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Verhey, K. J.

Publications and source records attributed to Verhey, K. J..

17 recordsLinked to original sources

Taccalonolide AJ uncouples tubulin GTP hydrolysis from microtubule depolymerization

Microtubules are dynamic polymers of tubulin subunits that are vital for a variety of eukaryotic cell functions, including intracellular trafficking and cell division. Microtubule-targeting drugs are among the oldest and most widely used chemotherapeutics. Despite their extensive use, the development and optimization of these drugs is hindered by our limited understanding of the molecular impacts on microtubules. Recent high-resolution structures have begun to explain how paclitaxel (Taxol) stabilizes microtubules: it reverses the hydrolysis-driven lateral strain at the microtubule seam and induces an expanded, GTP-like conformational state that promotes polymerization. In this work, we demonstrate that the microtubule-targeting natural product taccalonolide AJ (taccaAJ) stabilizes microtubules in a manner completely distinct from paclitaxel. Using cryo-EM, we show that taccaAJ stabilizes a compacted, post-GTP hydrolysis state, which is usually prone to depolymerization. In vitro assays show that taccaAJ-stabilized microtubules are more rigid than paclitaxel-stabilized microtubules, and reconstituted dynamics with taccaAJ exhibit increased rescue close to the plus-end. Finally, we use fluorescent biosensors for the compacted tubulin conformation to confirm that taccaAJ-stabilized microtubules in cells are compacted yet stable against depolymerization. We propose that taccaAJ preferentially binds a GDP lattice, promotes lateral interactions between protofilaments, and thus creates a rigid, stable microtubule in a compacted, post-GTP hydrolysis state.

biochemistry↗

A systems-level proteomic analysis identifies kinesin targets of KIFBP during neuronal development

Kinesins are molecular motor proteins essential for organizing and remodeling the cytoskeleton during neuronal development and maintenance. One key regulator is kinesin family binding protein (KIFBP), which inhibits a subset of kinesins by blocking motor-microtubule interactions. Homozygous mutations in KIFBP cause Goldberg-Shprintzen Syndrome (GOSHS), a neurodevelopmental disorder characterized by intellectual disability, microcephaly, and axonal neuropathy. Although loss of KIFBP has been linked to reduced neurite length and microtubule disorganization, the specific kinesins underlying these phenotypes remain unclear. Here we use a CRISPR-Cas9 generated KIFBP knockout Neuro-2a cell line to demonstrate that KIFBP is required for neurite extension and use inducible GFP-KIFBP to define the KIFBP interactome during neuronal differentiation. Immunoprecipitation coupled with mass spectrometry identified both known and novel KIFBP-associated kinesins. Single molecule TIRF microscopy confirmed direct inhibition of a subset of kinesins that co-immunoprecipitated with KIFBP. Notably, we identified KIF5A and KIF18B as previously unrecognized regulatory targets with potential roles in neuronal development. Together, these findings establish Neuro-2a cells as a model for studying KIFBP function and provide new insight into the regulation of kinesin activity and cytoskeletal dynamics in neurons.

cell biology↗

Accessibility of the unstructured α-tubulin C-terminal tail is controlled by microtubule lattice conformation

Microtubules are cytoskeletal filaments that self-assemble from the protein tubulin, a heterodimer of -tubulin and {beta}-tubulin, and are important for cell mechanics, migration, and division. Much work has focused on how the nucleotide state of {beta}-tubulin regulates the structure and dynamics of microtubules. In contrast, less is known about the structure and function of the C-terminal tails (CTTs) of - and {beta}-tubulin which are thought to freely protrude from the surface of the microtubule. To study the CTT of -tubulin, we developed three different biosensors that bind the tyrosinated -tubulin CTT (Y-CTT). Surprisingly, live imaging of the probes indicates that the Y-CTT is minimally accessible along the microtubule lattice under normal cellular conditions. Lattice binding of the Y-CTT probes can be increased by three different ways of changing the tubulin conformational state: the drug Taxol, expression of microtubule-associated proteins (MAPs) that recognize or promote an expanded tubulin conformation, or expression of tubulin that cannot hydrolyze GTP. Molecular dynamics simulations indicate that the Y-CTT undergoes numerous transient interactions with the bodies of -tubulin and {beta}-tubulin in the lattice, and that the frequency of these interactions is regulated by the tubulin nucleotide state. These findings suggest that accessibility of the Y-CTT is locally governed by nucleotide- and MAP-dependent conformational changes to tubulin subunits within the microtubule lattice.

