Compartmentalised RNA catalysis in membrane-free coacervate protocells

Response-Retaliation Behavior in Synthetic Protocell Communities

Two different artificial predation strategies are spatially and temporally coupled to generate a simple tit-for-tat mechanism in a ternary protocell network capable of antagonistic enzyme-mediated interactions. The consortium initially consists of protease-sensitive glucose-oxidase-containing proteinosomes (1), non-interacting pH-sensitive polypeptide/mononucleotide coacervate droplets containing proteinase K (2), and proteinosome-adhered pH-resistant polymer/polysaccharide coacervate droplets (3). On receiving a glucose signal, secretion of protons from 1 triggers the disassembly of 2 and the released protease is transferred to 3 to initiate a delayed contact-dependent killing of the proteinosomes and cessation of glucose oxidase activity. Our results provide a step towards complex mesoscale dynamics based on programmable response-retaliation behavior in artificial protocell consortia.

Physicochemical Characterization of Polymer-Stabilized Coacervate Protocells

The bottom-up construction of cell mimics has produced a range of membrane-bound protocells that have been endowed with functionality and biochemical processes reminiscent of living systems. The contents of these compartments, however, experience semidilute conditions, whereas macromolecules in the cytosol exist in protein-rich, crowded environments that affect their physicochemical properties, such as diffusion and catalytic activity. Recently, complex coacervates have emerged as attractive protocellular models because their condensed interiors would be expected to mimic this crowding better. Here we explore some relevant physicochemical properties of a recently developed polymer-stabilized coacervate system, such as the diffusion of macromolecules in the condensed coacervate phase, relative to in dilute solutions, the buffering capacity of the core, the molecular organization of the polymer membrane, the permeability characteristics of this membrane towards a wide range of compounds, and the behavior of a simple enzymatic reaction. In addition, either the coacervate charge or the cargo charge is engineered to allow the selective loading of protein cargo into the coacervate protocells. Our in-depth characterization has revealed that these polymer-stabilized coacervate protocells have many desirable properties, thus making them attractive candidates for the investigation of biochemical processes in stable, controlled, tunable, and increasingly cell-like environments.

Highly Photostable and Two-Photon Active Quantum Dot-Polymer Multicolor Hybrid Coacervate Droplets

Fabrication and precise control of the physicochemical properties of multifunctional organic-inorganic hybrid nanocomposites find great importance in various research fields. Herein, we report the fabrication of a new class of luminescent hybrid coacervate droplets from CdTe quantum dots (QDs) and a poly(diallyldimethylammonium chloride) (PDADMAC) aqueous mixture. The colloidal stability of these droplets has been explored over wide ranges of composition, pH, and ionic strength. Although these hybrid droplets are quite stable in a low-ionic-strength medium (<100 mM NaCl) and neutral/basic pH (pH >6.5), they are unstable in a higher-ionic-strength medium (>100 mM NaCl) and acidic pH (pH <5.5). Our findings indicate specific electrostatic interactions between negatively charged QDs and positively charged PDADMAC behind the observed coacervation. They exhibit the preferential sequestration of organic dyes and serum albumins. The intrinsic luminescent properties of these hybrid droplets have been explored using confocal laser scanning microscopy (CLSM) and epifluorescence microscopy. CLSM reveals the formation of intrinsically luminescent hybrid droplets. In addition, mixed two-color luminescent droplets have been fabricated by simultaneously mixing green- and red-emitting QDs with PDADMAC aqueous solution. Epifluorescence imaging reveals highly photostable and nonbleaching photoluminescence (PL) from individual droplets as a consequence of efficient surface passivation by polymeric chains of PDADMAC. Moreover, using two-photon (2P) confocal imaging we have shown that these hybrid droplets are ideal candidates for 2P confocal imaging applications. The present study can be easily extended to fabricate a wide range of hybrid droplets with various inorganic counterparts having unique optoelectronic properties, which will further expand their applicability in nanocatalysis, bioimaging, and biosensing.

Photoswitchable Phase Separation and Oligonucleotide Trafficking in DNA Coacervate Microdroplets

Coacervate microdroplets produced by liquid-liquid phase separation have been used as synthetic protocells that mimic the dynamical organization of membrane-free organelles in living systems. Achieving spatiotemporal control over droplet condensation and disassembly remains challenging. Herein, we describe the formation and photoswitchable behavior of light-responsive coacervate droplets prepared from mixtures of double-stranded DNA and an azobenzene cation. The droplets disassemble and reassemble under UV and blue light, respectively, due to azobenzene trans/cis photoisomerisation. Sequestration and release of captured oligonucleotides follow the dynamics of phase separation such that light-activated transfer, mixing, hybridization, and trafficking of the oligonucleotides can be controlled in binary populations of the droplets. Our results open perspectives for the spatiotemporal control of DNA coacervates and provide a step towards the dynamic regulation of synthetic protocells.

