Dissection of a single round of vesicular transport: sequential intermediates for intercisternal movement in the Golgi stack

Multi-view local hyperplane nearest neighbor model based on independence criterion for identifying vesicular transport proteins

Vesicular transport proteins participate in various biological processes and play a significant role in the movement of substances within cells. These proteins are associated with numerous human diseases, making their identification particularly important. In this study, we developed a novel strategy for accurately identifying vesicular transport proteins. We developed a novel multi-view classifier called graph-regularized k-local hyperplane distance nearest neighbor model (HSIC-GHKNN), which combines the Hilbert-Schmidt independence criterion (HSIC)-based multi-view learning method with a local hyperplane distance nearest-neighbor classifier. We first extracted protein evolution information using two feature extraction methods, pseudo-position-specific scoring matrix (PsePSSM) and AATP, and addressed dataset imbalance using the Edited Nearest Neighbors (ENN) algorithm. Subsequently, we employed a local hyperplane distance nearest-neighbor classifier for each view identification and added an HSIC term to maintain independence between views. We then assessed the performance of our identification strategy and analyzed the PsePSSM and AATP feature sets to determine the influencing factors of the classification results. The experimental results demonstrate that the accurate and Matthew correlation coefficients of our strategy on the independent test set are 85.8 % and 0.548, respectively. Our approach outperformed existing methods in most evaluation metrics. In addition, the proposed multi-view classification model can easily be applied to similar identification tasks.

Stack-VTP: prediction of vesicle transport proteins based on stacked ensemble classifier and evolutionary information

Vesicle transport proteins not only play an important role in the transmembrane transport of molecules, but also have a place in the field of biomedicine, so the identification of vesicle transport proteins is particularly important. We propose a method based on ensemble learning and evolutionary information to identify vesicle transport proteins. Firstly, we preprocess the imbalanced dataset by random undersampling. Secondly, we extract position-specific scoring matrix (PSSM) from protein sequences, and then further extract AADP-PSSM and RPSSM features from PSSM, and use the Max-Relevance-Max-Distance (MRMD) algorithm to select the optimal feature subset. Finally, the optimal feature subset is fed into the stacked classifier for vesicle transport proteins identification. The experimental results show that the of accuracy (ACC), sensitivity (SN) and specificity (SP) of our method on the independent testing set are 82.53%, 0.774 and 0.836, respectively. The SN, SP and ACC of our proposed method are 0.013, 0.007 and 0.76% higher than the current state-of-the-art methods.

VTP-Identifier: Vesicular Transport Proteins Identification Based on PSSM Profiles and XGBoost

Vesicular transport proteins are related to many human diseases, and they threaten human health when they undergo pathological changes. Protein function prediction has been one of the most in-depth topics in bioinformatics. In this work, we developed a useful tool to identify vesicular transport proteins. Our strategy is to extract transition probability composition, autocovariance transformation and other information from the position-specific scoring matrix as feature vectors. EditedNearesNeighbours (ENN) is used to address the imbalance of the data set, and the Max-Relevance-Max-Distance (MRMD) algorithm is adopted to reduce the dimension of the feature vector. We used 5-fold cross-validation and independent test sets to evaluate our model. On the test set, VTP-Identifier presented a higher performance compared with GRU. The accuracy, Matthew's correlation coefficient (MCC) and area under the ROC curve (AUC) were 83.6%, 0.531 and 0.873, respectively.

Computational identification of vesicular transport proteins from sequences using deep gated recurrent units architecture

Protein function prediction is one of the most well-studied topics, attracting attention from countless researchers in the field of computational biology. Implementing deep neural networks that help improve the prediction of protein function, however, is still a major challenge. In this research, we suggested a new strategy that includes gated recurrent units and position-specific scoring matrix profiles to predict vesicular transportation proteins, a biological function of great importance. Although it is difficult to discover its function, our model is able to achieve accuracies of 82.3% and 85.8% in the cross-validation and independent dataset, respectively. We also solve the problem of imbalance in the dataset via tuning class weight in the deep learning model. The results generated showed sensitivity, specificity, MCC, and AUC to have values of 79.2%, 82.9%, 0.52, and 0.861, respectively. Our strategy shows superiority in results on the same dataset against all other state-of-the-art algorithms. In our suggested research, we have suggested a technique for the discovery of more proteins, particularly proteins connected with vesicular transport. In addition, our accomplishment could encourage the use of gated recurrent units architecture in protein function prediction.

Lelio Orci, the modern master of morphology

Lelio Orci has made seminal contributions to our understanding of pancreatic islet structure and function. He introduced quantitative criteria to structural analysis in the study of endocrine pancreas in a series of works performed in collaboration with Albert Renold, Roger Unger, and Donald Steiner. Orci has moved islet cell morphology from the primitive era of histochemistry and electron microscopy into the modern era of cell biology, applying the most advanced techniques and covering every aspect of normal and pathological structure-function relationships. In collaboration with James Rothman in New York and Randy Schekman in Berkley, Orci discovered that the transport steps from the endoplasmic reticulum to the Golgi complex, and within the Golgi, are mediated by two sets of vesicles coated with protein envelopes different from clathrin.

COPI selectively drives maturation of the early Golgi

COPI coated vesicles carry material between Golgi compartments, but the role of COPI in the secretory pathway has been ambiguous. Previous studies of thermosensitive yeast COPI mutants yielded the surprising conclusion that COPI was dispensable both for the secretion of certain proteins and for Golgi cisternal maturation. To revisit these issues, we optimized the anchor-away method, which allows peripheral membrane proteins such as COPI to be sequestered rapidly by adding rapamycin. Video fluorescence microscopy revealed that COPI inactivation causes an early Golgi protein to remain in place while late Golgi proteins undergo cycles of arrival and departure. These dynamics generate partially functional hybrid Golgi structures that contain both early and late Golgi proteins, explaining how secretion can persist when COPI has been inactivated. Our findings suggest that cisternal maturation involves a COPI-dependent pathway that recycles early Golgi proteins, followed by multiple COPI-independent pathways that recycle late Golgi proteins.

