Compartmentalised RNA catalysis in membrane-free coacervate protocells

Enzyme- and DNAzyme-Driven Transient Assembly of DNA-Based Phase-Separated Coacervate Microdroplets

An assembly of dissipative, transient, DNA-based microdroplet (MD) coacervates in the presence of auxiliary enzymes (endonucleases and nickases) or MD-embedded DNAzyme is introduced. Two pairs of different Y-shaped DNA core frameworks modified with toehold tethers are cross-linked by complementary toehold-functionalized duplexes, engineered to be cleaved by EcoRI or HindIII endonucleases, or cross-linked by palindromic strands that include pre-engineered Nt.BbvCI or Nb.BtsI nicking sites, demonstrating transient evolution/depletion of phase-separated MD coacervates. By mixing the pairs of endonuclease- or nickase-responsive MDs, programmed or gated transient formation/depletion of MD frameworks is presented. In addition, by cross-linking a pre-engineered Y-shaped core framework with a sequence-designed fuel strand, phase separation of MD coacervates with embedded Mg2+-DNAzyme units is introduced. The DNAzyme-catalyzed cleavage of a ribonucleobase-modified hairpin substrate, generating the waste product of the metabolite fragments, leads to the metabolite-driven separation of the cross-linked coacervates, resulting in the temporal evolution and depletion of the DNAzyme-functionalized MDs. By employing a light-responsive caged hairpin structure, the light-modulated fueled evolution and depletion of the DNAzyme-active MDs are presented. The enzyme- or DNAzyme-catalyzed transient evolution/depletion of the MD coacervates provides protocell frameworks mimicking dynamic transient processes of native cells. The possible application of MDs as functional carriers for the temporal, dose-controlled release of loads is addressed.

A stepwise emergence of evolution in the RNA world

Building on experimental evidence and replicator theories, I propose a 3-stage scenario for a transition from autocatalysis into template-based replication of RNA, providing a pathway for the origin of life. In stage 1, self-reproduction occurs via autocatalysis using oligomer substrates, replicator viability relies on substrate-specificity, and heritable variations are mediated by structural interactions. In stage 2, autocatalysis coexists with the templated ligation of external substrates. This dual mode of reproduction combined with limited diffusion avoids the error catastrophe. In stage 3, template-based replication takes over and uses substrates of decreasing size, made possible by enhanced catalytic properties and compartmentalization. Structural complexity, catalytic efficiency, metabolic efficiency, and cellularization all evolve gradually and interdependently, ultimately leading to evolutionary processes similar to extant biology. Impact statement This perspective proposes a testable stepwise scenario for the emergence of evolution in an RNA origin of life. It shows how evolution could appear in a gradual manner, thanks to catalytic feedback among random mixtures of molecules. It highlights possible couplings between the different facets of molecular self-organization, which could bootstrap life.

Sequence-encoded intermolecular base pairing modulates fluidity in DNA and RNA condensates

Nature uses bottom-up self-assembly to build structures with remarkable complexity and functionality. Understanding how molecular-scale interactions translate to macroscopic properties remains a major challenge and requires systems that effectively bridge these two scales. Here, we generate DNA and RNA-based liquids with exquisite programmability in their macroscopic rheological properties. In the presence of multivalent cations, nucleic acids can condense to a liquid-like state. Within these liquids, DNA and RNA retain sequence-specific hybridization abilities. We show that sequence-specific inter-molecular hybridization in the condensed phase cross-links molecules and slows down chain dynamics. This reduced chain mobility is mirrored in the macroscopic properties of the condensates. Molecular diffusivity and material viscosity scale with the inter-molecular hybridization energy, enabling precise sequence-based modulation of condensate properties over several orders of magnitude. Our work offers a robust platform to create bottom-up programmable fluids and may help advance our understanding of liquid-like compartments in cells.

Dynamic Duos: Coacervate-Lipid Membrane Interactions in Regulating Membrane Transformation and Condensate Size

Biomolecular condensates interfacing with lipid membranes is crucial for several key cellular functions. However, the role of lipid membranes in regulating condensates in cells remains obscure. Here, in-depth interactions between condensates and lipid membranes are probed and unraveled by employing cell-mimetic systems like Giant unilamellar vesicles (GUVs). An unprecedented influence of the coacervate size and their electrostatic interaction with lipid membranes is revealed on the membrane properties and deformation. Importantly, these findings demonstrate that the large relative size of coacervates and minimal electrostatic interaction strength with membranes allow for budding transitions at the interface. Membranes act as nucleation site for coacervates when the charge-charge interaction is high, giving a wrinkled vesicle surface appearance. Molecular diffusion property of lipids, quantified using Fluorescence recovery after photobleaching (FRAP), is modulated at the coacervate-membrane interaction site restricting the coarsening of coacervates. Notably, these results reveal coacervate droplets are intertwined in between membrane folds and invaginations discerned using Transmission electron microscopy (TEM) and high-resolution imaging, which further controls the dimension of droplets resembling size distributions observed in cells. Finally, these findings provide mechanistic insights of lipid bilayers controlling condensate sizes that play a prominent role in comprehending nucleation and localization of cellular condensates.

An Overview of Liquid-Liquid Phase Separation and Its Mechanisms in Sepsis

Sepsis is a systemic inflammatory response syndrome triggered by the invasion of bacteria or pathogenic microorganisms into the human body, which may lead to a variety of serious complications and pose a serious threat to the patient's life and health. Liquid-liquid phase separation (LLPS) is a biomolecular process in which different biomolecules, such as proteins and nucleic acids, form liquid condensates through interactions, and these condensates play key roles in cellular physiological processes. LLPS may affect the development of sepsis through several pathways, such as modulation of inflammatory factors, immune responses, and cell death, by altering the function or activity of biomolecules, which, in turn, affect the cellular response to infection and inflammation. In this paper, we first discuss the mechanism of phase separation, then summarize the studies of LLPS in sepsis, and finally propose the potential application of LLPS in sepsis treatment strategies, while pointing out the limitations of the existing studies and the directions for future research.

Binary peptide coacervates as an active model for biomolecular condensates

Biomolecular condensates formed by proteins and nucleic acids are critical for cellular processes. Macromolecule-based coacervate droplets formed by liquid-liquid phase separation serve as synthetic analogues, but are limited by complex compositions and high molecular weights. Recently, short peptides have emerged as an alternative component of coacervates, but tend to form metastable microdroplets that evolve into rigid nanostructures. Here we present programmable coacervates using binary mixtures of diphenylalanine-based short peptides. We show that the presence of different short peptides stabilizes the coacervate phase and prevents the formation of rigid structures, allowing peptide coacervates to be used as stable adaptive compartments. This approach allows fine control of droplet formation and dynamic morphological changes in response to physiological triggers. As compartments, short peptide coacervates sequester hydrophobic molecules and enhance bio-orthogonal catalysis. In addition, the incorporation of coacervates into model synthetic cells enables the design of Boolean logic gates. Our findings highlight the potential of short peptide coacervates for creating adaptive biomimetic systems and provide insight into the principles of phase separation in biomolecular condensates.

