Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Non-equilibrium conditions inside rock pores drive fission, maintenance and selection of coacervate protocells.

ABSTRACT: Key requirements for the first cells on Earth include the ability to compartmentalize and evolve. Compartmentalization spatially localizes biomolecules from a dilute pool and an evolving cell, which, as it grows and divides, permits mixing and propagation of information to daughter cells. Complex coacervate microdroplets are excellent candidates as primordial cells with the ability to partition and concentrate molecules into their core and support primitive and complex biochemical reactions. However, the evolution of coacervate protocells by fusion, growth and fission has not yet been demonstrated. In this work, a primordial environment initiated the evolution of coacervate-based protocells. Gas bubbles inside heated rock pores perturb the coacervate protocell distribution and drive the growth, fusion, division and selection of coacervate microdroplets. Our findings provide a compelling scenario for the evolution of membrane-free coacervate microdroplets on the early Earth, induced by common gas bubbles within heated rock pores.

SUBMITTER: Ianeselli A

PROVIDER: S-EPMC8755537 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Non-equilibrium behaviour in coacervate-based protocells under electric-field-induced excitation.

Project description:Although numerous strategies are now available to generate rudimentary forms of synthetic cell-like entities, minimal progress has been made in the sustained excitation of artificial protocells under non-equilibrium conditions. Here we demonstrate that the electric field energization of coacervate microdroplets comprising polylysine and short single strands of DNA generates membrane-free protocells with complex, dynamical behaviours. By confining the droplets within a microfluidic channel and applying a range of electric field strengths, we produce protocells that exhibit repetitive cycles of vacuolarization, dynamical fluctuations in size and shape, chaotic growth and fusion, spontaneous ejection and sequestration of matter, directional capture of solute molecules, and pulsed enhancement of enzyme cascade reactions. Our results highlight new opportunities for the study of non-equilibrium phenomena in synthetic protocells, provide a strategy for inducing complex behaviour in electrostatically assembled soft matter microsystems and illustrate how dynamical properties can be activated and sustained in microcompartmentalized media.

| S-EPMC4756681 | biostudies-literature

Physicochemical Characterization of Polymer-Stabilized Coacervate Protocells.

Project description: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.

| S-EPMC6851677 | biostudies-literature

Catalytic processing in ruthenium-based polyoxometalate coacervate protocells.

Project description:The development of programmable microscale materials with cell-like functions, dynamics and collective behaviour is an important milestone in systems chemistry, soft matter bioengineering and synthetic protobiology. Here, polymer/nucleotide coacervate micro-droplets are reconfigured into membrane-bounded polyoxometalate coacervate vesicles (PCVs) in the presence of a bio-inspired Ru-based polyoxometalate catalyst to produce synzyme protocells (Ru4PCVs) with catalase-like activity. We exploit the synthetic protocells for the implementation of multi-compartmentalized cell-like models capable of collective synzyme-mediated buoyancy, parallel catalytic processing in individual horseradish peroxidase-containing Ru4PCVs, and chemical signalling in distributed or encapsulated multi-catalytic protocell communities. Our results highlight a new type of catalytic micro-compartment with multi-functional activity and provide a step towards the development of protocell reaction networks.

| S-EPMC6941959 | biostudies-literature

Compartmentalised RNA catalysis in membrane-free coacervate protocells.

Project description:Phase separation of mixtures of oppositely charged polymers provides a simple and direct route to compartmentalisation via complex coacervation, which may have been important for driving primitive reactions as part of the RNA world hypothesis. However, to date, RNA catalysis has not been reconciled with coacervation. Here we demonstrate that RNA catalysis is viable within coacervate microdroplets and further show that these membrane-free droplets can selectively retain longer length RNAs while permitting transfer of lower molecular weight oligonucleotides.

| S-EPMC6128941 | biostudies-literature

Construction of coacervate-in-coacervate multi-compartment protocells for spatial organization of enzymatic reactions.

Project description:Coacervate microdroplets, formed via liquid-liquid phase separation, have been extensively explored as a compartment model for the construction of artificial cells or organelles. In this study, coacervate-in-coacervate multi-compartment protocells were constructed using four polyelectrolytes, in which carboxymethyl-dextran and diethylaminoethyl-dextran were deposited on the surface of as-prepared polydiallyldimethyl ammonium/deoxyribonucleic acid coacervate microdroplets through layer-by-layer assembly. The resulting multi-compartment protocells were composed from two immiscible coacervate phases with distinct physical and chemical properties. Molecule transport experiments indicated that small molecules could diffuse between two coacervate phases and that macromolecular enzymes could be retained. Furthermore, a competitive cascade enzymatic reaction of glucose oxidase/horseradish peroxidase-catalase was performed in the multi-compartment protocells. The different enzyme organization and productions of H2O2 led to a distinct polymerization of dopamine. The spatial organization of different enzymes in immiscible coacervate phases, the distinct reaction fluxes between coacervate phases, and the enzymatic cascade network led to distinguishable signal generation and product outputs. The development of this multi-compartment structure could pave the way toward the spatial organization of multi-enzyme cascades and provide new ideas for the design of organelle-containing artificial cells.

| S-EPMC8163383 | biostudies-literature

Self-transformation and structural reconfiguration in coacervate-based protocells.

