Elucidating the Membrane Dynamics and Encapsulation Mechanism of Large DNA Molecules Under Molecular Crowding Conditions Using Giant Unilamellar Vesicles

Resilient Membranized Coacervates Formed through Spontaneous Wrapping of Heat-Destabilized Lipid Bilayers around Coacervate Droplets

Membranes and the membraneless biocondensates help organize cells and work synergistically to drive cellular processes. Separately, membrane-bound and membraneless compartments face difficulties as stable protocells or synthetic cell systems. Here, we present a new method to create membranized coacervates (MCs) for coacervates with any surface charge and a wide range of phospholipid membrane compositions. MCs are formed when liposomes, destabilized using heat and divalent ions, are mixed with coacervate dispersions. Unlike previous reports of hybrid coacervates surrounded by membranes, the MC membranes form an effective barrier also against small molecules, including calcein and TAMRA. The MC membranes provide excellent stability to the protocells at pH 2-10, salt concentrations of up to 0.5 м, hypotonic and hypertonic conditions, and repeated freeze-thaw cycles. MCs performed better in all the tested conditions than both coacervates and liposomes. We attribute this behavior to the increased stability that coacervates and liposomes confer to each other when together. MC membranes are unilamellar and fluid, allowing lateral lipid diffusion, and the lipids are more densely packed compared to their corresponding liposomes. MCs can help us understand how stable primitive cells might have emerged and build advanced synthetic cells with enhanced stability and selectivity.

Self-growing protocell models in aqueous two-phase system induced by internal DNA replication reaction

The bottom-up reconstitution of self-growing artificial cells is a critical milestone toward realizing autonomy and evolvability. However, building artificial cells that exhibit self-growth coupled with internal replication of gene-encoding DNA has not been achieved yet. Here, we report self-growing artificial cell models based on dextran-rich droplets in an aqueous two-phase system of poly(ethylene glycol) (PEG) and dextran (DEX). Motivated by the finding that DNA induces the generation of DEX-rich droplets, we integrate DNA amplification system with DEX-rich droplets, which exhibited active self-growth. We implement the protocells with cell-free transcription-translation systems coupled with DNA amplification/replication, which also show active self-growth. Considering the simplicities in terms of the chemical composition and the mechanism, these results underscore the potential of DEX droplets as a foundational platform for engineering protocells, giving implications for the emergence of protocells under prebiotic conditions.

Quest for space: Tenacity of DNA, Protein, and Lipid macromolecules in intracellular crowded environment

The biochemical processes in the cellular milieu involving biomacromolecular interaction usually occur in crowded and heterogeneous environments, impacting their structure, stability, and reactivity. The crowded environment in vivo is typically ignored for experimental investigations since the studies get complex due to intracellular biophysical interactions between nucleic acids, proteins, cellular membranes, and various cations/anions present in the cell. Thus, being a ubiquitous property of all cells, studying those biophysical aspects affecting biochemical processes under realistically crowded conditions is of prime importance. Crowders or crowding agents are usually exploited to mimic the in vivo conditions on interacting with such genomic species, revealing structural and functional changes resulting from excluded volume and soft interactions. In the last few years, studies including crowders of varied sizes have gained attention concerning the consequences of crowding agents on biomolecular structural transitions and stability. This review comprehensively summarizes macromolecular crowding, emphasizing the biophysical effects and contribution of soft interactions in the heterogeneous cellular environment.

Anomalous Colloidal Motion under Strong Confinement

Diffusion of biological macromolecules in the cytoplasm is a paradigm of colloidal diffusion in an environment characterized by a strong restriction of the accessible volume. This makes of the understanding of the physical rules governing colloidal diffusion under conditions mimicking the reduction in accessible volume occurring in the cell cytoplasm, a problem of a paramount importance. This work aims to study how the thermal motion of spherical colloidal beads in the inner cavity of giant unilamellar vesicles (GUVs) is modified by strong confinement conditions, and the viscoelastic character of the medium. Using single particle tracking, it is found that both the confinement and the environmental viscoelasticity lead to the emergence of anomalous motion pathways for colloidal microbeads encapsulated in the aqueous inner cavity of GUVs. This anomalous diffusion is strongly dependent on the ratio between the volume of the colloidal particle and that of the GUV under consideration as well as on the viscosity of the particle's liquid environment. Therefore, the results evidence that the reduction of the free volume accessible to colloidal motion pushes the diffusion far from a standard Brownian pathway as a result of the change in the hydrodynamic boundary conditions driving the particle motion.

