significant problem of the origin of life is the emergence of cellular self-replication. In the context of the “RNA world”, a crucial concern is how the RNA-based protocells could achieve the ability to produce their own membrane. Here we show, with the aid of a computer simulation, that for these protocells, there would be “immediately” a selection pressure for the emergence of a ribozyme synthesizing membrane components. The ribozyme would promote the enlargement of cellular space and favor the incoming (by permeation) of RNA's precursors, thus benefit the replication of inner RNA, including itself. Via growth and division, protocells containing the ribozyme would achieve superiority and spread in the system, and meanwhile the ribozyme would spread in the system. The present work is inspiring because it suggests that the transition from molecular self-replication to cellular self-replication might have occurred naturally (and necessarily) in the origin of life, leading to the emergence of Darwinian evolution at the cellular level.     

Imitational modeling of process of evolution: From organic macromolecules to protocell and animal cell

A dynamic imitational model of initial stages of cell evolution has been developed based on role of environmental calcium concentration. The model is designed from our hypothesis about the medium of the appearance of protocells, which could be potassium water reservoirs rather than sea salt water with its predominance of sodium salts. The necessary elements of the appearance of the protocells served organic molecules, code of their synthesis, and formation of macromolecules under favorable ion concentration in environment: a high K⁺ and Mg²⁺ and a low Na⁺ concentration. The model is based on an assumption that one of the first stages in evolution of life was the appearance in the potassium-magnesium water reservoirs of organic molecules capable for self-replication on the basis of genetic code and formation of protocell with the potassium cytoplasm. The model has demonstrated necessity of formation of cell envelope for development of the protocell. Replacement of the dominant cation in water reservoirs—potassium by sodium—required the appearance of ion-transporting devices in plasma membrane and their participation in adaptation of cells to environment. This stage of evolution was accompanied by the most important morphofunctional event—formation of the plasma membrane instead of cell envelope. The membrane provided the ion asymmetry in the cell (preservation of K⁺ in it) relatively to the sodium external medium for maintaining optimal intracellular medium. In the model system, predecessors of animal cells elaborated mechanism of maintenance of the potassium cytoplasm with the sodium counterion dominating in the environment.     

The Origins of Cellular Life

Understanding the origin of cellular life on Earth requires the discovery of plausible pathways for the transition from complex prebiotic chemistry to simple biology, defined as the emergence of chemical assemblies capable of Darwinian evolution. We have proposed that a simple primitive cell, or protocell, would consist of two key components: a protocell membrane that defines a spatially localized compartment, and an informational polymer that allows for the replication and inheritance of functional information. Recent studies of vesicles composed of fatty-acid membranes have shed considerable light on pathways for protocell growth and division, as well as means by which protocells could take up nutrients from their environment. Additional work with genetic polymers has provided insight into the potential for chemical genome replication and compatibility with membrane encapsulation. The integration of a dynamic fatty-acid compartment with robust, generalized genetic polymer replication would yield a laboratory model of a protocell with the potential for classical Darwinian biological evolution, and may help to evaluate potential pathways for the emergence of life on the early Earth. Here we discuss efforts to devise such an integrated protocell model.The emergence of the first cells on the early Earth was the culmination of a long history of prior chemical and geophysical processes. Although recognizing the many gaps in our knowledge of prebiotic chemistry and the early planetary setting in which life emerged, we will assume for the purpose of this review that the requisite chemical building blocks were available, in appropriate environmental settings. This assumption allows us to focus on the various spontaneous and catalyzed assembly processes that could have led to the formation of primitive membranes and early genetic polymers, their coassembly into membrane-encapsulated nucleic acids, and the chemical and physical processes that allowed for their replication. We will discuss recent progress toward the construction of laboratory models of a protocell (Fig. 1), evaluate the remaining steps that must be achieved before a complete protocell model can be constructed, and consider the prospects for the observation of spontaneous Darwinian evolution in laboratory protocells. Although such laboratory studies may not reflect the specific pathways that led to the origin of life on Earth, they are proving to be invaluable in uncovering surprising and unanticipated physical processes that help us to reconstruct plausible pathways and scenarios for the origin of life.Open in a separate windowFigure 1.A simple protocell model based on a replicating vesicle for compartmentalization, and a replicating genome to encode heritable information. A complex environment provides lipids, nucleotides capable of equilibrating across the membrane bilayer, and sources of energy (left), which leads to subsequent replication of the genetic material and growth of the protocell (middle), and finally protocellular division through physical and chemical processes (right). (Reproduced from Mansy et al. 2008 and reprinted with permission from Nature Publishing ©2008.)The term protocell has been used loosely to refer to primitive cells or to the first cells. Here we will use the term protocell to refer specifically to cell-like structures that are spatially delimited by a growing membrane boundary, and that contain replicating genetic information. A protocell differs from a true cell in that the evolution of genomically encoded advantageous functions has not yet occurred. With a genetic material such as RNA (or perhaps one of many other heteropolymers that could provide both heredity and function) and an appropriate environment, the continued replication of a population of protocells will lead inevitably to the spontaneous emergence of new coded functions by the classical mechanism of evolution through variation and natural selection. Once such genomically encoded and therefore heritable functions have evolved, we would consider the system to be a complete, living biological cell, albeit one much simpler than any modern cell (Szostak et al. 2001).     

