Spherical network contraction forms microtubule asters in confinement

Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies

Active matter systems can generate highly ordered structures, avoiding equilibrium through the consumption of energy by individual constituents. How the microscopic parameters that characterize the active agents are translated to the observed mesoscopic properties of the assembly has remained an open question. These active systems are prevalent in living matter; for example, in cells, the cytoskeleton is organized into structures such as the mitotic spindle through the coordinated activity of many motor proteins walking along microtubules. Here, we investigate how the microscopic motor-microtubule interactions affect the coherent structures formed in a reconstituted motor-microtubule system. This question is of deeper evolutionary significance as we suspect motor and microtubule type contribute to the shape and size of resulting structures. We explore key parameters experimentally and theoretically, using a variety of motors with different speeds, processivities, and directionalities. We demonstrate that aster size depends on the motor used to create the aster, and develop a model for the distribution of motors and microtubules in steady-state asters that depends on parameters related to motor speed and processivity. Further, we show that network contraction rates scale linearly with the single-motor speed in quasi-one-dimensional contraction experiments. In all, this theoretical and experimental work helps elucidate how microscopic motor properties are translated to the much larger scale of collective motor-microtubule assemblies.

Actin network architecture can ensure robust centering or sensitive decentering of the centrosome

The orientation of cell polarity depends on the position of the centrosome, the main microtubule-organizing center (MTOC). Microtubules (MTs) transmit pushing forces to the MTOC as they grow against the cell periphery. How the actin network regulates these forces remains unclear. Here, in a cell-free assay, we used purified proteins to reconstitute the interaction of a microtubule aster with actin networks of various architectures in cell-sized microwells. In the absence of actin filaments, MTOC positioning was highly sensitive to variations in microtubule length. The presence of a bulk actin network limited microtubule displacement, and MTOCs were held in place. In contrast, the assembly of a branched actin network along the well edges centered the MTOCs by maintaining an isotropic balance of pushing forces. An anisotropic peripheral actin network caused the MTOC to decenter by focusing the pushing forces. Overall, our results show that actin networks can limit the sensitivity of MTOC positioning to microtubule length and enforce robust MTOC centering or decentering depending on the isotropy of its architecture.

Multiple asters organize the yolk microtubule network during dclk2-GFP zebrafish epiboly

It is known that the organization of microtubule (MT) networks in cells is orchestrated by subcellular structures named MT organizing centers (MTOCs). In this work, we use Light Sheet Fluorescence and Confocal Microscopy to investigate how the MT network surrounding the spherical yolk is arranged in the dclk2-GFP zebrafish transgenic line. We found that during epiboly the MT network is organized by multiple aster-like MTOCS. These structures form rings around the yolk sphere. Importantly, in wt embryos, aster-like MTOCs are only found upon pharmacological or genetic induction. Using our microscopy approach, we underscore the variability in the number of such asters in the transgenic line and report on the variety of global configurations of the yolk MT network. The asters’ morphology, dynamics, and their distribution in the yolk sphere are also analyzed. We propose that these features are tightly linked to epiboly timing and geometry. Key molecules are identified which support this asters role as MTOCs, where MT nucleation and growth take place. We conclude that the yolk MT network of dclk2-GFP transgenic embryos can be used as a model to organize microtubules in a spherical geometry by means of multiple MTOCs.

Nano/Micromotors in Active Matter

Nano/micromotors (NMMs) are tiny objects capable of converting energy into mechanical motion. Recently, a wealth of active matter including synthetic colloids, cytoskeletons, bacteria, and cells have been used to construct NMMs. The self-sustained motion of active matter drives NMMs out of equilibrium, giving rise to rich dynamics and patterns. Alongside the spontaneous dynamics, external stimuli such as geometric confinements, light, magnetic field, and chemical potential are also harnessed to control the movements of NMMs, yielding new application paradigms of active matter. Here, we review the recent advances, both experimental and theoretical, in exploring biological NMMs. The unique dynamical features of collective NMMs are focused on, along with some possible applications of these intriguing systems.

Actomyosin-Assisted Pulling of Lipid Nanotubes from Lipid Vesicles and Cells

Molecular motors are pivotal for intracellular transport as well as cell motility and have great potential to be put to use outside cells. Here, we exploit engineered motor proteins in combination with self-assembly of actin filaments to actively pull lipid nanotubes from giant unilamellar vesicles (GUVs). In particular, actin filaments are bound to the outer GUV membrane and the GUVs are seeded on a heavy meromyosin-coated substrate. Upon addition of ATP, hollow lipid nanotubes with a length of tens of micrometer are pulled from single GUVs due to the motor activity. We employ the same mechanism to pull lipid nanotubes from different types of cells. We find that the length and number of nanotubes critically depends on the cell type, whereby suspension cells form bigger networks than adherent cells. This suggests that molecular machines can be used to exert forces on living cells to probe membrane-to-cortex attachment.

