Protocells: Milestones and Recent Advances

Droplet drinking in constrictions

Droplets generated through microfluidics serve as a common platform for assembling artificial cells, which are feasibly tailored using microfluidic methodology. The ability of natural cells to undergo shape changes, such as phagocytosis, is a typical characteristic that researchers aim to mimic in artificial cells. However, simulating the deformation behavior of natural cells within droplets is exceptionally challenging. Here, this study reports a pinocytosis-like phenomenon observed in droplets, termed "droplet drinking". When droplets traverse a capillary with constrictions, the shear force from the continuous-phase fluid induces relative motion within the droplets, creating concave regions at the rear. These regions facilitate engulfing of the continuous-phase fluid, resulting in the formation of multiple emulsions. This behavior is influenced by the capillary number, and the size of the ingested droplets is governed by the interfacial tension between the two phases. The production of multicore or multi-shell emulsions can be easily accomplished by making slight adjustments to the constrictions. Furthermore, this method demonstrates the integration of reactants into pre-existing droplets, facilitating biochemical reactions. This study presents a convenient approach for generating complex emulsions and an innovative strategy for studying deformation behavior in droplet-based artificial cells.

Chemotactic Interactions Drive Migration of Membraneless Active Droplets

In nature, chemotactic interactions are ubiquitous and play a critical role in driving the collective behavior of living organisms. Reproducing these interactions in vitro is still a paramount challenge due to the complexity of mimicking and controlling cellular features, such as tangled metabolic networks, cytosolic macromolecular crowding, and cellular migration, on a microorganism size scale. Here, we generate enzymatically active cell-sized droplets able to move freely, and by following a chemical gradient, able to interact with the surrounding droplets in a collective manner. The enzyme within the droplets generates a pH gradient that extends outside the edge of the droplets. We discovered that the external pH gradient triggers droplet migration and controls its directionality, which is selectively toward the neighboring droplets. Hence, by changing the enzyme activity inside the droplet, we tuned the droplet migration speed. Furthermore, we showed that these cellular-like features can facilitate the reconstitution of a simple and linear protometabolic pathway and increase the final reaction product generation. Our work suggests that simple and stable membraneless droplets can reproduce complex biological phenomena, opening new perspectives as bioinspired materials and synthetic biology tools.

Dynamics of giant vesicle assembly from thin lipid films

MOTIVATION

Giant unilamellar vesicles (GUVs), cell-like synthetic micrometer size structures, assemble when thin lipid films are hydrated in aqueous solutions. Quantitative measurements of static yields and distribution of sizes of GUVs obtained from thin film hydration methods were recently reported. Dynamic data such as the time evolution of yields and distribution of sizes, however, is not known. Dynamic data can provide insights into the assembly pathway of GUVs and guidelines for choosing conditions to obtain populations with desired size distributions.

APPROACH

We develop the 'stopped-time' technique to characterize the time evolution of the distribution of sizes and molar yields of populations of free-floating GUVs. We additionally capture high resolution time-lapse images of surface-attached GUV buds on the lipid films. We systematically study the dynamics of assembly of GUVs from three widely used thin film hydration methods, PAPYRUS (Paper-Abetted amPhiphile hYdRation in aqUeous Solutions), gentle hydration, and electroformation.

FINDINGS

We find that the molar yield versus time curves of GUVs demonstrate a characteristic sigmoidal shape, with an initial yield, a transient, and then a steady state plateau for all three methods. The population of GUVs showed a right-skewed distribution of diameters. The variance of the distributions increased with time. The systems reached steady state within 120 min. We rationalize the dynamics using the thermodynamically motivated budding and merging (BNM) model. These results further the understanding of lipid dynamics and provide for the first-time practical parameters to tailor the production of GUVs of specific sizes for applications.

Metal Ion-Induced Unusual Stability of the Metastable Vesicle-like Intermediates Evolving during the Self-Assembly of Phenylalanine: Prominent Role of Surface Charge Inversion

The underlying mechanism and intermediate formation in the self-assembly of aromatic amino acids, peptides, and proteins remain elusive despite numerous reports. We, for the first time, report that one can stabilize the intermediates by tuning the metal ion-amino acid interaction. Microscopic and spectroscopic investigations of the self-assembly of carboxybenzyl (Z)-protected phenylalanine (ZF) reveal that the bivalent metal ions eventually lead to the formation of fibrillar networks similar to blank ZF whereas the trivalent ions develop vesicle-like intermediates that do not undergo fibrillation for a prolonged time. The time-lapse measurement of surface charge reveals that the surface charge of blank ZF and in the presence of bivalent metal ions changes from a negative value to zero, implying unstable intermediates leading to the fibril network. Strikingly, a prominent charge inversion from an initial negative value to a positive value in the presence of trivalent metal ions imparts unusual stability to the metastable intermediates.