Synthetic organelles

One approach towards the creation of bottom-up synthetic biological systems of higher complexity relies on the subcompartmentalization of synthetic cell structures using artificially generated organelles — roughly mimicking the architecture of eukaryotic cells. Organelles create dedicated chemical environments for specific synthesis tasks — they separate incompatible processes from each other and help to create or maintain chemical gradients that drive other chemical processes. Artificial organelles have been used to compartmentalize enzyme reactions, to generate chemical fuels via photosynthesis and oxidative phosphorylation, and they have been utilized to spatially organize cell-free gene expression reactions. In this short review article, we provide an overview of recent developments in this field, which involve a wide variety of compartmentalization strategies ranging from lipid and polymer membrane systems to membraneless compartmentalization via coacervation.

Synthetic life on a chip

In this article, we argue that on-chip microfluidic systems provide an attractive technology when it comes to designing synthetic cells. We emphasize the importance of the surrounding environment for both living systems in nature and for developing artificial self-sustaining entities. On-chip microfluidic devices provide a high degree of control over the production of cell-like synthetic entities as well as over the local microenvironment that these soft-matter-based synthetic cells experience. Rapid progress in microfluidic fabrication technology has led to a variety of production and manipulation tools that establish on-chip environments as a versatile platform and arguably the best route forward for realizing synthetic life.

The Informational Substrate of Chemical Evolution: Implications for Abiogenesis

A key aspect of biological evolution is the capacity of living systems to process information, coded in deoxyribonucleic acid (DNA), and used to direct how the cell works. The overall picture that emerges today from fields such as developmental, synthetic, and systems biology indicates that information processing in cells occurs through a hierarchy of genes regulating the activity of other genes through complex metabolic networks. There is an implicit semiotic character in this way of dealing with information, based on functional molecules that act as signs to achieve self-regulation of the whole network. In contrast to cells, chemical systems are not thought of being able to process information, yet they must have preceded biological organisms, and evolved into them. Hence, there must have been prebiotic molecular assemblies that could somehow process information, in order to regulate their own constituent reactions and supramolecular organization processes. The purpose of this essay is then to reflect about the distinctive features of information in living and non-living matter, and on how the capacity of biological organisms for information processing was possibly rooted in a particular type of chemical systems (here referred to as autonomous chemical systems), which could self-sustain and reproduce through organizational closure of their molecular building blocks.

Dynamic Synthetic Cells Based on Liquid-Liquid Phase Separation

Living cells have long been a source of inspiration for chemists. Their capacity of performing complex tasks relies on the spatiotemporal coordination of matter and energy fluxes. Recent years have witnessed growing interest in the bottom-up construction of cell-like models capable of reproducing aspects of such dynamic organisation. Liquid-liquid phase-separation (LLPS) processes in water are increasingly recognised as representing a viable compartmentalisation strategy through which to produce dynamic synthetic cells. Herein, we highlight examples of the dynamic properties of LLPS used to assemble synthetic cells, including their biocatalytic activity, reversible condensation and dissolution, growth and division, and recent directions towards the design of higher-order structures and behaviour.

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

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

Spatial Positioning and Chemical Coupling in Coacervate-in-Proteinosome Protocells

The integration of molecularly crowded microenvironments into membrane-enclosed protocell models represents a step towards more realistic representations of cellular structure and organization. Herein, the membrane diffusion-mediated nucleation of either negatively or positively charged coacervate microdroplets within the aqueous lumen of individual proteinosomes is used to prepare nested hybrid protocells with spatially organized and chemically coupled enzyme activities. The location and reconfiguration of the entrapped droplets are regulated by tuning the electrostatic interactions between the encapsulated coacervate and surrounding negatively charged proteinosome membrane. As a consequence, alternative modes of a cascade reaction involving membrane- and coacervate-segregated enzymes can be implemented within the coacervate-in-proteinosome protocells.

Polyanion-Assisted Ribozyme Catalysis Inside Complex Coacervates

Owing to their ability to encapsulate biomolecules, complex coacervates formed by associative phase separation of oppositely charged polyelectrolytes have been postulated as prebiotic nonmembranous compartments (NMCs). Recent studies show that NMCs sequester RNA and enhance ribozyme reactions, a critical tenet of the RNA World Hypothesis. As RNA is negatively charged, it is expected to interact with polycationic coacervate components. The molecular basis for how identity and concentration of polyanionic components of complex coacervates affect ribozyme catalysis remains unexplored. We report here a general mechanism wherein diverse polyanions enhance ribozyme catalysis in complex coacervates. By competing for unproductive RNA-polycation interactions, polyanions enhance ribozyme reaction more than 12-fold. The generality of our findings is supported by similar behavior in three polyanions-polycarboxylates, polysulfates, and polysulfates/carboxylates-as well as two different ribozymes, the hammerhead and hairpin. These results reveal potential roles for polyanions in prebiotic chemistry and extant biology.

