Biology subjects

Carter, A. P.

Publications and source records attributed to Carter, A. P..

At least 19 recordsLinked to original sources

bioRxiv2026

Structural basis of dynein interaction with diverse activating adaptors

Cargo-specific activating adaptors enable dynein to assemble with dynactin into processive supercomplexes. Adaptors share a coiled-coil architecture, but are highly diverse in sequence and structure, raising the question of how they converge on a common activation mechanism. To address this, we determined near atomic cryo-EM structures of dynein-dynactin assembled with five adaptors: RAB11FIP3, NIN, TRAK1, BICD2 and HOOK3. Despite their heterogeneity, all complexes contain adaptor coiled coils which bridge two dynein dimers to the dynactin filament. Adaptors are defined by an N-terminal interaction at the HBS1 with the dynein heavy chain, additional contacts along the dynein-dynactin groove, and C-terminal binding to the dynactin pointed end. However, we also found distinct sequence features, coiled-coil breaks and pointed-end interfaces that tune complex stoichiometry and stability. Our results define shared principles of dynein activation while revealing unexpected plasticity in how adaptors recognise and organise the dynein-dynactin machinery.

molecular biology↗

bioRxiv2026

In situ cryo-ET of mammalian embryos reveals cytoplasmic lattices contain ubiquitin-charged E2-E3 ligase assemblies

Cytoplasmic lattices (CPLs) are filamentous assemblies essential for mammalian embryonic development that regulate organelle organization, spindle assembly, and protein homeostasis. However, their molecular functions remain unclear. Here, we develop a strategy combining cryo-focused ion beam milling and cryo-electron tomography to resolve macromolecular complexes directly in mammalian embryos. Using this approach, we determine the in situ structure of CPLs within mouse embryos at [~]4.7 [A] resolution. CPL filaments are built from multiple copies of fourteen proteins arranged into a [~]4.5 MDa repeating unit. These components form a scaffold that organizes a central cavity containing three complexes of the E2 ubiquitin-conjugating enzyme UBE2D, the E3 ligase UHRF1, NLRP14 and {beta}-tubulin. We observe states in which UBE2D is conjugated to ubiquitin, along with structural rearrangements within the cavity consistent with regulated ubiquitin transfer. Together, our findings suggest that CPLs are large ubiquitin ligase assemblies and play a role in post-translational protein modification during early embryonic development.

molecular biology↗

bioRxiv2025

Cryo-EM structures of Egl-BicD-RNA complexes reveal how diverse mRNAs are selected for subcellular localization

Localization of mRNAs is a widespread mechanism for controlling where proteins operate in cells and underpins many fundamental processes, from embryonic patterning to synaptic plasticity. This spatial control is mediated by RNA-binding proteins (RBPs) that interact with localization signals within target mRNAs. However, these signals lack overt sequence or structural patterns, even when targeted by the same protein, raising the question of how specificity is achieved. Here, we investigate this question using the Drosophila RBP Egalitarian (Egl), which couples developmentally important mRNAs to microtubule-based transport via Bicaudal D (BicD) and the dynein motor protein. We present cryo-EM structures of Egl- BicD in complex with six different RNAs. Egl uses multiple non-canonical double-stranded RNA-binding domains to cooperatively form a recognition pocket around a localization signal. Despite substantial variation in length and sequence, each signal adopts a bent stem-loop conformation that, together with base-pair identities at two defined sites, drives Egl binding. We further demonstrate that Egl dimers couple RNA binding to transport initiation through coincident detection of two RNA elements within the same transcript. Collectively, we show that diverse localizing mRNAs are recognized through a combination of shape, positional sequence features, and number of structured RNA elements. This work provides a framework for understanding how other RBPs engage highly variable mRNAs.

cell biology↗

bioRxiv2024

Structural and functional insights into activation and regulation of the dynein-dynactin-NuMA complex

