Cargo Adaptor Research Articles

Non-5q Spinal Muscular Atrophy in a Patient With a Novel BICD2 Missense Variant

Variants in BICD cargo adapter 2 (BICD2) cause autosomal dominant spinal muscular atrophy with lower extremity dominance (SMALED2) which is characterized with lower extremity muscle weakness and atrophy. We describe a novel, heterozygous BICD2 variant (c.1661T>C, [p.Leu554Pro]) in a 21-month-old female patient with a more severe phenotypic presentation than the typical SMALED2 expression including arthrogryposis multiplex congenita, absent deep tendon reflexes, respiratory insufficiency, and cerebral depression. The variant p.Leu554Pro is located just outside of a domain that interacts with the motor protein KIF5A. The detailed neuro-phenotyping and clinical course presented here expand the understanding of BICD2 related disease.

Trak adaptors regulate the recruitment and activation of dynein and kinesin in mitochondrial transport.

Mitochondria are cellular power plants that generate ATP and buffer cytosolic Ca2+. In neurons, mitochondria are distributed along microtubules where energy and Ca2+ is necessary and damaged mitochondria are transported back to the cell body for degradation. Deficiencies in mitochondrial transport are associated with neurodegenerative disorders. Mitochondrial transport is mediated by mitochondrial Rho GTPases Miro1 and TRAK adaptors that recruit kinesin-1 and dynein-dynactin. To understand how these opposing motors are regulated during mitochondrial transport, we reconstituted the bidirectional transport of Miro1/TRAK along microtubules in vitro.Motor proteins kinesin-1 and dynein, cargo adaptors TRAK1/2, MIRO1, and SNPH were recombinantly expressed and fluorescently labeled after purification. Using in vitro reconstitution, the velocity, run length, and landing rate of the motor proteins in the presence of TRAK1/2 were analyzed. In vitro pull-down assays revealed the interactions between motor proteins and TRAK. Force generation of motor-cargo adaptor complexes was measured by optical trapping. We show that the coiled-coil domain of TRAK activates dynein-dynactin and enhances the motility of kinesin-1 activated by its cofactor MAP7. TRAK adaptors that recruit both motors moved towards kinesin-1's direction, whereas kinesin-1 was excluded from binding TRAK transported by dynein-dynactin, demonstrating that TRAK coordinates the activity of these opposing motors to avoid tug-of-war. Using the reconstitution assay, we also tested whether disruption of the transport machinery or passive anchoring to microtubules stalls mitochondrial transport in regions with elevated Ca2+. Transport of Miro1/TRAK by kinesin-1 was not affected by Ca2+. Instead, the microtubule docking protein syntaphilin induced resistive forces that stall kinesin-1 and dynein-driven motility in vitro, supporting the model that mitochondrial transport stalls by Ca2+-mediated recruitment of syntaphilin to the mitochondrial membrane.

Architecture of the dynein adaptor complex Fts-Hook3-FHIP1B.

Organisation of the cell's diverse cargo is dependent on the opposing microtubule-based motors kinesin and dynein. Hook3 is a highly conserved cargo adaptor that can simultaneously scaffold kinesin-3 (Kif1C) and dynein to coordinate their activity. This adaptor exists within a Fts-Hook3-FHIP1B (FHF) complex, yet how Fts and FHIP1B reinforce the function of Hook3 is poorly understood. How FHF interacts with Kif1C is similarly unclear. To address these questions, we determined the cryo-EM structure of Fts-Hook3-FHIP1B in the absence or presence of the Kif1C tail. FHF adopts one major stable configuration that is characterised by four key binding sites. Within the FHF, Hook3 forms a coiled-coil that breaks and is captured by the alpha-solenoid protein FHIP1B. The Fts E2 variant protein is sandwiched between Hook3 and FHIP1B, contacting the side of the complex and wrapping around the Hook3 coiled-coil cargo adaptor to lock it in place. Together with cross-linking mass spectrometry, we show that Kif1C binds to the third coiled-coil region of Hook3. This density projects towards Fts/FHIP1B nexus without causing a major conformational change in the FHF complex. Collectively, these data reveal the molecular organisation of the FHF complex and the interaction network that enables Hook3 to bind a bidirectional motor complex.