DOI:http://dx.doi.org/10.7554/eLife.13232.001

Proteins play many important roles for cells, and these roles often require the proteins to be in particular locations in or around the cells. A set of cell compartments called the Golgi packages certain proteins into bubble-like structures called vesicles to enable the proteins to be used elsewhere in the cell or released to the outside of the cell, in a process called the secretory pathway. The operation of the secretory pathway requires the Golgi compartments to be continually remodeled.

Proteins and other materials can be ferried between the compartments of the Golgi by another type of vesicle. These vesicles are coated with a group, or complex, of proteins called COPI, which forms a curved lattice around the vesicles and helps them to capture the materials they will transport. However, it is not clear whether COPI is also involved in remodeling of the Golgi compartments.

Papanikou, Day et al. addressed this question using a technique called the “anchor-away method” combined with microscopy to study COPI in yeast cells. The yeast were genetically engineered so that COPI activity was effectively shut down in the presence of a drug called rapamycin. The experiments show that COPI is involved in the early stages of remodeling the Golgi compartments, but not the later stages. This finding supports the emerging view of the Golgi as a self-organizing cellular machine, and it provides a framework for uncovering the engineering principles that underlie the secretory pathway.

DOI:http://dx.doi.org/10.7554/eLife.13232.002

From fission to fusion: a perspective on the research that won the Nobel Prize in Physiology or Medicine, 2013

Secretion is widespread in all eukaryotic cells: all of us experience this in the course of daily life--saliva, mucus, sweat, tears, bile juice, adrenalin, etc.--the list is extremely long. How does a cell manage to repeatedly spit out some stuff without losing the rest? The answer is: through regulated vesicle trafficking within the cell. The Nobel Prize in Physiology or Medicine 2013 was awarded to Drs Randy Schekman, James E Rothman and Thomas C Südhof for their 'discoveries of machinery regulating vesicle traffic, a major transport system in our cells'. Dr Randy Schekman and his colleagues discovered a number of genes required for vesicle trafficking from the endoplasmic reticulum (ER) and Golgi; the James E Rothman group unravelled the protein machinery that allows vesicles to bud off from the membrane and fuse to their targets; and Dr Thomas C Südhof along with his colleagues revealed how calcium ions could instruct vesicles to fuse and discharge their contents with precision. These enabled the biotechnology industry to produce a variety of pharmaceutical and industrial products like insulin and hepatitis B vaccines, in a cost-efficient manner, using yeast and tissue cultured cells.

The principle of membrane fusion in the cell (Nobel lecture)

Cells contain small membrane-enclosed vesicles which transport many kinds of cargo between the compartments of the cell. The result is a choreographed program of secretory, biosynthetic, and endocytic protein traffic that serves the cell's internal physiologic needs.

Inter-Golgi transport mediated by COPI-containing vesicles carrying small cargoes

A core prediction of the vesicular transport model is that COPI vesicles are responsible for trafficking anterograde cargoes forward. In this study, we test this prediction by examining the properties and requirements of inter-Golgi transport within fused cells, which requires mobile carriers in order for exchange of constituents to occur. We report that both small soluble and membrane-bound secretory cargo and exogenous Golgi resident glycosyl-transferases are exchanged between separated Golgi. Large soluble aggregates, which traverse individual stacks, do not transfer between Golgi, implying that small cargoes (which can fit in a typical transport vesicle) are transported by a different mechanism. Super-resolution microscopy reveals that the carriers of both anterograde and retrograde cargoes are the size of COPI vesicles, contain coatomer, and functionally require ARF1 and coatomer for transport. The data suggest that COPI vesicles traffic both small secretory cargo and steady-state Golgi resident enzymes among stacked cisternae that are stationary.

DOI:http://dx.doi.org/10.7554/eLife.01296.001

All eukaryotic cells contain an organelle called the Golgi apparatus, which consists of a series of four to six flattened structures called cisternae. Proteins that are intended for secretion from the cell, or proteins that go on to become part of the cell membrane, must pass through the Golgi, where they undergo modifications that ensure they are targeted to the correct place.

There are two main models for how proteins are transported from the entry side of the Golgi, known as the cis face, to the exit side (trans face), through a process known as anterograde transport. One possibility is that the cargo protein matures within a single cisterna, which gradually moves from the cis to the trans face without the protein ever leaving it. Alternatively, the cisternae may remain fixed in position, while individual proteins are carried between them by specialized transport vesicles called COPI vesicles.

Now, Pellett et al. have used modern molecular biology techniques to revisit this question, more than 25 years after members of the same group first obtained evidence suggesting the involvement of COPI vesicles. To do this, they labelled the proteins that reside within the Golgi of one cell green, and those within the Golgi of another cell, red. They then fused the two cells together, and traced the movement of labelled proteins between the two organelles.

Proteins that are known to undergo anterograde transport were also transported between the two Golgi, whereas large protein aggregates were not. Super-resolution microscopy revealed that the transported proteins were carried in vesicles the size of COPI vesicles and surrounded by a coat protein that resembles COPI. Moreover, transport involved the adaptor protein ARF, which helps to load cargo into COPI vesicles.

By providing evidence that Golgi resident proteins and proteins that normally undergo anterograde transport can be carried by COPI vesicles between two physically separate Golgi, Pellett et al. increase the weight of evidence that COPI vesicles may also be responsible for both retrograde and anterograde transport within the Golgi itself.

DOI:http://dx.doi.org/10.7554/eLife.01296.002

Quantitative analysis of intra-Golgi transport shows intercisternal exchange for all cargo

The mechanisms controlling the transport of proteins through the Golgi stack of mammalian and plant cells is the subject of intense debate, with two models, cisternal progression and intercisternal exchange, emerging as major contenders. A variety of transport experiments have claimed support for each of these models. We reevaluate these experiments using a single quantitative coarse-grained framework of intra-Golgi transport that accounts for both transport models and their many variants. Our analysis makes a definitive case for the existence of intercisternal exchange both for small membrane proteins and large protein complexes--this implies that membrane structures larger than the typical protein-coated vesicles must be involved in transport. Notwithstanding, we find that current observations on protein transport cannot rule out cisternal progression as contributing significantly to the transport process. To discriminate between the different models of intra-Golgi transport, we suggest experiments and an analysis based on our extended theoretical framework that compare the dynamics of transiting and resident proteins.

