Myosin Va transport of liposomes in three-dimensional actin networks is modulated by actin filament density, position, and polarity

Kinesin-1-transported liposomes prefer to go straight in 3D microtubule intersections by a mechanism shared by other molecular motors

Kinesin-1 ensembles maneuver vesicular cargoes through the three-dimensional (3D) intracellular microtubule (MT) network. To define how such cargoes navigate MT intersections, we first determined how many kinesins from an ensemble on a lipid-based cargo simultaneously engage a MT, and then determined the directional outcomes (straight, turn, terminate) for liposome cargoes at perpendicular MT intersections. Run lengths of 350-nm diameter liposomes decorated with up to 20, constitutively active, truncated kinesin-1 KIF5B (K543) were longer than single motor transported cargo, suggesting multiple motor engagement. However, detachment forces of lipid-coated beads with ~20 kinesins, measured using an optical trap, showed no more than three simultaneously engaged motors, with a single engaged kinesin predominating, indicating anticooperative MT binding. At two-dimensional (2D) and 3D in vitro MT intersections, liposomes frequently paused (~2 s), suggesting kinesins simultaneously bind both MTs and engage in a tug-of-war. Liposomes showed no directional outcome bias in 2D (1.1 straight:turn ratio) but preferentially went straight (1.8 straight:turn ratio) in 3D intersections. To explain these data, we developed a mathematical model of liposome transport incorporating the known mechanochemistry of kinesins, which diffuse on the liposome surface, and have stiff tails in both compression and extension that impact how motors engage the intersecting MTs. Our model predicts the ~3 engaged motor limit observed in the optical trap and the bias toward going straight in 3D intersections. The striking similarity of these results to our previous study of liposome transport by myosin Va suggests a "universal" mechanism by which cargoes navigate 3D intersections.

Coordination, cooperation, competition, crowding and congestion of molecular motors: Theoretical models and computer simulations

Cytoskeletal motor proteins are biological nanomachines that convert chemical energy into mechanical work to carry out various functions such as cell division, cell motility, cargo transport, muscle contraction, beating of cilia and flagella, and ciliogenesis. Most of these processes are driven by the collective operation of several motors in the crowded viscous intracellular environment. Imaging and manipulation of the motors with powerful experimental probes have been complemented by mathematical analysis and computer simulations of the corresponding theoretical models. In this article, we illustrate some of the key theoretical approaches used to understand how coordination, cooperation and competition of multiple motors in the crowded intra-cellular environment drive the processes that are essential for biological function of a cell. In spite of the focus on theory, experimentalists will also find this article as an useful summary of the progress made so far in understanding multiple motor systems.

"Spatial Relationships Matter: Kinesin-1 Molecular Motors Transport Liposome Cargo Through 3D Microtubule Intersections In Vitro"

Kinesin-1 ensembles maneuver vesicular cargoes through intersections in the 3-dimensional (3D) intracellular microtubule (MT) network. To characterize directional outcomes (straight, turn, terminate) at MT intersections, we challenge 350 nm fluid-like liposomes transported by ~10 constitutively active, truncated kinesin-1 KIF5B (K543) with perpendicular 2-dimensional (2D) and 3D intersections in vitro. Liposomes frequently pause at 2D and 3D intersections (~2s), suggesting that motor teams can simultaneously engage each MT and undergo a tug-of-war. Once resolved, the directional outcomes at 2D MT intersections have a straight to turn ratio of 1.1; whereas at 3D MT intersections, liposomes more frequently go straight (straight to turn ratio of 1.8), highlighting that spatial relationships at intersections bias directional outcomes. Using 3D super-resolution microscopy (STORM), we define the gap between intersecting MTs and the liposome azimuthal approach angle heading into the intersection. We develop an in silico model in which kinesin-1 motors diffuse on the liposome surface, simultaneously engage the intersecting MTs, generate forces and detach from MTs governed by the motors' mechanochemical cycle, and undergo a tug-of-war with the winning team determining the directional outcome in 3D. The model predicts that 1-3 motors typically engage the MT, consistent with optical trapping measurements. Modeled liposomes also predominantly go straight through 3D intersections over a range of intersection gaps and liposome approach angles, even when obstructed by the crossing MT. Our observations and modeling offer mechanistic insights into how cells might tune the MT cytoskeleton, cargo, and motors to modulate cargo transport.

