The Capture of a Disabled Proteasome Identifies Erg25 as a Substrate for Endoplasmic Reticulum Associated Degradation

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Highlights

• •Epitope-tagging of a proteasome subunit allows for facile immuno-isolation.
• •An engineered yeast strain permits capture of proteasome-associated substrates.
• •MS/MS identified all 33 resident proteasome subunits in the 20S and 19S particles.
• •Analysis of associated proteins and characterization of newly identified ERAD substrate.

     

Transmembrane Protein 214 (TMEM214) Mediates Endoplasmic Reticulum Stress-induced Caspase 4 Enzyme Activation and Apoptosis

Endoplasmic reticulum (ER) stress caused by excessive aggregation of misfolded proteins induces apoptosis. Although ER stress-induced apoptosis has been implicated in many diseases, the detailed mechanisms are not well understood. Here, we identified human transmembrane protein 214 (TMEM214) as a critical mediator of ER stress-induced apoptosis. Overexpression of TMEM214 induced apoptosis, whereas knockdown of TMEM214 inhibited ER stress-induced apoptosis. TMEM214 was localized on the outer membrane of the ER and constitutively associated with procaspase 4, which was also critical for ER stress-induced apoptosis. TMEM214-induced apoptosis was abolished by a dominant negative mutant of procaspase 4, whereas caspase 4-induced apoptosis was inhibited by knockdown of TMEM214. Furthermore, knockdown of TMEM214 inhibited the activation and cleavage of procaspase 4 by impairing its recruitment to the ER. Our findings suggest that TMEM214 is essential for ER stress-induced apoptosis by acting as an anchor for recruitment of procaspase 4 to the ER and its subsequent activation.     

Sec62 Protein Mediates Membrane Insertion and Orientation of Moderately Hydrophobic Signal Anchor Proteins in the Endoplasmic Reticulum (ER)

Nascent chains are known to be targeted to the endoplasmic reticulum membrane either by a signal recognition particle (SRP)-dependent co-translational or by an SRP-independent post-translational translocation route depending on signal sequences. Using a set of model and cellular proteins carrying an N-terminal signal anchor sequence of controlled hydrophobicity and yeast mutant strains defective in SRP or Sec62 function, the hydrophobicity-dependent targeting efficiency and targeting pathway preference were systematically evaluated. Our results suggest that an SRP-dependent co-translational and an SRP-independent post-translational translocation are not mutually exclusive for signal anchor proteins and that moderately hydrophobic ones require both SRP and Sec62 for proper targeting and translocation to the endoplasmic reticulum. Further, defect in Sec62 selectively reduced signal sequences inserted in an N_in-C_out (type II) membrane topology, implying an undiscovered role of Sec62 in regulating the orientation of the signal sequence in an early stage of translocation.     

DiOC6(3): a Useful Dye for Staining the Endoplasmic Reticulum

The present review discusses the fluorescent organelle probe, DiOC₆(3), with reference to its structure, chemistry, availability, spectral properties, labeling procedures, vital staining characteristics, and major applications in cellular and molecular biology. The specificity of dye for endoplasmic reticulum is summarized. We examine the simplicity and advantages of the fluorescent dye system for evaluating structure and function of endoplasmic reticulum. Other significant uses of the dye are also discussed.     

A Low Affinity GCaMP3 Variant (GCaMPer) for Imaging the Endoplasmic Reticulum Calcium Store

Endoplasmic reticulum calcium homeostasis is critical for cellular functions and is disrupted in diverse pathologies including neurodegeneration and cardiovascular disease. Owing to the high concentration of calcium within the ER, studying this subcellular compartment requires tools that are optimized for these conditions. To develop a single-fluorophore genetically encoded calcium indicator for this organelle, we targeted a low affinity variant of GCaMP3 to the ER lumen (GCaMPer (10.19)). A set of viral vectors was constructed to express GCaMPer in human neuroblastoma cells, rat primary cortical neurons, and human induced pluripotent stem cell-derived cardiomyocytes. We observed dynamic changes in GCaMPer (10.19) fluorescence in response to pharmacologic manipulations of the ER calcium store. Additionally, periodic calcium efflux from the ER was observed during spontaneous beating of cardiomyocytes. GCaMPer (10.19) has utility in imaging ER calcium in living cells and providing insight into luminal calcium dynamics under physiologic and pathologic states.     

