Modelling lipid competition dynamics in heterogeneous protocell populations

Kinetic control of liposome size by direct lipid transfer

Spontaneous lipid vesiculation and related size distribution are traditionally studied in the framework of equilibrium thermodynamics and continuum mechanics, overlooking the kinetic aspects of the process. In the scenario of liposomes consisting of different lipid molecules dispersed in the same medium - a non-equilibrium situation -, the system evolves driven by lipid monomer transfer among the different liposomes. This process encompasses time-dependent changes in liposome size and size distribution, thus predicting size and composition at a given time would entail the control of the size of liposomes by kinetic means, an asset in the framework of diagnostics and synthetic biology. We introduce a direct transfer model, based on the fact that monomers are highly reactive species and apply it to saturated phospholipid molecules differing in hydrophobic chain length. Considering a well-defined gamma-type liposome size distribution, we demonstrate a clear liposome size-composition correlation and are able to predict liposome size and size distribution at any time in the transfer process. The size-composition correlation opens up new prospects for the control of the self-assembling properties of lipids and thereby the control of the liposome size.

Light energy transduction in liposome-based artificial cells

In this work we review the latest strategies for the bottom-up assembly of energetically autonomous artificial cells capable of transducing light energy into chemical energy and support internalized metabolic pathways. Such entities are built by taking inspiration from the photosynthetic machineries found in nature which are purified and reconstituted directly in the membrane of artificial compartments or encapsulated in form of organelle-like structures. Specifically, we report and discuss recent examples based on liposome-technology and multi-compartment (nested) architectures pointing out the importance of this matter for the artificial cell synthesis research field and some limitations and perspectives of the bottom-up approach.

When Is a Reaction Network a Metabolism? Criteria for Simple Metabolisms That Support Growth and Division of Protocells

With the aim of better understanding the nature of metabolism in the first cells and the relationship between the origin of life and the origin of metabolism, we propose three criteria that a chemical reaction system must satisfy in order to constitute a metabolism that would be capable of sustaining growth and division of a protocell. (1) Biomolecules produced by the reaction system must be maintained at high concentration inside the cell while they remain at low or zero concentration outside. (2) The total solute concentration inside the cell must be higher than outside, so there is a positive osmotic pressure that drives cell growth. (3) The metabolic rate (i.e., the rate of mass throughput) must be higher inside the cell than outside. We give examples of small-molecule reaction systems that satisfy these criteria, and others which do not, firstly considering fixed-volume compartments, and secondly, lipid vesicles that can grow and divide. If the criteria are satisfied, and if a supply of lipid is available outside the cell, then continued growth of membrane surface area occurs alongside the increase in volume of the cell. If the metabolism synthesizes more lipid inside the cell, then the membrane surface area can increase proportionately faster than the cell volume, in which case cell division is possible. The three criteria can be satisfied if the reaction system is bistable, because different concentrations can exist inside and out while the rate constants of all the reactions are the same. If the reaction system is monostable, the criteria can only be satisfied if there is a reason why the rate constants are different inside and out (for example, the decay rates of biomolecules are faster outside, or the formation rates of biomolecules are slower outside). If this difference between inside and outside does not exist, a monostable reaction system cannot sustain cell growth and division. We show that a reaction system for template-directed RNA polymerization can satisfy the requirements for a metabolism, even if the small-molecule reactions that make the single nucleotides do not.

Prebiological Membranes and Their Role in the Emergence of Early Cellular Life

Membrane compartmentalization is a fundamental feature of contemporary cellular life. Given this, it is rational to assume that at some stage in the early origins of life, membrane compartments would have potentially emerged to form a dynamic semipermeable barrier in primitive cells (protocells), protecting them from their surrounding environment. It is thought that such prebiological membranes would likely have played a crucial role in the emergence and evolution of life on the early Earth. Extant biological membranes are highly organized and complex, which is a consequence of a protracted evolutionary history. On the other hand, prebiotic membrane assemblies, which are thought to have preceded sophisticated contemporary membranes, are hypothesized to have been relatively simple and composed of single chain amphiphiles. Recent studies indicate that the evolution of prebiotic membranes potentially resulted from interactions between the membrane and its physicochemical environment. These studies have also speculated on the origin, composition, function and influence of environmental conditions on protocellular membranes as the niche parameters would have directly influenced their composition and biophysical properties. Nonetheless, the evolutionary pathways involved in the transition from prebiological membranes to contemporary membranes are largely unknown. This review critically evaluates existing research on prebiotic membranes in terms of their probable origin, composition, energetics, function and evolution. Notably, we outline new approaches that can further our understanding about how prebiotic membranes might have evolved in response to relevant physicochemical parameters that would have acted as pertinent selection pressures on the early Earth.