Kinesin-1, -2 and -3 use family-specific mechanochemical strategies to effectively compete with dynein during bidirectional transport.

Bidirectional cargo transport in neurons requires competing activity of motors from the kinesin-1, -2 and -3 superfamilies against cytoplasmic dynein-1. Previous studies demonstrated that when kinesin-1 attached to dynein-dynactin-BicD2 (DDB) complex, the tethered motors move slowly with a slight plus-end bias, suggesting kinesin-1 overpowers DDB but DDB generates a substantial hindering load. Compared to kinesin-1, motors from the kinesin-2 and -3 families display a higher sensitivity to load in single-molecule assays and are thus predicted to be overpowered by dynein complexes in cargo transport. To test this prediction, we used a DNA scaffold to pair DDB with members of the kinesin-1, -2 and -3 families to recreate bidirectional transport in vitro, and tracked the motor pairs using two-channel TIRF microscopy. Unexpectedly, we find that when both kinesin and dynein are engaged and stepping on the microtubule, kinesin-1, -2, and -3 motors are able to effectively withstand hindering loads generated by DDB. Stochastic stepping simulations reveal that kinesin-2 and -3 motors compensate for their faster detachment rates under load with faster reattachment kinetics. The similar performance between the three kinesin transport families highlights how motor kinetics play critical roles in balancing forces between kinesin and dynein, and emphasizes the importance of motor regulation by cargo adaptors, regulatory proteins, and the microtubule track for tuning the speed and directionality of cargo transport in cells.

Reconstitution of Dynein/Dynactin Transport Using Recombinant Dynein.

Cytoplasmic dynein-1 is activated by dynactin and a cargo adaptor for processive transport along microtubules. Dynein's motility can be visualized at the single-molecule level using total internal reflection fluorescence microscopy. Our understanding of the motile behavior of the dynein/dynactin complex has been aided by advances in recombinant expression, in particular for dynein. Here, I describe the purification of recombinant dynein and cargo adaptors, and endogenous dynactin and detail a protocol for the single-molecule motility assay. In this assay, microtubules are first immobilized on a coverslip. A fluorescently labeled dynein/dynactin/cargo adaptor complex is then added, allowing for the measurement of key motility parameters as the complex walks along the microtubule.

Native holdup (nHU) to measure binding affinities from cell extracts

Characterizing macromolecular interactions is essential for understanding cellular processes, yet most methods currently used to detect protein interactions from cells are qualitative. Here, we introduce the native holdup (nHU) approach to estimate equilibrium binding constants of protein interactions directly from cell extracts. Compared to other pull-down-based assays, nHU requires less sample preparation and can be coupled to any analytical methods as readouts, such as Western blotting or mass spectrometry. We use nHU to explore interactions of SNX27, a cargo adaptor of the retromer complex and find good agreement between in vitro affinities and those measured directly from cell extracts using nHU. We discuss the strengths and limitations of nHU and provide simple protocols that can be implemented in most laboratories.

Subretinal gene therapy delays vision loss in a Bardet-Biedl Syndrome type 10 mouse model

Blindness in Bardet-Biedl syndrome (BBS) is caused by dysfunction and loss of photoreceptor cells in the retina. BBS10, mutations of which account for approximately 21% of all BBS cases, encodes a chaperonin protein indispensable for the assembly of the BBSome, a cargo adaptor important for ciliary trafficking. The loss of BBSome function in the eye causes a reduced light sensitivity of photoreceptor cells, photoreceptor ciliary malformation, dysfunctional ciliary trafficking, and photoreceptor cell death. Cone photoreceptors lacking BBS10 have congenitally low electrical function in electroretinography. In this study, we performed gene augmentation therapy by injecting a viral construct subretinally to deliver the coding sequence of the mouse Bbs10 gene to treat retinal degeneration in a BBS10 mouse model. Long-term efficacy was assessed by measuring the electrical functions of the retina over time, imaging of the treated regions to visualize cell survival, conducting visually guided swim assays to measure functional vision, and performing retinal histology. We show that subretinal gene therapy slowed photoreceptor cell death and preserved retinal function in treated eyes. Notably, cone photoreceptors regained their electrical function after gene augmentation. Measurement of functional vision showed that subretinal gene therapy provided a significant benefit in delaying vision loss.