Evidence for a KATP Channel in Rough Endoplasmic Reticulum (rerKATP Channel) of Rat Hepatocytes

We report in a previous study the presence of a large conductance K⁺ channel in the membrane of rough endoplasmic reticulum (RER) from rat hepatocytes incorporated into lipid bilayers. Channel activity in this case was found to decrease in presence of ATP 100 µM on the cytoplasmic side and was totally inhibited at ATP concentrations greater than 0.25 mM. Although such features would be compatible with the presence of a K_ATP channel in the RER, recent data obtained from a brain mitochondrial inner membrane preparation have provided evidence for a Maxi-K channel which could also be blocked by ATP within the mM concentration range. A series of channel incorporation experiments was thus undertaken to determine if the ATP-sensitive channel originally observed in the RER corresponds to K_ATP channel. Our results indicate that the gating and permeation properties of this channel are unaffected by the addition of 800 nM charybdotoxin and 1 µM iberiotoxin, but appeared sensitive to 10 mM TEA and 2.5 mM ATP. Furthermore, adding 100 µM glibenclamide at positive potentials and 400 µM tolbutamide at negative or positive voltages caused a strong inhibition of channel activity. Finally Western blot analyses provided evidence for Kir6.2, SUR1 and/or SUR2B, and SUR2A expression in our RER fractions. It was concluded on the basis of these observations that the channel previously characterized in RER membranes corresponds to K_ATP, suggesting that opening of this channel may enhance Ca²⁺ releases, alter the dynamics of the Ca²⁺ transient and prevent accumulation of Ca²⁺ in the ER during Ca²⁺ overload.     

A High-Throughput Screen Identifies 2,9-Diazaspiro[5.5]Undecanes as Inducers of the Endoplasmic Reticulum Stress Response with Cytotoxic Activity in 3D Glioma Cell Models

The endoplasmic reticulum (ER) is involved in Ca²⁺ signaling and protein folding. ER Ca²⁺ depletion and accumulation of unfolded proteins activate the molecular chaperone GRP78 (glucose-regulated protein 78) which in turn triggers the ER stress response (ERSR) pathway aimed to restore ER homeostasis. Failure to adapt to stress, however, results in apoptosis. We and others have shown that malignant cells are more susceptible to ERSR-induced apoptosis than their normal counterparts, implicating the ERSR as a potential target for cancer therapeutics. Predicated on these findings, we developed an assay that uses a GRP78 biosensor to identify small molecule activators of ERSR in glioma cells. We performed a quantitative high-throughput screen (qHTS) against a collection of ~425,000 compounds and a comprehensive panel of orthogonal secondary assays was formulated for stringent compound validation. We identified novel activators of ERSR, including a compound with a 2,9-diazaspiro[5.5]undecane core, which depletes intracellular Ca²⁺ stores and induces apoptosis-mediated cell death in several cancer cell lines, including patient-derived and 3D cultures of glioma cells. This study demonstrates that our screening platform enables the identification and profiling of ERSR inducers with cytotoxic activity and advocates for characterization of these compound in in vivo models.     

The DNA-binding activity of protein disulfide isomerase ERp57 is associated with the a(') domain

ERp57 belongs to the protein disulfide isomerases, a family of homologous proteins mainly localized in the endoplasmic reticulum and characterized by the presence of a thioredoxin-like folding domain. ERp57 is a protein chaperone with thiol-dependent protein disulfide isomerase and additional activities and recently it has been shown to be involved, in cooperation with calnexin or with calreticulin, in the correct folding of glycoproteins. However, we have demonstrated that the same protein is also present in the nucleus, mainly associated with the internal nuclear matrix fraction. In vitro studies have shown that ERp57 has DNA-binding properties which are strongly dependent on its redox state, the oxidized form being the competent one. A comparison study on a recombinant form of ERp57 and several deletion mutants, obtained as fusion proteins and expressed in Escherichia coli, allowed us to identify the C-terminal a(') domain as directly involved in the DNA-binding activity of ERp57.     

A Conserved Endoplasmic Reticulum Membrane Protein Complex (EMC) Facilitates Phospholipid Transfer from the ER to Mitochondria

Mitochondrial membrane biogenesis and lipid metabolism require phospholipid transfer from the endoplasmic reticulum (ER) to mitochondria. Transfer is thought to occur at regions of close contact of these organelles and to be nonvesicular, but the mechanism is not known. Here we used a novel genetic screen in S. cerevisiae to identify mutants with defects in lipid exchange between the ER and mitochondria. We show that a strain missing multiple components of the conserved ER membrane protein complex (EMC) has decreased phosphatidylserine (PS) transfer from the ER to mitochondria. Mitochondria from this strain have significantly reduced levels of PS and its derivative phosphatidylethanolamine (PE). Cells lacking EMC proteins and the ER–mitochondria tethering complex called ERMES (the ER–mitochondria encounter structure) are inviable, suggesting that the EMC also functions as a tether. These defects are corrected by expression of an engineered ER–mitochondrial tethering protein that artificially tethers the ER to mitochondria. EMC mutants have a significant reduction in the amount of ER tethered to mitochondria even though ERMES remained intact in these mutants, suggesting that the EMC performs an additional tethering function to ERMES. We find that all Emc proteins interact with the mitochondrial translocase of the outer membrane (TOM) complex protein Tom5 and this interaction is important for PS transfer and cell growth, suggesting that the EMC forms a tether by associating with the TOM complex. Together, our findings support that the EMC tethers ER to mitochondria, which is required for phospholipid synthesis and cell growth.     

