Biology subjects

Kaksonen, M.

Publications and source records attributed to Kaksonen, M..

18 recordsLinked to original sources

bioRxiv2026

Adaptor interactions trigger Pan1 self-assembly during clathrin-mediated endocytosis in budding yeast

Clathrin-mediated endocytosis requires the coordinated assembly of a highly dynamic protein network that couples membrane remodeling to actin-driven force generation. The essential budding yeast protein, Pan1, scaffolds the endocytic protein network by linking adaptor proteins, and other coat components, and actin assembly regulators. How Pan1 coordinates all these different proteins in space and time is not well understood. We show that Pan1 undergoes biomolecular condensation. Elevated Pan1 expression induced the formation of condensates that exhibited partial rapid molecular exchange, temperature-dependent reversibility, and sensitivity to disruption of weak hydrophobic interactions. The Pan1 assemblies are compositionally selective, preferentially enriching late-stage endocytic factors while excluding early adaptor proteins. Truncation analysis demonstrated that condensation depends on cooperative contributions from intrinsically disordered regions, the EH2 domain, and the oligomerization module, whereas a C-terminal region negatively regulates condensation. Deletion of Pan1 regions promoting its self-assembly perturbed Pan1 assembly and function at endocytic sites. Disruption of interactions between Pan1 and endocytic adaptors did not alter the dynamics of endocytic events but instead reduced the number of endocytic events marked by Pan1 and caused the formation of ectopic Pan1 condensates. This indicates that adaptor-mediated interactions spatially constrain Pan1 localization by seeding Pan1 assembly at endocytic sites. Our findings support a model in which adaptor proteins seed Pan1 assembly at the endocytic sites while multivalent interactions drive Pan1 self-assembly to build the higher-order molecular network of the late endocytic coat.

cell biology↗

bioRxiv2026

A switch in clathrin turnover controls endocytic coat size and organisation

Endocytosis internalises nutrients, regulates extracellular signals, and recycles membrane components. Clathrin polymerises into a coat that shapes the endocytic vesicle from the plasma membrane. However, the role of clathrins dynamic assembly in the endocytic process remains unclear. We show, using two-colour fluorescence recovery after photobleaching assays in yeast, that the clathrin coat turns over rapidly in the early phase of endocytosis, dependent on the auxilin Swa2 and its ATPase. In the late phase the turnover is stopped by the coat protein Sla1. Regulated clathrin turnover is critical for the timing of endocytic progression and for controlling coat size. In the absence of this dynamic regulation the endocytic coats become abnormally large, resulting in the failure of the final actin-driven vesicle budding. These findings reveal that, in addition to its classic structural function, the dynamic properties of the clathrin lattice are critical for both the temporal and mechanical aspects of endocytosis.

cell biology↗

bioRxiv2025

Molecular basis for cellular compartmentalization by an ancient membrane fission mechanism

The emergence of cell compartmentalization depends on membrane fission to create the endomembrane compartments. In eukaryotes, membrane fission is commonly executed by ESCRT-III, a protein complex conserved in all domains of life. However, whether membrane fission was an ancestral ESCRT-III activity predating eukaryogenesis remains unknown. Here we show that ESCRT-IIIA from Asgard Heimdallarchaeota, the closest archaeal relatives of eukaryotes, performs membrane fission through an N-terminal amphipathic helix, which we term Hofund. In eukaryotes, Hofund is fragmented across ESCRT-IIIA paralogs, and disrupting these regions causes severe fission defect in yeast. Remarkably, Heimdallarchaeota Hofund restores fission when fused to defective eukaryotic paralogs. These findings suggest that ESCRT-III-mediated fission arose before eukaryogenesis and later diversified to support the regulatory complexity of eukaryotic compartmentalization.

cell biology↗

bioRxiv2025

The molecular basis of tricalbin-mediated membrane contact site organization in cells