Self-immolation Assisted Morphology Transformation of Prebiotic Lipidated-cationic Amino Acids: Electro-droplet Mediated C-C Coupling Reaction to Synthesize Macromolecules

Compartmentalization protected biomolecules from the fluctuating environments of early Earth. Although contemporary cells mostly use phospholipid-based bilayer membranes, the utility of non-bilayer compartments was not ruled out during the prebiotic and modern eras. In the present study, we demonstrated the prebiotic synthesis of lipidated cationic amino acid-based amphiphiles [lauryl ester of lysine (LysL); ornithine (OrnL); and 2,4-diamino butyric acid (DabL)] using model dry-down reaction. These amphiphiles self-assemble into micellar membranes. However, the OrnL and DabL-based micelles undergo pH-responsive transformation to lipid droplet-like morphologies, a modelcompartment in the prebiotic Earth. These cationic droplets encapsulated prebiotic molecules (isoprene) and assisted electron transfer reaction to synthesize isoprenoid derivatives at primitive Earth conditions. The self-assembly of prebiotic amphiphiles, their transformation to droplet compartments, and droplet-assisted C-C bond formation reaction might have helped the evolution to synthesize various biomolecules required for the origin of life.

Discretised Flux Balance Analysis for Reaction-Diffusion Simulation of Single-Cell Metabolism

Metabolites have to diffuse within the sub-cellular compartments they occupy to specific locations where enzymes are, so reactions could occur. Conventional flux balance analysis (FBA), a method based on linear programming that is commonly used to model metabolism, implicitly assumes that all enzymatic reactions are not diffusion-limited though that may not always be the case. In this work, we have developed a spatial method that implements FBA on a grid-based system, to enable the exploration of diffusion effects on metabolism. Specifically, the method discretises a living cell into a two-dimensional grid, represents the metabolic reactions in each grid element as well as the diffusion of metabolites to and from neighbouring elements, and simulates the system as a single linear programming problem. We varied the number of rows and columns in the grid to simulate different cell shapes, and the method was able to capture diffusion effects at different shapes. We then used the method to simulate heterogeneous enzyme distribution, which suggested a theoretical effect on variability at the population level. We propose the use of this method, and its future extensions, to explore how spatiotemporal organisation of sub-cellular compartments and the molecules within could affect cell behaviour.

Ultrasound-Stimulated "Exocytosis" by Cell-Like Microbubbles Enhances Antibacterial Species Penetration and Immune Activation Against Implant Infection

Host immune systems serving as crucial defense lines are vital resisting mechanisms against biofilm-associated implant infections. Nevertheless, biofilms hinder the penetration of anti-bacterial species, inhibit phagocytosis of immune cells, and frustrate host inflammatory responses, ultimately resulting in the weakness of the host immune system for biofilm elimination. Herein, a cell-like construct is developed through encapsulation of erythrocyte membrane fragments on the surface of Fe3 O4 nanoparticle-fabricated microbubbles and then loaded with hydroxyurea (EMB-Hu). Under ultrasound (US) stimulation, EMB-Hu undergoes a stable oscillation manner to act in an "exocytosis" mechanism for disrupting biofilm, releasing agents, and enhancing penetration of catalytically generated anti-bacterial species within biofilms. Additionally, the US-stimulated "exocytosis" by EMB-Hu can activate pro-inflammatory macrophage polarization and enhance macrophage phagocytosis for clearance of disrupted biofilms. Collectively, this work has exhibited cell-like microbubbles with US-stimulated "exocytosis" mechanisms to overcome the biofilm barrier and signal macrophages for inflammatory activation, finally achieving favorable therapeutic effects against implant infections caused by methicillin-resistant Staphylococcus aureus (MRSA) biofilms.

