Active contraction of microtubule networks

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.

The Spindle: Integrating Architecture and Mechanics across Scales

The spindle segregates chromosomes at cell division, and its task is a mechanical one. While we have a nearly complete list of spindle components, how their molecular-scale mechanics give rise to cellular-scale spindle architecture, mechanics, and function is not yet clear. Recent in vitro and in vivo measurements bring new levels of molecular and physical control and shed light on this question. Highlighting recent findings and open questions, we introduce the molecular force generators of the spindle, and discuss how they organize microtubules into diverse architectural modules and give rise to the emergent mechanics of the mammalian spindle. Throughout, we emphasize the breadth of space and time scales at play, and the feedback between spindle architecture, dynamics, and mechanics that drives robust function.

Determinants of Polar versus Nematic Organization in Networks of Dynamic Microtubules and Mitotic Motors

During cell division, mitotic motors organize microtubules in the bipolar spindle into either polar arrays at the spindle poles or a "nematic" network of aligned microtubules at the spindle center. The reasons for the distinct self-organizing capacities of dynamic microtubules and different motors are not understood. Using in vitro reconstitution experiments and computer simulations, we show that the human mitotic motors kinesin-5 KIF11 and kinesin-14 HSET, despite opposite directionalities, can both organize dynamic microtubules into either polar or nematic networks. We show that in addition to the motor properties the natural asymmetry between microtubule plus- and minus-end growth critically contributes to the organizational potential of the motors. We identify two control parameters that capture system composition and kinetic properties and predict the outcome of microtubule network organization. These results elucidate a fundamental design principle of spindle bipolarity and establish general rules for active filament network organization.

Kinetic theory of pattern formation in mixtures of microtubules and molecular motors

In this study we formulate a theoretical approach, based on a Boltzmann-like kinetic equation, to describe pattern formation in two-dimensional mixtures of microtubular filaments and molecular motors. Following the previous work by Aranson and Tsimring [Phys. Rev. E 74, 031915 (2006)PLEEE81539-375510.1103/PhysRevE.74.031915] we model the motor-induced reorientation of microtubules as collision rules, and devise a semianalytical method to calculate the corresponding interaction integrals. This procedure yields an infinite hierarchy of kinetic equations that we terminate by employing a well-established closure strategy, developed in the pattern-formation community and based on a power-counting argument. We thus arrive at a closed set of coupled equations for slowly varying local density and orientation of the microtubules, and study its behavior by performing a linear stability analysis and direct numerical simulations. By comparing our method with the work of Aranson and Tsimring, we assess the validity of the assumptions required to derive their and our theories. We demonstrate that our approximation-free evaluation of the interaction integrals and our choice of a systematic closure strategy result in a rather different dynamical behavior than was previously reported. Based on our theory, we discuss the ensuing phase diagram and the patterns observed.

Microtubule Dynamics, Kinesin-1 Sliding, and Dynein Action Drive Growth of Cell Processes

Recent experimental studies of the role of microtubule sliding in neurite outgrowth suggested a qualitative model, according to which kinesin-1 motors push the minus-end-out microtubules against the cell membrane and generate the early cell processes. At the later stage, dynein takes over the sliding, expels the minus-end-out microtubules from the neurites, and pulls in the plus-end-out microtubules that continue to elongate the nascent axon. This model leaves unanswered a number of questions: why is dynein unable to generate the processes alone, whereas kinesin-1 can? What is the role of microtubule dynamics in process initiation and growth? Can the model correctly predict the rates of process growth in control and dynein-inhibited cases? What triggers the transition from kinesin-driven to dynein-driven sliding? To answer these questions, we combine computational modeling of a network of elastic dynamic microtubules and kinesin-1 and dynein motors with measurements of the process growth kinetics and pharmacological perturbations in Drosophila S2 cells. The results verify quantitatively the qualitative model of the microtubule polarity sorting and suggest that dynein-powered elongation is effective only when the processes are longer than a threshold length, which explains why kinesin-1 alone, but not dynein, is sufficient for the process growth. Furthermore, we show that the mechanism of process elongation depends critically on microtubule dynamic instability. Both modeling and experimental measurements show, surprisingly, that dynein inhibition accelerates the process extension. We discuss implications of the model for the general problems of cell polarization, cytoskeletal polarity emergence, and cell process protrusion.