Dynamics of the vesicles composed of fatty acids and other amphiphile mixtures: unveiling the role of fatty acids as a model protocell membrane

Fundamental research at the interface of chemistry and biology has the potential to shine light on the question of how living cells can be synthesized from inanimate matter thereby providing plausible pathways for the emergence of cellular life. Compartmentalization of different biochemical reactions within a membrane bound water environment is considered an essential first step in any origin of life pathway. It has been suggested that fatty acid-based vesicles can be considered a model protocell having the potential for change via Darwinian evolution. As such, protocell models have the potential to assist in furthering our understanding of the origin of life in the laboratory. Fatty acids, both by themselves and in mixtures with other amphiphiles, can form different self-assembled structures depending on their surroundings. Recent studies of fatty acid-based membranes have suggested likely pathways of protocell growth, division and membrane permeabilisation for the transport of different nutrients, such as nucleotides across the membrane. In this review, different dynamic processes related to the growth and division of the protocell membrane are discussed and possible pathways for transition of the protocell to the modern cell are explored. These areas of research may lead to a better understanding of the synthesis of artificial cell-like entities and thus herald the possibility of creating new form of life distinct from existing biology. Graphical Abstract Table of Content (TOC) only.

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.

Replication of Simulated Prebiotic Amphiphilic Vesicles in a Finite Environment Exhibits Complex Behavior That Includes High Progeny Variability and Competition

We studied the simulated replication and growth of prebiotic vesicles composed of 140 phospholipids and cholesterol using our R-GARD (Real Graded Autocatalysis Replication Domain) formalism that utilizes currently extant lipids that have known rate constants of lipid-vesicle interactions from published experimental data. R-GARD normally modifies kinetic parameters of lipid-vesicle interactions based on vesicle composition and properties. Our original R-GARD model tracked the growth and division of one vesicle at a time in an environment with unlimited lipids at a constant concentration. We explore here a modified model where vesicles compete for a finite supply of lipids. We observed that vesicles exhibit complex behavior including initial fast unrestricted growth, followed by intervesicle competition for diminishing resources, then a second growth burst driven by better-adapted vesicles, and ending with a final steady state. Furthermore, in simulations without kinetic parameter modifications ("invariant kinetics"), the initial replication was an order of magnitude slower, and vesicles' composition variability at the final steady state was much lower. The complex kinetic behavior was not observed either in the previously published R-GARD simulations or in additional simulations presented here with only one lipid component. This demonstrates that both a finite environment (inducing selection) and multiple components (providing variation for selection to act upon) are crucial for portraying evolution-like behavior. Such properties can improve survival in a changing environment by increasing the ability of early protocellular entities to respond to rapid environmental fluctuations likely present during abiogenesis both on Earth and possibly on other planets. This in silico simulation predicts that a relatively simple in vitro chemical system containing only lipid molecules might exhibit properties that are relevant to prebiotic processes. Key Words: Phospholipid vesicles-Prebiotic compartments-Prebiotic vesicle competition-Prebiotic vesicle variability. Astrobiology 18, 419-430.

Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research

Conceiving the process of biogenesis as the evolutionary development of highly dynamic and integrated protocell populations provides the most appropriate framework to address the difficult problem of how prebiotic chemistry bridged the gap to full-fledged living organisms on the early Earth. In this contribution we briefly discuss the implications of taking dynamic, functionally integrated protocell systems (rather than complex reaction networks in bulk solution, sets of artificially evolvable replicating molecules, or even these same replicating molecules encapsulated in passive compartments) as the proper units of prebiotic evolution. We highlight, in particular, how the organisational features of those chemically active and reactive protocells, at different stages of the process, would strongly influence their corresponding evolutionary capacities. As a result of our analysis, we suggest three experimental challenges aimed at constructing protocell systems made of a diversity of functionally coupled components and, thereby, at characterizing more precisely the type of prebiotic evolutionary dynamics that such protocells could engage in.

First moves towards photoautotrophic synthetic cells: In vitro study of photosynthetic reaction centre and cytochrome bc1 complex interactions

Following a bottom-up synthetic biology approach it is shown that vesicle-based cell-like systems (shortly "synthetic cells") can be designed and assembled to perform specific function (for biotechnological applications) and for studies in the origin-of-life field. We recently focused on the construction of synthetic cells capable to converting light into chemical energy. Here we first present our approach, which has been realized so far by the reconstitution of photosynthetic reaction centre in the membrane of giant lipid vesicles. Next, the details of our ongoing research program are presented. It involves the use of the reaction centre, the coenzyme Q-cytochrome c oxidoreductase, and the ATP synthase for creating an autonomous synthetic cell. We show experimental results on the chemistry of the first two proteins showing that they can efficiently sustain light-driven chemical oscillations. Moreover, the cyclic pattern has been reproduced in silico by a minimal kinetic model.