Engineering pH-Responsive, Self-Healing Vesicle-Type Artificial Tissues with Higher-Order Cooperative Functionalities

Multicellular organisms demonstrate a hierarchical organization where multiple cells collectively form tissues, thereby enabling higher-order cooperative functionalities beyond the capabilities of individual cells. Drawing inspiration from this biological organization, assemblies of multiple protocells are developed to create novel functional materials with emergent higher-order cooperative functionalities. This paper presents new artificial tissues derived from multiple vesicles, which serve as protocellular models. These tissues are formed and manipulated through non-covalent interactions triggered by a salt bridge. Exhibiting pH-sensitive reversible formation and destruction under neutral conditions, these artificial vesicle tissues demonstrate three distinct higher-order cooperative functionalities: transportation of large cargoes, photo-induced contractions, and enhanced survivability against external threats. The rapid assembly and disassembly of these artificial tissues in response to pH variations enable controlled mechanical task performance. Additionally, the self-healing property of these artificial tissues indicates robustness against external mechanical damage. The research suggests that these vesicles can detect specific pH environments and spontaneously assemble into artificial tissues with advanced functionalities. This leads to the possibility of developing intelligent materials with high environmental specificity, particularly for applications in soft robotics.

Simulation of the emergence of cell-like morphologies with evolutionary potential based on virtual molecular interactions

This study explored the emergence of life using a simulation model approach. The "multiset chemical lattice model" allows the placement of virtual molecules of multiple types in each lattice cell in a two-dimensional space. This model was capable of describing a wide variety of states and interactions, such as the diffusion, chemical reaction, and polymerization of virtual molecules, in a limited number of lattice cell spaces. Moreover, this model was capable of describing a wide variety of states and interactions, even in the limited lattice cell space of 100 × 100 cells. In this study, I assumed 18 types of virtual molecules, i.e., 18 virtual numbers that do not correspond to real molecules with chemical reactions represented by transformation of the numbers that occur with a specified reaction rate probability. Furthermore, it considered the energy metabolism and energy resources in the environment, and was able to reproduce "evolution," in which a certain cell-like shape that adapted to the environment survived under conditions of decreasing amounts of energy resources in the environment. This enabled the simulation of the emergence of cell-like shapes with the four minimum cellular requirements, i.e., boundary, metabolism, replication, and evolution, based solely on the interaction of virtual molecules.

Chirality-Selected Coacervate by Chiral Gemini Surfactant

Chiral surfactants present opportunities to self-assemble into supramolecules with a chiral trait; however, the effects of stereochemistry on the formation of simple coacervates remain unclear. Here, we investigate the chirality-selected phase behavior in mixtures of chiral gemini surfactant 1,4-bis(dodecyl-N,N-dimethylammonium bromide)-2,3-butanediol (12-4(OH)2-12) with an oppositely charged chiral mandelic acid (MA). It demonstrates that altering the chirality of surfactants yields a heightened ability to regulate the phase behavior, leading to the formation of three different network-like structures, i.e., wormlike micelle, coacervate, and hydrogel, in the racemate, enantiomer, and mesomer, respectively. The different aggregate structures arise from the intermolecular and intramolecular hydrogen-bond interactions of the two hydroxyl groups located at stereogenic centers. Intriguingly, although they contain similar microstructures, the solid-like hydrogel and liquid-like wormlike micelle show similar low hydration ability and have no encapsulation capability, whereas only coacervate formed by the enantiomers of 12-4(OH)2-12 displays liquid-like characteristics, strong capacity to sequester diverse solutes, and high affinity for tightly bound water simultaneously. These findings further highlight the unique and advantageous properties of coacervates as a promising model for exploring the biological process and understanding how chirality plays a crucial role in early life scenarios and cell evolution at the molecular level.

Phosphate-Based Amphiphile and Lipidated Lysine Assemble into Superior Protocellular Membranes over Carboxylate and Sulfate-Based Systems: A Potential Missing Link between Prebiotic and the Modern Era?

Amphiphiles are among the most extensively studied building blocks that self-assemble into cell-like compartments. Most literature suggested that the building blocks/amphiphiles of early Earth (fatty acid-based membrane) were much simpler than today's phospholipids. To establish the bridge between the prebiotic fatty acid era and the modern phospholipid era, the investigation and characterization of alternate building blocks that form protocellular membranes are necessary. Herein, we report the potential prebiotic synthesis of alkyl phosphate, alkyl carboxylate, and alkyl sulfate amphiphiles (anionic) using dry-down reactions and demonstrate a more general role of cationic amino acid-based amphiphiles to recruit the anionic amphiphiles via ion-pair, hydrogen bonding, and hydrophobic interactions. The formation and self-assembly of the catanionic (mixed) amphiphilic system to vesicular morphology were characterized by turbidimetric, dynamic light scattering, transmission electron microscopy, fluorescence lifetime imaging microscopy, and glucose encapsulation experiments. Further experiments suggest that the phosphate-based vesicles were more stable than the alkyl sulfate and alkyl carboxylate-based systems. Moreover, the alkyl phosphate system can form vesicles at prebiotically relevant acidic pH (5.0), while alkyl carboxylate mainly forms cluster-type aggregates. An extended supramolecular polymer-type network formation via H-bonding and ion-pair interactions might order the membrane interface and stabilize the phosphate-based vesicles. The results suggest that phosphate-based amphiphiles might be a superior successor to fatty acids as early compartment building blocks. The work highlights the importance of previously unexplored building blocks that participate in protocellular membrane formation to encapsulate important precursors required for the functions of early life.