Polarized microtubule dynamics directs cell mechanics and coordinates forces during epithelial morphogenesis

Coordinated rearrangements of cytoskeletal structures are the principal source of forces that govern cell and tissue morphogenesis^1,2. However, unlike for actin-based mechanical forces, our knowledge about the contribution of forces originating from other cytoskeletal components remains scarce. Here, we establish microtubules as central components of cell mechanics during tissue morphogenesis. We find that individual cells are mechanically autonomous during early Drosophila wing epithelium development. Each cell contains a polarized apical non-centrosomal microtubule cytoskeleton that bears compressive forces, whereby acute elimination of microtubule-based forces leads to cell shortening. We further establish that the Fat planar cell polarity (Ft-PCP) signalling pathway^3,4 couples microtubules at adherens junctions (AJs) and patterns microtubule-based forces across a tissue via polarized transcellular stability, thus revealing a molecular mechanism bridging single cell and tissue mechanics. Together, these results provide a physical basis to explain how global patterning of microtubules controls cell mechanics to coordinate collective cell behaviour during tissue remodelling. These results also offer alternative paradigms towards the interplay of contractile and protrusive cytoskeletal forces at the single cell and tissue levels.

Microtubule minus-end aster organization is driven by processive HSET-tubulin clusters

Higher-order structures of the microtubule (MT) cytoskeleton are comprised of two architectures: bundles and asters. Although both architectures are critical for cellular function, the molecular pathways that drive aster formation are poorly understood. Here, we study aster formation by human minus-end-directed kinesin-14 (HSET/KIFC1). We show that HSET is incapable of forming asters from preformed, nongrowing MTs, but rapidly forms MT asters in the presence of soluble (non-MT) tubulin. HSET binds soluble (non-MT) tubulin via its N-terminal tail domain to form heterogeneous HSET-tubulin clusters containing multiple motors. Cluster formation induces motor processivity and rescues the formation of asters from nongrowing MTs. We then show that excess soluble (non-MT) tubulin stimulates aster formation in HeLa cells overexpressing HSET during mitosis. We propose a model where HSET can toggle between MT bundle and aster formation in a manner governed by the availability of soluble (non-MT) tubulin.

Spontaneous buckling of contractile poroelastic actomyosin sheets

Shape transitions in developing organisms can be driven by active stresses, notably, active contractility generated by myosin motors. The mechanisms generating tissue folding are typically studied in epithelia. There, the interaction between cells is also coupled to an elastic substrate, presenting a major difficulty for studying contraction induced folding. Here we study the contraction and buckling of active, initially homogeneous, thin elastic actomyosin networks isolated from bounding surfaces. The network behaves as a poroelastic material, where a flow of fluid is generated during contraction. Contraction starts at the system boundaries, proceeds into the bulk, and eventually leads to spontaneous buckling of the sheet at the periphery. The buckling instability resulted from system self-organization and from the spontaneous emergence of density gradients driven by the active contractility. The buckling wavelength increases linearly with sheet thickness. Our system offers a well-controlled way to study mechanically induced, spontaneous shape transitions in active matter.

Active matter composed of filaments and molecular motors can contract. Here, the authors report the spontaneous out-of-plane buckling of reconstituted contracting poroelastic actomyosin sheets in the absence of external cues.

Differential Activity-Driven Instabilities in Biphasic Active Matter

Active stresses can cause instabilities in contractile gels and living tissues. Here we provide a generic hydrodynamic theory that treats these systems as a mixture of two phases of varying activity and different mechanical properties. We find that differential activity between the phases causes a uniform mixture to undergo a demixing instability. We follow the nonlinear evolution of the instability and characterize a phase diagram of the resulting patterns. Our study complements other instability mechanisms in mixtures driven by differential adhesion, differential diffusion, differential growth, and differential motion.

