Actomyosin-Driven Division of a Synthetic Cell

Actin-membrane linkers: Insights from synthetic reconstituted systems

At the cell surface, the actin cytoskeleton and the plasma membrane interact reciprocally in a variety of processes related to the remodeling of the cell surface. The actin cytoskeleton has been known to modulate membrane organization and reshape the membrane. To this end, actin-membrane linking molecules play a major role in regulating actin assembly and spatially direct the interaction between the actin cytoskeleton and the membrane. While studies in cells have provided a wealth of knowledge on the molecular composition and interactions of the actin-membrane interface, the complex molecular interactions make it challenging to elucidate the precise actions of the actin-membrane linkers at the interface. Synthetic reconstituted systems, consisting of model membranes and purified proteins, have been a powerful approach to elucidate how actin-membrane linkers direct actin assembly to drive membrane shape changes. In this review, we will focus only on several actin-membrane linkers that have been studied by using reconstitution systems. We will discuss the design principles of these reconstitution systems and how they have contributed to the understanding of the cellular functions of actin-membrane linkers. Finally, we will provide a perspective on future research directions in understanding the intricate actin-membrane interaction.

Kinetic trapping organizes actin filaments within liquid-like protein droplets

Several actin-binding proteins (ABPs) phase separate to form condensates capable of curating the actin network shapes. Here, we use computational modeling to understand the principles of actin network organization within VASP condensate droplets. Our simulations reveal that the different actin shapes, namely shells, rings, and mixture states are highly dependent on the kinetics of VASP-actin interactions, suggesting that they arise from kinetic trapping. Specifically, we show that reducing the residence time of VASP on actin filaments reduces degree of bundling, thereby promoting assembly of shells rather than rings. We validate the model predictions experimentally using a VASP-mutant with decreased bundling capability. Finally, we investigate the ring opening within deformed droplets and found that the sphere-to-ellipsoid transition is favored under a wide range of filament lengths while the ellipsoid-to-rod transition is only permitted when filaments have a specific range of lengths. Our findings highlight key mechanisms of actin organization within phase-separated ABPs.

Benefits and challenges of reconstituting the actin cortex

The cell's ability to change shape is a central feature in many cellular processes, including cytokinesis, motility, migration, and tissue formation. The cell constructs a network of contractile proteins underneath the cell membrane to form the cortex, and the reorganization of these components directly contributes to cellular shape changes. The desire to mimic these cell shape changes to aid in the creation of a synthetic cell has been increasing. Therefore, membrane-based reconstitution experiments have flourished, furthering our understanding of the minimal components the cell uses throughout these processes. Although biochemical approaches increased our understanding of actin, myosin II, and actin-associated proteins, using membrane-based reconstituted systems has further expanded our understanding of actin structures and functions because membrane-cortex interactions can be analyzed. In this review, we highlight the recent developments in membrane-based reconstitution techniques. We examine the current findings on the minimal components needed to recapitulate distinct actin structures and functions and how they relate to the cortex's impact on cellular mechanical properties. We also explore how co-processing of computational models with wet-lab experiments enhances our understanding of these properties. Finally, we emphasize the benefits and challenges inherent to membrane-based, reconstitution assays, ranging from the advantage of precise control over the system to the difficulty of integrating these findings into the complex cellular environment.

Triggered contraction of self-assembled micron-scale DNA nanotube rings

Contractile rings are formed from cytoskeletal filaments during cell division. Ring formation is induced by specific crosslinkers, while contraction is typically associated with motor protein activity. Here, we engineer DNA nanotubes and peptide-functionalized starPEG constructs as synthetic crosslinkers to mimic this process. The crosslinker induces bundling of ten to hundred DNA nanotubes into closed micron-scale rings in a one-pot self-assembly process yielding several thousand rings per microliter. Molecular dynamics simulations reproduce the detailed architectural properties of the DNA rings observed in electron microscopy. Theory and simulations predict DNA ring contraction - without motor proteins - providing mechanistic insights into the parameter space relevant for efficient nanotube sliding. In agreement between simulation and experiment, we obtain ring contraction to less than half of the initial ring diameter. DNA-based contractile rings hold promise for an artificial division machinery or contractile muscle-like materials.

