Electron Tomography Revels that Milk Lipids Originate from Endoplasmic Reticulum Domains with Novel Structural Features.

Lipid droplets (LD) are dynamically-regulated organelles that originate from the endoplasmic reticulum (ER), and function in the storage, trafficking and metabolism of neutral lipids. In mammary epithelial cells (MEC) of lactating animals, intact LD are secreted intact into milk to form milk lipids by a novel apocrine mechanism. The secretion of intact LD and the relatively large amounts of lipid secreted by lactating MEC increase demands on the cellular processes responsible for lipid synthesis and LD formation. As yet these processes are poorly defined due to limited understanding of LD-ER interactions. To overcome these limitations, we used rapid-freezing and freeze-substitution methods in conjunction with 3D electron tomography and high resolution immunolocalization to define interactions between LD with ER in MEC of pregnant and lactating rats. Using these approaches, we identified distinct ER domains that contribute to lipid droplet formation and stabilization and which possess unique features previously unrecognized or not fully appreciated. Our results show nascent lipid droplets within the ER lumen and the association of both forming and mature droplets with structurally unique regions of ER cisternae, characterized by the presence of perilipin-2, a protein implicated in lipid droplet formation, and enzymes involved in lipid synthesis. These data demonstrate that milk lipids originate from LD-ER domains with novel structural features and suggest a mechanism for initial droplet formation in the ER lumen and subsequent maturation of the droplets in association with ER cisternae.

Proteomic analysis of the stacked Golgi complex.

Although a great deal is known about the structure and function of most mammalian organelles, comprehensive proteomes are necessary to provide a molecular framework to integrate this information. The Golgi complex is the central organelle of the secretory pathway and functions to posttranslationally modify newly synthesized proteins and lipids and to sort them to their sites of function. The methods described in this chapter facilitate the isolation of an enriched stacked Golgi fraction (GF) from rat liver (1,2) and the shotgun proteomic analysis of the fraction using multidimensional protein identification technology (MudPIT) (3,4).

Global approaches to study Golgi function.

Enormous insights into Golgi function have been provided by yeast genetics, biochemical assays and immuno-labeling methods and the emerging picture is of a very complex organelle with multiple levels of regulation. Despite many elegant experimental approaches, it remains unclear what mechanisms transport secretory proteins and lipids through the Golgi, and even the basic structure of the organelle is debated. Recently, new, global approaches such as proteomics and functional genomics have been applied to study the Golgi and its matrix. The data produced reveals great complexity and has potential to help address major unresolved questions concerning Golgi function.

Anion channels transport ATP into the Golgi lumen.

Anion channels provide a pathway for Cl(-) influx into the lumen of the Golgi cisternae. This influx permits luminal acidification by the organelle's H(+)-ATPase. Three different experimental approaches, electrophysiological, biochemical, and proteomic, demonstrated that two Golgi anion channels, GOLAC-1 and GOLAC-2, also mediate ATP anion transport into the Golgi lumen. First, GOLAC-1 and -2 were incorporated into planar lipid bilayers, and single-channel recordings were obtained. Low ionic activities of K(2)ATP added to the cis-chamber directly inhibited the Cl(-) subconductance levels of both channels, with K(m) values ranging from 16 to 115 microM. Substitution of either K(2)ATP or MgATP for Cl(-) on the cis, trans, or both sides indicated that ATP is conducted by the channels with a relative permeability sequence of Cl(-) > ATP(4-) > MgATP(2-). Single-channel currents were observed at physiological concentrations of Cl(-) and ATP, providing evidence for their importance in vivo. Second, transport of [alpha-(32)P]ATP into sealed Golgi vesicles that maintain in situ orientation was consistent with movement through the GOLACs because it exhibited little temperature dependence and was saturated with an apparent K(m) = 25 microM. Finally, after transport of [gamma-(32)P]ATP, a protease-protection assay demonstrated that proteins are phosphorylated within the Golgi lumen, and after SDS-PAGE, the proteins in the phosphorylated bands were identified by mass spectrometry. GOLAC conductances, [alpha-(32)P]ATP transport, and protein phosphorylation have identical pharmacological profiles. We conclude that the GOLACs play dual roles in the Golgi complex, providing pathways for Cl(-) and ATP influx into the Golgi lumen.