cell biology↗

The Kinesin-3 KIF1A Functions as a Diligent Worker during Axonal Transport

Long-distance intracellular transport is driven by motor proteins that walk along microtubule tracks. The fate of the motor protein after transport is unclear. Classically, motor proteins have been thought to function as Diligent Workers (DW) that remain attached to cargo during the entire transport event and are degraded at the end of the transport journey. In contrast, previous work suggests that kinesin-1 transport can be described by a Loose Bucket Brigade (LBB) model in which individual motor proteins participate in multiple rounds of transport. Here, we used live-cell imaging in iNeurons to test whether the kinesin-3 KIF1A functions as a DW during axonal transport. We demonstrate that the fluorescence intensity of KIF1A on particles undergoing axonal transport does not change over time, suggesting that KIF1A remains attached to its cargo for the entire transport event. We determined that KIF1A has a relatively short protein half-life, suggesting that KIF1A is degraded at the end of the journey. Moreover, protein turnover appears to be tightly controlled in iNeurons, as treating cells with proteasome inhibitors results in a cessation of KIF1A-driven transport and degradation of the KIF1A aggregates through autophagy. These results suggest that KIF1A transport fits the DW model and that KIF1A protein levels may play a role in signaling proteostatic stress in neuronal cells.

cell biology↗

MATCAP1 preferentially binds an expanded tubulin conformation to generate detyrosinated and ?C2 a-tubulin

Microtubules are cytoskeletal filaments with critical roles in cell division, cell motility, intracellular trafficking, and cilium function. In cells, subsets of microtubules are selectively marked by posttranslational modifications (PTMs), which control the ability of microtubule-associated proteins (MAPs) and molecular motors to engage microtubules. Detyrosination ({Delta}Y) and {Delta}C2 are PTMs of -tubulin, wherein one or two residues, respectively, are enzymatically removed from the C-terminus of the protein. How specific patterns of PTMs are generated in cells is not understood. Here, we use in vitro reconstitution assays to investigate the microtubule binding behavior of metallopeptidase MATCAP1 and the mechanism by which it generates {Delta}Y and {Delta}C2 modifications of -tubulin. We demonstrate that MATCAP1 preferentially binds to microtubules composed of tubulin subunits in an expanded conformation, which can be induced by preventing {beta}-tubulin GTP hydrolysis, Taxol treatment, or kinesin-1 stepping. MATCAP1 binds to expanded microtubule lattices with long dwell time and sequentially removes the terminal tyrosine residue to generate {Delta}Y-microtubules and the penultimate glutamate residue to generate {Delta}C2-microtubules. Thus, the lattice conformation of microtubules is a key factor that gates the binding and activity of MATCAP1.

cell biology↗

KIF1C, an RNA transporting kinesin-3, undergoes liquid-liquid phase separation through its C-terminal disordered domain

The spatial distribution of mRNA is critical for local control of protein production. Recent studies have identified the kinesin-3 family member KIF1C as an RNA transporter. However, it is not clear how KIF1C interacts with RNA molecules. Here, we show that KIF1Cs C-terminal tail domain is an intrinsically disordered region (IDR) containing a prion-like domain (PLD) that is unique compared to the C-terminal tails of other kinesin family members. In cells, KIF1C constructs undergo reversible formation of dynamic puncta that display physical properties of liquid condensates and incorporate RNA molecules in a sequence-selective manner. The IDR is necessary and sufficient for driving liquid-liquid phase separation (LLPS) but the condensate properties can be modulated by adjacent coiled-coil segments. The purified KIF1C IDR domain undergoes LLPS in vitro at near-endogenous nM concentrations in a salt-dependent manner. Deletion of the IDR abolished the ability of KIF1C to undergo LLPS and disrupted the distribution of mRNA cargoes to the cell periphery. Our work thus uncovers an intrinsic correlation between the LLPS activity of KIF1C and its role as an RNA transporter. In addition, as the first kinesin motor reported to undergo LLPS, our work reveals a previously uncharacterized mode of motor-cargo interaction that extends our understanding of the behavior of cytoskeletal motor proteins.