Acetylation of Short Glycopeptides Enables Phase Separation

Liquid-liquid phase separation (LLPS) of biomacromolecules is crucial for regulating cellular functions. To explore their molecular mechanisms, peptide-based coacervates mimicking natural proteins have been developed, but the role of side chain modifications such as glycosylation remains underexplored. Here, we demonstrate that acetylation of short glycopeptides can induce pH- and concentration-dependent phase separation, while removing acetyl groups abolishes this behavior. Circular dichroism spectroscopy revealed a strong link between peptide structural ordering and the phase separation propensity. Peptides capable of forming liquid droplets displayed a significant ellipticity change at 205 nm upon changing solution pH. Moreover, these peptide coacervates can interact with cells and enhance the antiproliferative property of doxorubicin. Therefore, this work highlights the critical role of O-acetylation in LLPS and provides a valuable tool for studying the parameters regulating LLPS and its implications in cellular processes.

Organelle-like structural evolution of coacervate droplets induced by photopolymerization

The dynamic study of coacervates in vitro contributes our understanding of phase separation mechanisms in cells due to complex intracellular physiology. However, current researches mainly involve the use of exogenous auxiliary agents to form multi-compartmental coacervates with short-term stability. Herein, we report the endogenous self-organizing of multi-component coacervates (HA/PDDA/BSA/DMAEMA) induced by a dynamic stimulation process of protein-mediated photopolymerization. As polymerization proceeds, the cycled structural evolution and maturation from coacervate droplets into multi-compartmental coacervates, coacervate vesicles and coacervate droplets are revealed, which are driven by electrostatic interaction and osmotic pressure difference supported by dynamic and thermodynamic control. Specially, by regulating the light stimulation time, a type of multi-compartmental coacervates can be widely obtained with high structural stability over 300 days. Being a promising artificial cell model, it shows the special characteristic of compartmentalized encapsulation of substrates, efficiently improving enzymatic interfacial catalytic efficiency of organelle-like communication. Our study holds great potential for advancing the understanding of the structural evolution mechanism of membraneless organelles and provides an instructive technique for constructing multi-compartmental coacervates with long-term stability.

Self-Assembled Luminescent Droplets from Graphene Quantum Dots Induced by a Gemini Surfactant for Selective Detection of Mercury(II)

Herein, we report the fabrication of a new class of luminescent coacervate droplets from graphene quantum dots (GQDs) and a gemini surfactant in aqueous medium and utilized them toward detection of mercuric ions (Hg2+). The self-assembly of negatively charged GQDs and positively charged gemini surfactant exists mainly because of their electrostatic interaction, leading to coacervation. Confocal laser scanning microscopy (CLSM) and field-emission scanning electron microscopy (FESEM) were utilized to analyze the luminescent and morphological structures of the self-assembled droplets. CLSM images display droplets that are naturally luminescent. The droplets exhibit luminescence quenching in the presence of Hg2+ ions. Our study demonstrates that Hg2+ ions interact through electrostatic interactions with the free carboxylate groups on the surface of GQDs in the hollow structure of the droplets. For Hg2+ ion sensing, the limit of detection (LOD) using the present system is found to be 30.5 nM, which is substantially lower than that of many of the previously reported similar systems. The sensor demonstrated high sensitivity for Hg2+ ions and exhibited a strong linear correlation within the concentration range of 100-500 nM. The current results indicate that the flexibility of surface ligands and organic nanoparticles in hybrid droplets plays a crucial role in the development of multifunctional materials for diverse applications.

Synthetic Biomolecular Condensates: Phase-Separation Control, Cytomimetic Modelling and Emerging Biomedical Potential

Liquid-liquid phase separation towards the formation of synthetic coacervate droplets represents a rapidly advancing frontier in the fields of synthetic biology, material science, and biomedicine. These artificial constructures mimic the biophysical principles and dynamic features of natural biomolecular condensates that are pivotal for cellular regulation and organization. Via adapting biological concepts, synthetic condensates with dynamic phase-separation control provide crucial insights into the fundamental cell processes and regulation of complex biological pathways. They are increasingly designed with the ability to display more complex and ambitious cell-like features and behaviors, which offer innovative solutions for cytomimetic modeling and engineering active materials with sophisticated functions. In this minireview, we highlight recent advancements in the design and construction of synthetic coacervate droplets; including their biomimicry structure and organization to replicate life-like properties and behaviors, and the dynamic control towards engineering active coacervates. Moreover, we highlight the unique applications of synthetic coacervates as catalytic centers and promising delivery vehicles, so that these biomimicry assemblies can be translated into practical applications.

Chemically Triggered Reactive Coacervates Show Life-Like Budding and Membrane Formation

Phase-separated coacervates can enhance reaction kinetics and guide multilevel self-assembly, mimicking early cellular evolution. In this work, we introduce "reactive" complex coacervates that undergo chemically triggered self-immolative transformations, directing the self-assembly of the reaction products within their matrix. These self-assemblies then evolve to show life-like properties such as budding and membrane formation. We find that the coacervate composition critically influences reaction rates and product distribution and guides the hierarchical self-assembly. This work showcases "reactive" coacervates as a versatile platform to influence reaction and self-assembly pathways for controlled supramolecular synthesis and hierarchical self-organization in confined spaces.

Selective peptide bond formation via side chain reactivity and self-assembly of abiotic phosphates

In the realm of biology, peptide bonds are formed via reactive phosphate-containing intermediates, facilitated by compartmentalized environments that ensure precise coupling and folding. Herein, we use aminoacyl phosphate esters, synthetic counterparts of biological aminoacyl adenylates, that drive selective peptide bond formation through side chain-controlled reactivity and self-assembly. This strategy results in the preferential incorporation of positively charged amino acids from mixtures containing natural and non-natural amino acids during the spontaneous formation of amide bonds in water. Conversely, aminoacyl phosphate esters that lack assembly and exhibit fast reactivity result in random peptide coupling. By introducing structural modifications to the phosphate esters (ethyl vs. phenyl) while retaining aggregation, we are able to tune the selectivity by incorporating aromatic amino acid residues. This approach enables the synthesis of sequences tailored to the specific phosphate esters, overcoming limitations posed by certain amino acid combinations. Furthermore, we demonstrate that a balance between electrostatic and aromatic stacking interactions facilitates covalent self-sorting or co-assembly during oligomerization reactions using unprotected N-terminus aminoacyl phosphate esters. These findings suggest that self-assembly of abiotic aminoacyl phosphate esters can activate a selection mechanism enabling the departure from randomness during the autonomous formation of amide bonds in water.

Photochemically Triggered and Autonomous Oscillatory pH-Modulated Transient Assembly/Disassembly of DNA Microdroplet Coacervates

The assembly of pH-responsive DNA-based, phase-separated microdroplets (MDs) coacervates, consisting of frameworks composed of Y-shaped nucleic acid modules crosslinked by pH-responsive strands, is introduced. The phase-separated MDs reveal dynamic pH-stimulated switchable or oscillatory transient depletion and reformation. In one system, a photoisomerizable merocyanine/spiropyran photoacid is used for the light-induced pH switchable modulation of the reaction medium between the values pH=6.0-4.4. The dynamic transient photochemically-induced switchable depletion/reformation of phase-separated MDs, follows the rhythm of pH changes in solution. In a second system, the Landolt oscillatory reaction mixture pH 7.5→4.2→7.5 is applied to stimulate the oscillatory depletion/reformation of the MDs. The autonomous dynamic oscillation of the assembly/disassembly of the MDs follows the oscillating pH rhythm of the reaction medium.

