Curved EFC/F-BAR-domain dimers are joined end to end into a filament for membrane invagination in endocytosis

The reticulon and DP1/Yop1p proteins form immobile oligomers in the tubular endoplasmic reticulum

We recently identified a class of membrane proteins, the reticulons and DP1/Yop1p, which shape the tubular endoplasmic reticulum (ER) in yeast and mammalian cells. These proteins are highly enriched in the tubular portions of the ER and virtually excluded from other regions. To understand how they promote tubule formation, we characterized their behavior in cellular membranes and addressed how their localization in the ER is determined. Using fluorescence recovery after photobleaching, we found that yeast Rtn1p and Yop1p are less mobile in the membrane than normal ER proteins. Sucrose gradient centrifugation and cross-linking analyses show that they form oligomers. Mutants of yeast Rtn1p, which no longer localize exclusively to the tubular ER or are even totally inactive in inducing ER tubules, are more mobile and oligomerize less extensively. The mammalian reticulons and DP1 are also relatively immobile and can form oligomers. The conserved reticulon homology domain that includes the two membrane-embedded segments is sufficient for the localization of the reticulons to the tubular ER, as well as for their diffusional immobility and oligomerization. Finally, ATP depletion in both yeast and mammalian cells further decreases the mobilities of the reticulons and DP1. We propose that oligomerization of the reticulons and DP1/Yop1p is important for both their localization to the tubular domains of the ER and for their ability to form tubules.

Four-scale description of membrane sculpting by BAR domains

BAR domains are proteins that sense and sculpt curved membranes in cells, furnishing a relatively well-studied example of mechanisms employed in cellular morphogenesis. We report a computational study of membrane bending by BAR domains at four levels of resolution, described by 1), all-atom molecular dynamics; 2), residue-based coarse-graining (resolving single amino acids and lipid molecules); 3), shape-based coarse-graining (resolving overall protein and membrane shapes); and 4), a continuum elastic membrane model. Membrane sculpting performed by BAR domains collectively is observed in agreement with experiments. Different arrangements of BAR domains on the membrane surface are found to lead to distinct membrane curvatures and bending dynamics.

Sorting nexin-1 defines an early phase of Salmonella-containing vacuole-remodeling during Salmonella infection

Salmonella enterica serovar Typhimurium replicate within host cells in a specialized membrane-bound compartment, the Salmonella-containing vacuole (SCV). Interaction of SCVs with the host endocytic network is modulated by bacterial effectors, some of which, such as SigD/SopB, manipulate the level of endosomal phosphoinositides. Here, we establish that at early stages of Salmonella infection, sorting nexin-1 (SNX1) - a host phosphoinositide-binding protein that normally associates with early endosomes and regulates transport to the trans-Golgi network (TGN) - undergoes a rapid and transient translocation to bacterial entry sites, an event promoted by SigD/SopB. Recruitment of SNX1 to SCVs results in the formation of extensive, long-range tubules that we have termed ;spacious vacuole-associated tubules'. Formation of these tubules is coupled with size reduction of vacuoles and the removal of TGN-resident cargo. SNX1 suppression perturbs intracellular progress of bacteria, resulting in a delayed replication. We propose that SNX1 is important in tubular-based re-modeling of nascent SCVs and, in doing so, regulates intracellular bacterial progression and replication.

Factors influencing local membrane curvature induction by N-BAR domains as revealed by molecular dynamics simulations

N-BAR domains are protein modules that bind to and induce curvature in membranes via a charged concave surface and N-terminal amphipathic helices. Recently, molecular dynamics simulations have demonstrated that the N-BAR domain can induce a strong local curvature that matches the curvature of the BAR domain surface facing the bilayer. Here we present further molecular dynamics simulations that examine in greater detail the roles of the concave surface and amphipathic helices in driving local membrane curvature. We find that the strong curvature induction observed in our previous simulations requires the stable presentation of the charged concave surface to the membrane and is not driven by the membrane-embedded amphipathic helices. Nevertheless, without these amphipathic helices embedded in the membrane, the N-BAR domain does not maintain a close association with the bilayer, and fails to drive membrane curvature. Increasing the membrane negative charge through the addition of PIP(2) facilitates closer association with the membrane in the absence of embedded helices. At sufficiently high concentrations, amphipathic helices embedded in the membrane drive membrane curvature independently of the BAR domain.