cell biology↗

Autoinhibited kinesin-1 adopts a hierarchical folding pattern

Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 remains unknown. Here, we combine cross-linking mass spectrometry (XL-MS), electron microscopy (EM), and AlphaFold structure prediction to determine the architecture of the full-length autoinhibited kinesin-1 homodimer [kinesin-1 heavy chain (KHC)] and kinesin-1 heterotetramer [KHC bound to kinesin light chain 1 (KLC1)]. Our integrative analysis shows that kinesin-1 forms a compact, bent conformation through a break in coiled coil 3. Moreover, our XL-MS analysis demonstrates that kinesin light chains stabilize the folded inhibited state rather than inducing a new structural state. Using our structural model, we show that disruption of multiple interactions between the motor, stalk, and tail domains is required to activate the full-length kinesin-1. Our work offers a conceptual framework for understanding how cargo adaptors and microtubule-associated proteins relieve autoinhibition to promote activation.

biophysics↗

Differences in single-motor and multi-motor motility properties across the kinesin-6 family

Kinesin motor proteins are responsible for orchestrating a variety of microtubule-based processes including intracellular transport, cell division, cytoskeletal organization, and cilium function. During cell division, members of the kinesin-6 family play critical roles in anaphase and cytokinesis, however little is known about their motility properties. We find that truncated versions of MKLP1 (HsKIF23), MKLP2 (HsKIF20A), and HsKIF20B predominately display non-processive behavior as single molecules although slow, processive motility was occasionally observed, most prominently for MKLP2. Despite their non-processive nature, all kinesin-6 proteins were able to work in teams to drive microtubule gliding. MKLP1 and KIF20B were also able to work in teams to drive robust transport of both peroxisomes, a low-load cargo, and Golgi, a high-load cargo, in cells. In contrast, MKLP2 showed minimal transport of peroxisomes and was unable to drive Golgi dispersion. These results indicate that while all three mammalian kinesin-6 motor proteins are generally non-processive as single motors, they differ in their ability to work in teams and generate forces needed to drive cargo transport in cells.

cell biology↗

A kinesin-1 variant reveals motor-induced microtubule damage in cells

Kinesins drive the transport of cellular cargoes as they walk along microtubule tracks, however, recent work has suggested that the physical act of kinesins walking along microtubules can stress the microtubule lattice. Here, we describe a kinesin-1 KIF5C mutant with an increased ability to generate defects in the microtubule lattice as compared to the wild-type motor. Expression of the mutant motor in cultured cells resulted in microtubule breakage and fragmentation, suggesting that kinesin-1 variants with increased damage activity would have been selected against during evolution. The increased ability to damage microtubules is not due to the altered motility properties of the mutant motor as expression of the kinesin-3 motor KIF1A, which has similar single-motor motility properties, also caused increased microtubule pausing, bending, and buckling but not breakage. In cells, motor-induced microtubule breakage could not be prevented by increased a-tubulin K40 acetylation, a post-translational modification known to increase microtubule flexibility. In vitro, lattice damage induced by wild-type KIF5C was repaired by soluble tubulin and resulted in increased rescues and microtubule growth whereas lattice damage induced by the KIF5C mutant resulted in larger repair sites that made the microtubule vulnerable to breakage and fragmentation when under mechanical stress. These results demonstrate that kinesin-1 motility causes defects in and damage to the microtubule lattice in cells. While cells have the capacity to repair lattice damage, conditions that exceed this capacity result in microtubule breakage and fragmentation and may contribute to human disease.

cell biology↗

Neurexin and Frizzled signaling intercept axonal-transport at microtubule minus-ends to control synapse formation

Precise synaptic connectivity defines neuronal circuits. Synapse formation is locally determined by transmembrane proteins, yet synaptic material is synthesized remotely and undergoes processive transport in axons. How local synaptogenic signals intercept synaptic cargo in transport to promote its delivery and synapse formation is unknown. We found that control of synaptic cargo delivery at microtubule (MT) minus-ends mediates pro- and anti-synaptogenic activities of presynaptic Neurexin and Frizzled in C. elegans, and identified the atypical kinesin VAB-8/KIF26 as a key molecule in this process. VAB-8/KIF26 levels at synaptic MT minus-ends are controlled by Frizzled and Neurexin, its loss mimics neurexin mutants or Frizzled hyperactivation, and its overexpression can rescue synapse-loss in these backgrounds. VAB-8/KIF26 is required for the synaptic localization of other minus-end proteins and promotes pausing of retrograde transport to allow delivery to synapses. Consistently, reducing retrograde transport rescues synapse-loss in vab-8 and neurexin mutants. These results uncover an important mechanistic link between synaptogenic signaling and axonal transport.