Double Emulsion Droplets as a Plausible Step to Fatty Acid Protocells

It is assumed that life originated on the Earth from vesicles made of fatty acids. These amphiphiles are the simplest chemicals, which can be present in the prebiotic soup, capable of self-assembling into compartments mimicking modern cells. Production of fatty acid vesicles is widely studied, as their growing and division. However, how prebiotic chemicals require to further yield living cells encapsulated within protocells remains unclear. Here, one suggests a scenario based on recent studies, which shows that phospholipid vesicles can form from double emulsions affording facile encapsulation of cargos. In these works, water-in-oil-in-water droplets are produced by microfluidics, having dispersed lipids in the oil. Dewetting of the oil droplet leaves the internal aqueous droplet covered by a lipid bilayer, entrapping cargos. In this review, formation of fatty acid protocells is briefly reviewed, together with the procedure for preparing double emulsions and vesicles from double emulsion and finally, it is proposed that double emulsion droplets formed in the deep ocean where undersea volcano expulsed materials, with fatty acids (under their carboxylic form) and alkanols as the oily phase, entrapping hydrosoluble prebiotic chemicals in a double emulsion droplet core. Once formed, double emulsion droplets can move up to the surface, where an increase of pH, variation of pressure and/or temperature may have allowed dewetting of the oily droplet, leaving a fatty acid vesicular protocell with encapsulated prebiotic materials.

The protometabolic nature of prebiotic chemistry

The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.

The Role of Chemically Innocent Polyanions in Active, Chemically Fueled Complex Coacervate Droplets

Complex coacervation describes the liquid-liquid phase separation of oppositely charged polymers. Active coacervates are droplets in which one of the electrolyte's affinity is regulated by chemical reactions. These droplets are particularly interesting because they are tightly regulated by reaction kinetics. For example, they serve as a model for membraneless organelles that are also often regulated by biochemical transformations such as post-translational modifications. They are also a great protocell model or could be used to synthesize life-they spontaneously emerge in response to reagents, compete, and decay when all nutrients have been consumed. However, the role of the unreactive building blocks, e.g., the polymeric compounds, is poorly understood. Here, we show the important role of the chemically innocent, unreactive polyanion of our chemically fueled coacervation droplets. We show that the polyanion drastically influences the resulting droplets' life cycle without influencing the chemical reaction cycle-either they are very dynamic or have a delayed dissolution. Additionally, we derive a mechanistic understanding of our observations and show how additives and rational polymer design help to create the desired coacervate emulsion life cycles.

Collective catalysis under spatial constraints: Phase separation and size-scaling effects on mass action kinetics

Chemical reactions are usually studied under the assumption that both substrates and catalysts are well-mixed (WM) throughout the system. Although this is often applicable to test-tube experimental conditions, it is not realistic in cellular environments, where biomolecules can undergo liquid-liquid phase separation (LLPS) and form condensates, leading to important functional outcomes, including the modulation of catalytic action. Similar processes may also play a role in protocellular systems, like primitive coacervates, or in membrane-assisted prebiotic pathways. Here we explore whether the demixing of catalysts could lead to the formation of microenvironments that influence the kinetics of a linear (multistep) reaction pathway, as compared to a WM system. We implemented a general lattice model to simulate LLPS of a collection of different catalysts and extended it to include diffusion and a sequence of reactions of small substrates. We carried out a quantitative analysis of how the phase separation of the catalysts affects reaction times depending on the affinity between substrates and catalysts, the length of the reaction pathway, the system size, and the degree of homogeneity of the condensate. A key aspect underlying the differences reported between the two scenarios is that the scale invariance observed in the WM system is broken by condensation processes. The main theoretical implications of our results for mean-field chemistry are drawn, extending the mass action kinetics scheme to include substrate initial "hitting times" to reach the catalysts condensate. We finally test this approach by considering open nonlinear conditions, where we successfully predict, through microscopic simulations, that phase separation inhibits chemical oscillatory behavior, providing a possible explanation for the marginal role that this complex dynamic behavior plays in real metabolisms.