During cell division, NuMA orchestrates the focusing of microtubule minus-ends in spindle poles and cortical force generation on astral microtubules by interacting with dynein motors, microtubules, and other cellular factors. Here, we used in vitro reconstitution, cryo-electron microscopy, and live cell imaging to understand the mechanism and regulation of NuMA. We determined the structure of the processive dynein/dynactin/NuMA complex (DDN) and showed that the NuMA N-terminus drives dynein motility in vitro and facilitates dynein-mediated transport in live cells. The C-terminus of NuMA directly binds to and suppresses the dynamics of the microtubule minus-end. Full-length NuMA is autoinhibited for its interactions with dynein and microtubules, but mitotically phosphorylated NuMA activates dynein in vitro and interphase cells. Together with dynein, activated full-length NuMA focuses microtubule minus-ends into aster-like structures. These results provide critical insights into the activation of NuMA and dynein for their mitotic functions.

biophysics↗

bioRxiv2024

CDR2 is a dynein adaptor recruited by kinectin to regulate ER sheet organization

The endoplasmic reticulum (ER) relies on the microtubule cytoskeleton for distribution and re-modelling of its extended membrane network, but how microtubule-based motors contribute to ER organization remains unclear. Using biochemical and cell-based assays, we identify cerebellar degeneration-related protein 2 (CDR2) and its paralog CDR2-like (CDR2L), onconeural antigens with poorly understood functions, as ER adaptors for cytoplasmic dynein-1 (dynein). We demonstrate that CDR2 is recruited by the integral ER membrane protein kinectin (KTN1) and that double knockout of CDR2 and CDR2L enhances KTN1-dependent ER sheet stacking, reversal of which by exogenous CDR2 requires its dynein-binding CC1 box motif. Exogenous CDR2 expression additionally promotes CC1 box-dependent clustering of ER sheets near centrosomes. CDR2 competes with the eEF1B{beta} subunit of translation elongation factor 1 for binding to KTN1, and eEF1B{beta} knockdown increases endogenous CDR2 levels on ER sheets, inducing their centrosome-proximal clustering. Our study describes a novel molecular pathway that implicates dynein in ER sheet organization and may be involved in the pathogenesis of paraneoplastic cerebellar degeneration.

cell biology↗

bioRxiv2024

Stepping dynamics of dynein characterized by MINFLUX

Cytoplasmic dynein is the principal motor for minus-end-directed motility and force generation functions along microtubules (MTs)1. Dynein converts the chemical energy of ATP hydrolysis into coordinated structural changes to step processively along MTs, but how dynein couples ATP hydrolysis to a minus-end-directed step remains controversial2, 3. The dynamics of dynein stepping have previously been characterized by tracking flexible regions of the motor with limited resolution4-6. Here, we site-specifically labeled yeast dynein at its MT-binding domain by developing a cysteine-light mutant and tracked its stepping at sub-millisecond and nanometer resolution at physiological ATP concentrations using MINFLUX7. We show that dynein hydrolyzes one ATP per step and takes multiples of 8 nm steps. Steps are preceded by a transient movement towards the plus end. These backward "dips" correspond to MT release upon ATP binding and subsequent diffusion of the stepping monomer around its MT-bound partner. Functional assays showed that dips terminate with a minus-end-directed movement upon ATP hydrolysis. These results provide critical insights into the order of mechanochemical events that result in a productive step of dynein.

biophysics↗

bioRxiv2024

The intracellular bacterium Orientia tsutsugamushi hijacks the adaptor protein BICD2 for dynein-based motility

The intracellular bacterium Orientia tsutsugamushi relies on the microtubule cytoskeleton and the motor protein dynein to traffic to the perinuclear region within infected cells. However, it remains unclear how the bacterium is coupled to the dynein machinery and how transport is regulated. Here, we discover that O. tsutsugamushi uses its autotransporter protein ScaC to recruit the dynein adaptor BICD2 to the bacterial surface. We show that ScaC is sufficient to engage dynein-based motility in the absence of other bacterial proteins and that BICD2 is required for efficient movement of O. tsutsugamushi during infection. Using TIRF single-molecule assays, we demonstrate that ScaC induces BICD2 to adopt an open conformation which activates the assembly of dynein-dynactin complexes. Our results reveal a novel role for BICD2 during bacterial infection and provide mechanistic insights into the life cycle of an important human pathogen.