Cooperative Accumulation of Dynein-Dynactin at Microtubule Minus-Ends Drives Microtubule Network Reorganization

Cytoplasmic dynein-1 is a minus-end-directed motor protein that transports cargo over long distances and organizes the intracellular microtubule (MT) network. How dynein motor activity is harnessed for these diverse functions remains unknown. Here, we have uncovered a mechanism for how processive dynein-dynactin complexes drive MT-MT sliding, reorganization, and focusing, activities required for mitotic spindle assembly. We find that motors cooperatively accumulate, in limited numbers, at MT minus-ends. Minus-end accumulations drive MT-MT sliding, independent of MT orientation, resulting in the clustering of MT minus-ends. At a mesoscale level, activated dynein-dynactin drives the formation and coalescence of MT asters. Macroscopically, dynein-dynactin activity leads to bulk contraction of millimeter-scale MT networks, suggesting that minus-end accumulations of motors produce network-scale contractile stresses. Our data provide a model for how localized dynein activity is harnessed by cells to produce contractile stresses within the cytoskeleton, for example, during mitotic spindle assembly.

Architecture shapes contractility in actomyosin networks

Myosin-driven contraction of the actin cytoskeleton is at the base of cell and tissue morphogenesis. At the molecular level, myosin motors drive contraction by sliding actin filaments past one another using energy produced by ATP hydrolysis. How this microscopic sliding activity gives rise to cell-scale contractions has been an active research question first in muscle cells, and over the last few decades in non-muscle cells. While many early investigations focused on myosin motor activity, increasingly, the nanoscale architecture of the actin network emerges as a key regulator of contractility. Here we review theoretical and in vitro reconstitution studies that have uncovered some of the key mechanisms by which actin network organization controls contractile tension generation. We then discuss recent findings indicating that similar principles apply in cells.

Spherical network contraction forms microtubule asters in confinement

Microtubules and motor proteins form active filament networks that are critical for a variety of functions in living cells. Network topology and dynamics are the result of a self-organisation process that takes place within the boundaries of the cell. Previous biochemical in vitro studies with biomimetic systems consisting of purified motors and microtubules have demonstrated that confinement has an important effect on the outcome of the self-organisation process. However, the pathway of motor/microtubule self-organisation under confinement and its effects on network morphology are still poorly understood. Here, we have investigated how minus-end directed microtubule cross-linking kinesins organise microtubules inside polymer-stabilised microfluidic droplets of well-controlled size. We find that confinement can impose a novel pathway of microtubule aster formation proceeding via the constriction of an initially spherical motor/microtubule network. This mechanism illustrates the close relationship between confinement, network contraction, and aster formation. The spherical constriction pathway robustly produces single, well-centred asters with remarkable reproducibility across thousands of droplets. These results show that the additional constraint of well-defined confinement can improve the robustness of active network self-organisation, providing insight into the design principles of self-organising active networks in micro-scale confinement.

Polarity sorting drives remodeling of actin-myosin networks

Cytoskeletal networks of actin filaments and myosin motors drive many dynamic cell processes. A key characteristic of these networks is their contractility. Despite intense experimental and theoretical efforts, it is not clear what mechanism favors network contraction over expansion. Recent work points to a dominant role for the nonlinear mechanical response of actin filaments, which can withstand stretching but buckle upon compression. Here we present an alternative mechanism. We study how interactions between actin and myosin-2 at the single filament level translate into contraction at the network scale by performing time-lapse imaging on reconstituted quasi-2D-networks mimicking the cell cortex. We observe myosin end-dwelling after it runs processively along actin filaments. This leads to transport and clustering of actin filament ends and the formation of transiently stable bipolar structures. Further we show that myosin-driven polarity sorting produces polar actin asters, which act as contractile nodes that drive contraction in crosslinked networks. Computer simulations comparing the roles of the end-dwelling mechanism and a buckling-dependent mechanism show that the relative contribution of end-dwelling contraction increases as the network mesh-size decreases.

A homeostatic apical microtubule network shortens cells for epithelial folding via a basal polarity shift

Epithelial folding is typically driven by localized actomyosin contractility. However, it remains unclear how epithelia deform when myosin levels are low and uniform. In the Drosophila gastrula, dorsal fold formation occurs despite a lack of localized myosin changes, while the fold-initiating cells reduce cell height following basal shifts of polarity via an unknown mechanism. We show that cell shortening depends on an apical microtubule network organized by the CAMSAP protein Patronin. Prior to gastrulation, microtubule forces generated by the minus-end motor dynein scaffold the apical cell cortex into a dome-like shape, while the severing enzyme Katanin facilitates network remodelling to ensure tissue-wide cell size homeostasis. During fold initiation, Patronin redistributes following basal polarity shifts in the initiating cells, apparently weakening the scaffolding forces to allow dome descent. The homeostatic network that ensures size/shape homogeneity is thus repurposed for cell shortening, linking epithelial polarity to folding via a microtubule-based mechanical mechanism.