Effects of cytoskeletal network mesh size on cargo transport

Intracellular transport of cargoes in the cell is essential for the organization and functioning cells, especially those that are large and elongated. The cytoskeletal networks inside large cells can be highly complex, and this cytoskeletal organization can have impacts on the distance and trajectories of travel. Here, we experimentally created microtubule networks with varying mesh sizes and examined the ability of kinesin-driven quantum dot cargoes to traverse the network. Using the experimental data, we deduced parameters for cargo detachment at intersections and away from intersections, allowing us to create an analytical theory for the run length as a function of mesh size. We also used these parameters to perform simulations of cargoes along paths extracted from the experimental networks. We find excellent agreement between the trends in run length, displacement, and trajectory persistence length comparing the experimental and simulated trajectories.

Exploring the Role of the Plant Actin Cytoskeleton: From Signaling to Cellular Functions

The plant actin cytoskeleton is characterized by the basic properties of dynamic array, which plays a central role in numerous conserved processes that are required for diverse cellular functions. Here, we focus on how actins and actin-related proteins (ARPs), which represent two classical branches of a greatly diverse superfamily of ATPases, are involved in fundamental functions underlying signal regulation of plant growth and development. Moreover, we review the structure, assembly dynamics, and biological functions of filamentous actin (F-actin) from a molecular perspective. The various accessory proteins known as actin-binding proteins (ABPs) partner with F-actin to finely tune actin dynamics, often in response to various cell signaling pathways. Our understanding of the significance of the actin cytoskeleton in vital cellular activities has been furthered by comparison of conserved functions of actin filaments across different species combined with advanced microscopic techniques and experimental methods. We discuss the current model of the plant actin cytoskeleton, followed by examples of the signaling mechanisms under the supervision of F-actin related to cell morphogenesis, polar growth, and cytoplasmic streaming. Determination of the theoretical basis of how the cytoskeleton works is important in itself and is beneficial to future applications aimed at improving crop biomass and production efficiency.

Spatiotemporal three-dimensional transport dynamics of endocytic cargos and their physical regulations in cells

Intracellular transport, regulated by complex cytoarchitectures and active driving forces, is crucial for biomolecule translocations and relates to many cellular functions. Despite extensive knowledge obtained from two-dimensional (2D) experiments, the real three-dimensional (3D) spatiotemporal characteristics of intracellular transport is still unclear. With 3D single-particle tracking, we comprehensively studied the transport dynamics of endocytic cargos. With varying timescale, the intracellular transport changes from thermal-dominated 3D-constrained motion to active-dominated quasi-2D motion. Spatially, the lateral motion is heterogeneous with peripheral regions being faster than perinuclear regions, while the axial motion is homogeneous across the cells. We further confirmed that such anisotropy and heterogeneity of vesicle transport result from actively directed motion on microtubules. Strikingly, inside the vesicles, we observed endocytic nanoparticles make diffusive motions on their inner membranes when microtubules are absent, suggesting endocytic cargos are normally localized at the inner vesicle membranes through a physical connection to the microtubules outside during transport.

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Endocytic transport changes from 3D-constrained to quasi-2D motions with timescales

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Lateral motion is heterogeneous while axial motion is homogeneous across the cells

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Microtubules cause the anisotropy and heterogeneity of vesicle transport

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Endocytic particles make diffusive motion on the inner membrane of vesicles

Chemically symmetric and asymmetric self-driven rigid dumbbells in a 2D polymer gel

We employ computer simulations to unveil the translational and rotational dynamics of self-driven chemically symmetric and asymmetric rigid dumbbells in a two-dimensional polymer gel. Our results show that the activity or the self-propulsion always enhances the dynamics of the dumbbells. Making the self-propelled dumbbell chemically asymmetric leads to further enhancement in dynamics. Additionally, the direction of self-propulsion is a key factor for chemically asymmetric dumbbells, where self-propulsion towards the non-sticky half of the dumbbell results in faster translational and rotational dynamics compared to the case with the self-propulsion towards the sticky half of the dumbbell. Our analyses show that both the symmetric and asymmetric passive rigid dumbbells get trapped inside the mesh of the polymer gel, but the chemical asymmetry always facilitates the mesh to mesh motion of the dumbbell and it is even more pronounced when the dumbbell is self-propelled. This results in multiple peaks in the van Hove function with increasing self-propulsion. In a nutshell, we believe that our in silico study can guide researchers to design efficient artificial microswimmers possessing potential applications in site-specific delivery.