Membrane contact sites facilitate molecular exchanges through physical interactions between organelles, connected by specific protein tethers. Among these tethers are the tricalbins, which mediate contacts between endoplasmic reticulum (ER) and plasma membrane in yeast. Tricalbins are integral to the ER, have a cytosolic lipid binding domain and bind the plasma membrane through C2 domains. Here, we combine fluorescence recovery after photobleaching with correlative light and 3D electron microscopy to dissect how tricalbins control their localization, dynamic distribution and contact site organization. We find that heteromerization via lipid binding domains is a prerequisite for tricalbin accumulation at contact sites, membrane curvature sensing and restrained mobility in the ER. By altering tricalbin protein domains, we show that intermembrane distances and intrinsically disordered regions interdependently control distribution and dynamics of contact site tethers. Our study reveals principles of contact site architecture that are fine-tuned by tricalbin domain organization.

cell biology↗

bioRxiv2025

Evolutionarily diverged on-switch for actin assembly in fungal endocytosis

Clathrin-mediated endocytosis is a conserved eukaryotic trafficking process where an Arp2/3 complex nucleated branched actin network provides force for vesicle formation. The mechanisms that initiate endocytic actin assembly are incompletely understood. In the fission yeast, Schizosaccharomyces pombe, actin assembly is initiated by Dip1, an Arp2/3 activator. In the budding yeast, Saccharomyces cerevisiae, the initiation of actin assembly has remained a mystery. Here we show that S. cerevisiae Ldb17, the homolog of Dip1, functions as an on-switch for endocytic actin assembly. Unexpectedly, the regulation of Ldb17 is more complicated than that of constitutively active Dip1. Ldb17 is controlled by a coat protein, Sla1, via separate recruitment and activation steps. This regulation was likely lost in the S. pombe lineage and this simplification may be related to other changes in actin assembly between these species. Our findings add a key missing piece in the understanding of endocytosis in S. cerevisiae and reveal an intriguing evolutionary tinkering of the actin on-switch.

cell biology↗

bioRxiv2025

High resolution mapping of the actin fusion focus reveals myosin V-dependent transport of formin for actin aster compaction

Many cellular processes such as polarized growth and secretion require the formation of specific actin networks. In fungi, the morphogenetic process of cell-cell fusion requires cell wall digestion mediated by the local secretion of lytic enzymes at the site of cell-cell contact. In Schizosaccharomyces pombe, lytic enzyme-containing secretory vesicles are transported by the myosin V Myo52 on the actin fusion focus, an aster-like actin network assembled by the condensate-forming formin Fus1. The fusion focus also concentrates proteins regulating cell polarity, cell-cell communication, actin cytoskeleton, exocytosis and membrane merging, but their precise position from the time of focus formation to cell fusion is unknown. Here, using centroid tracking and averaging, we present a first spatiotemporal map of the fusion site with a precision of 8 nm. We show that the bulk of secretory vesicles remains at constant distance from the plasma membrane as the actin structure condenses. Notably, though necessary to transport vesicles, Myo52 detaches from the vesicle pool and colocalizes with Fus1 in a more membrane-proximal position. We show that Myo52 physically interacts with Fus1 and transports it along actin filaments, and that Myo52 and Fus1 actin assembly activity contribute to focus compaction. Thus, myosin V-driven transport of the formin Fus1 along actin filaments nucleated by other Fus1 molecules underlies a positive feedback mechanism for actin aster formation.

cell biology↗

bioRxiv2024

Two-dimensional condensates of HRS drive the assembly of flat clathrin lattices on endosomes

In cells, the curved clathrin structures in vesicle budding are well characterized, while the flat ones remain poorly understood. We reconstituted the flat assembly of ESCRT-0 protein HRS and clathrin onto lipid membranes in vitro. HRS was found to form protein condensates. These condensates spread as a two-dimensional layer on negatively charged membranes and promoted the assembly of clathrin into a flat coat. Correlative cryo-tomography of HRS-labeled endosomes revealed a pure hexagonal lattice, consistent with flat clathrin structures. Cholesterol enhanced HRS recruitment to the membrane both in cells and in supported bilayers. Furthermore, cholesterol promoted the phase separation of HRS onto membranes, which in turn concentrated cholesterol underneath. This positive feedback promoted the formation of HRS-clathrin microdomains that sorted reconstituted ubiquitinated cargoes. Altogether, our results show that the unique architecture of ESCRT-0 is assembled by the two-dimensional phase-separation of HRS which drives the assembly of flat clathrin coats.