An overlooked riddle of life's origins: energy-dependent nucleic acid unzipping

The imposing progress in understanding contemporary life forms on Earth and in manipulating them has not been matched by a comparable progress in understanding the origins of life. This paper argues that a crucial problem of unzipping of the double helix molecule of nucleic acid during its replication has been underrated, if not plainly overlooked, in the theories of life's origin and evolution. A model is presented of how evolution may have solved the problem in its early phase. Similar to several previous models, the model envisages the existence of a protocell, in which osmotic disbalance is being created by accumulation of synthetic products resulting in expansion and division of the protocell. Novel in the model is the presence in the protocell of a double-stranded nucleic acid, with each of its two strands being affixed by its 3'-terminus to the opposite sides of the membrane of a protocell. In the course of the protocell expansion, osmotic force is utilized to pull the two strands longitudinally in opposite directions, unzipping the helix and partitioning the strands between the two daughter protocells. The model is also being used as a background for arguments of why life need operate in cycles. Many formal models of life's origin and evolution have not taken into account the fact that logical possibility does not equal thermodynamic feasibility. A system of self-replication has to consist of both replicators and replicants.     

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.     

On a kinetic origin of heredity: minority control in a replicating system with mutually catalytic molecules

As the first step in an investigation of the origin of genetic information, we study how some species of molecules are preserved over cell generations and play an important role in controlling the growth of a cell. We consider a model consisting of protocells. Each protocell contains two mutually catalysing molecule species (X and Y), each of which has catalytically active and inactive types. One of the species Y is assumed to have a slower synthesis speed. Through divisions of the protocells, the system reaches and remains in a state in which there are only a few active Y and almost no inactive Y molecules in most protocells, through the selection of very rare fluctuations. In this state, the active Y molecules are shown to control the behavior of the protocell. The minority molecule species act as the carrier of heredity, due to the relatively discrete nature of its population, in comparison with the majority species which behaves statistically in accordance with the law of large numbers. The minority controlled state may give rise to a selection pressure for mechanisms that ensure the transmission of the minority molecule. Once those mechanisms are in place, the minority molecule becomes the ideal storage device for information to be transmitted across generations, thus giving rise to "genetic information". The relevance of this minority controlled state to evolvability is also discussed.     

Mathematical modeling of a minimal protocell with coordinated growth and division

Self-replication is an essential attribute of life but the molecular-level mechanisms involved are not well understood. Cellular self-replication requires not only duplicating all cellular components and doubling volume and membrane area, but also replicating cellular geometry. A whole-cell modeling framework is presented in which an assumed reaction network determines both concentration changes of cellular components and cell geometry. Cell shape is calculated by minimizing membrane-bending energy. Using this framework, simultaneous doubling of volume, surface area, and all components was found to be insufficient to provide mid-cell “pinching” of the parental cell to form two daughter cells. This prompted the design of a minimal protocell that includes a growing shell, a cell-cycle engine, and a contractile ring to enforce cytokinesis. Kinetic parameters were found such that the system exhibited periodic behavior with fundamental aspects of self-replication. This involved simultaneous doubling of all cellular components during a cell cycle, doubling cell volume and membrane area, achieving periodic changes in surface/volume ratio, and forming daughter cells that were geometrically equivalent to each other and to the “newborn” parental cell. The results presented here impact the design of laboratory protocells and the development of a modular strategy for constructing a comprehensive in silico whole-cell model.     