Cis-Golgi matrix proteins move directly to endoplasmic reticulum exit sites by association with tubules.

The role of cis-medial Golgi matrix proteins in retrograde traffic is poorly understood. We have used imaging techniques to understand the relationship between the cis-medial Golgi matrix and transmembrane proteins during retrograde traffic in control and brefeldin A (BFA)-treated cells. All five of the cis-medial matrix proteins tested were associated with retrograde tubules within 2-3 min of initiation of tubule formation. Then, at later time points (3-10 min), transmembrane proteins are apparent in the same tubules. Strikingly, both the matrix proteins and the transmembrane proteins moved directly to endoplasmic reticulum (ER) exit sites labeled with p58 and Sec13, and there seemed to be a specific interaction between the ER exit sites and the tips or branch points of the tubules enriched for the matrix proteins. After the initial interaction, Golgi matrix proteins accumulated rapidly (5-10 min) at ER exit sites, and Golgi transmembrane proteins accumulated at the same sites approximately 2 h later. Our data suggest that Golgi cis-medial matrix proteins participate in Golgi-to-ER traffic and play a novel role in tubule formation and targeting.

GMx33 associates with the trans-Golgi matrix in a dynamic manner and sorts within tubules exiting the Golgi.

The trans-Golgi matrix consists of a group of proteins dynamically associated with the trans-Golgi and thought to be involved in anterograde and retrograde Golgi traffic, as well as interactions with the cytoskeleton and maintenance of the Golgi structure. GMx33 is localized to the cytoplasmic face of the trans-Golgi and is also present in a large cytoplasmic pool. Here we demonstrate that GMx33 is dynamically associated with the trans-Golgi matrix, associating and dissociating with the Golgi in seconds. GMx33 can be locked onto the trans-Golgi matrix by GTPgammaS, indicating that its association is regulated in a GTP-dependent manner like several other Golgi matrix proteins. Using live-cell imaging we show that GMx33 exits the Golgi associated with tubules and within these tubules GMx33 segregates from transmembrane proteins followed by fragmentation of the tubules into smaller tubules and vesicles. Within vesicles produced by an in vitro budding reaction, GMx33 remains segregated in a matrixlike tail region that sometimes contains Golgin-245. This trans-matrix often links a few vesicles together. Together these data suggest that GMx33 is a member of the trans-Golgi matrix and offer clues regarding the role of the trans-Golgi matrix in sorting and exit from the Golgi.

Proteomics of organelles and large cellular structures.

The mass-spectrometry-based identification of proteins has created opportunities for the study of organelles, transport intermediates and large subcellular structures. Traditional cell-biology techniques are used to enrich these structures for proteomics analyses, and such analyses provide insights into the biology and functions of these structures. Here, we review the state-of-the-art proteomics techniques for the analysis of subcellular structures and discuss the biological insights that have been derived from such studies.

Protein kinase C regulates the phosphorylation and oligomerization of ERM binding phosphoprotein 50.

Ezrin-Radixin-Moesin (ERM) binding phosphoprotein 50 (EBP50, a.k.a. NHERF-1) is a scaffold protein essential for the localization and coordinated activity of apical transporters, enzymes and receptors in epithelial cells. EBP50 acts via multiple protein binding interactions, including oligomerization through interactions of its PSD95-Dlg-ZO1 (PDZ) domains. EBP50 can be phosphorylated on multiple sites and phosphorylation of specific sites modulates the extent of oligomerization. The aim of the present study was to test the capacity of protein kinase C (PKC) to phosphorylate EBP50 and to regulate its oligomerization. In vitro experiments showed that the catalytic subunit of PKC directly phosphorylates EBP50. In HEK-293 cells transfected with rat EBP50 cDNA, a treatment with 12 myristate 13-acetate (PMA) induced a translocation of PKCalpha and beta isoforms to the membrane and increased 32P incorporation into EBP50. In co-transfection/co-precipitation studies, PMA treatment stimulated EBP50 oligomerization. Mass spectrometry analysis of full-length EBP50 and phosphorylation analyses of specific domains, and of mutated or truncated forms of EBP50, indicated that PKC-induced phosphorylation of EBP50 occurred on the Ser337/Ser338 residue within the carboxyl-tail domain of the protein. Truncation of Ser337/Ser338 also diminished PKC-induced oligomerization of EBP50. These results suggest the PKC signaling pathway can impact EBP50-dependent cellular functions by regulating EBP50 oligomerization.

Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis.

To quantify proteins on a global level from mammalian tissue, a method was developed to metabolically introduce 15N stable isotopes into the proteins of Rattus norvegicus for use as internal standards. The long-term metabolic labeling of rats with a diet enriched in 15N did not result in adverse health consequences. The average 15N amino acid enrichments reflected the relative turnover rates in the different tissues and ranged from 74.3 mpe in brain to 92.2 mpe in plasma. Using the 15N-enriched liver as a quantitative internal standard, changes in individual protein levels in response to cycloheximide treatment were measured for 310 proteins. These measurements revealed 127 proteins with altered protein level (p < 0.05). Most proteins with altered level have previously reported functions involving xenobiotic metabolism and protein-folding machinery of the endoplasmic reticulum. This approach is a powerful tool for the global quantitation of proteins, is capable of measuring proteome-wide changes in response to a drug, and will be useful for studying animal models of disease.

Direct continuities between cisternae at different levels of the Golgi complex in glucose-stimulated mouse islet beta cells.

Direct continuity between the membranes of cisternae in the Golgi complex in mammalian cells rarely has been observed; when seen, its documentation has been equivocal. Here we have used dual-axis electron microscope tomography to examine the architecture of the Golgi in three dimensions at approximately 6-nm resolution in rapidly frozen, freeze-substituted murine cells that make and secrete insulin in response to glucose challenge. Our data show three types of direct connections between Golgi cisternae that are normally distinct from one another. These connections all "bypass" interceding cisternae. We propose that when pancreatic beta cells are stimulated to synthesize and secrete insulin rapidly in vivo, such connections provide a continuous lumen that facilitates the rapid transit of large amounts of newly made protein for secretion. The heterotypic fusion of cisternae, even transiently, raises important questions about the molecular mechanisms that (i) facilitate the fusion/fission of cisternal membranes and control the directionality and specificity of such events, and (ii) retain Golgi processing enzymes at specific places within individual cisternae when two cisternae at different levels in the Golgi have fused, maintaining the sequential processing hierarchy that is a hallmark of Golgi organization.

Predicting function from structure: 3D structure studies of the mammalian Golgi complex.

3D electron tomography studies of the structure of the mammalian Golgi complex have led to four functional predictions (1). The sorting and exit site from the Golgi comprises two or three distinct trans-cisternae (2). The docking of vesicular-tubular clusters at the cis-face and the fragmentation of trans-cisternae are coordinated (3). The mechanisms of transport through, and exit from, the Golgi vary with physiological state, and in different cells and tissues (4). Specialized trans-ER functions in the delivery of ceramide to sphingomyelin synthase in the trans-Golgi membrane, for the regulated sorting via sphingolipid-cholesterol-rich domains. These structure-based predictions can now be tested using a variety of powerful cell and molecular tools.

Organellar proteomics reveals Golgi arginine dimethylation.

The Golgi complex functions to posttranslationally modify newly synthesized proteins and lipids and to sort them to their sites of function. In this study, a stacked Golgi fraction was isolated by classical cell fractionation, and the protein complement (the Golgi proteome) was characterized using multidimensional protein identification technology. Many of the proteins identified are known residents of the Golgi, and 64% of these are predicted transmembrane proteins. Proteins localized to other organelles also were identified, strengthening reports of functional interfacing between the Golgi and the endoplasmic reticulum and cytoskeleton. Importantly, 41 proteins of unknown function were identified. Two were selected for further analysis, and Golgi localization was confirmed. One of these, a putative methyltransferase, was shown to be arginine dimethylated, and upon further proteomic analysis, arginine dimethylation was identified on 18 total proteins in the Golgi proteome. This survey illustrates the utility of proteomics in the discovery of novel organellar functions and resulted in 1) a protein profile of an enriched Golgi fraction; 2) identification of 41 previously uncharacterized proteins, two with confirmed Golgi localization; 3) the identification of arginine dimethylated residues in Golgi proteins; and 4) a confirmation of methyltransferase activity within the Golgi fraction.