NuMA recruits dynein activity to microtubule minus-ends at mitosis

To build the spindle at mitosis, motors exert spatially regulated forces on microtubules. We know that dynein pulls on mammalian spindle microtubule minus-ends, and this localized activity at ends is predicted to allow dynein to cluster microtubules into poles. How dynein becomes enriched at minus-ends is not known. Here, we use quantitative imaging and laser ablation to show that NuMA targets dynactin to minus-ends, localizing dynein activity there. NuMA is recruited to new minus-ends independently of dynein and more quickly than dynactin; both NuMA and dynactin display specific, steady-state binding at minus-ends. NuMA localization to minus-ends involves a C-terminal region outside NuMA’s canonical microtubule-binding domain and is independent of minus-end binders γ-TuRC, CAMSAP1, and KANSL1/3. Both NuMA’s minus-end-binding and dynein-dynactin-binding modules are required to rescue focused, bipolar spindle organization. Thus, NuMA may serve as a mitosis-specific minus-end cargo adaptor, targeting dynein activity to minus-ends to cluster spindle microtubules into poles.

Every time a cell divides, it needs to duplicate its DNA and evenly distribute it between the two new ‘daughter’ cells. To move and distribute DNA, the cell builds a large machine called a spindle, which is made of stiff cables called microtubules.

Many proteins, including a motor called dynein, help to organize the spindle’s microtubules. One of dynein’s jobs is to cluster all microtubules at the two tips of the spindle, pulling them into shape. Without this clustering, spindles have the wrong shape and structure and can make mistakes when moving DNA.

Microtubules have a ‘plus’ end and a ‘minus’ end, and motor proteins usually only travel in one specified direction. Dynein, for example, moves towards the minus end of microtubules, which is where most of the clustering happens. It can form a complex with other proteins that help clustering, one of which is called NuMA. Until now, it was thought that dynein transports NuMA to the minus ends.

To test this model, Hueschen et al. studied dividing human cells under a microscope and isolated minus ends with the help of a laser. The experiments showed that, in fact, NuMA gets to minus ends independently of dynein. Once it is on the minus ends, NuMA grabs hold of another protein complex called dynactin, which then gathers dynein. Dynein then pulls the spindles into shape from the minus ends. When NuMA was experimentally removed from the cells, dynein-dynactin complexes were scattered along the entire length of the microtubule instead of pulling specifically on minus-ends, which resulted in disorganized spindles. Thus, where dynein complexes pull determines what spindle shape they build.

Hueschen et al. also showed that dynein complexes only pull on minus-ends while the cell divides, which makes sense, because NuMA remains hidden in the cell nucleus for the rest of the time. Together, these results suggest that NuMA makes sure dynein pulls specifically on the minus-ends of the microtubules to tighten the spindle at the right time.

A next step will be to test how the mechanical properties of the spindle are changed without dynein pulling on minus-ends. A better knowledge of how different proteins work together to build the spindle and help cells divide can help us understand what goes wrong when cells divide abnormally, as in the case of cancer cells.

A free-boundary model of a motile cell explains turning behavior

To understand shapes and movements of cells undergoing lamellipodial motility, we systematically explore minimal free-boundary models of actin-myosin contractility consisting of the force-balance and myosin transport equations. The models account for isotropic contraction proportional to myosin density, viscous stresses in the actin network, and constant-strength viscous-like adhesion. The contraction generates a spatially graded centripetal actin flow, which in turn reinforces the contraction via myosin redistribution and causes retraction of the lamellipodial boundary. Actin protrusion at the boundary counters the retraction, and the balance of the protrusion and retraction shapes the lamellipodium. The model analysis shows that initiation of motility critically depends on three dimensionless parameter combinations, which represent myosin-dependent contractility, a characteristic viscosity-adhesion length, and a rate of actin protrusion. When the contractility is sufficiently strong, cells break symmetry and move steadily along either straight or circular trajectories, and the motile behavior is sensitive to conditions at the cell boundary. Scanning of a model parameter space shows that the contractile mechanism of motility supports robust cell turning in conditions where short viscosity-adhesion lengths and fast protrusion cause an accumulation of myosin in a small region at the cell rear, destabilizing the axial symmetry of a moving cell.