Environmental Stability and Its Importance for the Emergence of Darwinian Evolution

The emergence of Darwinian evolution represents a central point in the history of life as we know it. However, it is generally assumed that the environments in which life appeared were hydrothermal environments, with highly variable conditions in terms of pH, temperature or redox levels. Are evolutionary processes favored to appear in such settings, where the target of biological adaptation changes over time? How would the first evolving populations compete with non-evolving populations? Using a numerical model, we explore the effect of environmental variation on the outcome of the competition between evolving and non-evolving populations of protocells. Our study found that, while evolving protocells consistently outcompete non-evolving populations in stable environments, they are outcompeted in variable environments when environmental variations occur on a timescale similar to the average duration of a generation. This is due to the energetic burden represented by adaptation to the wrong environmental conditions. Since the timescale of temperature variation in natural hydrothermal settings overlaps with the average prokaryote generation time, the current work indicates that a solution must have been found by early life to overcome this threshold.

Facile and Programmable Capillary-Induced Assembly of Prototissues via Hanging Drop Arrays

An important goal for bottom-up synthetic biology is to construct tissue-like structures from artificial cells. The key is the ability to control the assembly of the individual artificial cells. Unlike most methods resorting to external fields or sophisticated devices, inspired by the hanging drop method used for culturing spheroids of biological cells, we employ a capillary-driven approach to assemble giant unilamellar vesicles (GUVs)-based protocells into colonized prototissue arrays by means of a coverslip with patterned wettability. By spatially confining and controllably merging a mixed population of lipid-coated double-emulsion droplets that hang on a water/oil interface, an array of synthetic tissue-like constructs can be obtained. Each prototissue module in the array comprises multiple tightly packed droplet compartments where interfacial lipid bilayers are self-assembled at the interfaces both between two neighboring droplets and between the droplet and the external aqueous environment. The number, shape, and composition of the interconnected droplet compartments can be precisely controlled. Each prototissue module functions as a processer, in which fast signal transports of molecules via cell-cell and cell-environment communications have been demonstrated by molecular diffusions and cascade enzyme reactions, exhibiting the ability to be used as biochemical sensing and microreactor arrays. Our work provides a simple yet scalable and programmable method to form arrays of prototissues for synthetic biology, tissue engineering, and high-throughput assays.

Plant Cell-Inspired Membranization of Coacervate Protocells with a Structured Polysaccharide Layer

The design of compartmentalized colloids that exhibit biomimetic properties is providing model systems for developing synthetic cell-like entities (protocells). Inspired by the cell walls in plant cells, we developed a method to prepare membranized coacervates as protocell models by coating membraneless liquid-like microdroplets with a protective layer of rigid polysaccharides. Membranization not only endowed colloidal stability and prevented aggregation and coalescence but also facilitated selective biomolecule sequestration and chemical exchange across the membrane. The polysaccharide wall surrounding coacervate protocells acted as a stimuli-responsive structural barrier that enabled enzyme-triggered membrane lysis to initiate internalization and killing of Escherichia coli. The membranized coacervates were capable of spatial organization into structured tissue-like protocell assemblages, offering a means to mimic metabolism and cell-to-cell communication. We envision that surface engineering of protocells as developed in this work generates a platform for constructing advanced synthetic cell mimetics and sophisticated cell-like behaviors.

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.

Insights into Early Steps of Decanoic Acid Self-Assemblies under Prebiotic Temperatures Using Molecular Dynamics Simulations

The origin of life possibly required processes in confined systems that facilitated simple chemical reactions and other more complex reactions impossible to achieve under the condition of infinite dilution. In this context, the self-assembly of micelles or vesicles derived from prebiotic amphiphilic molecules is a cornerstone in the chemical evolution pathway. A prime example of these building blocks is decanoic acid, a short-chain fatty acid capable of self-assembling under ambient conditions. This study explored a simplified system made of decanoic acids under temperatures ranging from 0 °C to 110 °C to replicate prebiotic conditions. The study revealed the first point of aggregation of decanoic acid into vesicles and examined the insertion of a prebiotic-like peptide in a primitive bilayer. The information gathered from this research provides critical insights into molecule interactions with primitive membranes, allowing us to understand the first nanometric compartments needed to trigger further reactions that were essential for the origin of life.