An evolving paradigm for the secretory pathway?

The paradigm that the secretory pathway consists of a stable endoplasmic reticulum and Golgi apparatus, using discrete transport vesicles to exchange their contents, gained important support from groundbreaking biochemical and genetic studies during the 1980s. However, the subsequent development of new imaging technologies with green fluorescent protein introduced data on dynamic processes not fully accounted for by the paradigm. As a result, we may be seeing an example of how a paradigm is evolving to account for the results of new technologies and their new ways of describing cellular processes.

The future of Golgi research

This essay looks backward on the past three decades of research toward understanding the mechanism of macromolecular traffic through and within the Golgi apparatus with an eye to the future. I also explain why I feel the Golgi should continue to hold the attention of molecular cell biologists.

Photolysis of a caged peptide reveals rapid action of N-ethylmaleimide sensitive factor before neurotransmitter release

The time at which the N-ethylmaleimide-sensitive factor (NSF) acts during synaptic vesicle (SV) trafficking was identified by time-controlled perturbation of NSF function with a photoactivatable inhibitory peptide. Photolysis of this caged peptide in the squid giant presynaptic terminal caused an abrupt (0.2 s) slowing of the kinetics of the postsynaptic current (PSC) and a more gradual (2-3 s) reduction in PSC amplitude. Based on the rapid rate of these inhibitory effects relative to the speed of SV recycling, we conclude that NSF functions in reactions that immediately precede neurotransmitter release. Our results indicate the locus of SNARE protein recycling in presynaptic terminals and reveal NSF as a potential target for rapid regulation of transmitter release.

Ultrastructure of long-range transport carriers moving from the trans Golgi network to peripheral endosomes

The delivery of mannose 6-phosphate receptors carrying lysosomal hydrolases from the trans-Golgi network (TGN) to the endosomal system is mediated by selective incorporation of the receptor-hydrolase complexes into vesicular transport carriers (TCs) that are coated with clathrin and the adaptor proteins, GGA and AP-1. Previous electron microscopy (EM) and biochemical studies have shown that these TCs consist of spherical coated vesicles with a diameter of 60-100 nm. The use of fluorescent live cell imaging, however, has revealed that at least some of this transport relies on a subset of apparently larger and highly pleiomorphic carriers that detach from the TGN and translocate toward the peripheral cytoplasm until they meet with distally located endosomes. The ultrastructure of such long-range TCs has remained obscure because of the inability to examine by conventional EM the morphological details of rapidly moving organelles. The recent development of correlative light-EM has now allowed us to obtain ultrastructural 'snapshots' of these TCs immediately after their formation from the TGN in live cells. This approach has revealed that such carriers range from typical 60- to 100-nm clathrin-coated vesicles to larger, convoluted tubular-vesicular structures displaying several coated buds. We propose that this subset of TCs serve as vehicles for long-range distribution of biosynthetic or recycling cargo from the TGN to the peripheral endosomes.

Intra-Golgi transport: A way to a new paradigm?

The morpho-functional principles of intra-Golgi transport are, surprisingly, still not clear, which is in marked contrast to our advanced knowledge of the underlying molecular machineries. Recently, the conceptual and technological hindrances that had delayed progress in this area have been disappearing, and a cluster of powerful morphological techniques has been revealing new glimpses of the organization of traffic in intact cells. Here, we discuss the new concepts around the present models of intra-Golgi transport.

Fluoride causes reversible dispersal of Golgi cisternae and matrix in neuroendocrine cells

A role for heterotrimeric G proteins in the regulation of Golgi function and formation of secretory granules is generally accepted. We set out to study the effect of activation of heterotrimeric G proteins by aluminum fluoride on secretory granule formation in AtT-20 corticotropic tumor cells and in melanotrophs from the rat pituitary. In AtT-20 cells, treatment with aluminum fluoride or fluoride alone for 60 min induced complete dispersal of Golgi, ER-Golgi intermediate compartment and Golgi matrix markers, while betaCOP immunoreactiviy retained a juxtanuclear position and TGN38 was unaffected. Electron microscopy showed compression of Golgi cisternae followed by conversion of the Golgi stacks into clusters of tubular and vesicular elements. In the melanotroph of the rat pituitary a similar compression of Golgi cisternae was observed, followed by a progressive loss of cisternae from the stacks. As shown in other cells, brefeldin A induced redistribution of the Golgi matrix protein GM130 to punctate structures in the cytoplasm in AtT-20 cells, while mannosidase II immunoreactivity was completely dispersed. Fluoride induced a complete dispersal of mannosidase II and GM130 immunoreactivity. The effect of fluoride was fully reversible with reestablishment of normal mannosidase II and GM130 immunoreactivity within 2 h. After 1 h of recovery, showing varying stages of reassembly, the patterns of mannosidase II and GM130 immunoreactivity were identical in individual cells, indicating that Golgi matrix and cisternae reassemble with similar kinetics during recovery from fluoride treatment. Instead of a specific aluminum fluoride effect on secretory granule formation in the trans-Golgi network, we thus observe a unique form of Golgi dispersal induced by fluoride alone, possibly via its action as a phosphatase inhibitor.