biochemistry↗

bioRxiv2024

An evolutionary cell biology perspective into the diverging mechanisms of clathrin-mediated endocytosis in dikarya fungi

Clathrin-mediated endocytosis is an ancient eukaryotic trafficking pathway, which transports plasma membrane and associated cargo into the cell and is involved in numerous cell- and tissue-level processes. Cargo selection and clathrin-coated vesicle formation is mediated by over 60 proteins that assemble in a regular and sequential manner at the plasma membrane. Decades of endocytosis studies have followed the tenet that uncovering the conserved core molecular mechanisms is sufficient to understand a cellular process. However, this approach also revealed a number of cell type or species-related variations that challenge a universal conserved, core mechanism. In this paper, we refocus on the endocytic diversity to understand how evolution shapes endocytic mechanisms. We define a comparative evolutionary cell biology approach that uses dikarya fungi as a model clade and live-cell fluorescence microscopy to study endocytosis dynamics in three species: Saccharomyces cerevisiae, Schizosaccharomyces pombe and Ustilago maydis. Our results quantitatively define several phenotypic differences between the species. We uncover several differences that impact the endocytic early phase, the protein assembly order, actin regulation, membrane invagination and scission. These findings demonstrate a mosaic evolution of endocytic traits, suggest ancestral states and direction of changes. We also investigate the phenotypic plasticity and robustness against environmental conditions. Lastly, we demonstrate that relatively minor evolutionary changes can majorly impact endocytic phenotypes. These studies force an appreciation of endocytic variation as not auxiliary, but vital to mechanistic understanding of this conserved cellular pathway.

cell biology↗

bioRxiv2024

PyF2F: A robust and simplified fluorophore-to-fluorophore distance measurement tool for Protein interactions from Imaging Complexes after Translocation experiments

SummaryStructural knowledge of protein assemblies in their physiological environment is paramount to understand cellular functions at the molecular level. Protein interactions from Imaging Complexes after Translocation (PICT) is a live-cell imaging technique for the structural characterization of macromolecular assemblies in living cells. PICT relies on the measurement of the separation between labelled molecules using fluorescence microscopy and cell engineering. Unfortunately, the required computational tools to extract molecular distances involve a variety of sophisticated software that challenge reproducibility and limit their implementation by highly specialised researchers. Here we introduce PyF2F, a Python-based software that provides a workflow for measuring molecular distances from PICT data, with minimal user programming expertise. We used a published dataset to validate PyF2F performance.

bioinformatics↗

bioRxiv2023

Bsp1, a fungal CPI motif protein, regulates actin filament capping in endocytosis and cytokinesis

The capping of barbed filament ends is a fundamental mechanism for actin regulation. Capping protein controls filament growth and actin turnover in cells by binding to the barbed ends of the filaments with high affinity and slow off-rate. The interaction between Capping protein and actin is regulated by capping protein interaction (CPI) motif proteins. We identified a novel CPI motif protein, Bsp1, which is involved in cytokinesis and endocytosis in budding yeast. We demonstrate that Bsp1 is an actin binding protein with a high affinity for capping protein via its CPI motif. In cells, Bsp1 regulates capping protein at endocytic sites and is a major recruiter of capping protein to the cytokinetic actin ring. Lastly, we define Bsp1-related proteins as a distinct fungi-specific CPI protein group. Our results suggest that Bsp1 promotes actin filament capping by the capping protein. This study establishes Bsp1 as a new capping protein regulator and promising candidate to regulate actin networks in fungi.