Osmotic Pressure Enables High-Yield Assembly of Giant Vesicles in Solutions of Physiological Ionic Strengths

Giant unilamellar vesicles (GUVs) are micrometer-scale minimal cellular mimics that are useful for bottom-up synthetic biology and drug delivery. Unlike assembly in low-salt solutions, assembly of GUVs in solutions with ionic concentrations of 100-150 mM Na/KCl (salty solutions) is challenging. Chemical compounds deposited on the substrate or incorporated into the lipid mixture could assist in the assembly of GUVs. Here, we investigate quantitatively the effects of temperature and chemical identity of six polymeric compounds and one small molecule compound on the molar yields of GUVs composed of three different lipid mixtures using high-resolution confocal microscopy and large data set image analysis. All the polymers moderately increased the yields of GUVs either at 22 or 37 °C, whereas the small molecule compound was ineffective. Low-gelling temperature agarose is the singular compound that consistently produces yields of GUVs of greater than 10%. We propose a free energy model of budding to explain the effects of polymers in assisting the assembly of GUVs. The osmotic pressure exerted on the membranes by the dissolved polymer balances the increased adhesion between the membranes, thus reducing the free energy for bud formation. Data obtained by modulating the ionic strength and ion valency of the solution shows that the evolution of the yield of GUVs supports our model's prediction. In addition, polymer-specific interactions with the substrate and the lipid mixture affects yields. The uncovered mechanistic insights provide a quantitative experimental and theoretical framework to guide future studies. Additionally, this work shows a facile means for obtaining GUVs in solutions of physiological ionic strengths.

Confinement effect on hydrolysis in small lipid vesicles

In living organisms most chemical reactions take place within the confines of lipid-membrane bound compartments, while confinement within the bounds of a lipid membrane is thought to be a key step in abiogenesis. In previous work we demonstrated that confinement in the aqueous cavity of a lipid vesicle affords protection against hydrolysis, a phenomenon that we term here confinement effect (C _e) and that we attributed to the interaction with the lipid membrane. Here, we show that both the size and the shape of the cavity of the vesicle modulate the C _e. We link this observation to the packing of the lipid following changes in membrane curvature, and formulate a mathematical model that relates the C _e to the radius of a spherical vesicle and the packing parameter of the lipids. These results suggest that the shape of the compartment where a molecule is located plays a major role in controlling the chemical reactivity of non-enzymatic reactions. Moreover, the mathematical treatment we propose offers a useful tool for the design of vesicles with predictable reaction rates of the confined molecules, e.g., drug delivery vesicles with confined prodrugs. The results also show that a crude form of signal transduction, devoid of complex biological machinery, can be achieved by any external stimuli that drastically changes the structure of the membrane, like the osmotic shocks used in the present work.

Inorganic-organic coprecipitation: spontaneous formation of enclosed and porous silica compartments with enriched biopolymers

We show that it is possible to spontaneously form all-enclosed compartments with microporous shells and enriched biopolymers via simple coprecipitation of silica and biopolymers. The reaction involves mild conditions and tolerates the random mixing of multiple reagents. Such a synthetic advance points to a new direction for resolving the chicken-egg dilemma of how the early life forms were hosted: without a physical barrier it would be difficult to maintain organized reactions, but without organized reactions, it would be difficult to create a cell membrane. In our synthesis, the divalent cation Ca²⁺ plays a critical role in the co-precipitation and in creating hollow compartments after simple dilution with water. The precursor of silica, poly(silicic acid), is a negatively charged, cross-linked polymer. It could be co-precipitated with negatively charged biopolymers such as DNA and proteins, whereas the remaining silica precursor forms a conformal and microporous shell on the surface of the initial precipitate. After etching, the biopolymers are retained inside the hollow compartments. The fact that multiple favorable conditions are easily brought together in enclosed compartments opens new possibilities in theorizing the host of early life forms.

Model Atmospheric Aerosols Convert to Vesicles upon Entry into Aqueous Solution

Aerosols are abundant on the Earth and likely played a role in prebiotic chemistry. Aerosol particles coagulate, divide, and sample a wide variety of conditions conducive to synthesis. While much work has centered on the generation of aerosols and their chemistry, little effort has been expended on their fate after settling. Here, using a laboratory model, we show that aqueous aerosols transform into cell-sized protocellular structures upon entry into aqueous solution containing lipid. Such processes provide for a heretofore unexplored pathway for the assembly of the building blocks of life from disparate geochemical regions within cell-like vesicles with a lipid bilayer in a manner that does not lead to dilution. The efficiency of aerosol to vesicle transformation is high with prebiotically plausible lipids, such as decanoic acid and decanol, that were previously shown to be capable of forming growing and dividing vesicles. The high transformation efficiency with 10-carbon lipids in landing solutions is consistent with the surface properties and dynamics of short-chain lipids. Similar processes may be operative today as fatty acids are common constituents of both contemporary aerosols and the sea. Our work highlights a new pathway that may have facilitated the emergence of the Earth's first cells.