To understand shapes and movements of simple motile cells, we systematically explore minimal models describing a cell as a two-dimensional actin-myosin gel with a free boundary. The models account for actin-myosin contraction balanced by viscous stresses in the actin gel and uniform adhesion. The myosin contraction causes the lamellipodial boundary to retract. Actin protrusion at the boundary counters the retraction, and the balance of protrusion and retraction shapes the cell. The models reproduce a variety of motile shapes observed experimentally. The analysis shows that the mechanical state of a cell depends on a small number of parameters. We find that when the contractility is sufficiently strong, cells break symmetry and move steadily along either straight or circular trajectory. Scanning model parameters shows that the contractile mechanism of motility supports robust cell turning behavior in conditions where deformable actin gel and fast protrusion destabilize the axial symmetry of a moving cell.

Filament rigidity and connectivity tune the deformation modes of active biopolymer networks

Molecular motors embedded within collections of actin and microtubule filaments underlie the dynamics of cytoskeletal assemblies. Understanding the physics of such motor-filament materials is critical to developing a physical model of the cytoskeleton and designing biomimetic active materials. Here, we demonstrate through experiments and simulations that the rigidity and connectivity of filaments in active biopolymer networks regulates the anisotropy and the length scale of the underlying deformations, yielding materials with variable contractility. We find that semiflexible filaments can be compressed and bent by motor stresses, yielding materials that undergo predominantly biaxial deformations. By contrast, rigid filament bundles slide without bending under motor stress, yielding materials that undergo predominantly uniaxial deformations. Networks dominated by biaxial deformations are robustly contractile over a wide range of connectivities, while networks dominated by uniaxial deformations can be tuned from extensile to contractile through cross-linking. These results identify physical parameters that control the forces generated within motor-filament arrays and provide insight into the self-organization and mechanics of cytoskeletal assemblies.

A theory that predicts behaviors of disordered cytoskeletal networks

Morphogenesis in animal tissues is largely driven by actomyosin networks, through tensions generated by an active contractile process. Although the network components and their properties are known, and networks can be reconstituted in vitro, the requirements for contractility are still poorly understood. Here, we describe a theory that predicts whether an isotropic network will contract, expand, or conserve its dimensions. This analytical theory correctly predicts the behavior of simulated networks, consisting of filaments with varying combinations of connectors, and reveals conditions under which networks of rigid filaments are either contractile or expansile. Our results suggest that pulsatility is an intrinsic behavior of contractile networks if the filaments are not stable but turn over. The theory offers a unifying framework to think about mechanisms of contractions or expansion. It provides the foundation for studying a broad range of processes involving cytoskeletal networks and a basis for designing synthetic networks.

Force percolation of contractile active gels

Living systems provide a paradigmatic example of active soft matter. Cells and tissues comprise viscoelastic materials that exert forces and can actively change shape. This strikingly autonomous behavior is powered by the cytoskeleton, an active gel of semiflexible filaments, crosslinks, and molecular motors inside cells. Although individual motors are only a few nm in size and exert minute forces of a few pN, cells spatially integrate the activity of an ensemble of motors to produce larger contractile forces (∼nN and greater) on cellular, tissue, and organismal length scales. Here we review experimental and theoretical studies on contractile active gels composed of actin filaments and myosin motors. Unlike other active soft matter systems, which tend to form ordered patterns, actin-myosin systems exhibit a generic tendency to contract. Experimental studies of reconstituted actin-myosin model systems have long suggested that a mechanical interplay between motor activity and the network's connectivity governs this contractile behavior. Recent theoretical models indicate that this interplay can be understood in terms of percolation models, extended to include effects of motor activity on the network connectivity. Based on concepts from percolation theory, we propose a state diagram that unites a large body of experimental observations. This framework provides valuable insights into the mechanisms that drive cellular shape changes and also provides design principles for synthetic active materials.