Autoinhibition and activation mechanisms revealed by the triangular-shaped structure of myosin Va

As the prototype of unconventional myosin motor family, myosin Va (MyoVa) transport cellular cargos along actin filaments in diverse cellular processes. The off-duty MyoVa adopts a closed and autoinhibited state, which can be relieved by cargo binding. The molecular mechanisms governing the autoinhibition and activation of MyoVa remain unclear. Here, we report the cryo-electron microscopy structure of the two full-length, closed MyoVa heavy chains in complex with 12 calmodulin light chains at 4.78-Å resolution. The MyoVa adopts a triangular structure with multiple intra- and interpolypeptide chain interactions in establishing the closed state with cargo binding and adenosine triphosphatase activity inhibited. Structural, biochemical, and cellular analyses uncover an asymmetric autoinhibition mechanism, in which the cargo-binding sites in the two MyoVa heavy chains are differently protected. Thus, specific and efficient MyoVa activation requires coincident binding of multiple cargo adaptors, revealing an intricate and elegant activity regulation of the motor in response to cargos.

Assembly and stability of IFT-B complex and its function in BBSome trafficking.

The machinery of intraflagellar transport (IFT) consists of IFT motors and the ciliary cargo adaptors including IFT-A and IFT-B complexes and BBSome. IFT-B, which is composed of IFT-B1 and IFT-B2 subcomplexes, interacts with IFT motors and IFT-A during anterograde IFT and IFT-A during retrograde IFT while it is also implicated in BBSome trafficking. However, the assembly and stability of IFT-B and its regulation of anterograde IFT and BBSome trafficking remain not clear. Here, we show that IFT38 functions in the regulation of anterograde IFT and retrograde trafficking of BBSome. Deletion of IFT-B1 or IFT-B2 subunits results in differential instability of IFT-B1 and IFT-B2. The stability of IFT-B1 and IFT-B2 is mutually dependent and mediated by the connecting tetramer IFT38/5788/52. The formation of an intact IFT-B1 and IFT-B2 is not altered by the deletion of IFT38 of IFT-B2 and IFT52 of IFT-B1, respectively. Further analysis suggests a modular pathway for IFT-B assembly.

In vitro characterization of the full-length human dynein-1 cargo adaptor BicD2

Cargo adaptors are crucial in coupling motor proteins with their respective cargos and regulatory proteins. BicD2 is a prominent example within the cargo adaptor family. BicD2 is able to recruit the microtubule motor dynein to RNA, viral particles, and nuclei. The BicD2-mediated interaction between the nucleus and dynein is implicated in mitosis, interkinetic nuclear migration (INM) in radial glial progenitor cells, and neuron precursor migration during embryonic neocortex development. Invitro studies involving full-length cargo adaptors are difficult to perform due to the hydrophobic character, low-expression levels, and intrinsic flexibility of cargo adaptors. Here, we report the recombinant production of full-length human BicD2 and confirm its biochemical activity by interaction studies with RanBP2. We also describe pH-dependent conformational changes of BicD2 using cryoelectron microscopy (cryo-EM), template-free structure predictions, and biophysical tools. Our results will help define the biochemical parameters for the invitro reconstitution of higher-order BicD2 protein complexes.

Kinesin-1, -2, and -3 motors use family-specific mechanochemical strategies to effectively compete with dynein during bidirectional transport.