Perturbation of syndapin/PACSIN impairs synaptic vesicle recycling evoked by intense stimulation

Synaptic vesicle recycling has been proposed to depend on proteins which coordinate membrane and cytoskeletal dynamics. Here, we examine the role of the dynamin- and N-WASP (neural Wiskott-Aldrich syndrome protein)-binding protein syndapin/PACSIN at the lamprey reticulospinal synapse. We find that presynaptic microinjection of syndapin antibodies inhibits vesicle recycling evoked by intense (5 Hz or more), but not by light (0.2 Hz) stimulation. This contrasts with the inhibition at light stimulation induced by perturbation of amphiphysin (Shupliakov et al., 1997). Inhibition by syndapin antibodies was associated with massive accumulation of membranous cisternae and invaginations around release sites, but not of coated pits at the plasma membrane. Cisternae contained vesicle membrane, as shown by vesicle-associated membrane protein 2 (VAMP2)/synaptobrevin 2 immunolabeling. Similar effects were observed when syndapin was perturbed before onset of massive endocytosis induced by preceding intense stimulation. Selective perturbation of the Src homology 3 domain interactions of syndapin was sufficient to induce vesicle depletion and accumulation of cisternae. Our data show an involvement of syndapin in synaptic vesicle recycling evoked by intense stimulation. We propose that syndapin is required to stabilize the plasma membrane and/or facilitate bulk endocytosis at high release rates.

Structural basis of membrane invagination by F-BAR domains

BAR superfamily domains shape membranes through poorly understood mechanisms. We solved structures of F-BAR modules bound to flat and curved bilayers using electron (cryo)microscopy. We show that membrane tubules form when F-BARs polymerize into helical coats that are held together by lateral and tip-to-tip interactions. On gel-state membranes or after mutation of residues along the lateral interaction surface, F-BARs adsorb onto bilayers via surfaces other than their concave face. We conclude that membrane binding is separable from membrane bending, and that imposition of the module's concave surface forces fluid-phase bilayers to bend locally. Furthermore, exposure of the domain's lateral interaction surface through a change in orientation serves as the crucial trigger for assembly of the helical coat and propagation of bilayer bending. The geometric constraints and sequential assembly of the helical lattice explain how F-BAR and classical BAR domains segregate into distinct microdomains, and provide insight into the spatial regulation of membrane invagination.

Flexible scaffolding made of rigid BARs

Crescent-shaped BAR domains are generic actors in the creation of membrane curvature. In this issue, Frost et al. (2008) reveal how collective twisting of rigid F-BAR domains on a soft membrane surface may lead to different membrane curvatures.

Membrane recognition by phospholipid-binding domains

Many different globular domains bind to the surfaces of cellular membranes, or to specific phospholipid components in these membranes, and this binding is often tightly regulated. Examples include pleckstrin homology and C2 domains, which are among the largest domain families in the human proteome. Crystal structures, binding studies and analyses of subcellular localization have provided much insight into how members of this diverse group of domains bind to membranes, what features they recognize and how binding is controlled. A full appreciation of these processes is crucial for understanding how protein localization and membrane topography and trafficking are regulated in cells.

Membrane proteins of the endoplasmic reticulum induce high-curvature tubules

The tubular structure of the endoplasmic reticulum (ER) appears to be generated by integral membrane proteins, the reticulons and a protein family consisting of DP1 in mammals and Yop1p in yeast. Here, individual members of these families were found to be sufficient to generate membrane tubules. When we purified yeast Yop1p and incorporated it into proteoliposomes, narrow tubules (approximately 15 to 17 nanometers in diameter) were generated. Tubule formation occurred with different lipids; required essentially only the central portion of the protein, including its two long hydrophobic segments; and was prevented by mutations that affected tubule formation in vivo. Tubules were also formed by reconstituted purified yeast Rtn1p. Tubules made in vitro were narrower than normal ER tubules, due to a higher concentration of tubule-inducing proteins. The shape and oligomerization of the "morphogenic" proteins could explain the formation of the tubular ER.

Plasma membrane deformation by circular arrays of ESCRT-III protein filaments

Endosomal sorting complex required for transport III (ESCRT-III) proteins function in multivesicular body biogenesis and viral budding. They are recruited from the cytoplasm to the membrane, where they assemble into large complexes. We used “deep-etch” electron microscopy to examine polymers formed by the ESCRT-III proteins hSnf7-1 (CHMP4A) and hSnf7-2 (CHMP4B). When overexpressed, these proteins target to endosomes and the plasma membrane. Both hSnf7 proteins assemble into regular approximately 5-nm filaments that curve and self-associate to create circular arrays. Binding to a coexpressed adenosine triphosphate hydrolysis–deficient mutant of VPS4B draws these filaments together into tight circular scaffolds that bend the membrane away from the cytoplasm to form buds and tubules protruding from the cell surface. Similar buds develop in the absence of mutant VPS4B when hSnf7-1 is expressed without its regulatory C-terminal domain. We demonstrate that hSnf7 proteins form novel membrane-attached filaments that can promote or stabilize negative curvature and outward budding. We suggest that ESCRT-III polymers delineate and help generate the luminal vesicles of multivesicular bodies.