Single microtubules and small networks become significantly stiffer on short time-scales upon mechanical stimulation

The transfer of mechanical signals through cells is a complex phenomenon. To uncover a new mechanotransduction pathway, we study the frequency-dependent transport of mechanical stimuli by single microtubules and small networks in a bottom-up approach using optically trapped beads as anchor points. We interconnected microtubules to linear and triangular geometries to perform micro-rheology by defined oscillations of the beads relative to each other. We found a substantial stiffening of single filaments above a characteristic transition frequency of 1–30 Hz depending on the filament’s molecular composition. Below this frequency, filament elasticity only depends on its contour and persistence length. Interestingly, this elastic behavior is transferable to small networks, where we found the surprising effect that linear two filament connections act as transistor-like, angle dependent momentum filters, whereas triangular networks act as stabilizing elements. These observations implicate that cells can tune mechanical signals by temporal and spatial filtering stronger and more flexibly than expected.

Spontaneous Formation of a Globally Connected Contractile Network in a Microtubule-Motor System

Microtubule (MT) networks play key roles in cell division, intracellular transport, and cell motility. These functions of MT networks occur through interactions between MTs and various associated proteins, notably motor proteins that bundle and slide MTs. Our objective in this study was to address the question of how motors determine the nature of MT networks. We conducted in vitro assays using homotetrameric kinesin Eg5, a motor protein involved in the formation and maintenance of the mitotic spindle. The mixing of Eg5 and MTs produced a range of spatiotemporal dynamics depending on the motor/filament ratio. Low motor/filament ratios produced globally connected static MT networks with sparsely distributed contractile active nodes (motor-accumulating points with radially extending MTs). Increasing the motor/filament ratio facilitated the linking of contractile active nodes and led to a global contraction of the network. When the motor/filament ratio was further increased, densely distributed active nodes formed local clusters and segmented the network into pieces with their strong contractile forces. Altering the properties of the motor through the use of chimeric Eg5, which has kinesin-1 heads, resulted in the generation of many isolated asters. These results suggest that the spatial distribution of contractile active nodes determines the dynamics of MT-motor networks. We then developed a coarse-grained model of MT-motor networks and identified two essential features for reproducing the experimentally observed patterns: an accumulation of motors that form the active nodes necessary to generate contractile forces, and a nonlinear dependency of contractile force on motor densities. Our model also enabled us to characterize the mechanical properties of the contractile network. Our study provides insight into how local motor-MT interactions generate the spatiotemporal dynamics of macroscopic network structures.

Contractility in an extensile system

Essentially all biology is active and dynamic. Biological entities autonomously sense, compute, and respond using energy-coupled ratchets that can produce force and do work. The cytoskeleton, along with its associated proteins and motors, is a canonical example of biological active matter, which is responsible for cargo transport, cell motility, division, and morphology. Prior work on cytoskeletal active matter systems showed either extensile or contractile dynamics. Here, we demonstrate a cytoskeletal system that can control the direction of the network dynamics to be either extensile, contractile, or static depending on the concentration of filaments or weak, transient crosslinkers through systematic variation of the crosslinker or microtubule concentrations. Based on these new observations and our previously published results, we created a simple one-dimensional model of the interaction of filaments within a bundle. Despite its simplicity, our model recapitulates the observed activities of our experimental system, implying that the dynamics of our finite networks of bundles are driven by the local filament-filament interactions within the bundle. Finally, we show that contractile phases can result in autonomously motile networks that resemble cells. Our results reveal a fundamentally important aspect of cellular self-organization: weak, transient interacting species can tune their interaction strength directly by tuning the local concentration to act like a rheostat. In this case, when the weak, transient proteins crosslink microtubules, they can tune the dynamics of the network to change from extensile to contractile to static. Our experiments and model allow us to gain a deeper understanding of cytoskeletal dynamics and provide an new understanding of the importance of weak, transient interactions to soft and biological systems.