Bidirectional cargo transport in neurons requires competing activity of motors from the kinesin-1, -2, and -3 superfamilies against cytoplasmic dynein-1. Previous studies demonstrated that when kinesin-1 attached to dynein-dynactin-BicD2 (DDB) complex, the tethered motors move slowly with a slight plus-end bias, suggesting kinesin-1 overpowers DDB but DDB generates a substantial hindering load. Compared to kinesin-1, motors from the kinesin-2 and -3 families display a higher sensitivity to load in single-molecule assays and are thus predicted to be overpowered by dynein complexes in cargo transport. To test this prediction, we used a DNA scaffold to pair DDB with members of the kinesin-1, -2, and -3 families to recreate bidirectional transport in vitro, and tracked the motor pairs using two-channel TIRF microscopy. Unexpectedly, we find that when both kinesin and dynein are engaged and stepping on the microtubule, kinesin-1, -2, and -3 motors are able to effectively withstand hindering loads generated by DDB. Stochastic stepping simulations reveal that kinesin-2 and -3 motors compensate for their faster detachment rates under load with faster reattachment kinetics. The similar performance between the three kinesin transport families highlights how motor kinetics play critical roles in balancing forces between kinesin and dynein, and emphasizes the importance of motor regulation by cargo adaptors, regulatory proteins, and the microtubule track for tuning the speed and directionality of cargo transport in cells.

The sorting of cargo proteins in the plant trans-Golgi network.

Membrane trafficking contributes to distinct protein compositions of organelles and is essential for proper organellar maintenance and functions. The trans-Golgi network (TGN) acts as a sorting station where various cargo proteins are sorted and directed to post-Golgi compartments, such as the multivesicular body or pre-vacuolar compartment, vacuoles, and plasma membrane. The spatial and temporal segregation of cargo proteins within the TGN, which is mediated with different sets of regulators including small GTPases and cargo adaptors, is a fundamental process in the sorting machinery. Recent studies with powerful imaging technologies have suggested that the TGN possesses spatially distinct subdomains or zones for different trafficking pathways. In this review, we will summarize the spatially and dynamically characteristic features of the plant TGN and their relation to cargo protein trafficking.

The physiological cargo adaptor of kinesin-2 functions as an evolutionary conserved lockpick

Specific recognition of cellular cargo and efficient transport to its correct intracellular destination is an infrastructural challenge faced by most eukaryotic cells. This remarkable deed is accomplished by processive motor proteins that are subject to robust regulatory mechanisms. The first level of regulation entails the ability of the motor to suppress its own activity. This autoinhibition is eventually relieved by specific cargo binding. To better understand the role of the cargo during motor activation, we dissected the activation mechanism of the ciliary homodimeric kinesin-2 from Caenorhabditis elegans by its physiological cargo. In functional reconstitution assays, we identified two cargo adaptor proteins that together are necessary and sufficient to allosterically activate the autoinhibited motor. Surprisingly, the orthologous adaptor proteins from the unicellular green algae Chlamydomonasreinhardtii also fully activated the kinesin-2 from worm, even though C. reinhardtii itself lacks a homodimeric kinesin-2 motor. The latter suggested that a motor activation mechanism similar to the C. elegans model existed already well before metazoans evolved, and prompted us to scrutinize predicted homodimeric kinesin-2 orthologs in other evolutionarily distant eukaryotes. We show that the ciliate Tetrahymena thermophila not only possesses a homodimeric kinesin-2 but that it also shares the same allosteric activation mechanism that we delineated in the C. elegans model. Our results point to a much more fundamental role of homodimeric kinesin-2 in intraflagellar transport (IFT) than previously thought and warrant further scrutiny of distantly related organisms toward a comprehensive picture of the IFT process and its evolution.