microbiology↗

bioRxiv2023

KIF1C activates and extends dynein movement through the FHF cargo adaptor

Cellular cargos move bidirectionally on microtubules due to the presence of opposite polarity motors dynein and kinesin. Many studies show these motors are co-dependent, whereby one requires the activity of the other, although the mechanism is unknown. Here, using in vitro motility assays, we show that the kinesin-3 KIF1C acts both as an activator and a processivity factor for dynein. Activation only requires a fragment of the non-motor tail of KIF1C (KIF1C-stalk) to bind the cargo adaptor HOOK3. Cryo-EM, crosslinking mass spectrometry and AlphaFold2 predictions reveal this binding site to be separate from that of two constitutive factors (FTS and FHIP), which link HOOK3 to small G-proteins on cargos. We provide a structural model for how the FTS-HOOK3-FHIP1B (FHF) complex is auto-inhibited and explain how the KIF1C-stalk relieves this inhibition. Collectively, our work provides a molecular explanation for co-dependency by revealing that the mutual activation of dynein and kinesin is mediated through their shared adaptor. Many adaptors bind both dynein and kinesins, suggesting this mechanism could be generalised to other bidirectional complexes.

cell biology↗

bioRxiv2023

A cryo-ET study of ciliary rootlet organization

Ciliary rootlets are striated bundles of filaments that connect the base of cilia to internal cellular structures. Rootlets are critical for the sensory and motile functions of cilia. However, the mechanisms underlying these functions remain unknown, in part due to a lack of structural information of rootlet organization. In this study, we obtain 3D reconstructions of membrane-associated and purified rootlets using cryo-electron tomography (cryo-ET). We show that flexible protrusions on the rootlet surface, which emanate from the cross-striations, connect to intracellular membranes. In purified rootlets, the striations were classified into amorphous (A)-bands, associated with accumulations on the rootlet surface, and discrete (D)-bands corresponding to punctate lines of density that run through the rootlet. These striations connect a flexible network of longitudinal filaments. Subtomogram averaging suggests the filaments consist of two intertwined coiled coils. The rootlets filamentous architecture, with frequent membrane-connecting cross-striations, lends itself well for anchoring large membranes in the cell.

molecular biology↗

bioRxiv2023

A force-sensitive mutation reveals a spindle assembly checkpoint-independent role for dynein in anaphase progression

The cytoplasmic dynein-1 (dynein) motor organizes cells by shaping microtubule networks and moving a large variety of cargoes along them. However, dyneins diverse roles complicate in vivo studies of its functions significantly. To address this issue, we have used gene editing to generate a series of missense mutations in Drosophila Dynein heavy chain (Dhc). We find that mutations associated with human neurological disease cause a range of defects in larval and adult flies, including impaired cargo trafficking in neurons. We also describe a novel mutation in the microtubule-binding domain (MTBD) of Dhc that, remarkably, causes metaphase arrest of mitotic spindles in the embryo but does not impair other dynein-dependent processes. We demonstrate that the mitotic arrest is independent of dyneins well-established roles in silencing the spindle assembly checkpoint. In vitro reconstitution and optical trapping assays reveal that the mutation only impairs the performance of dynein under load. In silico all-atom molecular dynamics simulations show that this effect correlates with increased flexibility of the MTBD, as well as an altered orientation of the stalk domain, with respect to the microtubule. Collectively, our data point to a novel role of dynein in anaphase progression that depends on the motor operating in a specific load regime. More broadly, our work illustrates how cytoskeletal transport processes can be dissected in vivo by manipulating mechanical properties of motors.