Confinement size determines the architecture of Ran-induced microtubule networks

The organization of microtubules (MTs) is critical for cells during interphase and mitosis. During mitotic spindle assembly, MTs are made and organized around chromosomes in a process regulated by RanGTP. The role of RanGTP has been explored in Xenopus egg extracts, which are not limited by a cell membrane. Here, we investigated whether cell-sized confinements affect the assembly of RanGTP-induced MT networks in Xenopus egg extracts. We used microfluidics to encapsulate extracts within monodisperse extract-in-oil droplets. Importantly, we find that the architecture of Ran-induced MT networks depends on the droplet diameter and the Ran concentration, and differs from structures formed in bulk extracts. Our results highlight that both MT nucleation and physical confinement play critical roles in determining the spatial organization of the MT cytoskeleton.

Patterning Microtubule Network Organization Reshapes Cell-Like Compartments

Eukaryotic cells contain a cytoskeletal network comprised of dynamic microtubule filaments whose spatial organization is highly plastic. Specialized microtubule architectures are optimized for different cell types and remodel with the oscillatory cell cycle. These spatially distinct microtubule networks are thought to arise from the activity and localization of microtubule regulators and motors and are further shaped by physical forces from the cell boundary. Given complexities and redundancies of a living cell, it is challenging to disentangle the separate biochemical and physical contributions to microtubule network organization. Therefore, we sought to develop a minimal cell-like system to manipulate and spatially pattern the organization of cytoskeletal components in real-time, providing an opportunity to build distinct spatial structures and to determine how they are shaped by or reshape cell boundaries. We constructed a system for induced spatial patterning of protein components within cell-sized emulsion compartments and used it to drive microtubule network organization in real-time. We controlled dynamic protein relocalization using small molecules and light and slowed lateral diffusion within the lipid monolayer to create stable micropatterns with focused illumination. By fusing microtubule interacting proteins to optochemical dimerization domains, we directed the spatial organization of microtubule networks. Cortical patterning of polymerizing microtubules leads to symmetry breaking and forces that dramatically reshape the compartment. Our system has applications in cell biology to characterize the contributions of biochemical components and physical boundary conditions to microtubule network organization. Additionally, active shape control has uses in protocell engineering and for augmenting the functionalities of synthetic cells.

In Vitro Reconstitution of Dynamic Co-organization of Microtubules and Actin Filaments in Emulsion Droplets

In vitro (or cell-free) reconstitution is a powerful tool to study the physical basis of cytoskeletal organization in eukaryotic cells. Cytoskeletal reconstitution studies have mostly been done for individual cytoskeleton systems in unconfined 3D or quasi-2D geometries, which lack complexity relative to a cellular environment. To increase the level of complexity, we present a method to study co-organization of two cytoskeletal components, namely microtubules and actin filaments, confined in cell-sized water-in-oil emulsion droplets. We show that centrosome-nucleated dynamic microtubules can be made to interact with actin filaments through a tip-tracking complex consisting of microtubule end-binding proteins and an actin-microtubule cytolinker. In addition to the protocols themselves, we discuss the optimization steps required in order to build these more complex in vitro model systems of cytoskeletal interactions.

Microtubule-dependent pushing forces contribute to long-distance aster movement and centration in Xenopus laevis egg extracts

During interphase of the eukaryotic cell cycle, the microtubule (MT) cytoskeleton serves as both a supportive scaffold for organelles and an arborized system of tracks for intracellular transport. At the onset of mitosis, the position of the astral MT network, specifically its center, determines the eventual location of the spindle apparatus and ultimately the cytokinetic furrow. Positioning of the MT aster often results in its movement to the center of a cell, even in large blastomeres hundreds of microns in diameter. This translocation requires positioning forces, yet how these forces are generated and then integrated within cells of various sizes and geometries remains an open question. Here we describe a method that combines microfluidics, hydrogels, and Xenopus laevis egg extract to investigate the mechanics of aster movement and centration. We determined that asters were able to find the center of artificial channels and annular cylinders, even when cytoplasmic dynein-dependent pulling mechanisms were inhibited. Characterization of aster movement away from V-shaped hydrogel barriers provided additional evidence for a MT-based pushing mechanism. Importantly, the distance over which this mechanism seemed to operate was longer than that predicted by radial aster growth models, agreeing with recent models of a more complex MT network architecture within the aster.