Synthetic transitions: towards a new synthesis

The evolution of life in our biosphere has been marked by several major innovations. Such major complexity shifts include the origin of cells, genetic codes or multicellularity to the emergence of non-genetic information, language or even consciousness. Understanding the nature and conditions for their rise and success is a major challenge for evolutionary biology. Along with data analysis, phylogenetic studies and dedicated experimental work, theoretical and computational studies are an essential part of this exploration. With the rise of synthetic biology, evolutionary robotics, artificial life and advanced simulations, novel perspectives to these problems have led to a rather interesting scenario, where not only the major transitions can be studied or even reproduced, but even new ones might be potentially identified. In both cases, transitions can be understood in terms of phase transitions, as defined in physics. Such mapping (if correct) would help in defining a general framework to establish a theory of major transitions, both natural and artificial. Here, we review some advances made at the crossroads between statistical physics, artificial life, synthetic biology and evolutionary robotics.This article is part of the themed issue 'The major synthetic evolutionary transitions'.

Filamentation as primitive growth mode?

Osmotic pressure influences cellular shape. In a growing cell, chemical reactions and dilution induce changes in osmolarity, which in turn influence the cellular shape. Using a protocell model relying upon random conservative chemical reaction networks with arbitrary stoichiometry, we find that when the membrane is so flexible that its shape adjusts itself quasi-instantaneously to balance the osmotic pressure, the protocell either grows filamentous or fails to grow. This behavior is consistent with a mathematical proof. This suggests that filamentation may be a primitive growth mode resulting from the simple physical property of balanced osmotic pressure. We also find that growth is favored if some chemical species are only present inside the protocell, but not in the outside growth medium. Such an insulation requires specific chemical schemes. Modern evolved cells such as E. coli meet these requirements through active transport mechanisms such as the phosphotransferase system.

New Insights into the Growth and Transformation of Vesicles: A Free-Flow Electrophoresis Study

The spontaneous formation of lipid vesicles, in particular fatty acid vesicles, is considered an important physical process at the roots of cellular life. It has been demonstrated previously that the addition of fatty acid micelles to preformed vesicles induces vesicle self-reproduction by a growth-division mechanism. Despite multiple experimental efforts, it remains unresolved how vesicles rearrange upon the addition of fresh membrane-forming compounds, and whether solutes that are initially encapsulated inside the mother vesicles are evenly redistributed among the daughter ones. Here we investigate the growth-division of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) vesicles, which, following the addition of oleate micelles, form mixed oleate/POPC vesicles. Our approach is based on free-flow electrophoresis (FFE) and cryogenic transmission electronmicroscopy (cryo-TEM). Two new features emerge from this study. FFE analysis unexpectedly reveals that the uptake of oleate micelles by POPC vesicles follows two different pathways depending on the micelles/vesicles ratio. At low oleate molar fractions (<0.35), plain incorporation of oleate into pre-existing POPC vesicles is our dominant observation. In contrast, oleate-rich and oleate-poor daughter vesicles are generated from parent POPC vesicles when the oleate molar fraction exceeds 0.35. Cryo-TEM reveals that when ferritin-filled vesicles grow and divide, some vesicles contain ferritin at increased concentrations, others are empty. Intriguingly, in some cases, ferritin appears to be highly concentrated inside the vesicles. These observations imply a specific redistribution (partitioning) of encapsulated solutes among nascent vesicles during the growth-division steps. We have interpreted our observations by assuming that freshly added oleate molecules are taken-up preferentially (cooperatively) by oleate-rich membrane regions that form spontaneously in POPC/oleate vesicles when a certain threshold (oleate molar fraction ca. 0.35) is surpassed. The proposed cooperative mechanism could be based on differential microscopic constants for oleate/oleic acid dynamics in oleate-rich and oleate-poor membrane regions, which eventually generate populations of oleate-rich and oleate-poor vesicles.

Emergent chemical behavior in variable-volume protocells

Artificial protocellular compartments and lipid vesicles have been used as model systems to understand the origins and requirements for early cells, as well as to design encapsulated reactors for biotechnology. One prominent feature of vesicles is the semi-permeable nature of their membranes, able to support passive diffusion of individual solute species into/out of the compartment, in addition to an osmotic water flow in the opposite direction to the net solute concentration gradient. Crucially, this water flow affects the internal aqueous volume of the vesicle in response to osmotic imbalances, in particular those created by ongoing reactions within the system. In this theoretical study, we pay attention to this often overlooked aspect and show, via the use of a simple semi-spatial vesicle reactor model, that a changing solvent volume introduces interesting non-linearities into an encapsulated chemistry. Focusing on bistability, we demonstrate how a changing volume compartment can degenerate existing bistable reactions, but also promote emergent bistability from very simple reactions, which are not bistable in bulk conditions. One particularly remarkable effect is that two or more chemically-independent reactions, with mutually exclusive reaction kinetics, are able to couple their dynamics through the variation of solvent volume inside the vesicle. Our results suggest that other chemical innovations should be expected when more realistic and active properties of protocellular compartments are taken into account.

Paley's watchmaker analogy and prebiotic synthetic chemistry in surfactant assemblies. Formaldehyde scavenging by pyrroles leading to porphyrins as a case study

Facile exchange of micromolar dialkylpyrrolic constituents among a Poisson distribution of aqueous micelles overcomes immense statistical odds against reaction.