Concomitant formation of protocells and prebiotic compounds under a plausible early Earth atmosphere

Revealing the origin of life and unambiguously detecting fossil remains of the earliest organisms are closely related aspects of the same scientific research. The synthesis of prebiotic molecular building blocks of life and the first compartmentalization into protocells have been considered two events apart in time, space, or both. We conducted lightning experiments in borosilicate reactors filled with a mixture of gases mimicking plausible geochemical conditions of early Earth. In addition to the variety of prebiotic organic molecules synthesized in these experiments, we investigated the micrometer-thick silica-induced organic film that covers the walls of the reactors and floats at the water-gas interface. We found that the film is formed by aggregation of HCN-polymer nanoclusters whenever water is present, either in the liquid or vapor phase. The organic film morphs into micrometer-scale biomorphic vesicular structures hanging from the organic film into the water. We also show that these structures are hollow and may act as microreactors facilitating chemical pathways toward increasing complexity. We propose that these organic biomorphs form through a bubble-driven mechanism and interfacial precipitation of HCN-polymers. The concomitant synthesis of biomorphic poly-HCN protocells and prebiotic molecules under plausible geochemical conditions of early Earth-like planets and moons and opens a different geochemical scenario for the emergence of life. Our results suggest that the coexistence of molecular building blocks of life and submicron biomorphic structures in the oldest rocks on Earth or any other celestial body does not necessarily mean evidence of life.

Peptides for Liquid-Liquid Phase Separation: An Emerging Biomaterial

Liquid-liquid phase separation (LLPS) refers to a spontaneous separation behavior of biomacromolecules under specific physiological conditions, playing a crucial role in regulating various biological processes. Recent advances in synthetic peptides have greatly improved our understanding of peptide-based coacervate droplets and expanded their applications in biomedicine. Numerous peptide sequences have been reported that undergo phase separation, enabling the concentration and sequestration of different guest molecules for purposes such as drug delivery, catalytic performance, and bioanalytical techniques. Particularly, some of these peptides offer significant advantages in controlled drug release, efficient cell transfection, accelerated reaction kinetics, and selective biomarker detection. This review provides an overview of recent developments in peptide-based LLPS, exploring various strategies for designing peptide sequences and their biomedical applications. It also addresses the challenges and future directions for LLPS peptide vehicles as promising biomaterials.

Construction of Somatostatin-Based Multiphase "Core-Shell" Coacervates as Photodynamic Biomimetic Organelles

Biomimetic coacervates have recently attracted great interest in biomedical fields, especially for drug delivery and as protocells. However, these membraneless structures are easily coalesced and poorly targetable, limiting their real biomedical applications. Here multiphase "core-shell" coacervate (CSC) constructed by dsDNA and somatostatin (SST), a 14-mer cyclopeptide is designed. The CSC shows enhanced tumor targetability through SST binding to SST receptors on the tumor cells' surface. G4 quadruplex-hemin complex can be embedded in the CSC by interaction with SST, as demonstrated by molecular simulation and isothermal titration calorimetry. The G4-hemin embedded CSC can further recruit photosensitizers such as tetracarboxyphenyl porphyrin to form the CSC-GHT composite for photodynamic therapy (PDT). As photodynamic biomimetic organelles, CSC-GHT can convert oxygen to singlet oxygen (catalyzed by the catalase-mimetic activity of G4-hemin), resulting in enhanced PDT effect, which allows the inhibition of cellular migration in vitro and tumor growth in vivo. Owing to high stability, targetability, and biosafety, the proposed CSC can recruit various cargos from small dyes to large biomacromolecules (up to 430 kDa), providing promising theranostic applications.

A pH-Dependent Phase Separation Drives Polyamine-Mediated Silicification from Undersaturated Solutions

Silica polymerization from its soluble monomers is fundamental to many chemical processes. Although industrial methods require harsh conditions and concentrated precursors, biological silica precipitation occurs under ambient conditions from dilute solutions. The hallmark of biosilica is the presence of amine-rich organic macromolecules, but their functional role remains elusive. Here, we show a pH-dependent stimulatory effect of such polyamines on silica polymerization. Notably, this process is decoupled from the saturation degree, allowing the synthesis of polymer-silica hybrid products with controlled network morphologies from undersaturated solutions. The data suggest a two-step phase separation process. First, an associative liquid-liquid phase separation forms a micrometer-size dense phase. Second, silica undergoes a liquid-to-solid transition in the supersaturated condensates to form a bicontinuous silica structure. This study can inspire "soft chemistry" routes to design organic-inorganic nanomaterials with regulatory principles optimized by evolution.

Coacervate Droplets as Biomimetic Models for Designing Cell-Like Microreactors

Coacervates are versatile compartments formed by liquid-liquid phase separation. Their dynamic behavior and molecularly crowded microenvironment make them ideal materials for creating cell-like systems such as synthetic cells and microreactors. Recently, combinations of synthetic and natural molecules have been exploited via simple or complex coacervation to create compartments that can be used to build hierarchical chemical systems with life-like properties. This review highlights recent advances in the design of coacervate compartments and their application as biomimetic compartments for the design of cell-like chemical reactors and cell mimicking systems. It first explores the variety of materials used for coacervation and the influence of their chemical structure on their controlled dynamic behavior. Then, the applications of coacervates as cell-like systems are reviewed, focusing on how they can be used as cell-like microreactors through their ability to sequester molecules and provide a distinct and regulatory microenvironment for chemical reactions in aqueous media.

Viral N protein hijacks deaminase-containing RNA granules to enhance SARS-CoV-2 mutagenesis

Host cell-encoded deaminases act as antiviral restriction factors to impair viral replication and production through introducing mutations in the viral genome. We sought to understand whether deaminases are involved in SARS-CoV-2 mutation and replication, and how the viral factors interact with deaminases to trigger these processes. Here, we show that APOBEC and ADAR deaminases act as the driving forces for SARS-CoV-2 mutagenesis, thereby blocking viral infection and production. Mechanistically, SARS-CoV-2 nucleocapsid (N) protein, which is responsible for packaging viral genomic RNA, interacts with host deaminases and co-localizes with them at stress granules to facilitate viral RNA mutagenesis. N proteins from several coronaviruses interact with host deaminases at RNA granules in a manner dependent on its F17 residue, suggesting a conserved role in modulation of viral mutagenesis in other coronaviruses. Furthermore, mutant N protein bearing a F17A substitution cannot localize to deaminase-containing RNA granules and leads to reduced mutagenesis of viral RNA, providing support for its function in enhancing deaminase-dependent viral RNA editing. Our study thus provides further insight into virus-host cell interactions mediating SARS-CoV-2 evolution.