Project description:A functionalized small-molecule dipeptide capable of structural adaptation is used to prepare coacervate-based protocells that exhibit a pH-triggered process of self-transformation and structural reconfiguration. Polymer-dipeptide coacervate micro-droplets are prepared at pH 8.5 from aqueous mixtures of poly(diallyldimethylammonium chloride) and deprotonated N-(fluorenyl-9-methoxycarbonyl)-d-Ala-d-Ala, and transform into discrete aster-like micro-architectures by controlled lowering of the pH to 4.5. Reconfiguration of the micro-droplets results in entanglement and formation of an interpenetrating fibrous network that subsequently develops into a polymer-containing dipeptide hydrogel. Our results provide a step towards the assembly of synthetic protocells exhibiting rudimentary aspects of metamorphosis, and should offer a new approach to the design and construction of soft reconfigurable chemical micro-ensembles.

| S-EPMC6024302 | biostudies-other

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

Project description: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.

| S-EPMC6618027 | biostudies-literature

Programmed spatial organization of biomacromolecules into discrete, coacervate-based protocells.

Project description:The cell cytosol is crowded with high concentrations of many different biomacromolecules, which is difficult to mimic in bottom-up synthetic cell research and limits the functionality of existing protocellular platforms. There is thus a clear need for a general, biocompatible, and accessible tool to more accurately emulate this environment. Herein, we describe the development of a discrete, membrane-bound coacervate-based protocellular platform that utilizes the well-known binding motif between Ni2+-nitrilotriacetic acid and His-tagged proteins to exercise a high level of control over the loading of biologically relevant macromolecules. This platform can accrete proteins in a controlled, efficient, and benign manner, culminating in the enhancement of an encapsulated two-enzyme cascade and protease-mediated cargo secretion, highlighting the potency of this methodology. This versatile approach for programmed spatial organization of biologically relevant proteins expands the protocellular toolbox, and paves the way for the development of the next generation of complex yet well-regulated synthetic cells.

| S-EPMC7722712 | biostudies-literature

Active coacervate droplets as a model for membraneless organelles and protocells.

Project description:Membraneless organelles like stress granules are active liquid-liquid phase-separated droplets that are involved in many intracellular processes. Their active and dynamic behavior is often regulated by ATP-dependent reactions. However, how exactly membraneless organelles control their dynamic composition remains poorly understood. Herein, we present a model for membraneless organelles based on RNA-containing active coacervate droplets regulated by a fuel-driven reaction cycle. These droplets emerge when fuel is present, but decay without. Moreover, we find these droplets can transiently up-concentrate functional RNA which remains in its active folded state inside the droplets. Finally, we show that in their pathway towards decay, these droplets break apart in multiple droplet fragments. Emergence, decay, rapid exchange of building blocks, and functionality are all hallmarks of membrane-less organelles, and we believe that our work could be powerful as a model to study such organelles.

| S-EPMC7560875 | biostudies-literature

Active coacervate droplets are protocells that grow and resist Ostwald ripening.

Project description:Active coacervate droplets are liquid condensates coupled to a chemical reaction that turns over their components, keeping the droplets out of equilibrium. This turnover can be used to drive active processes such as growth, and provide an insight into the chemical requirements underlying (proto)cellular behaviour. Moreover, controlled growth is a key requirement to achieve population fitness and survival. Here we present a minimal, nucleotide-based coacervate model for active droplets, and report three key findings that make these droplets into evolvable protocells. First, we show that coacervate droplets form and grow by the fuel-driven synthesis of new coacervate material. Second, we find that these droplets do not undergo Ostwald ripening, which we attribute to the attractive electrostatic interactions and translational entropy within complex coacervates, active or passive. Finally, we show that the droplet growth rate reflects experimental conditions such as substrate, enzyme and protein concentration, and that a different droplet composition (addition of RNA) leads to altered growth rates and droplet fitness. These findings together make active coacervate droplets a powerful platform to mimic cellular growth at a single-droplet level, and to study fitness at a population level.

| S-EPMC8217494 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data