Aster swarming by symmetry breaking of cortical dynein transport and coupling kinesins

Microtubule (MT) radial arrays or asters establish the internal topology of a cell by interacting with organelles and molecular motors. We proceed to understand the general pattern forming potential of aster-motor systems using a computational model of multiple MT asters interacting with motors in cellular confinement. In this model dynein motors are attached to the cell cortex and plus-ended motors resembling kinesin-5 diffuse in the cell interior. The introduction of 'noise' in the form of MT length fluctuations spontaneously results in the emergence of coordinated, achiral vortex-like rotation of asters. The coherence and persistence of rotation require a threshold density of both cortical dyneins and coupling kinesins, while the onset is diffusion-limited with relation to the cortical dynein mobility. The coordinated rotational motion emerges due to the resolution of a 'tug-of-war' of multiple cortical dynein motors bound to MTs of the same aster by 'noise' in the form of MT dynamic instability. This transient symmetry breaking is amplified by local coupling by kinesin-5 complexes. The lack of widespread aster rotation across cell types suggests that biophysical mechanisms that suppress such intrinsic dynamics may have evolved. This model is analogous to more general models of locally coupled self-propelled particles (SPP) that spontaneously undergo collective transport in the presence of 'noise' that have been invoked to explain swarming in birds and fish. However, the aster-motor system is distinct from SPP models with regard to the particle density and 'noise' dependence, providing a set of experimentally testable predictions for a novel sub-cellular pattern forming system.

Actin and microtubule crosslinkers tune mobility and control co-localization in a composite cytoskeletal network

Actin and microtubule filaments, with their auxiliary proteins, enable the cytoskeleton to carry out vital processes in the cell by tuning the organizational and mechanical properties of the network. Despite their critical importance and interactions in cells, we are only beginning to uncover information about the composite network. The challenge is due to the high complexity of combining actin, microtubules, and their hundreds of known associated proteins. Here, we use fluorescence microscopy, fluctuation, and cross-correlation analysis to examine the role of actin and microtubules in the presence of an antiparallel microtubule crosslinker, MAP65, and a generic, strong actin crosslinker, biotin-NeutrAvidin. For a fixed ratio of actin and microtubule filaments, we vary the amount of each crosslinker and measure the organization and fluctuations of the filaments. We find that the microtubule crosslinker plays the principle role in the organization of the system, while, actin crosslinking dictates the mobility of the filaments. We have previously demonstrated that the fluctuations of filaments are related to the mechanics, implying that actin crosslinking controls the mechanical properties of the network, independent of the microtubule-driven re-organization.

Engineering Light-Responsive Contractile Actomyosin Networks with DNA Nanotechnology

External control and precise manipulation is key for the bottom-up engineering of complex synthetic cells. Minimal actomyosin networks have been reconstituted into synthetic cells; however, their light-triggered symmetry breaking contraction has not yet been demonstrated. Here, light-activated directional contractility of a minimal synthetic actomyosin network inside microfluidic cell-sized compartments is engineered. Actin filaments, heavy-meromyosin-coated beads, and caged ATP are co-encapsulated into water-in-oil droplets. ATP is released upon illumination, leading to a myosin-generated force which results in a motion of the beads along the filaments and hence a contraction of the network. Symmetry breaking is achieved using DNA nanotechnology to establish a link between the network and the compartment periphery. It is demonstrated that the DNA-linked actin filaments contract to one side of the compartment forming actin asters and quantify the dynamics of this process. This work exemplifies that an engineering approach to bottom-up synthetic biology, combining biological and artificial elements, can circumvent challenges related to active multi-component systems and thereby greatly enrich the complexity of synthetic cellular systems.

Bottom-Up Assembly of Functional Intracellular Synthetic Organelles by Droplet-Based Microfluidics

Bottom-up synthetic biology has directed most efforts toward the construction of artificial compartmentalized systems that recreate living cell functions in their mechanical, morphological, or metabolic characteristics. However, bottom-up synthetic biology also offers great potential to study subcellular structures like organelles. Because of their intricate and complex structure, these key elements of eukaryotic life forms remain poorly understood. Here, the controlled assembly of lipid enclosed, organelle-like architectures is explored by droplet-based microfluidics. Three types of giant unilamellar vesicles (GUVs)-based synthetic organelles (SOs) functioning within natural living cells are procedured: (A) synthetic peroxisomes supporting cellular stress-management, mimicking an organelle innate to the host cell by using analogous enzymatic modules; (B) synthetic endoplasmic reticulum (ER) as intracellular light-responsive calcium stores involved in intercellular calcium signalling, mimicking an organelle innate to the host cell but utilizing a fundamentally different mechanism; and (C) synthetic magnetosomes providing eukaryotic cells with a magnetotactic sense, mimicking an organelle that is not natural to the host cell but transplanting its functionality from other branches of the phylogenetic tree. Microfluidic assembly of functional SOs paves the way for high-throughput generation of versatile intracellular structures implantable into living cells. This in-droplet SO design may support or expand cellular functionalities in translational nanomedicine.