RNA-driven phase transitions in biomolecular condensates

RNAs and RNA-binding proteins can undergo spontaneous or active condensation into phase-separated liquid-like droplets. These condensates are cellular hubs for various physiological processes, and their dysregulation leads to diseases. Although RNAs are core components of many cellular condensates, the underlying molecular determinants for the formation, regulation, and function of ribonucleoprotein condensates have largely been studied from a protein-centric perspective. Here, we highlight recent developments in ribonucleoprotein condensate biology with a particular emphasis on RNA-driven phase transitions. We also present emerging future directions that might shed light on the role of RNA condensates in spatiotemporal regulation of cellular processes and inspire bioengineering of RNA-based therapeutics.

Stem Life: A Framework for Understanding the Prebiotic-Biotic Transition

Abiogenesis is frequently envisioned as a linear, ladder-like progression of increasingly complex chemical systems, eventually leading to the ancestors of extant cellular life. This "pre-cladistics" view is in stark contrast to the well-accepted principles of organismal evolutionary biology, as informed by paleontology and phylogenetics. Applying this perspective to origins, I explore the paradigm of "Stem Life," which embeds abiogenesis within a broader continuity of diversification and extinction of both hereditary lineages and chemical systems. In this new paradigm, extant life's ancestral lineage emerged alongside and was dependent upon many other complex prebiotic chemical systems, as part of a diverse and fecund prebiosphere. Drawing from several natural history analogies, I show how this shift in perspective enriches our understanding of Origins and directly informs debates on defining Life, the emergence of the Last Universal Common Ancestor (LUCA), and the implications of prebiotic chemical experiments.

The molecular picture of the local environment in a stable model coacervate

Complex coacervates play essential roles in various biological processes and applications. Although substantial progress has been made in understanding the molecular interactions driving complex coacervation, the mechanisms stabilizing coacervates against coalescence remain experimentally challenging and not fully elucidated. We recently showed that polydiallyldimethylammonium chloride (PDDA) and adenosine triphosphate (ATP) coacervates stabilize upon their transfer to deionized (DI) water. Here, we perform molecular dynamics simulations of PDDA-ATP coacervates in supernatant and DI water, to understand the ion dynamics and structure within stable coacervates. We found that transferring the coacervates to DI water results in an immediate ejection of a significant fraction of small ions (Na+ and Cl-) from the surface of the coacervates to DI water. We also observed a notable reduction in the mobility of these counterions in coacervates when in DI water, both in the cluster-forming and slab simulations, together with a lowered displacement of PDDA and ATP. These results suggest that the initial ejection of the ions from the coacervates in DI water may induce an interfacial skin layer formation, inhibiting further mobility of ions in the skin layer.

Peptide-Based Biomimetic Condensates via Liquid-Liquid Phase Separation as Biomedical Delivery Vehicles

Biomolecular condensates are dynamic liquid droplets through intracellular liquid-liquid phase separation that function as membraneless organelles, which are highly involved in various complex cellular processes and functions. Artificial analogs formed via similar pathways that can be integrated with biological complexity and advanced functions have received tremendous research interest in the field of synthetic biology. The coacervate droplet-based compartments can partition and concentrate a wide range of solutes, which are regarded as attractive candidates for mimicking phase-separation behaviors and biophysical features of biomolecular condensates. The use of peptide-based materials as phase-separating components has advantages such as the diversity of amino acid residues and customized sequence design, which allows for programming their phase-separation behaviors and the physicochemical properties of the resulting compartments. In this Perspective, we highlight the recent advancements in the design and construction of biomimicry condensates from synthetic peptides relevant to intracellular phase-separating protein, with specific reference to their molecular design, self-assembly via phase separation, and biorelated applications, to envisage the use of peptide-based droplets as emerging biomedical delivery vehicles.

Continuous Transformation from Membrane-Less Coacervates to Membranized Coacervates and Giant Vesicles: Toward Multicompartmental Protocells with Complex (Membrane) Architectures

The membranization of membrane-less coacervates paves the way for the exploitation of complex protocells with regard to structural and cell-like functional behaviors. However, the controlled transformation from membranized coacervates to vesicles remains a challenge. This can provide stable (multi)phase and (multi)compartmental architectures through the reconfiguration of coacervate droplets in the presence of (bioactive) polymers, bio(macro)molecules and/or nanoobjects. Herein, we present a continuous protocell transformation from membrane-less coacervates to membranized coacervates and, ultimately, to giant hybrid vesicles. This transformation process is orchestrated by altering the balance of non-covalent interactions through varying concentrations of an anionic terpolymer, leading to dynamic processes such as spontaneous membranization of terpolymer nanoparticles at the coacervate surface, disassembly of the coacervate phase mediated by the excess anionic charge, and the redistribution of coacervate components in membrane. The diverse protocells during the transformation course provide distinct structural features and molecular permeability. Notably, the introduction of multiphase coacervates in this continuous transformation process signifies advancements toward the creation of synthetic cells with different diffusible compartments. Our findings emphasize the highly controlled continuous structural reorganization of coacervate protocells and represents a novel step toward the development of advanced and sophisticated synthetic protocells with more precise compositions and complex (membrane) structures.

Protocell Effects on RNA Folding, Function, and Evolution

Creating a living system from nonliving matter is a great challenge in chemistry and biophysics. The early history of life can provide inspiration from the idea of the prebiotic "RNA World" established by ribozymes, in which all genetic and catalytic activities were executed by RNA. Such a system could be much simpler than the interdependent central dogma characterizing life today. At the same time, cooperative systems require a mechanism such as cellular compartmentalization in order to survive and evolve. Minimal cells might therefore consist of simple vesicles enclosing a prebiotic RNA metabolism. The internal volume of a vesicle is a distinctive environment due to its closed boundary, which alters diffusion and available volume for macromolecules and changes effective molecular concentrations, among other considerations. These physical effects are mechanistically distinct from chemical interactions, such as electrostatic repulsion, that might also occur between the membrane boundary and encapsulated contents. Both indirect and direct interactions between the membrane and RNA can give rise to nonintuitive, "emergent" behaviors in the model protocell system. We have been examining how encapsulation inside membrane vesicles would affect the folding and activity of entrapped RNA. Using biophysical techniques such as FRET, we characterized ribozyme folding and activity inside vesicles. Encapsulation inside model protocells generally promoted RNA folding, consistent with an excluded volume effect, independently of chemical interactions. This energetic stabilization translated into increased ribozyme activity in two different systems that were studied (hairpin ribozyme and self-aminoacylating RNAs). A particularly intriguing finding was that encapsulation could rescue the activity of mutant ribozymes, suggesting that encapsulation could affect not only folding and activity but also evolution. To study this further, we developed a high-throughput sequencing assay to measure the aminoacylation kinetics of many thousands of ribozyme variants in parallel. The results revealed an unexpected tendency for encapsulation to improve the better ribozyme variants more than worse variants. During evolution, this effect would create a tilted playing field, so to speak, that would give additional fitness gains to already-high-activity variants. According to Fisher's Fundamental Theorem of Natural Selection, the increased variance in fitness should manifest as faster evolutionary adaptation. This prediction was borne out experimentally during in vitro evolution, where we observed that the initially diverse ribozyme population converged more quickly to the most active sequences when they were encapsulated inside vesicles. The studies in this Account have expanded our understanding of emergent protocell behavior, by showing how simply entrapping an RNA inside a vesicle, which could occur spontaneously during vesicle formation, might profoundly affect the evolutionary landscape of the RNA. Because of the exponential dynamics of replication and selection, even small changes to activity and function could lead to major evolutionary consequences. By closely studying the details of minimal yet surprisingly complex protocells, we might one day trace a pathway from encapsulated RNA to a living system.