Distinct roles for the AAA ATPases NSF and p97 in the secretory pathway

NSF and p97 are related AAA proteins implicated in membrane trafficking and organelle biogenesis. p97 is also involved in pathways that lead to ubiquitin-dependent proteolysis, including ER-associated degradation (ERAD). In this study, we have used dominant interfering ATP-hydrolysis deficient mutants (NSF(E329Q) and p97(E578Q)) to compare the function of these AAA proteins in the secretory pathway of mammalian cells. Expressing NSF(E329Q) promotes disassembly of Golgi stacks into dispersed vesicular structures. It also rapidly inhibits glycosaminoglycan sulfation, reflecting disruption of intra-Golgi transport. In contrast, expressing p97(E578Q) does not affect Golgi structure or function; glycosaminoglycans are normally sulfated and secreted, as is the VSV-G ts045 protein. Instead, expression of p97(E578Q) causes ubiquitinated proteins to accumulate on ER membranes and slows degradation of the ERAD substrate cystic-fibrosis transmembrane-conductance regulator. In addition, expression of p97(E578Q) eventually causes the ER to swell. More specific assessment of effects of p97(E578Q) on organelle assembly shows that the Golgi apparatus disperses and reassembles normally after treatment with brefeldin A and during mitosis. These findings demonstrate that ATP-hydrolysis-dependent activities of NSF and p97 in the cell are not equivalent and suggest that only NSF is directly involved in regulating membrane fusion.

Cholesterol trafficking in the secretory and endocytic systems

Cells maintain a cholesterol gradient across the secretory system, with the lowest concentrations in the endoplasmic reticulum (ER) and the highest in the plasma membrane (PM). Cholesterol is also heterogeneously distributed in the endocytic pathway. Little is known about how this heterogeneous distribution of cholesterol is maintained despite continuous vesicular traffic between organelles. Both the modulation of the cholesterol content of transport vesicles and the non-vesicular transport of cholesterol between organelles are likely to contribute. This review summarizes what is known about the pathways and mechanisms of intracellular sterol trafficking.

A novel assay to study autophagy: regulation of autophagosome vacuole size by amino acid deprivation

Autophagy is a normal degradative pathway that involves the sequestration of cytoplasmic portions and intracellular organelles in a membrane vacuole called the autophagosome. These vesicles fuse with lysosomes and the sequestered material is degraded. Owing to the complexity of the autophagic pathway and to its inaccessibility to external probes, little is known about the molecular mechanisms that regulate autophagy in higher eukaryotic cells. We used the autofluorescent drug monodansylcadaverine (MDC), a specific autophagolysosome marker to analyze at the molecular level the machinery involved in the autophagic process. We have developed a morphological and biochemical assay to study authophagy in living cells based on the incorporation of MDC. With this assay we observed that the accumulation of MDC was specifically induced by amino acid deprivation and was inhibited by 3-methlyadenine, a classical inhibitor of the autophagic pathway. Additionally, wortmannin, an inhibitor of PI3-kinases that blocks autophagy at an early stage, inhibited the accumulation of MDC in autophagic vacuoles. We also found that treatment of the cells with N-ethylmaleimide (NEM), an agent known to inhibit several vesicular transport events, completely blocked the incorporation of MDC, suggesting that an NEM-sensitive protein is required for the formation of autophagic vacuoles. Conversely, vinblastine, a microtubule depolymerizing agent that induces the accumulation of autophagic vacuoles by preventing their degradation, increased the accumulation of MDC and altered the distribution and size of the autophagic vacuoles. Our results indicate that in the presence of vinblastine very large MDC-vacuoles accumulated mainly under starvation conditions, indicating that the expansion of autophagosomes is upregulated by amino acid deprivation. Furthermore, these MDC-vacuoles were labeled with LC3, one of the mammalian homologues of the yeast protein Apg8/Aut7 that plays an important role in autophagosome formation.

The organizing potential of sphingolipids in intracellular membrane transport

Eukaryotes are characterized by endomembranes that are connected by vesicular transport along secretory and endocytic pathways. The compositional differences between the various cellular membranes are maintained by sorting events, and it has long been believed that sorting is based solely on protein-protein interactions. However, the central sorting station along the secretory pathway is the Golgi apparatus, and this is the site of synthesis of the sphingolipids. Sphingolipids are essential for eukaryotic life, and this review ascribes the sorting power of the Golgi to its capability to act as a distillation apparatus for sphingolipids and cholesterol. As Golgi cisternae mature, ongoing sphingolipid synthesis attracts endoplasmic reticulum-derived cholesterol and drives a fluid-fluid lipid phase separation that segregates sphingolipids and sterols from unsaturated glycerolipids into lateral domains. While sphingolipid domains move forward, unsaturated glycerolipids are retrieved by recycling vesicles budding from the sphingolipid-poor environment. We hypothesize that by this mechanism, the composition of the sphingolipid domains, and the surrounding membrane changes along the cis-trans axis. At the same time the membrane thickens. These features are recognized by a number of membrane proteins that as a consequence of partitioning between domain and environment follow the domains but can enter recycling vesicles at any stage of the pathway. The interplay between protein- and lipid-mediated sorting is discussed.

Protein kinase D regulates the fission of cell surface destined transport carriers from the trans-Golgi network

When a kinase inactive form of Protein Kinase D (PKD-K618N) was expressed in HeLa cells, it localized to the trans-Golgi network (TGN) and caused extensive tubulation. Cargo that was destined for the plasma membrane was found in PKD-K618N-containing tubes but the tubes did not detach from the TGN. As a result, the transfer of cargo from TGN to the plasma membrane was inhibited. We have also demonstrated the formation and subsequent detachment of cargo-containing tubes from the TGN in cells stably expressing low levels of PKD-K618N. Our results suggest that PKD regulates the fission from the TGN of transport carriers that are en route to the cell surface.

N-ethylmaleimide sensitive factor (NSF) structure and function

Our understanding of the molecular mechanisms of membrane trafficking advanced at a rapid rate during the 1990s. As one of the initial protein components of the trafficking machinery to be identified, N-ethylmaleimide sensitive factor (NSF) has served as a reference point in many of these recent studies. This hexameric ATPase is essential for most of the membrane-trafficking events in a cell. Initially, due to its ATPase activity, NSF was thought to be the motor that drove membrane fusion. Subsequent studies have shown that NSF actually plays the role of a chaperone by activating SNAP receptor proteins (SNAREs) so that they can participate in membrane fusion. In this review we will examine the initial characterization of NSF, its role in membrane fusion events, and what new structural information can tell us about NSF's mechanism of action.

