Dynamin, a membrane-remodelling GTPase

Abstract

Dynamin, the founding member of a family of dynamin-like proteins (DLPs) implicated in membrane remodelling, has a critical role in endocytic membrane fission events. The use of complementary approaches, including live-cell imaging, cell-free studies, X-ray crystallography and genetic studies in mice, has greatly advanced our understanding of the mechanisms by which dynamin acts, its essential roles in cell physiology and the specific function of different dynamin isoforms. In addition, several connections between dynamin and human disease have also emerged, highlighting specific contributions of this GTPase to the physiology of different tissues.

Figure 1. Sites of action of dynamin and dynamin related proteins (DLPs) in a mammalian cell

(a) Dynamin is localized at sites of endocytosis. It is also found at actin meshworks nucleated by the Arp2/3 complex such as membrane ruffles, podosomes and invadopodia, and at actin pedestals induced by pathogenic bacteria. Other DLPs, including atlastin, Drp1, OPA1 and mitofusin, localize to sites of intracellular membrane fission and fusion in the endoplasmic reticulum and mitochondria. The location of dynamin and DLPs is shown in red while F-actin is coloured green. The endosymbiotic origin of mitochondria (i.e. their formation by the endocytosis of an ancient prokaryote) may explain the role of a DLP in the fission of their outer mitochondrial membrane

Figure 2. Structure of dynamin and putative mechanism of dynamin-mediated membrane fission

(a) Top: Linear representation of the domain organization of dynamin based on its 3D structure as revealed by crystallographic studies (numbers indicate amino acid position within the primary sequence of human dynamin 1, xa splice variant). Regions that belong to the same folded module are shown in the same color. Bottom: crystal structure of a dynamin dimer (color coded to match the linear representation). Molecular graphics were created with Pymol, PDB code 3SNH ). (b) Schematic representation of dynamin dimers and of helical dynamin polymers around a tubular template in two different orientations (90 degrees rotation). The colour-coding of the domains matches the colors of panel (a). The approximate location of the bound nucleotide is highlighted in yellow. Dynamin polymerization occurs as a result of interactions between the stalks of dynamin monomers (interface 2) and between stalk dimers (interfaces 1 and 3). The GTP-dependent dimerization of G domains between adjacent rungs of the dynamin helix (highlighted in yellow stars, longitudinal view of the helix), is thought to promote assembly-stimulated GTPase activity, resulting in membrane constriction and ultimately fission. (d) Proposed GTP hydrolysis-dependent lever-like movement of dynamin's neck (BSE) relative to the G domain. (e) Schematic view of the key steps leading to dynamin-mediated membrane fission. (e) Cryo-EM image showing a helical polymer of purified dynamin that has driven the formation of a tubule from a liposome. Image kindly provided by Adam Frost and Vincenz Unger (University of Utah and Northwestern University respectively).

Figure 3. Dynamin and clathrin-mediated endocytosis

(a) Putative sequence of action of actin, BAR proteins and dynamin at clathrin coated endocytic pits as revealed by studies of cells that lack dynamin (dynamin 1,2 double KO fibroblasts) . Lack of dynamin results in an arrest of the endocytic reaction at the stage of deeply invaginated pits and in the actin-dependent elongation of their BAR protein coated tubular necks (EM micrograph at lower right, reproduced with permission from ). When actin is depolymerized (latrunculin B treatment), clathrin coated buds collapse to omega shaped pits with short wide necks (upper left EM micrograph, reproduced with permission from ). The fluorescence micrograph shows tubulated endocytic clathrin coated pits in dynamin 1,2 double KO fibroblasts as revealed by live cell imaging of the BAR protein endophilin 2-GFP (tubular neck) and of RFP-clathrin light chain (reproduced with permission from ) (b) Schematic timeline showing the accumulation of endocytic proteins at endocytic pits. The zero time represents the fission reaction, as determined by the loss of accessibility of the bud lumen to the extracellular medium (sketched based on data from ). Note that the role of actin may be non-essential under some conditions ^, .

Figure 4. Dynamin participates in synaptic vesicle recycling at neuronal synapses

(a) From electron microscopy analysis, wild type synapses (left) are characterized by an abundance of synaptic vesicles and very few clathrin-coated pits or clathrin-coated vesicles, consistent with the transient nature of clathrin-coated structures even during intense synaptic activity. At synapses that lack the great majority of their normal dynamin content (for example, from dynamin 1 knockout neurons or even more strikingly from dynamin 1,3 double KO neurons) (right) there is a depletion of synaptic vesicles and a striking accumulation of uniformly sized clathrin coated pits which bud from long invaginations of the plasma membrane ^{, ,} . A small increase in the abundance of clathrin coated pits is also observed post-synaptically, where pits are heterogeneous in size. (b) Representative electron micrograph of a presynaptic terminal from a dynamin 1 knockout neuron. Presynaptic vesicle clusters at two synaptic junctions are very small (regions defined by dashed lines) while clathrin-coated vesicular structures are highly abundant and occupy the bulk of the terminal. As shown by electron tomography (see field c), all such structures are coated pits, although in this thin section (~60nm) their tubular stalks can only seen in few cases and their connection with the plasma membrane cannot be appreciated ^, . (c) Partial electron tomography reconstruction from a dynamin 1,3 double KO nerve terminals showing a long tubular plasma membrane invagination studded with numerous individual clathrin coated pits. The arrow indicates the opening of this tubular structure at the peripheral presynaptic plasma membrane. (d) In resting synapses, the PRD region of dynamin 1 is phosphorylated, preventing association with syndapin. Upon stimulation and increased cytosolic [Ca²⁺], the protein phosphatase calcineurin, which directly binds a dynamin 1 splice variant (xb), dephosphorylates dynamin 1, allowing its interaction with syndapin. This regulated interaction is thought to promote synaptic vesicle endocytosis at times of elevated neuronal activity.