Polymer-Carrying Ability of Actin Filaments Interacting with Myosin Motors in a Biological Motility System In Vitro

The reconstituted motility system of actin-myosin is expected to be used in bioinspired transport devices, in which carried materials are attached to either moving actin filaments or walking myosin molecules. However, the dependence of the ability to transport on the size of the attached materials is still inadequately understood. Here, as carried materials, polyethylene glycols (PEGs) of various sizes are covalently bound to actin filaments, and the motility of PEG-attached filaments on a heavy meromyosin immobilized on a glass surface is observed via fluorescence microscopy. Full attachment of 2 kDa PEG, with an approximately 2 nm gyration radius, decreases the velocity and fraction of moving actin filaments by approximately 10% relative to unattached filaments. For the 5 kDa PEG, the fraction of moving filaments is decreased by approximately 70% even when the filaments contain only 20% PEG-attached actin. The attachment of both sizes of PEGs suppresses the actin-activated ATPase activity at the same level. These results suggest that actin filaments can carry PEGs up to 2 kDa having the same size as actin monomers, while the rate of ATP hydrolysis is limited. The size-dependence may provide a criterion for material delivery via actin filaments in nanotransport applications. This article is protected by copyright. All rights reserved.

Morphology and Transport in Eukaryotic Cells

Transport of intracellular components relies on a variety of active and passive mechanisms, ranging from the diffusive spreading of small molecules over short distances to motor-driven motion across long distances. The cell-scale behavior of these mechanisms is fundamentally dependent on the morphology of the underlying cellular structures. Diffusion-limited reaction times can be qualitatively altered by the presence of occluding barriers or by confinement in complex architectures, such as those of reticulated organelles. Motor-driven transport is modulated by the architecture of cytoskeletal filaments that serve as transport highways. In this review, we discuss the impact of geometry on intracellular transport processes that fulfill a broad range of functional objectives, including delivery, distribution, and sorting of cellular components. By unraveling the interplay between morphology and transport efficiency, we aim to elucidate key structure-function relationships that govern the architecture of transport systems at the cellular scale. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Modeling myosin Va liposome transport through actin filament networks reveals a percolation threshold that modulates transport properties

Myosin Va (myoVa) motors transport membrane-bound cargo through three-dimensional, intracellular actin filament networks. We developed a coarse-grained, in silico model to predict how actin filament density (3-800 filaments) within a randomly oriented actin network affects fluid-like liposome (350 nm vs. 1750 nm) transport by myoVa motors. Five thousand simulated liposomes transported within each network adopted one of three states: transport, tug-of-war, or diffusion. Diffusion due to liposome detachment from actin rarely occurred given at least 10 motors on the liposome surface. However, with increased actin density, liposomes transitioned from primarily directed transport on single actin filaments to an apparent random walk, resulting from a mixture of transport and tug-of-wars as the probability of encountering additional actin filaments increased. This phase transition arises from a percolation phase transition at a critical number of accessible actin filaments, N_c. N_c is a geometric property of the actin network that depends only on the position and polarity of the actin filaments, transport distance, and the liposome diameter, as evidenced by a fivefold increase in liposome diameter resulting in a fivefold decrease in N_c. Thus in cells, actin network density and cargo size may be regulated to match cargo delivery to the cell’s physiological demands.

Optimizing microtubule arrangements for rapid cargo capture

Cellular functions such as autophagy, cell signaling, and vesicular trafficking involve the retrograde transport of motor-driven cargo along microtubules. Typically, newly formed cargo engages in slow undirected movement from its point of origin before attaching to a microtubule. In some cell types, cargo destined for delivery to the perinuclear region relies on capture at dynein-enriched loading zones located near microtubule plus ends. Such systems include extended cell regions of neurites and fungal hyphae, where the efficiency of the initial diffusive loading process depends on the axial distribution of microtubule plus ends relative to the initial cargo position. We use analytic mean first-passage time calculations and numerical simulations to model diffusive capture processes in tubular cells, exploring how the spatial arrangement of microtubule plus ends affects the efficiency of retrograde cargo transport. Our model delineates the key features of optimal microtubule arrangements that minimize mean cargo capture times. Namely, we show that configurations with a single microtubule plus end abutting the distal tip and broadly distributed other plus ends allow for efficient capture in a variety of different scenarios for retrograde transport. Live-cell imaging of microtubule plus ends in Aspergillus nidulans hyphae indicates that their distributions exhibit these optimal qualitative features. Our results highlight important coupling effects between the distribution of microtubule tips and retrograde cargo transport, providing guiding principles for the spatial arrangement of microtubules within tubular cell regions.