Reconstitution of clathrin-independent endocytosis at the apical domain of permeabilized MDCK II cells: requirement for a Rho-family GTPase

This paper studies the endocytosis of ricin at the apical pole of polarized MDCK II cells after permeabilization of the cells basolaterally with streptolysin O. Ricin endocytosis after the addition of cytosol with an ATP-regenerating system was 2-3-fold higher than after the addition of a transport medium. A similar increase in ricin endocytosis was obtained by reconstitution of dialyzed cytosol with the nonhydrolyzable GTP analog, GTP gamma S, in the presence of an ATP-regenerating system. The nonhydrolyzable GDP analog, GDP beta S, did not increase ricin uptake. In contrast to the data obtained with ricin, GTP gamma S was found to inhibit apical transferrin uptake in MDCK II cells transfected with the human transferrin receptor, and the data thus imply that GTP gamma S supports clathrin-independent endocytosis. Electron microscopy (EM) demonstrated that free endocytic vesicles were formed from the apical pole of permeabilized MDCK II cells in the presence of GTP gamma S and that both a ricin-HRP conjugate, HRP, and cationized gold were endocytosed. Ricin endocytosis in the presence of intact cytosol, as well as GTP gamma S-stimulated ricin uptake, was inhibited by Clostridium botulinum C3 transferase, an enzyme found to inactivate Rho proteins. The data demonstrate that apical clathrin-independent endocytosis functions in the presence of GTP gamma S, and suggest that one or more of the small GTP binding proteins of the Rho family is involved in regulation of the apical clathrin-independent endocytosis in MDCK II cells.

Evidence for segregation of sphingomyelin and cholesterol during formation of COPI-coated vesicles

In higher eukaryotes, phospholipid and cholesterol synthesis occurs mainly in the endoplasmic reticulum, whereas sphingomyelin and higher glycosphingolipids are synthesized in the Golgi apparatus. Lipids like cholesterol and sphingomyelin are gradually enriched along the secretory pathway, with their highest concentration at the plasma membrane. How a cell succeeds in maintaining organelle-specific lipid compositions, despite a steady flow of incoming and outgoing transport carriers along the secretory pathway, is not yet clear. Transport and sorting along the secretory pathway of both proteins and most lipids are thought to be mediated by vesicular transport, with coat protein I (COPI) vesicles operating in the early secretory pathway. Although the protein constituents of these transport intermediates are characterized in great detail, much less is known about their lipid content. Using nano-electrospray ionization tandem mass spectrometry for quantitative lipid analysis of COPI-coated vesicles and their parental Golgi membranes, we find only low amounts of sphingomyelin and cholesterol in COPI-coated vesicles compared with their donor Golgi membranes, providing evidence for a significant segregation from COPI vesicles of these lipids. In addition, our data indicate a sorting of individual sphingomyelin molecular species. The possible molecular mechanisms underlying this segregation, as well as implications on COPI function, are discussed.

Exclusion of golgi residents from transport vesicles budding from Golgi cisternae in intact cells

A central feature of cisternal progression/maturation models for anterograde transport across the Golgi stack is the requirement that the entire population of steady-state residents of this organelle be continuously transported backward to earlier cisternae to avoid loss of these residents as the membrane of the oldest (trans-most) cisterna departs the stack. For this to occur, resident proteins must be packaged into retrograde-directed transport vesicles, and to occur at the rate of anterograde transport, resident proteins must be present in vesicles at a higher concentration than in cisternal membranes. We have tested this prediction by localizing two steady-state residents of medial Golgi cisternae (mannosidase II and N-acetylglucosaminyl transferase I) at the electron microscopic level in intact cells. In both cases, these abundant cisternal constituents were strongly excluded from buds and vesicles. This result suggests that cisternal progression takes place substantially more slowly than most protein transport and therefore is unlikely to be the predominant mechanism of anterograde movement.

Anterograde flow of cargo across the golgi stack potentially mediated via bidirectional "percolating" COPI vesicles

How do secretory proteins and other cargo targeted to post-Golgi locations traverse the Golgi stack? We report immunoelectron microscopy experiments establishing that a Golgi-restricted SNARE, GOS 28, is present in the same population of COPI vesicles as anterograde cargo marked by vesicular stomatitis virus glycoprotein, but is excluded from the COPI vesicles containing retrograde-targeted cargo (marked by KDEL receptor). We also report that GOS 28 and its partnering t-SNARE heavy chain, syntaxin 5, reside together in every cisterna of the stack. Taken together, these data raise the possibility that the anterograde cargo-laden COPI vesicles, retained locally by means of tethers, are inherently capable of fusing with neighboring cisternae on either side. If so, quanta of exported proteins would transit the stack in GOS 28-COPI vesicles via a bidirectional random walk, entering at the cis face and leaving at the trans face and percolating up and down the stack in between. Percolating vesicles carrying both post-Golgi cargo and Golgi residents up and down the stack would reconcile disparate observations on Golgi transport in cells and in cell-free systems.

Megavesicles implicated in the rapid transport of intracisternal aggregates across the Golgi stack

Engineered protein aggregates ranging up to 400 nm in diameter were selectively deposited within the cis-most cisternae of the Golgi stack following a 15 degrees C block. These aggregates are much larger than the standard volume of Golgi vesicles, yet they are transported across the stack within 10 min after warming the cells to 20 degrees C. Serial sectioning reveals that during the peak of anterograde transport, about 20% of the aggregates were enclosed in topologically free "megavesicles" which appear to pinch off from the rims of the cisternae. These megavesicles can explain the rapid transport of aggregates without cisternal progression on this time scale.