Dynamic Actuation of DNA-Assembled Plasmonic Nanostructures in Microfluidic Cell-Sized Compartments

Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been integrated or operated inside synthetic cells toward the goal of realizing artificial biological systems entirely from the bottom-up. In this Letter, we encapsulate and actuate DNA-assembled dynamic nanostructures inside cell-sized microfluidic compartments. These encapsulated DNA nanostructures not only exhibit structural reconfigurability owing to their pH-sensitive molecular switches upon external stimuli but also possess optical feedback enabled by the integrated plasmonic probes. In particular, we demonstrate the power of microfluidic compartmentalization for achieving on-chip plasmonic enantiomer separation and substrate filtration. Our work exemplifies that the two unique tools, droplet-based microfluidics and DNA technology, offering high precision on the microscale and nanoscale, respectively, can be brought together to greatly enrich the complexity and diversity of functional synthetic systems.

Synthetic asters as elastic and radial skeletons

The radial geometry with rays radiated from a common core occurs ubiquitously in nature for its symmetry and functions. Herein, we report a class of synthetic asters with well-defined core-ray geometry that can function as elastic and radial skeletons to harbor nano- and microparticles. We fabricate the asters in a single, facile, and high-yield step that can be readily scaled up; specifically, amphiphilic gemini molecules self-assemble in water into asters with an amorphous core and divergently growing, twisted crystalline ribbons. The asters can spontaneously position microparticles in the cores, along the radial ribbons, or by the outer rims depending on particle sizes and surface chemistry. Their mechanical properties are determined on single- and multiple-aster levels. We further maneuver the synthetic asters as building blocks to form higher-order structures in virtue of aster-aster adhesion induced by ribbon intertwining. We envision the astral structures to act as rudimentary spatial organizers in nanoscience for coordinated multicomponent systems, possibly leading to emergent, synergistic functions.

Nanosystems capable of organisation and the formation of structures are of interest in nanotechnology. Here, the authors report on synthetic asters made of gemini surfactant which are able to position microparticles based on size and chemical composition which can also be organised into higher order structures.

From isolated structures to continuous networks: A categorization of cytoskeleton-based motile engineered biological microstructures

As technology at the small scale is advancing, motile engineered microstructures are becoming useful in drug delivery, biomedicine, and lab-on-a-chip devices. However, traditional engineering methods and materials can be inefficient or functionally inadequate for small-scale applications. Increasingly, researchers are turning to the biology of the cytoskeleton, including microtubules, actin filaments, kinesins, dyneins, myosins, and associated proteins, for both inspiration and solutions. They are engineering structures with components that range from being entirely biological to being entirely synthetic mimics of biology and on scales that range from isotropic continuous networks to single isolated structures. Motile biological microstructures trace their origins from the development of assays used to study the cytoskeleton to the array of structures currently available today. We define 12 types of motile biological microstructures, based on four categories: entirely biological, modular, hybrid, and synthetic, and three scales: networks, clusters, and isolated structures. We highlight some key examples, the unique functionalities, and the potential applications of each microstructure type, and we summarize the quantitative models that enable engineering them. By categorizing the diversity of motile biological microstructures in this way, we aim to establish a framework to classify these structures, define the gaps in current research, and spur ideas to fill those gaps. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Nanotechnology Approaches to Biology > Cells at the Nanoscale Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.

Microfluidics for Artificial Life: Techniques for Bottom-Up Synthetic Biology

Synthetic biology is a rapidly growing multidisciplinary branch of science that exploits the advancement of molecular and cellular biology. Conventional modification of pre-existing cells is referred to as the top-down approach. Bottom-up synthetic biology is an emerging complementary branch that seeks to construct artificial cells from natural or synthetic components. One of the aims in bottom-up synthetic biology is to construct or mimic the complex pathways present in living cells. The recent, and rapidly growing, application of microfluidics in the field is driven by the central tenet of the bottom-up approach-the pursuit of controllably generating artificial cells with precisely defined parameters, in terms of molecular and geometrical composition. In this review we survey conventional methods of artificial cell synthesis and their limitations. We proceed to show how microfluidic approaches have been pivotal in overcoming these limitations and ushering in a new generation of complexity that may be imbued in artificial cells and the milieu of applications that result.