FERARI and cargo adaptors coordinate cargo flow through sorting endosomes

Cellular organization, compartmentalization and cell-to-cell communication are crucially dependent on endosomal pathways. Sorting endosomes provide a transit point for various trafficking pathways and decide the fate of proteins: recycling, secretion or degradation. FERARI (Factors for Endosome Recycling and Rab Interactions) play a key role in shaping these compartments and coordinate Rab GTPase function with membrane fusion and fission of vesicles through a kiss-and-run mechanism. Here, we show that FERARI also mediate kiss-and-run of Rab5-positive vesicles with sorting endosomes. During these encounters, cargo flows from Rab5-positive vesicles into sorting endosomes and from there in Rab11-positive vesicles. Cargo flow from sorting endosomes into Rab11 structures relies on the cargo adaptor SNX6, while cargo retention in the Rab11 compartment is dependent on AP1. The available cargo amount appears to regulate the duration of kisses. We propose that FERARI, together with cargo adaptors, coordinate the vectorial flow of cargo through sorting endosomes.

Selective inhibition of protein secretion by abrogating receptor–coat interactions during ER export

Protein secretion is an essential process that drives cell growth, movement, and communication. Protein traffic within the secretory pathway occurs via transport intermediates that bud from one compartment and fuse with a downstream compartment to deliver their contents. Here, we explore the possibility that protein secretion can be selectively inhibited by perturbing protein-protein interactions that drive capture into transport vesicles. Human proprotein convertase subtilisin/kexin type 9 (PCSK9) is a determinant of cholesterol metabolism whose secretion is mediated by a specific cargo adaptor protein, SEC24A. We map a series of protein-protein interactions between PCSK9, its endoplasmic reticulum (ER) export receptor SURF4, and SEC24A that mediate secretion of PCSK9. We show that the interaction between SURF4 and SEC24A can be inhibited by 4-phenylbutyrate (4-PBA), a small molecule that occludes a cargo-binding domain of SEC24. This inhibition reduces secretion of PCSK9 and additional SURF4 clients that we identify by mass spectrometry, leaving other secreted cargoes unaffected. We propose that selective small-molecule inhibition of cargo recognition by SEC24 is a potential therapeutic intervention for atherosclerosis and other diseases that are modulated by secreted proteins.

Cargo Recognition Mechanisms of Yeast Myo2 Revealed by AlphaFold2-Powered Protein Complex Prediction.

Myo2, a yeast class V myosin, transports a broad range of organelles and plays important roles in various cellular processes, including cell division in budding yeast. Despite the fact that several structures of Myo2/cargo adaptor complexes have been determined, the understanding of the versatile cargo-binding modes of Myo2 is still very limited, given the large number of cargo adaptors identified for Myo2. Here, we used ColabFold, an AlphaFold2-powered and easy-to-use tool, to predict the complex structures of Myo2-GTD and its several cargo adaptors. After benchmarking the prediction strategy with three Myo2/cargo adaptor complexes that have been determined previously, we successfully predicted the atomic structures of Myo2-GTD in complex with another three cargo adaptors, Vac17, Kar9 and Pea2, which were confirmed by our biochemical characterizations. By systematically comparing the interaction details of the six complexes of Myo2 and its cargo adaptors, we summarized the cargo-binding modes on the three conserved sites of Myo2-GTD, providing an overall picture of the versatile cargo-recognition mechanisms of Myo2. In addition, our study demonstrates an efficient and effective solution to study protein–protein interactions in the future via the AlphaFold2-powered prediction.

Cargo receptors and adaptors for selective autophagy in plant cells.

Plant selective (macro)autophagy is a highly regulated process where eukaryotic cells spatiotemporally degrade some of their constituents that have become superfluous or harmful. The identification and characterization of the factors determining this selectivity make it possible to integrate selective (macro)autophagy into plant cell physiology and homeostasis. The specific cargo receptors and/or scaffold proteins involved in this pathway are generally not structurally conserved, as are the biochemical mechanisms underlying recognition and integration of a given cargo into the autophagosome in different cell types. This review discusses the few specific cargo receptors described in plant cells to highlight key features of selective autophagy in the plant kingdom and its integration with plant physiology, aiming to identify evolutionary convergence and knowledge gaps to be filled by future research.