Coatomer vesicles are not required for inhibition of Golgi transport by G-protein activators

The G-protein activators guanosine 5'-O-(3-thiodiphosphate) (GTP gamma S) and aluminum fluoride (AIF) are thought to inhibit transport between Golgi cisternae by causing the accumulation of nonfunctional coatomer-coated transport vesicles on the Golgi. Although GTP gamma S and AIF inhibit transport in cell-free intra-Golgi transport systems, blocking coatomer vesicle formation does not. We therefore determined whether inhibition of in vitro Golgi transport by these agents requires coatomer vesicle formation. Depletion of coatomer was found to completely block coated vesicle formation on Golgi cisternae without affecting inhibition of in vitro transport by either GTP gamma S or AIF. Depletion of ADP-ribosylation factor (ARF) prevented inhibition of transport by GTP gamma S, but not by AIF, suggesting that the AIF-sensitive component in transport may not be a GTP-binding protein. Surprisingly, depletion of cytosolic ARF did not prevent the GTP gamma S-induced formation of Golgi-coated vesicles, whereas ARF was required for AIF-induced vesicle formation. Although ARF or coatomer depletion caused an increase in the fenestration of cisternae, no other ultrastructural changes were observed that might explain the inhibition of transport by GTP gamma S or AIF. These findings suggest that ARF-GTP gamma S and AIF act by distinct and coatomer-independent mechanisms to inhibit membrane fusion in cell-free intra-Golgi transport.

Coat proteins regulating membrane traffic

This review focuses on the roles of coat proteins in regulating the membrane traffic of eukaryotic cells. Coat proteins are recruited to the donor organelle membrane from a cytosolic pool by specific small GTP-binding proteins and are required for the budding of coated vesicles. This review first describes the four types of coat complexes that have been characterized so far: clathrin and its adaptors, the adaptor-related AP-3 complex, COPI, and COPII. It then discusses the ascribed functions of coat proteins in vesicular transport, including the physical deformation of the membrane into a bud, the selection of cargo, and the targeting of the budded vesicle. It also mentions how the coat proteins may function in an alternative model for transport, namely via tubular connections, and how traffic is regulated. Finally, this review outlines the evidence that related coat proteins may regulate other steps of membrane traffic.

A role for ADP ribosylation factor in the control of cargo uptake during COPI-coated vesicle biogenesis

ARF-mediated hydrolysis of GTP has been demonstrated to regulate coat disassembly of Golgi-derived COPI transport vesicles (Tanigawa, G., Orci, L., Amherdt, M., Ravazzola, M., Helms, J.B. and Rothman, J.E. (1993) J. Cell Biol. 123, 1365-1371). In addition, a requirement for GTP hydrolysis at an early stage of COPI vesicle biogenesis has been established since cargo uptake is impaired in the presence of GTPgammaS (Nickel, W., Malsam, J., Gorgas, K., Ravazzola, M., Jenne, N., Helms, J.B. and Wieland, F.T. (1998) J. Cell Sci. 111, 3081-3090), a non-hydrolyzable analogue of GTP. We now demonstrate that the GTPase involved in the regulation of cargo uptake is ARF, revealing a multi-functional role of this GTPase in COPI-mediated vesicular transport. The molecular mechanism of cargo uptake as well as the functional implications of these findings on the overall process of COPI vesicle biogenesis are discussed.

Cell-free transfer of the vesicular stomatitis virus G protein from an endoplasmic reticulum compartment of baby hamster kidney cells to a rat liver Golgi apparatus compartment for Man8-9 to Man5 processing

We report the reconstitution of the transfer of a membrane glycoprotein (vesicular stomatitis virus glycoprotein, VSV-G protein) from endoplasmic reticulum to Golgi apparatus and its subsequent Man8-9GlcNAc2 to Man5GlcNAc2 processing in a completely cell-free system. The acceptor was Golgi apparatus from rat liver immobilized on nitrocellulose. The endoplasmic reticulum donor was from homogenates of VSV-G-infected BHK cells. Nucleoside triphosphate plus cytosol-dependent transfer and processing of radiolabeled VSV-G protein was observed with donor from BHK cells infected at 37 degrees C with wild-type VSV or at the permissive temperature of 34 degrees C with the ts045 mutant. With Golgi apparatus as acceptor, specific transfer at 37 degrees C in the presence of nucleoside triphosphate was eightfold that at 4 degrees C or in the absence of ATP. About 40% of the VSV-G protein transferred was processed to the Man5GlcNAc2 form. Processing was specific for cis Golgi apparatus fractions purified by preparative free-flow electrophoresis. Fractions derived from the trans Golgi apparatus were inactive in processing. With the ts045 temperature-sensitive mutant, transfer and processing were much reduced even in the complete system when microsomes were from cells infected with mutant virus and incubated at the restrictive temperature of 39.5 degrees C but were able to proceed at the permissive temperature of 34 degrees C. Thus, Man8-9GlcNAc2 to Man5GlcNAc2 processing of VSV-G protein occurs following transfer in a completely cell-free system using immobilized intact Golgi apparatus or cis Golgi apparatus cisternae as the acceptor and shows temperature sensitivity, donor specificity, requirement for ATP, and response to inhibitors similar to those exhibited by transfer and processing of VSV-G protein in vivo.

Golgi structure in three dimensions: functional insights from the normal rat kidney cell

Three-dimensional reconstructions of portions of the Golgi complex from cryofixed, freeze-substituted normal rat kidney cells have been made by dual-axis, high-voltage EM tomography at approximately 7-nm resolution. The reconstruction shown here ( approximately 1 x 1 x 4 microm3) contains two stacks of seven cisternae separated by a noncompact region across which bridges connect some cisternae at equivalent levels, but none at nonequivalent levels. The rest of the noncompact region is filled with both vesicles and polymorphic membranous elements. All cisternae are fenestrated and display coated buds. They all have about the same surface area, but they differ in volume by as much as 50%. The trans-most cisterna produces exclusively clathrin-coated buds, whereas the others display only nonclathrin coated buds. This finding challenges traditional views of where sorting occurs within the Golgi complex. Tubules with budding profiles extend from the margins of both cis and trans cisternae. They pass beyond neighboring cisternae, suggesting that these tubules contribute to traffic to and/or from the Golgi. Vesicle-filled "wells" open to both the cis and lateral sides of the stacks. The stacks of cisternae are positioned between two types of ER, cis and trans. The cis ER lies adjacent to the ER-Golgi intermediate compartment, which consists of discrete polymorphic membranous elements layered in front of the cis-most Golgi cisterna. The extensive trans ER forms close contacts with the two trans-most cisternae; this apposition may permit direct transfer of lipids between ER and Golgi membranes. Within 0.2 microm of the cisternae studied, there are 394 vesicles (8 clathrin coated, 190 nonclathrin coated, and 196 noncoated), indicating considerable vesicular traffic in this Golgi region. Our data place structural constraints on models of trafficking to, through, and from the Golgi complex.