Tension sensors reveal how the kinetochore shares its load

At metaphase in mitotic cells, pulling forces at the kinetochore-microtubule interface create tension by stretching the centromeric chromatin between oppositely oriented sister kinetochores. This tension is important for stabilizing the end-on kinetochore microtubule attachment required for proper bi-orientation of sister chromosomes as well as for satisfaction of the Spindle Assembly Checkpoint and entry into anaphase. How force is coupled by proteins to kinetochore microtubules and resisted by centromere stretch is becoming better understood as many of the proteins involved have been identified. Recent application of genetically encoded fluorescent tension sensors within the mechanical linkage between the centromere and kinetochore microtubules are beginning to reveal - from live cell assays - protein specific contributions that are functionally important.

Probing the biology of cell boundary conditions through confinement of Xenopus cell-free cytoplasmic extracts

Cell-free cytoplasmic extracts prepared from Xenopus eggs and embryos have for decades provided a biochemical system with which to interrogate complex cell biological processes in vitro. Recently, the application of microfabrication and microfluidic strategies in biology has narrowed the gap between in vitro and in vivo studies by enabling formation of cell-size compartments containing functional cytoplasm. These approaches provide numerous advantages over traditional biochemical experiments performed in a test tube. Most notably, the cell-free cytoplasm is confined using a two- or three-dimensional boundary, which mimics the natural configuration of a cell. This strategy enables characterization of the spatial organization of a cell, and the role that boundaries play in regulating intracellular assembly and function. In this review, we describe the marriage of Xenopus cell-free cytoplasm and confinement technologies to generate synthetic cell-like systems, the recent biological insights they have enabled, and the promise they hold for future scientific discovery.

Bridging length scales to measure polymer assembly

Time-resolvable quantitative measurements of polymer concentration are very useful to elucidate protein polymerization pathways. There are numerous techniques to measure polymer concentrations in purified protein solutions, but few are applicable in vivo. Here we develop a methodology combining microscopy and spectroscopy to overcome the limitations of both approaches for measuring polymer concentration in cells and cell extracts. This technique is based on quantifying the relationship between microscopy and spectroscopy measurements at many locations. We apply this methodology to measure microtubule assembly in tissue culture cells and Xenopus egg extracts using two-photon microscopy with FLIM measurements of FRET. We find that the relationship between FRET and two-photon intensity quantitatively agrees with predictions. Furthermore, FRET and intensity measurements change as expected with changes in acquisition time, labeling ratios, and polymer concentration. Taken together, these results demonstrate that this approach can quantitatively measure microtubule assembly in complex environments. This methodology should be broadly useful for studying microtubule nucleation and assembly pathways of other polymers.

Buckling-induced F-actin fragmentation modulates the contraction of active cytoskeletal networks

Actomyosin contractility originating from interactions between F-actin and myosin facilitates various structural reorganizations of the actin cytoskeleton. Cross-linked actomyosin networks show a tendency to contract to single or multiple foci, which has been investigated extensively in numerous studies. Recently, it was suggested that suppression of F-actin buckling via an increase in bending rigidity significantly reduces network contraction. In this study, we demonstrate that networks may show the largest contraction at intermediate bending rigidity, not at the lowest rigidity, if filaments are severed by buckling arising from myosin activity as demonstrated in recent experiments; if filaments are very flexible, frequent severing events can severely deteriorate network connectivity, leading to the formation of multiple small foci and low network contraction. By contrast, if filaments are too stiff, the networks exhibit minimal contraction due to the inhibition of filament buckling. This study reveals that buckling-induced filament severing can modulate the contraction of active cytoskeletal networks, which has been neglected to date.

Spatial confinement of active microtubule networks induces large-scale rotational cytoplasmic flow

Collective behaviors of motile units through hydrodynamic interactions induce directed fluid flow on a larger length scale than individual units. In cells, active cytoskeletal systems composed of polar filaments and molecular motors drive fluid flow, a process known as cytoplasmic streaming. The motor-driven elongation of microtubule bundles generates turbulent-like flow in purified systems; however, it remains unclear whether and how microtubule bundles induce large-scale directed flow like the cytoplasmic streaming observed in cells. Here, we adopted Xenopus egg extracts as a model system of the cytoplasm and found that microtubule bundle elongation induces directed flow for which the length scale and timescale depend on the existence of geometrical constraints. At the lower activity of dynein, kinesins bundle and slide microtubules, organizing extensile microtubule bundles. In bulk extracts, the extensile bundles connected with each other and formed a random network, and vortex flows with a length scale comparable to the bundle length continually emerged and persisted for 1 min at multiple places. When the extracts were encapsulated in droplets, the extensile bundles pushed the droplet boundary. This pushing force initiated symmetry breaking of the randomly oriented bundle network, leading to bundles aligning into a rotating vortex structure. This vortex induced rotational cytoplasmic flows on the length scale and timescale that were 10- to 100-fold longer than the vortex flows emerging in bulk extracts. Our results suggest that microtubule systems use not only hydrodynamic interactions but also mechanical interactions to induce large-scale temporally stable cytoplasmic flow.