Imitational modeling of evolution: from organic macromolecules to protocell and animal cell

A dynamic imitational model is developed of initial stages of cell evolution based on role of environmental cation concentration. The model is developed on our hypothesis, concerning the medium of the appearance of protocells. Could be potassium water reservoirs rather than sea salt water with its predominance of sodium salts. The necessary elements of appearance the protocells served organic molecules, code of their synthesis, and formation of macromolecules under favorable ion concentration in environment High K+ and Mg2+ concentration and bow Na+. The model is based on an assumption that one of the first stages in evolution of life was the appearance in potassium-magnesium water reservoirs of organic molecules capable for selfreplication on the basis of genetic code and formation of protocells with potassium cytoplasm. The model has demonstrated necessity of formation of cell envelope for development of the protocell. Replacement of the dominant cation in water reservoirs-potassium by sodium-required the appearance of ion-transporting devices in plasma membrane and their participation in adaptation of cells to environment. This stage of evolution was accompanied by the most important morpho-functional event--formation of the plasma membrane instead of cell envelope. The membrane provided the ion asymmetry in the cell (preservation of K+ in it) relatively to the sodium external medium for maintaining optimal intracellular medium. In the model system, predecessors of animal cells elaborated mechanism of maintenance of the potassium cytoplasm with the sodium counter-ion dominating in the environment.     

Computational studies on conditions of the emergence of autopoietic protocells

It has been pointed out that the acquisition of self-maintaining protocells was one of the most important evolutionary steps in the earliest stage of life. However, there remains little evidence to show what the components of the protocells were and how they were acquired. A theoretical study to investigate the possible process of the emergence of protocells is therefore required. In this paper, we present a computational model that demonstrates the emergence and evolution of self-maintaining and self-reproducing structures to analyze conditions under which precellular autocatalytic molecules could evolve into self-reproducing protocells. We focused on the supply rates of molecular resources as environmental parameters and explored the pathways of evolution from molecular replication to cellular reproduction under various conditions. The results showed that the spontaneous organization of protocells from a random initial state takes place in a parameter region where the metabolism becomes difficult because of an insufficient supply of resources, but once cell structures are organized, they can survive in a wider range of environments. We investigated the evolution in temporally or spatially changing environments and found that the protocells can take over the precellular metabolic system after the transition. These results suggest a possible scenario for the evolution from precellular to cellular reproduction.     

Less can be more: RNA-adapters may enhance coding capacity of replicators

It is still not clear how prebiotic replicators evolved towards the complexity found in present day organisms. Within the most realistic scenario for prebiotic evolution, known as the RNA world hypothesis, such complexity has arisen from replicators consisting solely of RNA. Within contemporary life, remarkably many RNAs are involved in modifying other RNAs. In hindsight, such RNA-RNA modification might have helped in alleviating the limits of complexity posed by the information threshold for RNA-only replicators. Here we study the possible role of such self-modification in early evolution, by modeling the evolution of protocells as evolving replicators, which have the opportunity to incorporate these mechanisms as a molecular tool. Evolution is studied towards a set of 25 arbitrary 'functional' structures, while avoiding all other (misfolded) structures, which are considered to be toxic and increase the death-rate of a protocell. The modeled protocells contain a genotype of different RNA-sequences while their phenotype is the ensemble of secondary structures they can potentially produce from these RNA-sequences. One of the secondary structures explicitly codes for a simple sequence-modification tool. This 'RNA-adapter' can block certain positions on other RNA-sequences through antisense base-pairing. The altered sequence can produce an alternative secondary structure, which may or may not be functional. We show that the modifying potential of interacting RNA-sequences enables these protocells to evolve high fitness under high mutation rates. Moreover, our model shows that because of toxicity of misfolded molecules, redundant coding impedes the evolution of self-modification machinery, in effect restraining the evolvability of coding structures. Hence, high mutation rates can actually promote the evolution of complex coding structures by reducing redundant coding. Protocells can successfully use RNA-adapters to modify their genotype-phenotype mapping in order to enhance the coding capacity of their genome and fit more information on smaller sized genomes.     