Binding forces of hepatic microsomal and plasma membrane proteins in normal and pancreatitic rats: an AFM force spectroscopic study

The docking and fusion of membrane-bound vesicles at the cell plasma membrane are brought about by several participating vesicle membrane, plasma membrane, and soluble cytosolic proteins. An understanding of the interactions between these participating proteins will provide an estimate of the potency and efficacy of secretory vesicle docking and fusion at the plasma membrane in cells of a given tissue. Earlier studies suggest that in chronic pancreatitis, glucose intolerance may be associated with impaired exocytosis/endocytosis of hepatic insulin receptor and glucose transporter proteins. In this study, the binding force profiles between microsome membrane proteins and plasma membrane proteins in liver obtained from normal and pancreatitic rats have been examined using atomic force microscopy. The ability of a VAMP-specific antibody to alter binding between microsome- and plasma membrane-associated membrane proteins was examined. In pancreatitic livers, a significant loss in microsome-plasma membrane binding is observed. Furthermore, our study shows that, in contrast to control livers, the microsome-plasma membrane binding in pancreatitic livers is VAMP-independent, which suggests an absence of VAMP participation in membrane-microsome binding. In confirmation with our earlier findings, these studies suggest altered membrane recycling in liver of rats with chronic pancreatitis.

Synaptic physiology and ultrastructure in comatose mutants define an in vivo role for NSF in neurotransmitter release

N-Ethylmaleimide-sensitive fusion protein (NSF) is a cytosolic protein thought to play a key role in vesicular transport in all eukaryotic cells. Although NSF was proposed to function in the trafficking of synaptic vesicles responsible for neurotransmitter release, only recently have in vivo experiments begun to reveal a specific function for NSF in this process. Our previous work showed that mutations in a Drosophila NSF gene, dNSF1, are responsible for the temperature-sensitive paralytic phenotype in comatose (comt) mutants. In this study, we perform electrophysiological and ultrastructural analyses in three different comt alleles to investigate the function of dNSF1 at native synapses in vivo. Electrophysiological analysis of postsynaptic potentials and currents at adult neuromuscular synapses revealed that in the absence of repetitive stimulation, comt synapses exhibit wild-type neurotransmitter release at restrictive (paralytic) temperatures. In contrast, repetitive stimulation at restrictive temperatures revealed a progressive, activity-dependent reduction in neurotransmitter release in comt but not in wild type. These results indicate that dNSF1 does not participate directly in the fusion of vesicles with the target membrane but rather functions in maintaining the pool of readily releasable vesicles competent for fast calcium-triggered fusion. To define dNSF1 function further, we used transmission electron microscopy to examine the distribution of vesicles within synaptic terminals, and observed a marked accumulation of docked vesicles at restrictive temperatures in comt. Together, the results reported here define a role for dNSF1 in the priming of docked synaptic vesicles for calcium-triggered fusion.

Coupling of coat assembly and vesicle budding to packaging of putative cargo receptors

COPI-coated vesicle budding from lipid bilayers whose composition resembles mammalian Golgi membranes requires coatomer, ARF, GTP, and cytoplasmic tails of putative cargo receptors (p24 family proteins) or membrane cargo proteins (containing the KKXX retrieval signal) emanating from the bilayer surface. Liposome-derived COPI-coated vesicles are similar to their native counterparts with respect to diameter, buoyant density, morphology, and the requirement for an elevated temperature for budding. These results suggest that a bivalent interaction of coatomer with membrane-bound ARF[GTP] and with the cytoplasmic tails of cargo or putative cargo receptors is the molecular basis of COPI coat assembly and provide a simple mechanism to couple uptake of cargo to transport vesicle formation.

Purification and characterization of a novel 13 S hetero-oligomeric protein complex that stimulates in vitro Golgi transport

Intracellular protein traffic involves a tightly regulated series of events in which a membrane-bounded vesicles bud from one compartment and are specifically targeted to the next compartment, where they dock and fuse. A cell-free system that reconstitutes vesicle trafficking between the cis and medial Golgi cisternae has been used previously to identify several proteins involved in vesicular transport (N-ethylmaleimide-sensitive fusion protein, soluble N-ethylmaleimide-sensitive fusion protein attachment proteins, p115, and p16); however, these factors are insufficient to drive the transport reaction. We have used a modified version of this in vitro intra-Golgi transport assay to guide purification of a new transport-stimulating activity. The active component is a 13 S hetero-oligomeric complex consisting of at least five polypeptides (approximately 110, 109, 90, 82, and 71 kDa), which we term Golgi transport complex (GTC). Hydrodynamic properties suggest that GTC is approximately 800 kDa and nonglobular. We obtained peptide sequence information from the 90-kDa subunit (GTC-90) that allowed us to identify a number of GTC-90 cDNAs. Comparison of these cDNAs with one another and with the genomic sequence suggests that the GTC-90 mRNA is alternatively spliced. Anti-GTC-90 antibodies inhibit the in vitro Golgi transport assay, confirming the functionality of the purified complex. Subcellular fractionation indicates that GTC-90 exists in both membrane and cytosolic pools, with the cytosolic pool associated exclusively with the GTC complex. The membrane-associated pool of GTC-90 is localized to the Golgi apparatus.