What remains from living cells in bacterial lysate-based cell-free systems

Because they mimic cells while offering an accessible and controllable environment, lysate-based cell-free systems (CFS) have emerged as valuable biotechnology tools for synthetic biology. Historically used to uncover fundamental mechanisms of life, CFS are nowadays used for a multitude of purposes, including protein production and prototyping of synthetic circuits. Despite the conservation of fundamental functions in CFS like transcription and translation, RNAs and certain membrane-embedded or membrane-bound proteins of the host cell are lost when preparing the lysate. As a result, CFS largely lack some essential properties of living cells, such as the ability to adapt to changing conditions, to maintain homeostasis and spatial organization. Regardless of the application, shedding light on the black-box of the bacterial lysate is necessary to fully exploit the potential of CFS. Most measurements of the activity of synthetic circuits in CFS and in vivo show significant correlations because these only require processes that are preserved in CFS, like transcription and translation. However, prototyping circuits of higher complexity that require functions that are lost in CFS (cell adaptation, homeostasis, spatial organization) will not show such a good correlation with in vivo conditions. Both for prototyping circuits of higher complexity and for building artificial cells, the cell-free community has developed devices to reconstruct cellular functions. This mini-review compares bacterial CFS to living cells, focusing on functional and cellular process differences and the latest developments in restoring lost functions through complementation of the lysate or device engineering.

Sucrose Osmotic Self-Oscillation Drives Membrane Permeability

Molecular permeation through phospholipid membranes is a fundamental biological process for small molecules. Sucrose is one of the most widely used sweeteners and a key factor in the pathogenesis of obesity and diabetes, yet a detailed understanding of its mechanism involved in permeability into phospholipid membranes is still lacking. Here, using giant unimolecular vesicles (GUVs) reconstituting membrane properties, we compared the osmotic behavior of sucrose in GUVs and HepG2 cells to explore the effect of sucrose on membrane stability in the absence of protein enhancers. The results suggested that the particle size and potential of GUVs and the cellular membrane potential changed significantly with increasing the sucrose concentration (p < 0.05). In microscopic images of cells containing GUVs and sucrose, the fluorescence intensity of vesicles was 537 ± 17.69 after 15 min, and the value was significantly higher than that of microscopic images of cells without sucrose addition (p < 0.05). These changes suggested that the permeability of the phospholipid membrane became larger under a sucrose environment. This study provides a theoretical basis for better insight on the role of sucrose in the physiological environment.

Crowding-Induced Spatial Organization of Gene Expression in Cell-Sized Vesicles

Cell-free protein synthesis is an important tool for studying gene expression and harnessing it for applications. In cells, gene expression is regulated in part by the spatial organization of transcription and translation. Unfortunately, current cell-free approaches are unable to control the organization of molecular components needed for gene expression, which limits the ability to probe and utilize its effects. Here, we show, using complementary computational and experimental approaches, that macromolecular crowding can be used to control the spatial organization and translational efficiency of gene expression in cell-sized vesicles. Computer simulations and imaging experiments reveal that, as crowding is increased, DNA plasmids become localized at the inner surface of vesicles. Ribosomes, in contrast, remain uniformly distributed, demonstrating that crowding can be used to differentially organize components of gene expression. We further carried out cell-free protein synthesis reactions in cell-sized vesicles and quantified mRNA and protein abundance. At sufficiently high levels of crowding, we observed localization of mRNA near vesicle surfaces, a decrease in translational efficiency and protein abundance, and anomalous scaling of protein abundance as a function of vesicle size. These results are consistent with high levels of crowding causing altered spatial organization and slower diffusion. Our work demonstrates a straightforward way to control the organization of gene expression in cell-sized vesicles and provides insight into the spatial regulation of gene expression in cells.

Thermo-Statistical Effects of Inclusions on Vesicles: Division into Multispheres and Polyhedral Deformation

The construction of simple cellular models has attracted much attention as a way to explore the origin of life or elucidate the mechanisms of cell division. In the absence of complex regulatory systems, some bacteria spontaneously divide through thermostatistically elucidated mechanisms, and incorporating these simple physical principles could help to construct primitive or artificial cells. Because thermodynamic interactions play an essential role in such mechanisms, this review discusses the thermodynamic aspects of spontaneous division models of vesicles that contain a high density of inclusions, with their membrane serving as a boundary. Vesicles with highly dense inclusions are deformed according to the volume-to-area ratio. The phase separation of beads at specific intermediate volume fractions and the associated polyhedral deformation of the membrane are considered in relation to the Alder transition. Current advances in the development of a membrane-growth vesicular model are summarized. The thermostatistical understanding of these mechanisms could become a cornerstone for the construction of vesicular models that display spontaneous cell division.