Kymolyzer, a Semi-Autonomous Kymography Tool to Analyze Intracellular Motility

The movement of intracellular cargo, such as transcripts, proteins, and organelles, is fundamental to cellular function. Neurons, due to their long axons and dendrites, are particularly dependent on proper intracellular trafficking and vulnerable to defects in the movement of intracellular cargo that are noted in neurodegenerative and neurodevelopmental disorders. Accurate quantification of intracellular transport is therefore needed for studying the mechanisms of cargo trafficking, the influence of mutations, and the effects of potentially therapeutic pharmaceuticals. In this article, we introduce an algorithm called "Kymolyzer." The algorithm can quantify intracellular trafficking along a defined path, such as that formed by the aligned microtubules of axons and dendrites. Kymolyzer works as a semi-autonomous kymography software application. It constructs and analyzes kymographs to measure the movement and distribution of fluorescently tagged objects along a user-defined path. The algorithm can be used under a wide variety of experimental conditions and can extract a diverse array of motility parameters describing intracellular movement, including time spent in motion, percentage of objects in motion, percentage of objects that are stationary, and velocities of motile objects. This article serves as a user manual describing the design of Kymolyzer, providing a stepwise protocol for its use and illustrating its functions with common examples. © 2020 Wiley Periodicals LLC Basic Protocol: Kymolyzer, a semi-autonomous kymography tool to analyze intracellular motility.

Clinical and Neurobiological Aspects of TAO Kinase Family in Neurodevelopmental Disorders

Despite the complexity of neurodevelopmental disorders (NDDs), from their genotype to phenotype, in the last few decades substantial progress has been made in understanding their pathophysiology. Recent accumulating evidence shows the relevance of genetic variants in thousand and one (TAO) kinases as major contributors to several NDDs. Although it is well-known that TAO kinases are a highly conserved family of STE20 kinase and play important roles in multiple biological processes, the emerging roles of TAO kinases in neurodevelopment and NDDs have yet to be intensively discussed. In this review article, we summarize the potential roles of the TAO kinases based on structural and biochemical analyses, present the genetic data from clinical investigations, and assess the mechanistic link between the mutations of TAO kinases, neuropathology, and behavioral impairment in NDDs. We then offer potential perspectives from basic research to clinical therapies, which may contribute to fully understanding how TAO kinases are involved in NDDs.

Roles and regulation of myosin V interaction with cargo

A major question in cell biology is, how are organelles and large macromolecular complexes transported within a cell? Myosin V molecular motors play critical roles in the distribution of organelles, vesicles, and mRNA. Mis-localization of organelles that depend on myosin V motors underlie diseases in the skin, gut, and brain. Thus, the delivery of organelles to their proper destination is important for animal physiology and cellular function. Cargoes attach to myosin V motors via cargo specific adaptor proteins, which transiently bridge motors to their cargoes. Regulation of these adaptor proteins play key roles in the regulation of cargo transport. Emerging studies reveal that cargo adaptors play additional essential roles in the activation of myosin V, and the regulation of actin filaments. Here, we review how motor-adaptor interactions are controlled to regulate the proper loading and unloading of cargoes, as well as roles of adaptor proteins in the regulation of myosin V activity and the dynamics of actin filaments.

F-actin disassembly factor MICAL1 binding to Myosin Va mediates cargo unloading during cytokinesis

Motor-mediated intracellular trafficking requires motors to position cargoes at proper locations. Myosin Va (MyoVa), an actin-based motor, is a classic model for studying cargo transport. However, the molecular basis underlying cargo unloading in MyoVa-mediated transport has remained enigmatic. We have identified MICAL1, an F-actin disassembly regulator, as a binding partner of MyoVa and shown that MICAL1-MyoVa interaction is critical for localization of MyoVa at the midbody. By binding to MICAL1, MyoVa-mediated transport is terminated, resulting in vesicle unloading at the midbody for efficient cytokinesis. The MyoVa/MICAL1 complex structure reveals that MICAL1 and F-actin assembly factors, Spires, share an overlapped binding surface on MyoVa, suggesting a regulatory role of F-actin dynamics in cargo unloading. Down-regulating F-actin disassembly by a MICAL1 mutant significantly reduces MyoVa and vesicles accumulating at the midbody. Collectively, our findings demonstrate that MyoVa binds to MICAL1 at the midbody destination and triggers F-actin disassembly to unload the vesicle cargo.