Uptake by COPI-coated vesicles of both anterograde and retrograde cargo is inhibited by GTPgammaS in vitro

On the basis of the cell surface protein CD8 we have constructed reporter molecules for both anterograde and retrograde transport from the Golgi complex. The cytoplasmic tail of CD8 was exchanged by a construct comprising a hemagglutinin (HA) epitope, the C-terminal sequence of the viral protein E19 (containing a KKXX retrieval signal) followed by a myc epitope (CD8-LT). Due to this masking of the KKXX retrieval signal CD8-LT is transported to the cell surface. Since the KKXX motif is joined to the myc epitope via a thrombin cleavage site, CD8-LT in isolated Golgi membranes can be proteolytically converted into an unmasked reporter molecule for retrograde transport (CD8-ST) in vitro. A CHO cell line stably expressing CD8-LT was generated and used for the isolation of Golgi membranes. These membranes were shown to contain CD8-LT en route to the cell surface. By addition of thrombin, CD8-LT could be efficiently converted into CD8-ST, and this allows us to study the sorting into coat protein COPI-coated vesicles of these different kinds of cargo on a comparative basis. COPI-coated vesicles were generated in vitro from Golgi membranes containing either CD8-LT or CD8-ST. When the incubation was performed in the presence of GTP, both CD8-LT and CD8-ST were packaged into COPI-coated vesicles. However, COPI-coated vesicles generated in the presence of the slowly hydrolyzable analogue of GTP, GTP(γ)S contained strikingly lower amounts of CD8-LT and CD8-ST. While COPI-coated vesicles accumulated about 12-fold in the presence of GTPgammaS these vesicles together contained only one fifth of cargo compared to the few vesicles generated in the absence of GTPgammaS. These data indicate that cargo packaging into COPI-coated vesicles requires hydrolysis of GTP.

Vesicle budding on Golgi membranes: regulation by G proteins and myosin motors

One of the main functions of the Golgi complex is to generate transport vesicles for the post-Golgi trafficking of proteins in secretory pathways. Many different populations of vesicles are distinguished by unique sets of structural and regulatory proteins which participate in vesicle budding and fusion. Monomeric and heterotrimeric G proteins regulate vesicle budding and secretory traffic into and out of the Golgi complex. An inventory of G protein alpha subunits associated with Golgi membranes highlights their diverse involvement and potential for coupling Golgi trafficking, through various signal transduction pathways, to cell growth or other more specialized cell functions. Cytoskeletal proteins are now also known to associate specifically with the Golgi complex and Golgi-derived vesicles. Amongst these, conventional and unconventional myosins are recruited to vesicle membranes. Several roles in vesicle budding and vesicle trafficking can be proposed for these actin-based motors.

SNAREs and membrane fusion in the Golgi apparatus

Soluble factors, NSF and SNAPs, are required at many membrane fusion events within the cell. They interact with a class of type II integral membrane proteins termed SNAP receptors, or SNAREs. Interaction between cognate SNAREs on opposing membranes is a prerequisite for NSF dependent membrane fusion. NSF is an ATPase which will disrupt complexes composed of different SNAREs. However, there is increasingly abundant evidence that the SNARE complex recognised by NSF does not bridge the two fusing membranes, but rather is composed of SNAREs in the same membrane. The essential role of NSF may be to prime SNAREs for a direct role during fusion. The best characterised SNAREs in the Golgi are Sed5p in yeast and its mammalian homologue syntaxin 5, both of which are predominantly localised to the cis Golgi. The SNARE-SNARE interactions in which these two proteins are involved are strikingly similar. Sed5p and syntaxin 5 may mediate three distinct pathways for membrane flow into the cis Golgi, one from the ER, one from later Golgi cisternae, and possibly a third from endosomes. Syntaxin 5 is itself likely to cycle through the ER, and thus may be involved in homotypic fusion of ER derived transport vesicles. In all well characterised SNARE dependent membrane fusion events one of the interacting SNAREs is a syntaxin homologue. There are only eight members of the syntaxin family in yeast. Besides Sed5p two others, Tlg1p and Tlg2p, are found in the Golgi complex. They are present in a late Golgi compartment, but neither is required for transit of secreted proteins through the Golgi. We suggest that these observations are most compatible with a model for transit through the Golgi in which anterograde cargo is carried in cisternae, the enzymatic composition of which changes with time as Golgi resident enzymes are delivered in retrograde transport vesicles.

Temperature-sensitive paralytic mutations demonstrate that synaptic exocytosis requires SNARE complex assembly and disassembly

The neuronal SNARE complex is formed via the interaction of synaptobrevin with syntaxin and SNAP-25. Purified SNARE proteins assemble spontaneously, while disassembly requires the ATPase NSF. Cycles of assembly and disassembly have been proposed to drive lipid bilayer fusion. However, this hypothesis remains to be tested in vivo. We have isolated a Drosophila temperature-sensitive paralytic mutation in syntaxin that rapidly blocks synaptic transmission at nonpermissive temperatures. This paralytic mutation specifically and selectively decreases binding to synaptobrevin and abolishes assembly of the 7S SNARE complex. Temperature-sensitive paralytic mutations in NSF (comatose) also block synaptic transmission, but over a much slower time course and with the accumulation of syntaxin and SNARE complexes on synaptic vesicles. These results provide in vivo evidence that cycles of assembly and disassembly of SNARE complexes drive membrane trafficking at synapses.

Phosphatidylinositol transfer protein (PITPalpha) stimulates in vitro intra-Golgi transport

Using a cell-free assay designed to reconstitute cis-to-medial intra-Golgi vesicular transport, we identified at least four crude activities in bovine brain cytosol that stimulate this assay. We have purified one of these activities to near homogeneity and have identified this Mr 36 kDa protein to be the alpha isoform of phosphatidylinositol transfer protein (PITPalpha) by N-terminal peptide sequencing, immunoreactivity with PITP-specific antisera, and the ability of recombinant PITPalpha to stimulate in vitro intra-Golgi transport. From these data, we conclude that in vitro Golgi transport is facilitated by PITPalpha.

The mammalian Golgi apparatus during M-phase

The Golgi apparatus in mammalian cells disassembles into several thousand vesicles as cells enter M-phase. Disassembly is dependent on the action of cdc2-kinase and at least two pathways contribute to the fragmentation: One involves the budding of COP-coated vesicles from Golgi cisternae with concomitant inhibition of fusion with their target membranes, the other is a less well characterised COP-independent pathway. During telophase, the Golgi fragments reassemble and fuse into a fully functional Golgi stack, using at least two distinct fusion pathways. The morphological changes of the Golgi apparatus during M-phase offer an ideal system to study how cellular organelles are generated and how their structure is maintained during interphase.