Ferric heme b in aqueous micellar and vesicular systems: state-of-the-art and challenges

Ferric heme b (= ferric protoporphyrin IX = hemin) is an important prosthetic group of different types of enzymes, including the intensively investigated and widely applied horseradish peroxidase (HRP). In HRP, hemin is present in monomeric form in a hydrophobic pocket containing among other amino acid side chains the two imidazoyl groups of His170 and His42. Both amino acids are important for the peroxidase activity of HRP as an axial ligand of hemin (proximal His170) and as an acid/base catalyst (distal His42). A key feature of the peroxidase mechanism of HRP is the initial formation of compound I under heterolytic cleavage of added hydrogen peroxide as a terminal oxidant. Investigations of free hemin dispersed in aqueous solution showed that different types of hemin dimers can form, depending on the experimental conditions, possibly resulting in hemin crystallization. Although it has been recognized already in the 1970s that hemin aggregation can be prevented in aqueous solution by using micelle-forming amphiphiles, it remains a challenge to prepare hemin-containing micellar and vesicular systems with peroxidase-like activities. Such systems are of interest as cheap HRP-mimicking catalysts for analytical and synthetic applications. Some of the key concepts on which research in this fascinating and interdisciplinary field is based are summarized, along with major accomplishments and possible directions for further improvement. A systematic analysis of the physico-chemical properties of hemin in aqueous micellar solutions and vesicular dispersions must be combined with a reliable evaluation of its catalytic activity. Future studies should show how well the molecular complexity around hemin in HRP can be mimicked by using micelles or vesicles. Because of the importance of heme b in virtually all biological systems and the fact that porphyrins and hemes can be obtained under potentially prebiotic conditions, ideas exist about the possible role of heme-containing micellar and vesicular systems in prebiotic times.

Emergence Simulation of Biological Cell-like Shapes Satisfying the Conditions of Life Using a Lattice-Type Multiset Chemical Model

Simple Summary

One of the great challenges in science is determining when, where, why, and how life first arose as well as the form taken by this life. In the present study, life was assumed to be (1) bounded, (2) replicating, (3) able to inherit information, and (4) able to metabolize energy. The various existing hypotheses provide little explanation of how these four conditions for life were established. Indeed, “how” a chemical process that simultaneously satisfies all four conditions emerged after the materials for life were in place is not always clear. In this study, a multiset chemical lattice model, which allows for virtual molecules of multiple types to be placed in each cell on a two-dimensional space, was considered. Using only the processes of molecular diffusion, reaction, and polymerization and modeling the chemical reactions of 15 types of molecules and 2 types of polymerized molecules, as well as using the morphogenesis rule of the Turing model, the process of emergence of a cell-like form with all three conditions except evolution ability was modeled and demonstrated.

Abstract

Although numerous reports using methods such as molecular dynamics, cellular automata, and artificial chemistry have clarified the process connecting non-life and life on protocell simulations, none of the models could simultaneously explain the emergence of cell shape, continuous self-replication, and replication control solely from molecular reactions and diffusion. Herein, we developed a model to generate all three conditions, except evolution ability, from hypothetical chains of chemical and molecular polymerization reactions. The present model considers a 2D lattice cell space, where virtual molecules are placed in each cell, and molecular reactions in each cell are based on a multiset rewriting rule, indicating stochastic transition of molecular species. The reaction paths of virtual molecules were implemented by replacing the rules of cellular automata that generate Turing patterns with molecular reactions. The emergence of a cell-like form with all three conditions except evolution ability was modeled and demonstrated using only molecular diffusion, reaction, and polymerization for modeling the chemical reactions of 15 types of molecules and 2 types of polymerized molecules. Furthermore, controlling self-replication is possible by changing the initial arrangement of a specific molecule. In summary, the present model is capable of investigating and refining existing hypotheses on the emergence of life.