neuroscience↗

A Cytoskeletal Function for PBRM1 Reading Methylated Microtubules

The chromatin modifier SETD2 was recently shown to be a dual-function methyltransferase that "writes" methyl marks on both chromatin and the mitotic spindle, revealing -tubulin methylation as a new posttranslational modification of microtubules. Here, we report the first cytoskeletal "reader" for this SETD2 methyl mark: the polybromo protein PBRM1. We found PBRM1 directly binds the -Tub-K40me3 mark on tubulin, and localizes to the mitotic spindle and spindle pole during cell division. PBRM1 can assemble a PBAF complex in the absence of chromatin as revealed by mass spectrometry, and can recruit other PBAF complex components including SMARCA4 and ARID2 to -tubulin. In addition to PBRM1, other PBAF components were also localized to the mitotic spindle and spindle pole. This PBAF localization was dependent on recruitment to microtubules by PBRM1, and loss of spindle-associated PBRM1/PBAF led to genomic instability as assessed by increased formation of micronuclei. These data reveal a previously unknown function for PBRM1 beyond its role remodeling chromatin, and expand the repertoire of chromatin remodelers involved in writing and reading methyl marks on the cytoskeleton. The results of this study lay the foundation for a new paradigm for the epigenetic machinery as chromatocytoskeletal modifiers, with coordinated nuclear and cytoskeletal functions.

cell biology↗

SETD2 is an actin lysine methyltransferase

SET-domain-containing-2 (SETD2) was identified as the methyltransferase responsible for the histone 3 lysine 36 trimethyl (H3K36me3) mark of the histone code. Most recently, SETD2 has been shown to be a dual-function remodeler that regulates genome stability via methylation of dynamic microtubules during mitosis and cytokinesis. Here we show that actin is a bona fide target for methylation by SETD2 in vitro and in cells. Antibodies against the SETD2 trimethyl lysine epitope recognize methylated actin, with this methyl mark localizing to areas of active actin cytoskeleton reorganization in migrating cells. Disruption of this methylation activity causes defects in actin polymerization and impairs collective cell migration. Together, these data identify SETD2 as a multifunctional cytoskeletal remodeler regulating methylation and polymerization of actin filaments, and provide new avenues for understanding how defects in SETD2 drive disease via aberrant cytoskeletal methylation.

cell biology↗

Microtubule binding of the kinesin-4 KIF7 and its regulation by autoinhibition

KIF7 is a member of the kinesin-4 family and plays critical roles in Hedgehog signaling in vertebrate cells. KIF7 is an atypical kinesin as it binds to microtubules but is immotile. We demonstrate that, like conventional kinesins, KIF7 is regulated by autoinhibition as the full-length motor cannot bind to microtubules whereas truncated versions bind statically to microtubules in cells. Previous work suggested that truncated KIF7 motors bind preferentially to the plus ends of microtubules in vitro, however, we find that truncated KIF7 does not bind preferentially to or track the plus ends of growing microtubules in mammalian cells or in cell extracts. Although the truncated KIF7 did alter microtubule dynamics in cells, this property is not specific to KIF7 as expression of an active kinesin-1 motor also altered microtubule growth rates. The immotile behavior of KIF7 is not due to the extended neck linker domain as its deletion does not activate KIF7 for motility and its presence in a KIF5C/KIF7 chimeric motor does not prevent processive motility. Together this work indicates that the atypical kinesin KIF7 is regulated by autoinhibition to prevent binding to microtubules and alteration of microtubule dynamics in cells.

cell biology↗

The Ciliary Lumen Accommodates Passive Diffusion and Vesicle Trafficking in Cytoplasmic-Ciliary Transport

Transport of membrane and cytosolic proteins into the primary cilium is essential for its role in cellular signaling. Using single molecule microscopy, we mapped the movement of membrane and soluble proteins at the base of the primary cilium. In addition to the well-known intraflagellar transport (IFT) route, we identified two new pathways within the lumen of the primary cilium - passive diffusional and vesicle transport routes - that are adopted by proteins for cytoplasmic-cilium transport in live cells. Independent of the IFT path, approximately half of IFT motors (KIF3A) and cargo (-tubulin) take the passive diffusion route and more than half of membrane-embedded G protein coupled receptors (SSTR3 and HTR6) use RAB8A-regulated vesicles to transport into and inside cilia. Furthermore, ciliary lumen transport is the preferred route for membrane proteins in the early stages of ciliogenesis and inhibition of SSTR3 vesicle transport completely blocks ciliogenesis. Furthermore, clathrin-mediated, signal-dependent internalization of SSTR3 also occurs through the ciliary lumen. These transport routes were also observed in Chlamydomonas reinhardtii flagella, suggesting their conserved roles in trafficking of ciliary proteins.