A method for the comprehensive proteomic analysis of membrane proteins.

We describe a method that allows for the concurrent proteomic analysis of both membrane and soluble proteins from complex membrane-containing samples. When coupled with multidimensional protein identification technology (MudPIT), this method results in (i) the identification of soluble and membrane proteins, (ii) the identification of post-translational modification sites on soluble and membrane proteins, and (iii) the characterization of membrane protein topology and relative localization of soluble proteins. Overlapping peptides produced from digestion with the robust nonspecific protease proteinase K facilitates the identification of covalent modifications (phosphorylation and methylation). High-pH treatment disrupts sealed membrane compartments without solubilizing or denaturing the lipid bilayer to allow mapping of the soluble domains of integral membrane proteins. Furthermore, coupling protease protection strategies to this method permits characterization of the relative sidedness of the hydrophilic domains of membrane proteins.

The mammalian Golgi--complex debates.

Since the first description of the Golgi in 1898, key issues regarding this organelle have remained contentious among cell biologists. Resolving these complex debates, which revolve around Golgi structure-function relationships, is prerequisite to understanding how the Golgi fulfils its role as the central organelle and sorting station of the mammalian secretory pathway.

Structure of the Golgi and distribution of reporter molecules at 20 degrees C reveals the complexity of the exit compartments.

Incubating cells at 20 degrees C blocks transport out of the Golgi complex and amplifies the exit compartments. We have used the 20 degrees C block, followed by EM tomography and serial section reconstruction, to study the structure of Golgi exit sites in NRK cells. The dominant feature of Golgi structure in temperature-blocked cells is the presence of large bulging domains on the three trans-most cisternae. These domains extend laterally from the stack and are continuous with "cisternal" domains that maintain normal thickness and alignment with the other stacked Golgi cisternae. The bulging domains do not resemble the perpendicularly extending tubules associated with the trans-cisternae of control cells. Such tubules are completely absent in temperature-blocked cells. The three cisternae with bulging domains can be identified as trans by their association with specialized ER and the presence of clathrin-coated buds on the trans-most cisterna only. Immunogold labeling and immunoblots show a significant degradation of a medial- and a trans-Golgi marker with no evidence for their redistribution within the Golgi or to other organelles. These data suggest that exit from the Golgi occurs directly from three trans-cisternae and that specialized ER plays a significant role in trans-Golgi function.

A large-conductance anion channel of the Golgi complex.

An acidic lumenal pH is vital for the proper posttranslational modifications and sorting of proteins and lipids from the Golgi complex. We characterized ion channels present in Golgi fractions that have been cleared of transiting proteins. A large conductance anion channel was observed in approximately 30% of successful channel incorporations into the planar lipid bilayer. The channel, GOLAC-2, has six levels (one closed and five open). The open states are each approximately 20% increments of the maximal, 325 pS conductance. The channel was approximately 6 times more selective for Cl(-) over K(+). Binomial analysis of percent occupancy for each conducting level supports the hypothesis of five independent conducting pathways. The conducting levels can coordinately gate because full openings and closings were often observed. Addition of 3 to 5 mM reduced glutathione to the cis chamber caused dose-dependent increases in single channel conductance, indicating that the channel may be regulated by the oxidation-reduction state of the cell. We propose that GOLAC-2 is a co-channel complex consisting of five identical pores that have a coordinated gating mechanism. GOALC-2 may function as a source of counter anions for the H(+)-ATPase and may be involved in regulating charge balance and membrane potential of the Golgi complex.