Reactions Driven by Primitive Nonbiological Polyesters

All life on Earth is composed of cells, which are built from and run by biological reactions and structures. These reactions and structures are generally the result of action by cellular biomolecules, which are indispensable for the function and survival of all living organisms. Specifically, biological catalysis, namely by protein enzymes, but also by other biomolecules including nucleic acids, is an essential component of life. How the biomolecules themselves that perform biological catalysis came to exist in the first place is a major unanswered question that plagues researchers to this day, which is generally the focus of the origins of life (OoL) research field. Based on current knowledge, it is generally postulated that early Earth was full of a myriad of different chemicals, and that these chemicals reacted in specific ways that led to the emergence of biochemistry, cells, and later, life. In particular, a significant part of OoL research focuses on the synthesis, evolution, and function of biomolecules potentially present under early Earth conditions, as a way to understand their eventual transition into modern life. However, this narrative overlooks possibilities that other molecules contributed to the OoL, as while biomolecules that led to life were certainly present on early Earth, at the same time, other molecules that may not have strict, direct biological lineage were also widely and abundantly present. For example, hydroxy acids, although playing a role in metabolism or as parts of certain biological structures, are not generally considered to be as essential to modern biology as amino acids (a chemically similar monomer), and thus research in the OoL field tends to perhaps focus more on amino acids than hydroxy acids. However, their likely abundance on early Earth coupled with their ability to spontaneously condense into polymers (i.e., polyesters) make hydroxy acids, and their subsequent products, functions, and reactions, a reasonable target of investigation for prebiotic chemists. Whether "non-biological" hydroxy acids or polyesters can contribute to the emergence of life on early Earth is an inquiry that deserves attention within the OoL community, as this knowledge can also contribute to our understanding of the plausibility of extraterrestrial life that does not exactly use the biochemical set found in terrestrial organisms. While some demonstrations have been made with respect to compartment assembly, compartmentalization, and growth of primitive polyester-based systems, whether these "non-biological" polymers can contribute any catalytic function and/or drive primitive reactions is still an important step toward the development of early life. Here, we review research both from the OoL field as well as from industry and applied sciences regarding potential catalysis or reaction driven by "non-biological" polyesters in various forms: as linear polymers, as hyperbranched polyesters, and as membraneless microdroplets.

Sequence programmable nucleic acid coacervates

Nature uses bottom-up self-assembly to build structures with remarkable complexity and functionality. Understanding how molecular-scale interactions translate to macroscopic properties remains a major challenge and requires systems that effectively bridge these two scales. Here, we generate DNA and RNA liquids with exquisite programmability in their material properties. Nucleic acids are negatively charged, and in the presence of polycations, they may condense to a liquid-like state. Within these liquids, DNA and RNA retain sequence-specific hybridization abilities. We show that intermolecular hybridization in the condensed phase cross-links molecules and slows down chain dynamics. This reduced chain mobility is mirrored in the macroscopic properties of the condensates. Molecular diffusivity and material viscosity scale with the intermolecular hybridization energy, enabling precise sequence-based modulation of condensate properties over orders of magnitude. Our work offers a robust platform to create self-assembling programmable fluids and may help advance our understanding of liquid-like compartments in cells.

How Droplets Can Accelerate Reactions─Coacervate Protocells as Catalytic Microcompartments

Coacervates are droplets formed by liquid-liquid phase separation (LLPS) and are often used as model protocells-primitive cell-like compartments that could have aided the emergence of life. Their continued presence as membraneless organelles in modern cells gives further credit to their relevance. The local physicochemical environment inside coacervates is distinctly different from the surrounding dilute solution and offers an interesting microenvironment for prebiotic reactions. Coacervates can selectively take up reactants and enhance their effective concentration, stabilize products, destabilize reactants and lower transition states, and can therefore play a similar role as micellar catalysts in providing rate enhancement and selectivity in reaction outcome. Rate enhancement and selectivity must have been essential for the origins of life by enabling chemical reactions to occur at appreciable rates and overcoming competition from hydrolysis. In this Accounts, we dissect the mechanisms by which coacervate protocells can accelerate reactions and provide selectivity. These mechanisms can similarly be exploited by membraneless organelles to control cellular processes. First, coacervates can affect the local concentration of reactants and accelerate reactions by copartitioning of reactants or exclusion of a product or inhibitor. Second, the local environment inside the coacervate can change the energy landscape for reactions taking place inside the droplets. The coacervate is more apolar than the surrounding solution and often rich in charged moieties, which can affect the stability of reactants, transition states and products. The crowded nature of the droplets can favor complexation of large molecules such as ribozymes. Their locally different proton and water activity can facilitate reactions involving a (de)protonation step, condensation reactions and reactions that are sensitive to hydrolysis. Not only the coacervate core, but also the surface can accelerate reactions and provides an interesting site for chemical reactions with gradients in pH, water activity and charge. The coacervate is often rich in catalytic amino acids and can localize catalysts like divalent metal ions, leading to further rate enhancement inside the droplets. Lastly, these coacervate properties can favor certain reaction pathways, and thereby give selectivity over the reaction outcome. These mechanisms are further illustrated with a case study on ribozyme reactions inside coacervates, for which there is a fine balance between concentration and reactivity that can be tuned by the coacervate composition. Furthermore, coacervates can both catalyze ribozyme reactions and provide product selectivity, demonstrating that coacervates could have functioned as enzyme-like catalytic microcompartments at the origins of life.

Reaction-Driven Diffusiophoresis of Liquid Condensates: Potential Mechanisms for Intracellular Organization

The cellular environment, characterized by its intricate composition and spatial organization, hosts a variety of organelles, ranging from membrane-bound ones to membraneless structures that are formed through liquid-liquid phase separation. Cells show precise control over the position of such condensates. We demonstrate that organelle movement in external concentration gradients, diffusiophoresis, is distinct from the one of colloids because fluxes can remain finite inside the liquid-phase droplets and movement of the latter arises from incompressibility. Within cellular domains diffusiophoresis naturally arises from biochemical reactions that are driven by a chemical fuel and produce waste. Simulations and analytical arguments within a minimal model of reaction-driven phase separation reveal that the directed movement stems from two contributions: Fuel and waste are refilled or extracted at the boundary, resulting in concentration gradients, which (i) induce product fluxes via incompressibility and (ii) result in an asymmetric forward reaction in the droplet's surroundings (as well as asymmetric backward reaction inside the droplet), thereby shifting the droplet's position. We show that the former contribution dominates and sets the direction of the movement, toward or away from fuel source and waste sink, depending on the product molecules' affinity toward fuel and waste, respectively. The mechanism thus provides a simple means to organize condensates with different composition. Particle-based simulations and systems with more complex reaction cycles corroborate the robustness and universality of this mechanism.