Growth, replication and division enable evolution of coacervate protocells

Living and proliferating cells undergo repeated cycles of growth, replication and division, all orchestrated by complex molecular networks. How a minimal cell cycle emerged and helped primitive cells to evolve remains one of the biggest mysteries in modern science, and is an active area of research in chemistry. Protocells are cell-like compartments that recapitulate features of living cells and may be seen as the chemical ancestors of modern life. While compartmentalization is not strictly required for primitive, open-ended evolution of self-replicating systems, it gives such systems a clear identity by setting the boundaries and it can help them overcome three major obstacles of dilution, parasitism and compatibility. Compartmentalization is therefore widely considered to be a central hallmark of primitive life, and various types of protocells are actively investigated, with the ultimate goal of developing a protocell capable of autonomous proliferation by mimicking the well-known cell cycle of growth, replication and division. We and others have found that coacervates are promising protocell candidates in which chemical building blocks required for life are naturally concentrated, and chemical reactions can be selectively enhanced or suppressed. This feature article provides an overview of how growth, replication and division can be realized with coacervates as protocells and what the bottlenecks are. Considerations are given for designing chemical networks in coacervates that can lead to sustained growth, selective replication and controlled division, in a way that they are linked together like in the cell cycle. Ultimately, such a system may undergo evolution by natural selection of certain phenotypes, leading to adaptation and the gain of new functions, and we end with a brief discussion of the opportunities for coacervates to facilitate this.

Distinguishing cellular from abiotic spheroidal microstructures in the ca. 3.4 Ga Strelley Pool Formation

The morphogenesis of most carbonaceous microstructures that resemble microfossils in Archean (4-2.5 Ga old) rocks remains debated. The associated carbonaceous matter may even-in some cases-derive from abiotic organic molecules. Mineral growths associated with organic matter migration may mimic microbial cells, some anatomical features, and known microfossils-in particular those with simple spheroid shapes. Here, spheroid microstructures from a chert of the ca. 3.4 Ga Strelley Pool Formation (SPF) of the Pilbara Craton (Western Australia) were imaged and analyzed with a combination of high-resolution in situ techniques. This provides new insights into carbonaceous matter distributions and their relationships with the crystallographic textures of associated quartz. Thus, we describe five new types of spheroids and discuss their morphogenesis. In at least three types of microstructures, wall coalescence argues for migration of carbonaceous matter onto abiotic siliceous spherulites or diffusion in poorly crystalline silica. The nanoparticulate walls of these coalescent structures often cut across multiple quartz crystals, consistent with migration in/on silica prior to quartz recrystallization. Sub-continuous walls lying at quartz boundaries occur in some coalescent vesicles. This weakens the "continuous carbonaceous wall" criterion proposed to support cellular inferences. In contrast, some clustered spheroids display wrinkled sub-continuous double walls, and a large sphere shows a thick sub-continuous wall with pustules and depressions. These features appear consistent with post-mortem cell alteration, although abiotic morphogenesis remains difficult to rule out. We compared these siliceous and carbonaceous microstructures to coalescent pyritic spheroids from the same sample, which likely formed as "colloidal" structures in hydrothermal context. The pyrites display a smaller size and only limited carbonaceous coatings, arguing that they could not have acted as precursors to siliceous spheroids. This study revealed new textural features arguing for abiotic morphogenesis of some Archean spheroids. The absence of these features in distinct types of spheroids leaves open the microfossil hypothesis in the same rock. Distinction of such characteristics could help addressing further the origin of other candidate microfossils. This study calls for similar investigations of metamorphosed microfossiliferous rocks and of the products of in vitro growth of cell-mimicking structures in presence of organics and silica.

From vesicles toward protocells and minimal cells

In contrast to ordinary condensed matter systems, "living systems" are unique. They are based on molecular compartments that reproduce themselves through (i) an uptake of ingredients and energy from the environment, and (ii) spatially and timely coordinated internal chemical transformations. These occur on the basis of instructions encoded in information molecules (DNAs). Life originated on Earth about 4 billion years ago as self-organised systems of inorganic compounds and organic molecules including macromolecules (e.g. nucleic acids and proteins) and low molar mass amphiphiles (lipids). Before the first living systems emerged from non-living forms of matter, functional molecules and dynamic molecular assemblies must have been formed as prebiotic soft matter systems. These hypothetical cell-like compartment systems often are called "protocells". Other systems that are considered as bridging units between non-living and living systems are called "minimal cells". They are synthetic, autonomous and sustainable reproducing compartment systems, but their constituents are not limited to prebiotic substances. In this review, we focus on both membrane-bounded (vesicular) protocells and minimal cells, and provide a membrane physics background which helps to understand how morphological transformations of vesicle systems might have happened and how vesicle reproduction might be coupled with metabolic reactions and information molecules. This research, which bridges matter and life, is a great challenge in which soft matter physics, systems chemistry, and synthetic biology must take joined efforts to better understand how the transformation of protocells into living systems might have occurred at the origin of life.