HAP1 interacts with 14–3-3 to regulate epileptic seizure via GABAAR-mediated inhibitory synaptic transmission in pentylenetetrazole rat model

Disruption of γ-aminobutyric acid type A receptors (GABAARs) synaptic clustering and a decrease number in the plasma membrane are thought to contribute to the alteration in the balance between excitatory and inhibitory neurotransmission in the epilepsy. Thus, it is important to elucidate the molecular mechanisms that regulate the stabilities of surface GABAARs populations as well as their concentrations at inhibitory synapses. However, the mechanism that delivers GABAARs to plasma membrane has not been conclusively determined. Our previous research indicated that huntingtin-associated protein 1 (HAP1), a major facilitator of pathological variations in membrane trafficking, modulates epileptic seizure by regulating GABAARs-mediated inhibitory synaptic transmission in pentylenetetrazole (PTZ)-induced epileptic rats. However, a detailed molecular interaction networks comprising GABAARs and HAP1 is necessary for studying and investigating new treatment targets for epilepsy. In this study, we indicate that HAP1 specifically interacts with 14–3–3, a protein that functions as a chaperone, forming a cargo adaptor complex to regulate surface GABAARs expression and the inhibitory post-synaptic current amplitudes. Disrupting the HAP1/14–3–3 complex decreases the strength of GABAARs-mediated inhibitory synaptic transmission in epilepsy. Taken together, HAP1/14–3–3 complex is linked to inhibitory synaptic transmission in evoking seizures, therefore, it is a possible drug target for epilepsy.

Synergistic autoinhibition and activation mechanisms control kinesin-1 motor activity.

SUMMARYKinesin-1 activity is regulated by autoinhibition. Intramolecular interactions within the kinesin heavy chain (KHC) are proposed to be one facet of motor regulation. The KHC also binds to the kinesin light chain (KLC), which has been implicated in both autoinhibition and activation of the motor. We show that the KLC inhibits the kinesin-microtubule interaction independently from the proposed intramolecular interaction within KHC. Cargo-adaptor proteins that bind the KLC stimulated processive movement, but the landing rate of activated kinesin complexes remained low. Microtubule-associated protein 7 (MAP7) enhanced motility by increasing the landing rate and run length of the activated kinesin motors. Our results support a model whereby the motor activity of the kinesin is regulated by synergistic inhibition mechanisms and that cargo-adaptor binding to the KLC releases both mechanisms. However, a non-motor MAP is required for robust microtubule association of the activated motor. Thus, human kinesin is regulated by synergistic autoinhibition and activation mechanisms.

Filling in the GAPs‐ Mapping the Spatiotemporal Kinetics of Arf1 and its Regulators

The Golgi serves as a hub for intracellular membrane trafficking. The small GTPase Arf1 coordinates several Golgi trafficking pathways by directly recruiting many effectors, such as cargo adaptors and lipid regulators, to the Golgi at precise and distinct points of cisternal maturation. To accomplish this, Arf1 distribution at the Golgi is tightly controlled by GEFs and GAPs, which activate and inactivate Arf1, respectively. Once active, Arf1 becomes stabilized on the membrane where it can then carryout its functions. Despite the significance of Arf1 Golgi localization in properly orchestrating Golgi trafficking, its maturation kinetics remain largely unknown due to its sensitivity to tagging. Furthermore, while the maturation kinetics of the Arf‐GEFs are well‐characterized, they are yet to be determined for the ArfGAPs. Here, I have utilized time‐lapse fluorescence microscopy and novel approaches for Arf1 visualization to begin to map the spatiotemporal dynamics of Arf1 and its GAPs. I have made a breakthrough in developing a method for directly visualizing the location of Arf1 in living cells that does not interfere with Arf1 function. Additionally, I have established the timing of each of the yeast Golgi‐localized ArfGAPs relative to the major Golgi trafficking pathways. Further, I am investigating the role of a highly conserved sequence in the TGN‐localized ArfGAP, Age2. This work will ultimately provide important insights into fundamental questions about Golgi trafficking and function.