cell biology↗

bioRxiv2023

Dynein and dynactin move long-range but are delivered separately to the axon tip

Axonal transport is essential for neuronal survival. This is driven by microtubule motors including dynein, which transports cargo from the axon tip back to the cell body. This function requires its cofactor dynactin and regulators LIS1 and NDEL1. Due to difficulties imaging dynein at a single-molecule level, it is unclear how this motor and its regulators coordinate transport along the length of the axon. Here we use neuron-inducible human stem-celllines (NGN2-OPTi-OX) to endogenously tag dynein components and visualise them at a near-single molecule regime. In the retrograde direction, we find that dynein and dynactin can move the entire length of the axon (>500 m) in one go. Furthermore, LIS1 and NDEL1 also undergo longdistance movement, despite being mainly implicated with initiation of dynein transport. Intriguingly, in the anterograde direction, dynein/LIS1 move faster than dynactin/NDEL1 consistent with transport on different cargos. Therefore, neurons ensure efficient transport by holding dynein/dynactin on cargos over long distances, but keeping them separate until required.

cell biology↗

bioRxiv2023

CryoET shows cofilactin filaments inside the microtubule lumen

Cytoplasmic microtubules are tubular polymers that can harbor small proteins or filaments inside their lumen. The identity of these objects and what causes their accumulation has not been conclusively established. Here, we used cryogenic electron tomography (cryoET) of Drosophila S2 cell protrusions and found filaments inside the microtubule lumen, which resemble those reported recently in human HAP1 cells. The frequency of these filaments increased upon inhibition of the sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) with the small-molecule drug thapsigargin. Subtomogram averaging showed that the luminal filaments adopt a helical structure reminiscent of cofilin-bound actin (cofilactin). Consistent with this, cofilin was activated in cells under the same conditions that increased luminal filament occurrence. Furthermore, RNAi knock-down of cofilin reduced the frequency of luminal filaments with cofilactin morphology. These results suggest that cofilin activation stimulates its accumulation on actin filaments inside the microtubule lumen.

cell biology↗

bioRxiv2022

The lysosomal adaptor JIP3 activates dynein-dynactin via a short coiled coil

Microtubule motors, like cytoplasmic dynein-1, are tightly regulated to prevent inappropriate activity in cells. Dynein functions as a [~]4 MDa complex containing its cofactor dynactin and a cargo-specific coiled-coil adaptor. However, how dynein and dynactin recognise diverse adaptors, how they interact with each other during complex formation, and the role of critical regulators such as LIS1 remain unclear. To address this, we determine the cryo-EM structure of dynein-dynactin on microtubules with LIS1 and the lysosomal adaptor JIP3. We show how JIP3 specifies complex formation despite a shorter coiled coil and lack of identifiable motifs compared to typical adaptors. We find LIS1 directly binds dynactins p150 subunit, closely tethering it to dynein. This interaction is necessary for dyneins cellular and in vitro activity. We also show how dyneins intermediate chain relieves p150s autoinhibition to enable LIS1 binding. Together, our data suggest LIS1 and p150 constrain dynein-dynactin to ensure efficient complex formation.

molecular biology↗

bioRxiv2022

Structure of dynein-dynactin on microtubules shows tandem recruitment of cargo adaptors

Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor. There is currently limited structural information on how the resulting complex interacts with microtubules and how adaptors are recruited. Here, we develop a cryo-EM processing pipeline to solve the high-resolution structure of dynein-dynactin and the adaptor BICDR1 bound to microtubules. This reveals the asymmetric interactions between neighbouring dynein motor domains and how it relates to their motile behaviour. We find unexpectedly that two adaptors occupy the complex. Both adaptors make similar interactions with the dyneins but diverge in their contacts with each other and dynactin. Our structure has implications for the stability and stoichiometry of motor recruitment by cargos.

molecular biology↗

bioRxiv2022

Conformational transitions of the mitotic adaptor Spindly underlie its interaction with Dynein and Dynactin