Domain protolife

We propose the Thermal Protein First Paradigm (protocell theory) that affirms that first life was cellular. The first cells emerged from molecular (chemical) evolution as protocells (heated amino acids self-order in copolymerization reactions to form thermal proteins which self-organize when in contact with water to form protocells). Metaprotocells are specialized protocells capable of synthesizing ATP (light energy conversion to chemical energy), polypeptides, and polynucleotides. Aggregations of protocells in thermal protein matrices form distinctive morphologies (protocellular networks). Prokaryotic cells emerged from metaprotocells. We classify protocells and metaprotocells as members of the Domain Protolife. We revised the cell theory to include protolife.     

Sufficient conditions for emergent synchronization in protocell models

In this paper, we study general protocell models aiming to understand the synchronization phenomenon of genetic material and container productions, a necessary condition to ensure sustainable growth in protocells and eventually leading to Darwinian evolution when applied to a population of protocells.Synchronization has been proved to be an emergent property in many relevant protocell models in the class of the so-called surface reaction models, assuming both linear- and non-linear dynamics for the involved chemical reactions. We here extend this analysis by introducing and studying a new class of models where the relevant chemical reactions are assumed to occur inside the protocell, in contrast with the former model where the reaction site was the external surface.While in our previous studies, the replicators were assumed to compete for resources, without any direct interaction among them, we here improve both models by allowing linear interaction between replicators: catalysis and/or inhibition. Extending some techniques previously introduced, we are able to give a quite general analytical answer about the synchronization phenomenon in this more general context. We also report on results of numerical simulations to support the theory, where applicable, and allow the investigation of cases which are not amenable to analytical calculations.     

Generic Darwinian selection in catalytic protocell assemblies

To satisfy the minimal requirements for life, an information carrying molecular structure must be able to convert resources into building blocks and also be able to adapt to or modify its environment to enhance its own proliferation. Furthermore, new copies of itself must have variable fitness such that evolution is possible. In practical terms, a minimal protocell should be characterized by a strong coupling between its metabolism and genetic subsystem, which is made possible by the container. There is still no general agreement on how such a complex system might have been naturally selected for in a prebiotic environment. However, the historical details are not important for our investigations as they are related to assembling and evolution of protocells in the laboratory. Here, we study three different minimal protocell models of increasing complexity, all of them incorporating the coupling between a 'genetic template', a container and, eventually, a toy metabolism. We show that for any local growth law associated with template self-replication, the overall temporal evolution of all protocell's components follows an exponential growth (efficient or uninhibited autocatalysis). Thus, such a system attains exponential growth through coordinated catalytic growth of its component subsystems, independent of the replication efficiency of the involved subsystems. As exponential growth implies the survival of the fittest in a competitive environment, these results suggest that protocell assemblies could be efficient vehicles in terms of evolving through Darwinian selection.     

The "protocell": a mathematical model of self-maintenance

The concepts of self-generation, autonomous boundary and self-maintenance are explained briefly. The "protocell" is presented as a model of self-maintenance which is based on simple physical mechanisms of diffusion and reaction. The time evolution of the surface of the protocell is taken into account explicitly in the form of a Stefan condition giving rise to a non-linear feedback of the surface motion to the reaction and diffusion processes inside the protocell. The spatio-temporal dynamics are investigated, particularly in the neighbourhood of the stationary states, showing a self-maintaining behaviour under a certain range of nutritional conditions. Under another set of conditions we find an instability leading to a division process so that the population of protocells becomes self-maintaining instead of the single individual. The presented formulation of the protocell model is crucially improved compared with a previous version which required boundary conditions at infinity. The previous version was not strictly self-maintaining since dynamics outside the cell were essential for its behaviour.     

Phenomenon of Quantum Entanglement in a System Composed of Two Minimal Protocells

The quantum mechanical self-assembly of two separate photoactive supramolecular systems with different photosynthetic centers was investigated by means of density functional theory methods. Quantum entangled energy transitions from one subsystem to the other and the assembly of logically controlled artificial minimal protocells were modeled. The systems studied were based on different photoactive sensitizer molecules covalently bonded to a non-canonical oxo-guanine::cytosine supramolecule with the precursor of a fatty acid (pFA) molecule attached via Van der Waals forces, all surrounded by water molecules. The electron correlation interactions responsible for the weak hydrogen and Van der Waals chemical bonds increased due to the addition of polar water solvent molecules. The distances between the separated sensitizer, nucleotide, pFA, and water molecules are comparable to Van der Waals and hydrogen bonding radii. As a result, the overall system becomes compressed, resulting in photo-excited electron tunneling from the sensitizer (bis(4-diphenylamine-2-phenyl)-squarine or 1,4-bis(N,N-dimethylamino)naphthalene) to the pFA molecules. Absorption spectra as well as electron transfer trajectories associated with the different excited states were calculated using time dependent density functional theory methods. The results allow separation of the quantum entangled photosynthetic transitions within the same minimal protocell and with the neighboring minimal protocell. The transferred electron is used to cleave a “waste” organic molecule resulting in the formation of the desired product. A two variable, quantum entangled AND logic gate was proposed, consisting of two input photoactive sensitizer molecules and one output (pFA molecule). It is proposed that a similar process might be applied for the destruction of tumor cancer cells or to yield building blocks in artificial cells.     