Shocker─A Molecular Dynamics Protocol and Tool for Accelerating and Analyzing the Effects of Osmotic Shocks

The process of osmosis, a fundamental phenomenon in life, drives water through a semipermeable membrane in response to a solute concentration gradient across this membrane. In vitro, osmotic shocks are often used to drive shape changes in lipid vesicles, for instance, to study fission events in the context of artificial cells. While experimental techniques provide a macroscopic picture of large-scale membrane remodeling processes, molecular dynamics (MD) simulations are a powerful tool to study membrane deformations at the molecular level. However, simulating an osmotic shock is a time-consuming process due to slow water diffusion across the membrane, making it practically impossible to examine its effects in classic MD simulations. In this article, we present Shocker, a Python-based MD tool for simulating the effects of an osmotic shock by selecting and relocating water particles across a membrane over the course of several pumping cycles. Although this method is primarily aimed at efficiently simulating volume changes in vesicles, it can also handle membrane tubes and double bilayer systems. Additionally, Shocker is force field-independent and compatible with both coarse-grained and all-atom systems. We demonstrate that our tool is applicable to simulate both hypertonic and hypotonic osmotic shocks for a range of vesicular and bilamellar setups, including complex multicomponent systems containing membrane proteins or crowded internal solutions.

Reconstitution of actin-based cellular processes: Why encapsulation changes the rules

While in vitro reconstitution of cellular processes is progressing rapidly, the encapsulation of biomimetic systems to reproduce the cellular environment is a major challenge. Here we review the difficulties, using reconstitution of processes dependent on actin polymerization as an example. Some of the problems are purely technical, due to the need for engineering strategies to encapsulate concentrated solutions in micrometer-sized compartments. However, other significant issues arise from the reduction of experimental volumes, which alters the chemical evolution of these non-equilibrium systems. Important parameters to consider for successful reconstitutions are the amount of each component, their consumption and renewal rates to guarantee their continuous availability.

Spatial Control of Arp2/3-Induced Actin Polymerization on Phase-Separated Giant Unilamellar Vesicles

Deciphering the physical mechanisms underlying cell shape changes, while avoiding the cellular interior's complexity, involves the development of controlled basic biomimetic systems that imitate cell functions. In particular, the reconstruction of cytoskeletal dynamics on cell-sized giant unilamellar vesicles (GUVs) has allowed for the reconstituting of some cell-like processes in vitro. In fact, such a bottom-up strategy could be the basis for forming protocells able to reorganize or even move autonomously. However, reconstituting the subtle and controlled dynamics of the cytoskeleton-membrane interface in vitro remains an experimental challenge. Taking advantage of the lipid-induced segregation of an actin polymerization activator, we present a system that targets actin polymerization in specific domains of phase-separated GUVs. We observe actin networks localized on Lo, Ld, or on both types of domains and the actin-induced deformation or reorganization of these domains. These results suggest that the system we have developed here could pave the way for future experiments further detailing the interplay between actin dynamics and membrane heterogeneities.

Out With a Bang: Celebrating Global Chemical Biology

On November 8-10, 2022, 163 participants from all over the world gathered at the Campus Biotech in Geneva, Switzerland to share in the latest research in chemical biology. The fourth international symposium of the Swiss National Centres of Competence in Research (NCCR) Chemical Biology coincided with the end of this successful research consortium, and as such this event marked a celebration of the past 12 years of chemical biology research in Switzerland. The inspiring talks delivered by the 15 well-known scientists, balanced in gender, expertise, and geographic location, as well as the numerous poster presentations by junior scientists showcased the breadth of global chemical biology and the bright future ahead.

Bottom-Up Synthetic Biology Using Cell-Free Protein Synthesis

Technical advances in biotechnology have greatly accelerated the development of bottom-up synthetic biology. Unlike top-down approaches, bottom-up synthetic biology focuses on the construction of a minimal cell from scratch and the application of these principles to solve challenges. Cell-free protein synthesis (CFPS) systems provide minimal machinery for transcription and translation, from either a fractionated cell lysate or individual purified protein elements, thus speeding up the development of synthetic cell projects. In this review, we trace the history of the cell-free technique back to the first in vitro fermentation experiment using yeast cell lysate. Furthermore, we summarized progresses of individual cell mimicry modules, such as compartmentalization, gene expression regulation, energy regeneration and metabolism, growth and division, communication, and motility. Finally, current challenges and future perspectives on the field are outlined.

Scratching beyond the surface - minimal actin assemblies as tools to elucidate mechanical reinforcement and shape change

The interaction between the actin cytoskeleton and the plasma membrane in eukaryotic cells is integral to a large number of functions such as shape change, mechanical reinforcement and contraction. These phenomena are driven by the architectural regulation of a thin actin network, directly beneath the membrane through interactions with a variety of binding proteins, membrane anchoring proteins and molecular motors. An increasingly common approach to understanding the mechanisms that drive these processes is to build model systems from reconstituted lipids, actin filaments and associated actin-binding proteins. Here we review recent progress in this field, with a particular emphasis on how the actin cytoskeleton provides mechanical reinforcement, drives shape change and induces contraction. Finally, we discuss potential future developments in the field, which would allow the extension of these techniques to more complex cellular processes.