Constrained dynamics of DNA oligonucleotides in phase-separated droplets

Understanding the dynamics of biomolecules in complex environments is crucial for elucidating the effect of condensed and heterogeneous environments on their functional properties. A relevant environment-and one that can also be mimicked easily in vitro-is that of phase-separated droplets. While phase-separated droplet systems have been shown to compartmentalize a wide range of functional biomolecules, the effects of internal structuration of droplets on the dynamics and mobility of internalized molecules remain poorly understood. Here, we use fluorescence correlation spectroscopy to measure the dynamics of short oligonucleotides encapsulated within two representative kinds of uncharged and charged phase-separated droplets. We find that the internal structuration controls the oligonucleotide dynamics in these droplets, revealed by measuring physical parameters at high spatiotemporal resolution. By varying oligonucleotide length and salt concentrations (and thereby charge screening), we found that the dynamics are significantly affected in the noncharged droplets compared to the charged system. Our work lays the foundation for unraveling and quantifying the physical parameters governing biomolecular transport in the condensed environment.

DNA-empowered synthetic cells as minimalistic life forms

Cells, the fundamental units of life, orchestrate intricate functions - motility, adaptation, replication, communication, and self-organization within tissues. Originating from spatiotemporally organized structures and machinery, coupled with information processing in signalling networks, cells embody the 'sensor-processor-actuator' paradigm. Can we glean insights from these processes to construct primitive artificial systems with life-like properties? Using de novo design approaches, what can we uncover about the evolutionary path of life? This Review discusses the strides made in crafting synthetic cells, utilizing the powerful toolbox of structural and dynamic DNA nanoscience. We describe how DNA can serve as a versatile tool for engineering entire synthetic cells or subcellular entities, and how DNA enables complex behaviour, including motility and information processing for adaptive and interactive processes. We chart future directions for DNA-empowered synthetic cells, envisioning interactive systems wherein synthetic cells communicate within communities and with living cells.

Nucleic acid liquids

The confluence of recent discoveries of the roles of biomolecular liquids in living systems and modern abilities to precisely synthesize and modify nucleic acids (NAs) has led to a surge of interest in liquid phases of NAs. These phases can be formed primarily from NAs, as driven by base-pairing interactions, or from the electrostatic combination (coacervation) of negatively charged NAs and positively charged molecules. Generally, the use of sequence-engineered NAs provides the means to tune microsopic particle properties, and thus imbue specific, customizable behaviors into the resulting liquids. In this way, researchers have used NA liquids to tackle fundamental problems in the physics of finite valence soft materials, and to create liquids with novel structured and/or multi-functional properties. Here, we review this growing field, discussing the theoretical background of NA liquid phase separation, quantitative understanding of liquid material properties, and the broad and growing array of functional demonstrations in these materials. We close with a few comments discussing remaining open questions and challenges in the field.

Self-assembly of stabilized droplets from liquid-liquid phase separation for higher-order structures and functions

Dynamic microscale droplets produced by liquid-liquid phase separation (LLPS) have emerged as appealing biomaterials due to their remarkable features. However, the instability of droplets limits the construction of population-level structures with collective behaviors. Here we first provide a brief background of droplets in the context of materials properties. Subsequently, we discuss current strategies for stabilizing droplets including physical separation and chemical modulation. We also discuss the recent development of LLPS droplets for various applications such as synthetic cells and biomedical materials. Finally, we give insights on how stabilized droplets can self-assemble into higher-order structures displaying coordinated functions to fully exploit their potentials in bottom-up synthetic biology and biomedical applications.

Phase-separated biomolecular condensates for biocatalysis

Nature often uses dynamically assembling multienzymatic complexes called metabolons to achieve spatiotemporal control of complex metabolic reactions. Researchers are aiming to mimic this strategy of organizing enzymes to enhance the performance of artificial biocatalytic systems. Biomolecular condensates formed through liquid-liquid phase separation (LLPS) can serve as a powerful tool to drive controlled assembly of enzymes. Diverse enzymatic pathways have been reconstituted within catalytic condensates in vitro as well as synthetic membraneless organelles in living cells. Furthermore, in vivo condensates have been engineered to regulate metabolic pathways by selectively sequestering enzymes. Thus, harnessing LLPS for controlled organization of enzymes provides an opportunity to dynamically regulate biocatalytic processes.

Chapter 9: Life as We Don't Know It

While Earth contains the only known example of life in the universe, it is possible that life elsewhere is fundamentally different from what we are familiar with. There is an increased recognition in the astrobiology community that the search for life should steer away from terran-specific biosignatures to those that are more inclusive to all life-forms. To start exploring the space of possibilities that life could occupy, we can try to dissociate life from the chemistry that composes it on Earth by envisioning how different life elsewhere could be in composition, lifestyle, medium, and form, and by exploring how the general principles that govern living systems on Earth might be found in different forms and environments across the Solar System. Exotic life-forms could exist on Mars or Venus, or icy moons like Europa and Enceladus, or even as a shadow biosphere on Earth. New perspectives on agnostic biosignature detection have also begun to emerge, allowing for a broader and more inclusive approach to seeking exotic life with unknown chemistry that is distinct from life as we know it on Earth.

RNA Condensate as a Versatile Platform for Improving Fluorogenic RNA Aptamer Properties and Cell Imaging

Fluorogenic RNA aptamers are valuable tools for cell imaging, but they still suffer from shortcomings such as easy degradation, limited photostability, and low fluorescence enhancement. Molecular crowding conditions enable the stabilization of the structure, promotion of folding, and improvement of activity of functional RNA. Based on artificial RNA condensates, here we present a versatile platform to improve fluorogenic RNA aptamer properties and develop sensors for target analyte imaging in living cells. Using the CUG repeat as a general tag to drive phase separation, various fluorogenic aptamer-based RNA condensates (FLARE) were prepared. We show that the molecular crowding of FLARE can improve the enzymatic resistance, thermostability, photostability, and binding affinity of fluorogenic RNA aptamers. Moreover, the FLARE systems can be modularly engineered into sensors (FLARES), which demonstrate enhanced brightness and sensitivity compared to free sensors dispersed in homogeneous solution. This scalable design principle provides new insights into RNA aptamer property regulation and cellular imaging.

Multicompartmental coacervate-based protocell by spontaneous droplet evaporation

Hierarchical compartmentalization, a hallmark of both primitive and modern cells, enables the concentration and isolation of biomolecules, and facilitates spatial organization of biochemical reactions. Coacervate-based compartments can sequester and recruit a large variety of molecules, making it an attractive protocell model. In this work, we report the spontaneous formation of core-shell cell-sized coacervate-based compartments driven by spontaneous evaporation of a sessile droplet on a thin-oil-coated substrate. Our analysis reveals that such far-from-equilibrium architectures arise from multiple, coupled segregative and associative liquid-liquid phase separation, and are stabilized by stagnation points within the evaporating droplet. The formation of stagnation points results from convective capillary flows induced by the maximum evaporation rate at the liquid-liquid-air contact line. This work provides valuable insights into the spontaneous formation and maintenance of hierarchical compartments under non-equilibrium conditions, offering a glimpse into the real-life scenario.