Minimal in vitro systems shed light on cell polarity

Cell polarity - the morphological and functional differentiation of cellular compartments in a directional manner - is required for processes such as orientation of cell division, directed cellular growth and motility. How the interplay of components within the complexity of a cell leads to cell polarity is still heavily debated. In this Review, we focus on one specific aspect of cell polarity: the non-uniform accumulation of proteins on the cell membrane. In cells, this is achieved through reaction-diffusion and/or cytoskeleton-based mechanisms. In reaction-diffusion systems, components are transformed into each other by chemical reactions and are moving through space by diffusion. In cytoskeleton-based processes, cellular components (i.e. proteins) are actively transported by microtubules (MTs) and actin filaments to specific locations in the cell. We examine how minimal systems - in vitro reconstitutions of a particular cellular function with a minimal number of components - are designed, how they contribute to our understanding of cell polarity (i.e. protein accumulation), and how they complement in vivo investigations. We start by discussing the Min protein system from Escherichia coli, which represents a reaction-diffusion system with a well-established minimal system. This is followed by a discussion of MT-based directed transport for cell polarity markers as an example of a cytoskeleton-based mechanism. To conclude, we discuss, as an example, the interplay of reaction-diffusion and cytoskeleton-based mechanisms during polarity establishment in budding yeast.

From cytoskeletal assemblies to living materials

Many subcellular structures contain large numbers of cytoskeletal filaments. Such assemblies underlie much of cell division, motility, signaling, metabolism, and growth. Thus, understanding cell biology requires understanding the properties of networks of cytoskeletal filaments. While there are well established disciplines in biology dedicated to studying isolated proteins - their structure (Structural Biology) and behaviors (Biochemistry) - it is much less clear how to investigate, or even just describe, the structure and behaviors of collections of cytoskeletal filaments. One approach is to use methodologies from Mechanics and Soft Condensed Matter Physics, which have been phenomenally successful in the domains where they have been traditionally applied. From this perspective, collections of cytoskeletal filaments are viewed as materials, albeit very complex, 'active' materials, composed of molecules which use chemical energy to perform mechanical work. A major challenge is to relate these material level properties to the behaviors of the molecular constituents. Here we discuss this materials perspective and review recent work bridging molecular and network scale properties of the cytoskeleton, focusing on the organization of microtubules by dynein as an illustrative example.

Charge-controlled microfluidic formation of lipid-based single- and multicompartment systems

In this manuscript, we introduce a simple, off-the-shelf approach for the on-demand creation of giant unilamellar vesicles (GUVs) or multicompartment synthetic cell model systems in a high-throughput manner. To achieve this, we use microfluidics to encapsulate small unilamellar vesicles in block-copolymer surfactant-stabilized water-in-oil droplets. By tuning the charge of the inner droplet interface, adsorption of lipids can be either inhibited, leading to multicompartment systems, or induced, leading to the formation of droplet-stabilized GUVs. To control the charge density, we formed droplets using different molar ratios of an uncharged PEG-based fluorosurfactant and a negatively-charged PFPE carboxylic acid fluorosurfactant (Krytox). We systematically studied the transition from a multicompartment system to 3D-supported lipid bilayers as a function of lipid charge and Krytox concentration using confocal fluorescence microscopy, cryo-scanning electron microscopy and interfacial tension measurements. Moreover, we demonstrate a simple method to release GUVs from the surfactant shell and the oil phase into a physiological buffer - providing a remarkably high-yield approach for GUV formation. This widely applicable microfluidics-based technology will increase the scope of GUVs as adaptable cell-like compartments in bottom-up synthetic biology applications and beyond.

Mastering Complexity: Towards Bottom-up Construction of Multifunctional Eukaryotic Synthetic Cells

With the ultimate aim to construct a living cell, bottom-up synthetic biology strives to reconstitute cellular phenomena in vitro - disentangled from the complex environment of a cell. Recent work towards this ambitious goal has provided new insights into the mechanisms governing life. With the fast-growing library of functional modules for synthetic cells, their classification and integration become increasingly important. We discuss strategies to reverse-engineer and recombine functional parts for synthetic eukaryotes, mimicking the characteristics of nature's own prototype. Particularly, we focus on large outer compartments, complex endomembrane systems with organelles, and versatile cytoskeletons as hallmarks of eukaryotic life. Moreover, we identify microfluidics and DNA nanotechnology as two technologies that can integrate these functional modules into sophisticated multifunctional synthetic cells.