biophysics↗

Regulation of KIF1A motility via polyglutamylation of tubulin C-terminal tails

Axonal transport is a highly regulated cellular process responsible for site-specific neuronal cargo delivery. This process is mediated in part by KIF1A, a member of the kinesin-3 family of molecular motors. It is imperative that KIF1As highly efficient, superprocessive motility along microtubules is tightly regulated as misregulation of KIF1A cargo delivery is observed in many neurodegenerative diseases. However, the regulatory mechanisms responsible for KIF1As motility, and subsequent proper spatiotemporal cargo delivery, are largely unknown. One potential regulatory mechanism of KIF1A motility is through the posttranslational modifications (PTMs) of axonal microtubules. These PTMs, often occurring on the C-terminal tails of the microtubule tracks, act as molecular \"traffic signals\" helping to direct kinesin motor cargo delivery. Occurring on neuronal microtubules, C-terminal tail polygutamylation is known to be important for KIF1A cargo transport. KIF1As initial interaction with microtubule C-terminal tails is facilitated by the K-loop, a positively charged surface loop of the KIF1A motor domain. However, the K-loops role in KIF1A motility and response to perturbations in C-terminal tail polyglutamylation is underexplored. Using single-molecule imaging, we present evidence of KIF1As previously unreported pausing behavior on multiple microtubule structures. Further analysis revealed that these pauses link multiple processive segments together, contributing to KIF1As characteristic superprocessive run length. We further demonstrate that KIF1A pausing is mediated by a K-loop/polyglutamylated C-terminal tail interaction and is a regulatory mechanism of KIF1A motility. In summary, we introduce a new mechanism of KIF1A motility regulation, providing further insight into KIF1As role in axonal transport.

biophysics↗

Acute inhibition of heterotrimeric kinesin-2 function reveals mechanisms of intraflagellar transport in mammalian cilia

The trafficking of components within cilia, called intraflagellar transport (IFT), is powered by kinesin-2 and dynein-2 motors. Loss of function in any subunit of the heterotrimeric KIF3A/KIF3B/KAP kinesin-2 motor prevents ciliogenesis in mammalian cells and has hindered an understanding of how kinesin-2 motors function in IFT. We used a chemical-genetic approach to engineer an inhibitable KIF3A/KIF3B (i3A/i3B) kinesin-2 motor that is capable of rescuing WT motor function in Kif3a/Kif3b double-knockout cells. Inhibitor addition blocks ciliogenesis or, if added to ciliated cells, blocks IFT within two minutes, which leads to a complete loss of primary cilia within six hours. The kinesin-2 family members KIF3A/KIF3C and KIF17 cannot rescue ciliogenesis in Kif3a/Kif3b double-knockout cells nor delay the disassembly of full-formed cilia upon i3A/i3B inhibition. These data suggest that KIF3A/KIF3B/KAP is the sole and essential motor for cilia assembly and function in mammalian cells, indicating a species-specific adaptation of kinesin-2 motors for IFT function.

cell biology↗

Autoinhibition of kinesin-1 is essential to the dendrite-specific localization of Golgi outposts

Neuronal polarity relies on the selective localization of cargo to axons or dendrites. The molecular motor kinesin-1 moves cargo into axons but is also active in dendrites. This raises the question of how kinesin-1 activity is regulated to maintain the compartment-specific localization of cargo. Our in vivo structure-function analysis of endogenous Drosophila kinesin-1 reveals a novel role for autoinhibition in enabling the dendrite-specific localization of Golgi outposts. Mutations that disrupt kinesin-1 autoinhibition result in the axonal mislocalization of Golgi outposts. Autoinhibition also regulates kinesin-1 localization. Uninhibited kinesin-1 accumulates in axons and is depleted from dendrites, correlating with the change in outpost distribution and dendrite growth defects. Genetic interaction tests show that a balance of kinesin-1 inhibition and dynein activity is necessary to localize Golgi outposts to dendrites and keep them from entering axons. Our data indicate that kinesin-1 activity is precisely regulated by autoinhibition to achieve the selective localization of dendritic cargo.\n\nSummaryNeuronal polarity relies on the axon-or dendrite-specific localization of cargo by molecular motors such as kinesin-1. These studies show autoinhibition regulates both kinesin-1 activity and localization to keep dendritic cargo from entering axons.

cell biology↗