Superstructural ordering in self-sorting coacervate-based protocell networks

Bottom-up assembly of higher-order cytomimetic systems capable of coordinated physical behaviours, collective chemical signalling and spatially integrated processing is a key challenge in the study of artificial multicellularity. Here we develop an interactive binary population of coacervate microdroplets that spontaneously self-sort into chain-like protocell networks with an alternating sequence of structurally and compositionally dissimilar microdomains with hemispherical contact points. The protocell superstructures exhibit macromolecular self-sorting, spatially localized enzyme/ribozyme biocatalysis and interdroplet molecular translocation. They are capable of topographical reconfiguration using chemical or light-mediated stimuli and can be used as a micro-extraction system for macroscale biomolecular sorting. Our methodology opens a pathway towards the self-assembly of multicomponent protocell networks based on selective processes of coacervate droplet-droplet adhesion and fusion, and provides a step towards the spontaneous orchestration of protocell models into artificial tissues and colonies with ordered architectures and collective functions.

Dipeptide coacervates as artificial membraneless organelles for bioorthogonal catalysis

Artificial organelles can manipulate cellular functions and introduce non-biological processes into cells. Coacervate droplets have emerged as a close analog of membraneless cellular organelles. Their biomimetic properties, such as molecular crowding and selective partitioning, make them promising components for designing cell-like materials. However, their use as artificial organelles has been limited by their complex molecular structure, limited control over internal microenvironment properties, and inherent colloidal instability. Here we report the design of dipeptide coacervates that exhibit enhanced stability, biocompatibility, and a hydrophobic microenvironment. The hydrophobic character facilitates the encapsulation of hydrophobic species, including transition metal-based catalysts, enhancing their efficiency in aqueous environments. Dipeptide coacervates carrying a metal-based catalyst are incorporated as active artificial organelles in cells and trigger an internal non-biological chemical reaction. The development of coacervates with a hydrophobic microenvironment opens an alternative avenue in the field of biomimetic materials with applications in catalysis and synthetic biology.

The RNA-DNA world and the emergence of DNA-encoded heritable traits

The RNA world hypothesis confers a central role to RNA molecules in information encoding and catalysis. Even though evidence in support of this hypothesis has accumulated from both experiments and computational modelling, the transition from an RNA world to a world where heritable genetic information is encoded in DNA remains an open question. Recent experiments show that both RNA and DNA templates can extend complementary primers using free RNA/DNA nucleotides, either non-enzymatically or in the presence of a replicase ribozyme. Guided by these experiments, we analyse protocellular evolution with an expanded set of reaction pathways made possible through the presence of DNA nucleotides. By encapsulating these reactions inside three different types of protocellular compartments, each subject to distinct modes of selection, we show how protocells containing DNA-encoded replicases in low copy numbers and replicases in high copy numbers can dominate the population. This is facilitated by a reaction that leads to auto-catalytic synthesis of replicase ribozymes from DNA templates encoding the replicase after the chance emergence of a replicase through non-enzymatic reactions. Our work unveils a pathway for the transition from an RNA world to a mixed RNA-DNA world characterized by Darwinian evolution, where DNA sequences encode heritable phenotypes.

Leveraging liquid-liquid phase separation and volume modulation to regulate the enzymatic activity of formate dehydrogenase

Engineering of reaction media is an exciting alternative for modulating kinetic properties of biocatalytic reactions. We addressed the combined effect of an aqueous two-phase system (ATPS) and high hydrostatic pressure on the kinetics of the Candida boidinii formate dehydrogenase-catalyzed oxidation of formate to CO2. Pressurization was found to lead to an increase of the binding affinity (decrease of KM, respectively) and a decrease of the turnover number, kcat. The experimental approach was supported using thermodynamic modeling with the electrolyte Perturbed-Chain Statistical Associating Fluid Theory (ePC-SAFT) equation of state to predict the liquid-liquid phase separation and the molecular crowding effect of the ATPS on the kinetic properties. The ePC-SAFT was able to quantitatively predict the KM-values of the substrate in both phases at 1 bar as well as up to a pressure of 1000 bar. The framework presented enables significant advances in bioprocess engineering, including the design of processes with significantly fewer experiments and trial-and-error approaches.

Selective amide bond formation in redox-active coacervate protocells

Coacervate droplets are promising protocell models because they sequester a wide range of guest molecules and may catalyze their conversion. However, it remains unclear how life's building blocks, including peptides, could be synthesized from primitive precursor molecules inside such protocells. Here, we develop a redox-active protocell model formed by phase separation of prebiotically relevant ferricyanide (Fe(CN)63-) molecules and cationic peptides. Their assembly into coacervates can be regulated by redox chemistry and the coacervates act as oxidizing hubs for sequestered metabolites, like NAD(P)H and gluthathione. Interestingly, the oxidizing potential of Fe(CN)63- inside coacervates can be harnessed to drive the formation of new amide bonds between prebiotically relevant amino acids and α-amidothioacids. Aminoacylation is enhanced in Fe(CN)63-/peptide coacervates and selective for amino acids that interact less strongly with the coacervates. We finally use Fe(CN)63--containing coacervates to spatially control assembly of fibrous networks inside and at the surface of coacervate protocells. These results provide an important step towards the prebiotically relevant integration of redox chemistry in primitive cell-like compartments.

Construction of Membraneless and Multicompartmentalized Coacervate Protocells Controlling a Cell Metabolism-like Cascade Reaction

In recent years, there has been growing attention to designing synthetic protocells, capable of mimicking micrometric and multicompartmental structures and highly complex physicochemical and biological processes with spatiotemporal control. Controlling metabolism-like cascade reactions in coacervate protocells is still challenging since signal transduction has to be involved in sequential and parallelized actions mediated by a pH change. Herein, we report the hierarchical construction of membraneless and multicompartmentalized protocells composed of (i) a cytosol-like scaffold based on complex coacervate droplets stable under flow conditions, (ii) enzyme-active artificial organelles and a substrate nanoreservoir capable of triggering a cascade reaction between them in response to a pH increase, and (iii) a signal transduction component based on the urease enzyme capable of the conversion of an exogenous biological fuel (urea) into an endogenous signal (ammonia and pH increase). Overall, this strategy allows a synergistic communication between their components within the membraneless and multicompartment protocells and, thus, metabolism-like enzymatic cascade reactions. This signal communication is transmitted through a scaffold protocell from an "inactive state" (nonfluorescent protocell) to an "active state" (fluorescent protocell capable of consuming stored metabolites).