cell biology↗

bioRxiv2022

Spatio-temporal regulation of endocytic protein assembly by SH3 domains in yeast

Clathrin-mediated endocytosis is a conserved eukaryotic membrane trafficking pathway that is driven by a sequentially assembled molecular machinery that contains over 60 different proteins. SH3 domains are the most abundant protein-protein interaction domain in this process, but the function of most SH3 domains in protein dynamics remains elusive. Using mutagenesis and live-cell fluorescence microscopy in the budding yeast Saccharomyces cerevisiae, we dissected SH3-mediated regulation of the endocytic pathway. Our data suggest that multiple SH3 domains regulate the actin nucleation promoting Las17/Vrp1 complex, and that the network of SH3 interactions coordinate both Las17/Vrp1 assembly and dissociation. Furthermore, most endocytic SH3 domain proteins use the SH3 domain for their own recruitment, while a minority uses the SH3 domain to recruit other proteins, and not themselves. Our results provide a dynamic map of SH3 functions in yeast endocytosis and a framework for SH3 interaction network studies across biology.

cell biology↗

bioRxiv2021

Superresolution microscopy reveals partial preassembly and subsequent bending of the clathrin coat during endocytosis

Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargos. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle. Here, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area, before they become rapidly and continuously bent, and confirm this mechanism in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane.

cell biology↗

bioRxiv2021

Regulation of membrane scission in yeast endocytosis

During clathrin-mediated endocytosis, a flat plasma membrane is shaped into an invagination that undergoes scission to form a vesicle. In mammalian cells, the force that drives the transition from invagination to vesicle is primarily provided by the GTPase dynamin that acts in concert with crescent-shaped BAR domain proteins. In yeast cells, the mechanism of endocytic scission is unclear. The yeast BAR domain protein complex Rvs161/167 (Rvs) nevertheless plays an important role in this process: deletion of Rvs dramatically reduces scission efficiency. A mechanistic understanding of the influence of Rvs on scission however, remains incomplete. We used quantitative live-cell imaging and genetic manipulation to understand the recruitment and function of Rvs and other late-stage proteins at yeast endocytic sites. We found that arrival of Rvs at endocytic sites is timed by interaction of its BAR domain with specific membrane curvature. A second domain of Rvs167- the SH3 domain-affects localization efficiency of Rvs. We show that Myo3, one of the two type-I myosins in Saccharomyces cerevisiae, has a role in recruiting Rvs167 via the SH3 domain. Removal of the SH3 domain also affects assembly and disassembly of actin and impedes membrane invagination. Our results indicate that both BAR and SH3 domains are important for the role of Rvs as a regulator of scission. We tested other proteins implicated in vesicle formation in Saccharomyces cerevisiae, and found that neither synaptojanins nor dynamin contribute directly to membrane scission. We propose that recruitment of Rvs BAR domains delays scission and allows invaginations to grow by stabilizing them. We also propose that vesicle formation is dependent on the force exerted by the actin network component of the endocytic machinery.

cell biology↗

bioRxiv2020

Autoregulation clamps the synaptic membrane-remodeling machinery and promotes productive actin-dependent endocytosis

Synaptic membrane-remodeling events such as endocytosis require force-generating actin assembly. The endocytic machinery that regulates these actin and membrane dynamics localizes at high concentrations to large areas of the presynaptic membrane, but actin assembly and productive endocytosis are far more restricted in space and time. Here we describe a mechanism whereby autoinhibition clamps the presynaptic endocytic machinery to limit actin assembly to discrete functional events. We found that collective interactions between the Drosophila endocytic proteins Nwk/FCHSD2, Dap160/Intersectin, and WASp relieve Nwk autoinhibition and promote robust membrane-coupled actin assembly in vitro. Using automated particle tracking to quantify synaptic actin dynamics in vivo, we discovered that Nwk-Dap160 interactions constrain spurious assembly of WASp-dependent actin structures. These interactions also promote synaptic endocytosis, suggesting that autoinhibition both clamps and primes the synaptic endocytic machinery, thereby constraining actin assembly to drive productive membrane remodeling in response to physiological cues.