Cytoplasmic Dynein 1, or Dynein, is a microtubule minus-end directed motor. Dynein motility requires Dynactin and a family of activating adaptors that stabilize the Dynein-Dynactin complex and promote regulated interactions with cargo in space and time. How activating adaptors limit Dynein activation to specialized subcellular locales is unclear. Here, we reveal that Spindly, a mitotic Dynein adaptor at the kinetochore corona, exists natively in a closed conformation that occludes binding of Dynein-Dynactin to its CC1 box and Spindly motif. A structure-based analysis identified various mutations promoting an open conformation of Spindly that binds Dynein-Dynactin. A region of Spindly downstream from the Spindly motif and not required for cargo binding faces the CC1 box and stabilizes the intramolecular closed conformation. This region is also required for robust kinetochore localization of Spindly, suggesting that kinetochores promote Spindly activation to recruit Dynein. This mechanism may be paradigmatic for Dynein activation by other adaptors at various cellular locales.

biochemistry↗

bioRxiv2021

A cryo-ET survey of intracellular compartments within mammalian axons

The neuronal axon contains many intracellular compartments which travel between the cell body and axon tip. The nature of these cargos and the complex axonal environment through which they traverse is unclear. Here, we describe the internal components of mammalian sensory axons using cryo-electron tomography. We show that axonal endoplasmic reticulum has thin, beaded appearance and is tethered to microtubules at multiple sites. The tethers are elongated, [~] 7 nm long proteins which cluster in small groups. We survey the different membrane-bound cargos in axons, quantify their abundance and describe novel internal features including granules and broken membranes. We observe connecting density between membranes and microtubules which may correspond to motor proteins. In addition to membrane-bound organelles, we detect numerous proteinaceous compartments, including vaults and previously undescribed virus-like capsid particles. The abundance of these compartments suggests they undergo trafficking in axons. Our observations outline the physical characteristics of axonal cargo and provide a platform for identification of their constituents.

cell biology↗

bioRxiv2021

A cryo-ET study of microtubules in axons

The microtubule cytoskeleton in axons plays key roles in intracellular transport and in defining cell shape. Despite many years of study of microtubules, many questions regarding their native architecture remain unanswered. Here, we performed cryo-electron tomography of mouse dorsal root ganglion (DRG) and Drosophila melanogaster (Dm) neurons and examined their microtubule ultrastructure in situ. We found that the microtubule minus and plus ends in DRG axons are structurally similar and frequently contact nearby components. The microtubules in DRG axons maintained a 13 protofilament (pf) architecture, even close to lattice break sites. In contrast, microtubules in Dm neurons had 12 or 13 pfs and we detected sites of pf number transition. The microtubule lumen in DRG axons is filled with globular microtubule inner proteins (MIPs). Our data suggest these have a defined structure, which is surprising given they are thought to contain the disordered protein MAP6. In summary, we reveal novel morphological and structural features of microtubules in their native environment.

cell biology↗

bioRxiv2021

Structures and function of locked conformations of SARS-CoV-2 spike

The spike (S) protein of SARS-CoV-2 has been observed in three distinct pre-fusion conformations: locked, closed and open. Of these, the function of the locked conformation remains poorly understood. Here we engineered a SARS-CoV-2 S protein construct "S-R/x3" to arrest SARS-CoV-2 spikes in the locked conformation by a disulfide bond. Using this construct we determined high-resolution structures confirming that the x3 disulfide bond has the ability to stabilize the otherwise transient locked conformations. Structural analyses reveal that wild-type SARS-CoV-2 spike can adopt two distinct locked-1 and locked-2 conformations. For the D614G spike, based on which all variants of concern were evolved, only the locked-2 conformation was observed. Analysis of the structures suggests that rigidified domain D in the locked conformations interacts with the hinge to domain C and thereby restrains RBD movement. Structural change in domain D correlates with spike conformational change. We propose that the locked-1 and locked-2 conformations of S are present in the acidic high-lipid cellular compartments during virus assembly and egress. In this model, release of the virion into the neutral pH extracellular space would favour transition to the closed or open conformations. The dynamics of this transition can be altered by mutations that modulate domain D structure, as is the case for the D614G mutation, leading to changes in viral fitness. The S-R/x3 construct provides a tool for the further structural and functional characterization of the locked conformations of S, as well as how sequence changes might alter S assembly and regulation of receptor binding domain dynamics.

microbiology↗