Vesicle, mitochondrial, and plastid division machineries with emphasis on dynamin and electron-dense rings

The original eukaryotic cells contained at least one set of double-membrane-bounded organelles (cell nucleus and mitochondria) and single-membrane-bounded organelles [endoplasmic reticulum, Golgi apparatus, lysosomes (vacuoles), and microbodies (peroxisomes)]. An increase in the number of organelles accompanied the evolution of these cells into Amoebozoa and Opisthokonta. Furthermore, the basic cells, containing mitochondria, engulfed photosynthetic Cyanobacteria, which were converted to plastids, and the cells thereby evolved into cells characteristic of the Bikonta. How did basic single- and double-membrane-bounded organelles originate from bacteria-like cells during early eukaryotic evolution? To answer this question, the important roles of the GTPase dynamin- and electron-dense rings in the promotion of diverse cellular activities in eukaryotes, including endocytosis, vesicular transport, mitochondrial division, and plastid division, must be considered. In this review, vesicle division, mitochondrial division, and plastid division machineries, including the dynamin- and electron-dense rings, and their roles in the origin and biogenesis of organelles in eukaryote cells are summarized.

Roles of F-BAR/PCH proteins in the regulation of membrane dynamics and actin reorganization

The Pombe Cdc15 Homology (PCH) proteins have emerged in many species as important coordinators of signaling pathways that regulate actomyosin assembly and membrane dynamics. The hallmark of the PCH proteins is the presence of a Fes/CIP4 homology-Bin/Amphiphysin/Rvsp (F-BAR) domain; therefore they are commonly referred to as F-BAR proteins. The prototype F-BAR protein, Cdc15p of Schizosaccharomyces pombe, has a role in the formation of the contractile actomyosin ring during cytokinesis. Vertebrate F-BAR proteins have an established role in binding phospholipids and they participate in membrane deformations, for instance, during the internalization of transmembrane receptors. This way the F-BAR proteins will function as linkers between the actin polymerization apparatus and the machinery regulating membrane dynamics. Interestingly, some members of the F-BAR proteins are implicated in inflammatory or neurodegenerative disorders and the observations can be expected to have clinical implications for the treatment of the diseases.

The Fer tyrosine kinase regulates an axon retraction response to Semaphorin 3A in dorsal root ganglion neurons

Background

Fps/Fes and Fer are the only two members of a distinct subclass of cytoplasmic protein tyrosine kinases. Fps/Fes was previously implicated in Semaphorin 3A (Sema3A)-induced growth cone collapse signaling in neurons from the dorsal root ganglion (DRG) through interaction with and phosphorylation of the Sema3A receptor component PlexinA1, and members of the collapsin response mediator protein (CRMP) family of microtubule regulators. However, the potential role of the closely related Fer kinase has not been examined.

Results

Here we provide novel biochemical and genetic evidence that Fer plays a prominent role in microtubule regulation in DRG neurons in response to Sema3A. Although Fps/Fes and Fer were both expressed in neonatal brains and isolated DRGs, Fer was expressed at higher levels; and Fer, but not Fps/Fes kinase activity was detected in vivo. Fer also showed higher in vitro kinase activity toward tubulin, as an exogenous substrate; and this activity was higher when the kinases were isolated from perinatal relative to adult brain stages. CRMP2 was a substrate for both kinases in vitro, but both CRMP2 and PlexinA1 inhibited their autophosphorylation activities. Cultured mouse DRG neurons retracted their axons upon exposure to Sema3A, and this response was significantly diminished in Fer-deficient, but only slightly attenuated in Fps/Fes-deficient DRG neurons.

Conclusion

Fps/Fes and Fer are both capable of phosphorylating tubulin and the microtubule regulator CRMP2 in vitro; and their in vitro kinase activities were both inhibited by CRMP2 or PlexinA1, suggesting a possible regulatory interaction. Furthermore, Fer plays a more prominent role than Fps/Fes in regulating the axon retraction response to Sema3A in DRG neurons. Therefore, Fps/Fes and Fer may play important roles in developmental or regenerative axon pathfinding through signaling from Sema3A to the microtubule cytoskeleton.

The PX-BAR membrane-remodeling unit of sorting nexin 9

Sorting nexins (SNXs) form a family of proteins known to interact with components in the endosomal system and to regulate various steps of vesicle transport. Sorting nexin 9 (SNX9) is involved in the late stages of clathrin-mediated endocytosis in non-neuronal cells, where together with the GTPase dynamin, it participates in the formation and scission of the vesicle neck. We report here crystal structures of the functional membrane-remodeling unit of SNX9 and show that it efficiently tubulates lipid membranes in vivo and in vitro. Elucidation of the protein superdomain structure, together with mutational analysis and biochemical and cell biological experiments, demonstrated how the SNX9 PX and BAR domains work in concert in targeting and tubulation of phosphoinositide-containing membranes. The study provides insights into the SNX9-induced membrane modulation mechanism.

F-BAR Proteins Join the BAR Family Fold

Expanding the range of curvature generating and curvature stabilizing protein modules, the first F-BAR domain structures support their assignment to the BAR domain superfamily and emphasize how modifications to a basic structural frame can generate a broad spectrum of properties.