Automated Multi-Peak Tracking Kymography (AMTraK): A Tool to Quantify Sub-Cellular Dynamics with Sub-Pixel Accuracy

Kymographs or space-time plots are widely used in cell biology to reduce the dimensions of a time-series in microscopy for both qualitative and quantitative insight into spatio-temporal dynamics. While multiple tools for image kymography have been described before, quantification remains largely manual. Here, we describe a novel software tool for automated multi-peak tracking kymography (AMTraK), which uses peak information and distance minimization to track and automatically quantify kymographs, integrated in a GUI. The program takes fluorescence time-series data as an input and tracks contours in the kymographs based on intensity and gradient peaks. By integrating a branch-point detection method, it can be used to identify merging and splitting events of tracks, important in separation and coalescence events. In tests with synthetic images, we demonstrate sub-pixel positional accuracy of the program. We test the program by quantifying sub-cellular dynamics in rod-shaped bacteria, microtubule (MT) transport and vesicle dynamics. A time-series of E. coli cell division with labeled nucleoid DNA is used to identify the time-point and rate at which the nucleoid segregates. The mean velocity of microtubule (MT) gliding motility due to a recombinant kinesin motor is estimated as 0.5 μm/s, in agreement with published values, and comparable to estimates using software for nanometer precision filament-tracking. We proceed to employ AMTraK to analyze previously published time-series microscopy data where kymographs had been manually quantified: clathrin polymerization kinetics during vesicle formation and anterograde and retrograde transport in axons. AMTraK analysis not only reproduces the reported parameters, it also provides an objective and automated method for reproducible analysis of kymographs from in vitro and in vivo fluorescence microscopy time-series of sub-cellular dynamics.

Isomorphic coalescence of aster cores formed in vitro from microtubules and kinesin motors

We report fluorescence microscopy studies of the formation of aster-like structures emerging from a cellular element-based active system and a novel analysis of the aster condensation. The system consists of rhodamine labeled microtubules which are dynamically coupled by functionalized kinesin motor proteins cross-linked via streptavidin-coated quantum dots (QDs). The aster-shaped objects contain core structures. The cores are aggregates of the QD-motor protein complexes, and result from the dynamic condensation of sub-clusters that are connected to each other randomly. The structural specificity of the aster core reflects a configuration of the initial connectivity between sub-clusters. Detailed image analysis allows us to extract a novel correlation between the condensation speed and the sub-cluster separation. The size of the core is scaled down during the condensation process, following a power law dependence on the distance between sub-clusters. The exponent of the power law is close to two, as expected from a geometric model. This single exponent common to all the contractile lines implies that there exists a time regime during which an isomorphic contraction of the aster core continues during the condensation process. We analyze the observed contraction by using a model system with potential applicability in a wide range of emergent phenomena in randomly coupled active networks, which are prevalent in the cellular environment.

Meeting report - New York Symposium on Quantitative Biology of the Cell

In the city that never sleeps, great science never takes a break. On 15 January 2016, the 'New York Symposium on Quantitative Biology of the Cell', a one-day local meeting of the American Society for Cell Biology (ASCB), took place at Columbia University Medical Center in upper Manhattan. Focusing on the quantitative understanding of cellular and multicellular systems, this meeting created an otherwise rare opportunity for interaction among scientists at various career levels with differing but complementary backgrounds. Highlighting cutting-edge experimental measurements and theoretical modeling, the symposium broke the barrier between disciplines and ignited a hopefully continuing regional dialogue on the emergent topic of quantitative biology of the cell.

Large-scale microtubule networks contract quite well

The quantitative investigation of how networks of microtubules contract can boost our understanding of actin biology.