Physics of active emulsions

Phase separating systems that are maintained away from thermodynamic equilibrium via molecular processes represent a class of active systems, which we call active emulsions. These systems are driven by external energy input, for example provided by an external fuel reservoir. The external energy input gives rise to novel phenomena that are not present in passive systems. For instance, concentration gradients can spatially organise emulsions and cause novel droplet size distributions. Another example are active droplets that are subject to chemical reactions such that their nucleation and size can be controlled, and they can divide spontaneously. In this review, we discuss the physics of phase separation and emulsions and show how the concepts that govern such phenomena can be extended to capture the physics of active emulsions. This physics is relevant to the spatial organisation of the biochemistry in living cells, for the development of novel applications in chemical engineering and models for the origin of life.

Mass Transport in Coacervate-Based Protocell Coated with Fatty Acid under Nonequilibrium Conditions

Construction of protocell models from prebiotically plausible components to mimic the basic features or functions of living cells is still a challenge. In this work, we prepare a hybrid protocell model by coating sodium oleate on the coacervate droplet constituted by poly(l-lysine) and oligonucleotide and investigate the transport of different molecules under electric field. Results show that sodium oleate forms a layered viscoelastic membrane on the droplet surface, which is selectively permeable to small, polar molecules, such as oligolysine. As the droplet is stimulated at 10 V cm^-1, the oleate membrane slips along the direction of electric field while maintaining its integrity. Most of the molecules are still excluded under such conditions. As repetitive cycles of vacuolization occur at 20 V cm^-1, all molecules are internalized and sequestrated in the droplet through their specific pathways except enzyme, which anchors in the oleate membrane and is immune to electric field. Cascade enzymatic reactions are then carried out, and the product generated from the membrane exhibits a time-dependent concentration gradient across the droplet. Our work makes a step toward the nonequilibrium functionalization of synthetic protocells capable of biomimetic operations.

Biomolecular Chemistry in Liquid Phase Separated Compartments

Biochemical processes inside the cell take place in a complex environment that is highly crowded, heterogeneous, and replete with interfaces. The recently recognized importance of biomolecular condensates in cellular organization has added new elements of complexity to our understanding of chemistry in the cell. Many of these condensates are formed by liquid-liquid phase separation (LLPS) and behave like liquid droplets. Such droplet organelles can be reproduced and studied in vitro by using coacervates and have some remarkable features, including regulated assembly, differential partitioning of macromolecules, permeability to small molecules, and a uniquely crowded environment. Here, we review the main principles of biochemical organization in model membraneless compartments. We focus on some promising in vitro coacervate model systems that aptly mimic part of the compartmentalized cellular environment. We address the physicochemical characteristics of these liquid phase separated compartments, and their impact on biomolecular chemistry and assembly. These model systems enable a systematic investigation of the role of spatiotemporal organization of biomolecules in controlling biochemical processes in the cell, and they provide crucial insights for the development of functional artificial organelles and cells.

Cytoskeletal and Actin-Based Polymerization Motors and Their Role in Minimal Cell Design

Life implies motion. In cells, protein-based active molecular machines drive cell locomotion and intracellular transport, control cell shape, segregate genetic material, and split a cell in two parts. Key players among molecular machines driving these various cell functions are the cytoskeleton and motor proteins that convert chemical bound energy into mechanical work. Findings over the last decades in the field of in vitro reconstitutions of cytoskeletal and motor proteins have elucidated mechanistic details of these active protein systems. For example, a complex spatial and temporal interplay between the cytoskeleton and motor proteins is responsible for the translation of chemically bound energy into (directed) movement and force generation, which eventually governs the emergence of complex cellular functions. Understanding these mechanisms and the design principles of the cytoskeleton and motor proteins builds the basis for mimicking fundamental life processes. Here, a brief overview of actin, prokaryotic actin analogs, and motor proteins and their potential role in the design of a minimal cell from the bottom-up is provided.

Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates

Membraneless compartments, such as complex coacervates, have been hypothesized as plausible prebiotic micro-compartments due to their ability to sequester RNA; however, their compatibility with essential RNA World chemistries is unclear. We show that such compartments can enhance key prebiotically-relevant RNA chemistries. We demonstrate that template-directed RNA polymerization is sensitive to polycation identity, with polydiallyldimethylammonium chloride (PDAC) outperforming poly(allylamine), poly(lysine), and poly(arginine) in polycation/RNA coacervates. Differences in RNA diffusion rates between PDAC/RNA and oligoarginine/RNA coacervates imply distinct biophysical environments. Template-directed RNA polymerization is relatively insensitive to Mg²⁺ concentration when performed in PDAC/RNA coacervates as compared to buffer, even enabling partial rescue of the reaction in the absence of magnesium. Finally, we show enhanced activities of multiple nucleic acid enzymes including two ribozymes and a deoxyribozyme, underscoring the generality of this approach, in which functional nucleic acids like aptamers and ribozymes, and in some cases key cosolutes localize within the coacervate microenvironments.

Membraneless compartments have been theorized to be prebiotic micro-compartments as they spontaneously encapsulate RNA and proteins. Here, the authors report membraneless compartments can enhance RNA chemistries, affecting template directed RNA polymerization and stimulating nucleic acid enzymes.

Liquid–liquid phase separation rescues the conformational stability of a DNA hairpin from pressure–stress

Aqueous two-phase systems are able to rescue the conformational stability of DNA hairpins under harsh environmental conditions.