cell biology↗

bioRxiv2019

Phase separation of Ede1 promotes the initiation of endocytic events

Clathrin-mediated endocytosis is a major pathway that eukaryotic cells use to produce transport vesicles from the plasma membrane. The assembly of the endocytic coat is initiated by a dynamic network of weakly interacting proteins, but the exact mechanism of initiation is unknown. Ede1, the yeast homologue of mammalian Eps15, is one of the early-arriving endocytic proteins and a key initiation factor. In the absence of Ede1, most other early endocytic proteins lose their punctate localization and the frequency of endocytic initiation is decreased. We show here that in mutants with increased amounts of cytoplasmic Ede1, the excess protein forms large condensates which exhibit properties of phase separated liquid protein droplets. These Ede1 condensates recruit many other early-arriving endocytic proteins. Their formation depends on the core region of Ede1 that contains a coiled coil and a low-complexity domain. We demonstrate that Ede1 core region is essential for the endocytic function of Ede1. The core region can also promote clustering of a heterologous lipid-binding domain into discrete sites on the plasma membrane that initiate endocytic events. We propose that the clustering of the early endocytic proteins and cargo depend on phase separation mediated by Ede1.

cell biology↗

bioRxiv2018

Type-I myosins promote actin polymerization to drive membrane bending in endocytosis

Clathrin-mediated endocytosis in budding yeast requires the formation of a dynamic actin network that produces the force to invaginate the plasma membrane against the intracellular turgor pressure. The type-I myosins Myo3 and Myo5 are important for endocytic membrane reshaping, but mechanistic details of their function remain scarce. Here, we studied the function of Myo3 and Myo5 during endocytosis using quantitative live-cell imaging and genetic perturbations. We show that the type-I myosins promote, in a dose-dependent way, the growth and expansion of the actin network, which controls the speed of membrane and coat internalization. We found that this myosin-activity is independent of the actin nucleation promoting activity of myosins, and cannot be compensated for by increasing actin nucleation. Our results suggest a new mechanism for type-I myosins to produce force by promoting actin filament polymerization.

cell biology↗

bioRxiv2017

Systematic analysis of the molecular architecture of endocytosis reveals a nanoscale actin nucleation template that drives efficient vesicle formation

Clathrin-mediated endocytosis is an essential cellular function in all eukaryotes that is driven by a self-assembled macromolecular machine of over 50 different proteins in tens to hundreds of copies. How these proteins are organized to produce endocytic vesicles with high precision and efficiency is not understood. Here, we developed high-throughput superresolution microscopy to reconstruct the nanoscale structural organization of 23 endocytic proteins from over 100,000 endocytic sites in yeast. We found that proteins assemble by radially-ordered recruitment according to function. WASP family proteins form a circular nano-scale template on the membrane to spatially control actin nucleation during vesicle formation. Mathematical modeling of actin polymerization showed that this WASP nano-template creates sufficient force for membrane invagination and substantially increases the efficiency of endocytosis. Such nanoscale pre-patterning of actin nucleation may represent a general design principle for directional force generation in membrane remodeling processes such as during cell migration and division.

cell biology↗

bioRxiv2017

The contributions of the actin machinery to endocytic membrane bending and vesicle formation

Branched and crosslinked actin networks mediate cellular processes that move and shape membranes. To understand how actin contributes during the different stages of endocytic membrane reshaping, we analysed deletion mutants of yeast actin network components using a hybrid imaging approach that combines live imaging with correlative microscopy. We could thereby temporally dissect the effects of different actin network perturbations, revealing distinct stages of actin-based membrane reshaping. Our data show that initiation of membrane bending requires the actin network to be physically linked to the plasma membrane and to be optimally crosslinked. Once initiated, the membrane invagination process is driven by nucleation and polymerization of new actin filaments, independently of the degree of cross-linking and unaffected by a surplus of actin network components. A key transition occurs 2 seconds before scission when the filament nucleation rate drops. From that time point on, invagination growth and vesicle scission are driven by an expansion of the assembled actin network. The expansion is sensitive to the amount of filamentous actin and its crosslinking. Our results suggest that the mechanism by which actin reshapes the membrane adapts to force requirements that vary during the progress of endocytosis.

cell biology↗