Facilitated diffusion as a method for selective accumulation of materials from the primordial oceans by a lipid-vesicle protocell

A model is proposed for the selective accumulation of amino acids, sugars, nucleotides, cations and protons from the primordial oceans into a lipid vesicle type of protocell. The model is built on facilitated diffusion using simple, primordial, lipid-soluble carriers. The advantages a lipid vesicle protocell would have had over the other potential types of protocells are discussed.     

Steps Towards the Formation of A Protocell: The Possible Role of Short Peptides

The paper deals with molecular self-organization leading to formation of a protocell. Plausible steps towards a protocell include: polymerization of peptides and oligonucleotides on mineral surfaces; coevolution of peptides and oligonucleotides with formation of collectively autocatalytic sets; self-organization of short peptides into vesicles; entrapment of the peptide/oligonucleotide systems in mixed peptide and simple amphiphile membranes; and formation of functioning protocells with metabolism and cell division. The established propensity of short peptides to self-ordering and to formation of vesicles makes this sequence plausible. We further suggest that evolution of a protocell produced cellular ancestors of viruses as well as ancestors of cellular organisms.     

Monte Carlo simulation of early molecular evolution in the RNA World

The origin of life remains a highly speculative field, mainly due to the shortage of our knowledge on prebiotic chemistry and basic understanding on the essence of life. In this context, computer simulation is expected to play an important role. For instance, the scenario concerning the genesis of the widely accepted RNA World remains blurry, though we have gathered some circumstantial evidence and fragmented knowledge on several supposed stages, including formation of polynucleotides from a prebiotic nucleotide pool, emergence of RNA replicases (RNA molecules catalyzing their own replication), and evolution of RNA replicases. It is highly valuable to simulate the stages as a continuous process to evaluate the plausibility of the supposition and study the rules involved. Here we construct a computer simulation on the process using Monte Carlo method. It demonstrates that primordial RNA replicases may appear and spread in a nucleotide pool provided they could recognize their own sequence and their complements as catalytic targets, and then may evolve to more efficient RNA replicases. Apart from its indication on the genesis of the RNA World, the vivid simulation of emergence of the “first replicative molecules” and their subsequent evolution is impressive and may help to get insight into “how could self-replication and Darwinian evolution, two key features of life, emerge in a non-life background?” thus improve our understanding of “what is life” when studying origins of life.     

Origin of Sex Revisited

Why did sex ever arise in the first place? Why it does not disappear in view of the greater efficiency of asexuals? These are clearly two different questions, and we suggest here that the solution for the origin of sex does not necessarily come from theoretical considerations based on currently existing genetic systems. Thus, while we agree with a number of authors in that the emergence of sex (understood as the exchange of genetic material between genomes) is deeply rooted in the origin of life and happened during the very early stages in the transition from individual genes (`replicators') to bacteria-like cells (`reproducers'), we challenge the idea that recombinational repair was the major selective force for the emergence of sex. Taking the stochastic corrector model as a starting point, we provide arguments that question the putative costs of redundancy in primitive protocells. In addition, if genes that cause intragenomic conflict (i.e., parasites) are taken into account, it is certainly wrong to suggest that cellular fusion would be beneficial at the population level (although this strong claim needs some qualifications). However, when a continuous input of deleterious mutations that impair the fitness of the protocell as a whole is considered in the model (in the realistic range in which stable mutant distributions of quasi-species within compartments are established), there are circumstances when sex could be beneficial as a side effect of the dynamic equilibrium between cellular fusion-mutation-selection. The scenario we have explored numerically is fully consistent with the idea that the universal ancestor was not a discrete entity but an ensemble of proto-organisms that exchanged much genetic information.