RNAs undergo phase transitions with lower critical solution temperatures

Co-phase separation of RNAs and RNA-binding proteins drives the biogenesis of ribonucleoprotein granules. RNAs can also undergo phase transitions in the absence of proteins. However, the physicochemical driving forces of protein-free, RNA-driven phase transitions remain unclear. Here we report that various types of RNA undergo phase separation with system-specific lower critical solution temperatures. This entropically driven phase separation is an intrinsic feature of the phosphate backbone that requires Mg2+ ions and is modulated by RNA bases. RNA-only condensates can additionally undergo enthalpically favourable percolation transitions within dense phases. This is enabled by a combination of Mg2+-dependent bridging interactions between phosphate groups and RNA-specific base stacking and base pairing. Phase separation coupled to percolation can cause dynamic arrest of RNAs within condensates and suppress the catalytic activity of an RNase P ribozyme. Our work highlights the need to incorporate RNA-driven phase transitions into models for ribonucleoprotein granule biogenesis.

Coacervate Droplets for Synthetic Cells

The design and construction of synthetic cells - human-made microcompartments that mimic features of living cells - have experienced a real boom in the past decade. While many efforts have been geared toward assembling membrane-bounded compartments, coacervate droplets produced by liquid-liquid phase separation have emerged as an alternative membrane-free compartmentalization paradigm. Here, the dual role of coacervate droplets in synthetic cell research is discussed: encapsulated within membrane-enclosed compartments, coacervates act as surrogates of membraneless organelles ubiquitously found in living cells; alternatively, they can be viewed as crowded cytosol-like chassis for constructing integrated synthetic cells. After introducing key concepts of coacervation and illustrating the chemical diversity of coacervate systems, their physicochemical properties and resulting bioinspired functions are emphasized. Moving from suspensions of free floating coacervates, the two nascent roles of these droplets in synthetic cell research are highlighted: organelle-like modules and cytosol-like templates. Building the discussion on recent studies from the literature, the potential of coacervate droplets to assemble integrated synthetic cells capable of multiple life-inspired functions is showcased. Future challenges that are still to be tackled in the field are finally discussed.

Epistemology of synthetic biology: a new theoretical framework based on its potential objects and objectives

Synthetic biology is a new research field which attempts to understand, modify, and create new biological entities by adopting a modular and systemic conception of the living organisms. The development of synthetic biology has generated a pluralism of different approaches, bringing together a set of heterogeneous practices and conceptualizations from various disciplines, which can lead to confusion within the synthetic biology community as well as with other biological disciplines. I present in this manuscript an epistemological analysis of synthetic biology in order to better define this new discipline in terms of objects of study and specific objectives. First, I present and analyze the principal research projects developed at the foundation of synthetic biology, in order to establish an overview of the practices in this new emerging discipline. Then, I analyze an important scientometric study on synthetic biology to complete this overview. Afterwards, considering this analysis, I suggest a three-level classification of the object of study for synthetic biology (which are different kinds of living entities that can be built in the laboratory), based on three successive criteria: structural hierarchy, structural origin, functional origin. Finally, I propose three successively linked objectives in which synthetic biology can contribute (where the achievement of one objective led to the development of the other): interdisciplinarity collaboration (between natural, artificial, and theoretical sciences), knowledge of natural living entities (past, present, future, and alternative), pragmatic definition of the concept of "living" (that can be used by biologists in different contexts). Considering this new theoretical framework, based on its potential objects and objectives, I take the position that synthetic biology has not only the potential to develop its own new approach (which includes methods, objects, and objectives), distinct from other subdisciplines in biology, but also the ability to develop new knowledge on living entities.

Understanding the Impacts of Molecular and Macromolecular Crowding Agents on Protein-Polymer Complex Coacervates

Complex coacervation refers to the liquid-liquid phase separation (LLPS) process occurring between charged macromolecules. The study of complex coacervation is of great interest due to its implications in the formation of membraneless organelles (MLOs) in living cells. However, the impacts of the crowded intracellular environment on the behavior and interactions of biomolecules involved in MLO formation are not fully understood. To address this knowledge gap, we investigated the effects of crowding on a model protein-polymer complex coacervate system. Specifically, we examined the influence of sucrose as a molecular crowder and polyethylene glycol (PEG) as a macromolecular crowder. Our results reveal that the presence of crowders led to the formation of larger coacervate droplets that remained stable over a 25-day period. While sucrose had a minimal effect on the physical properties of the coacervates, PEG led to the formation of coacervates with distinct characteristics, including higher density, increased protein and polymer content, and a more compact internal structure. These differences in coacervate properties can be attributed to the effects of crowders on individual macromolecules, such as the conformation of model polymers, and nonspecific interactions among model protein molecules. Moreover, our results show that sucrose and PEG have different partition behaviors: sucrose was present in both the coacervate and dilute phases, while PEG was observed to be excluded from the coacervate phase. Collectively, our findings provide insights into the understanding of crowding effects on complex coacervation, shedding light on the formation and properties of coacervates in the context of MLOs.

Emergent properties of melanin-inspired peptide/RNA condensates

Most biocatalytic processes in eukaryotic cells are regulated by subcellular microenvironments such as membrane-bound or membraneless organelles. These natural compartmentalization systems have inspired the design of synthetic compartments composed of a variety of building blocks. Recently, the emerging field of liquid-liquid phase separation has facilitated the design of biomolecular condensates composed of proteins and nucleic acids, with controllable properties including polarity, diffusivity, surface tension, and encapsulation efficiency. However, utilizing phase-separated condensates as optical sensors has not yet been attempted. Here, we were inspired by the biosynthesis of melanin pigments, a key biocatalytic process that is regulated by compartmentalization in organelles, to design minimalistic biomolecular condensates with emergent optical properties. Melanins are ubiquitous pigment materials with a range of functionalities including photoprotection, coloration, and free radical scavenging activity. Their biosynthesis in the confined melanosomes involves oxidation-polymerization of tyrosine (Tyr), catalyzed by the enzyme tyrosinase. We have now developed condensates that are formed by an interaction between a Tyr-containing peptide and RNA and can serve as both microreactors and substrates for tyrosinase. Importantly, partitioning of Tyr into the condensates and subsequent oxidation-polymerization gives rise to unique optical properties including far-red fluorescence. We now demonstrate that individual condensates can serve as sensors to detect tyrosinase activity, with a limit of detection similar to that of synthetic fluorescent probes. This approach opens opportunities to utilize designer biomolecular condensates as diagnostic tools for various disorders involving abnormal enzymatic activity.

Liquid spherical shells are a non-equilibrium steady state of active droplets

Liquid-liquid phase separation yields spherical droplets that eventually coarsen to one large, stable droplet governed by the principle of minimal free energy. In chemically fueled phase separation, the formation of phase-separating molecules is coupled to a fuel-driven, non-equilibrium reaction cycle. It thus yields dissipative structures sustained by a continuous fuel conversion. Such dissipative structures are ubiquitous in biology but are poorly understood as they are governed by non-equilibrium thermodynamics. Here, we bridge the gap between passive, close-to-equilibrium, and active, dissipative structures with chemically fueled phase separation. We observe that spherical, active droplets can undergo a morphological transition into a liquid, spherical shell. We demonstrate that the mechanism is related to gradients of short-lived droplet material. We characterize how far out of equilibrium the spherical shell state is and the chemical power necessary to sustain it. Our work suggests alternative avenues for assembling complex stable morphologies, which might already be exploited to form membraneless organelles by cells.