A novel labeling strategy reveals that myosin Va and myosin Vb bind the same dendritically polarized vesicle population

Neurons are specialized cells with a polarized geometry and several distinct subdomains that require specific complements of proteins. Delivery of transmembrane proteins requires vesicle transport, which is mediated by molecular motor proteins. The myosin V family of motor proteins mediates transport to the barbed end of actin filaments, and little is known about the vesicles bound by myosin V in neurons. We developed a novel strategy to visualize myosin V-labeled vesicles in cultured hippocampal neurons and systematically characterized the vesicle populations labeled by myosin Va and Vb. We find that both myosins bind vesicles that are polarized to the somatodendritic domain where they undergo bidirectional long-range transport. A series of two-color imaging experiments showed that myosin V specifically colocalized with two different vesicle populations: vesicles labeled with the transferrin receptor and vesicles labeled by low-density lipoprotein receptor. Finally, coexpression with Kinesin-3 family members found that myosin V binds vesicles concurrently with KIF13A or KIF13B, supporting the hypothesis that coregulation of kinesins and myosin V on vesicles is likely to play an important role in neuronal vesicle transport. We anticipate that this new assay will be applicable in a broad range of cell types to determine the function of myosin V motor proteins.

The role of the Arp2/3 complex in shaping the dynamics and structures of branched actomyosin networks

Actomyosin networks give cells the ability to move and divide. These networks contract and expand while being driven by active energy-consuming processes such as motor protein walking and actin polymerization. Actin dynamics is also regulated by actin-binding proteins, such as the actin-related protein 2/3 (Arp2/3) complex. This complex generates branched filaments, thereby changing the overall organization of the network. In this work, the spatiotemporal patterns of dynamical actin assembly accompanying the branching-induced reorganization caused by Arp2/3 were studied using a computational model (mechanochemical dynamics of active networks [MEDYAN]); this model simulates actomyosin network dynamics as a result of chemical reactions whose rates are modulated by rapid mechanical equilibration. We show that branched actomyosin networks relax significantly more slowly than do unbranched networks. Also, branched networks undergo rare convulsive movements, "avalanches," that release strain in the network. These avalanches are associated with the more heterogeneous distribution of mechanically linked filaments displayed by branched networks. These far-from-equilibrium events arising from the marginal stability of growing actomyosin networks provide a possible mechanism of the "cytoquakes" recently seen in experiments.

Tuning molecular motor transport through cytoskeletal filament network organization

Within cells, crosslinking proteins organize cytoskeletal filaments both temporally and spatially to create dynamic and structurally diverse networks. Molecular motors move on these networks for both force generation and transport processes. How the transport statistics depend on the network architecture remains poorly characterized. Using cross-linking proteins (α-actinin, fimbrin, fascin, or filamin) and purified actin, we create cytoskeletal networks with diverse microscopic architectures. We track the motion of myosin II motor proteins moving on these networks and calculate transport statistics. We observe that motor dynamics change predictably based on the bundling of filaments within the underlying networks and discuss implications for network function.

How Myosin 5 Walks Deduced from Single-Molecule Biophysical Approaches

Myosin 5a is a two-headed myosin that functions as a cargo transporter in cells. To accomplish this task it has evolved several unique structural and kinetic features that allow it to move processively as a single molecule along actin filaments. A plethora of biophysical techniques have been used to elucidate the detailed mechanism of its movement along actin filaments in vitro. This chapter describes how this mechanism was deduced.

Dynamic motions of molecular motors in the actin cytoskeleton

During intracellular transport, cellular cargos, such as organelles, vesicles, and proteins, are transported within cells. Intracellular transport plays an important role in diverse cellular functions. Molecular motors walking on the cytoskeleton facilitate active intracellular transport, which is more efficient than diffusion-based passive transport. Active transport driven by kinesin and dynein walking on microtubules has been studied well during recent decades. However, mechanisms of active transport occurring in disorganized actin networks via myosin motors remain elusive. To provide physiologically relevant insights, we probed motions of myosin motors in actin networks under various conditions using our well-established computational model that rigorously accounts for the mechanical and dynamical behaviors of the actin cytoskeleton. We demonstrated that myosin motions can be confined due to three different reasons in the absence of F-actin turnover. We verified mechanisms of motor stalling using in vitro reconstituted actomyosin networks. We also found that with F-actin turnover, motors consistently move for a long time without significant confinement. Our study sheds light on the importance of F-actin turnover for effective active transport in the actin cytoskeleton.