A Small Molecule Inhibitor of Endoplasmic Reticulum Oxidation 1 (ERO1) with Selectively Reversible Thiol Reactivity

Endoplasmic reticulum oxidation 1 (ERO1) is a conserved eukaryotic flavin adenine nucleotide-containing enzyme that promotes disulfide bond formation by accepting electrons from reduced protein disulfide isomerase (PDI) and passing them on to molecular oxygen. Although disulfide bond formation is an essential process, recent experiments suggest a surprisingly broad tolerance to genetic manipulations that attenuate the rate of disulfide bond formation and that a hyperoxidizing ER may place stressed cells at a disadvantage. In this study, we report on the development of a high throughput in vitro assay for mammalian ERO1α activity and its application to identify small molecule inhibitors. The inhibitor EN460 (IC₅₀, 1.9 μm) interacts selectively with the reduced, active form of ERO1α and prevents its reoxidation. Despite rapid and promiscuous reactivity with thiolates, EN460 exhibits selectivity for ERO1. This selectivity is explained by the rapid reversibility of the reaction of EN460 with unstructured thiols, in contrast to the formation of a stable bond with ERO1α followed by displacement of bound flavin adenine dinucleotide from the active site of the enzyme. Modest concentrations of EN460 and a functionally related inhibitor, QM295, promote signaling in the unfolded protein response and precondition cells against severe ER stress. Together, these observations point to the feasibility of targeting the enzymatic activity of ERO1α with small molecule inhibitors.     

A Review of the Role of ERp57 in Cancerous and Non-Cancerous Cell Physiology and its Potential as a Therapeutic Target

The protein ERp57 is a stress-responsive protein, mainly exists in the endoplasmic reticulum (ER), and a small amount in the cell membrane, cytoplasm, nucleus and mitochondria, which is involved in the signal transduction from the cell surface, the regulation process that occurs in the nucleus, and the formation of polymer protein complexes involved in DNA repair. Various degrees of ERp57 dysregulation has been observed in many types of non-communicable diseases especially in cancers. Previous studies showed that the expression of ERp57 could play a key role in occurrence and development of cancers such as breast cancer, gastric cancer, ovarian cancer, etc.; in addition, it has been suggested to play a pivotal role in disease progression of non-cancerous diseases such as neurodegeneration, liver disease, kidney disease, intestinal irritability syndrome and airway hypersensitivity. Thus, abnormal expression of ERp57 could be used as promising biomarker for cancer diagnosis and prognosis based on the previous studies. In this regard, current study was aimed to review the literature, which have been elucidate the role of ERp57 protein expression in both non-cancer and cancer disease. Overall, most studies have shown that inhibiting/knocking out of ERp57 could inhibit the cell proliferation and also induce apoptosis in both human cancerous and non-cancerous cells. Also, it has been suggested that the overexpression of ERp57 could intensify the cancer development. Therefore, it could be hypothesized that targeting of ERp57 might be a potential treatment in cancerous and non-cancerous diseases.     

Protein Interaction Screening for the Ankyrin Repeats and Suppressor of Cytokine Signaling (SOCS) Box (ASB) Family Identify Asb11 as a Novel Endoplasmic Reticulum Resident Ubiquitin Ligase

The ankyrin and SOCS (suppressor of cytokine signaling) box (ASB) family of proteins function as the substrate recognition subunit in a subset of Elongin-Cullin-SOCS (ECS) E3 ubiquitin ligases. Despite counting 18 members in humans, the identity of the physiological targets of the Asb proteins remains largely unexplored. To increase our understanding of the function of ASB proteins, we conducted a family-wide SILAC (stable isotope labeling by amino acids in cell culture)-based protein/protein interaction analysis. This investigation led to the identification of novel as well as known ASB-associated proteins like Cullin 5 and Elongins B/C. We observed that several proteins can be bound by more than one Asb protein. The additional exploration of this phenomenon demonstrated that ASB-Cullin 5 complexes can oligomerize and provides evidence that Cullin 5 forms heterodimeric complexes with the Cullin 4a-DDB1 complex. We also demonstrated that ASB11 is a novel endoplasmic reticulum-associated ubiquitin ligase with the ability to interact and promote the ubiquitination of Ribophorin 1, an integral protein of the oligosaccharyltransferase (OST) glycosylation complex. Moreover, expression of ASB11 can increase Ribophorin 1 protein turnover in vivo. In summary, we provide a comprehensive protein/protein interaction data resource that can aid the biological and functional characterization of ASB ubiquitin ligases.     

Arabidopsis Stromal-derived Factor2 (SDF2) Is a Crucial Target of the Unfolded Protein Response in the Endoplasmic Reticulum

Stresses increasing the load of unfolded proteins that enter the endoplasmic reticulum (ER) trigger a protective response termed the unfolded protein response (UPR). Stromal cell-derived factor2 (SDF2)-type proteins are highly conserved throughout the plant and animal kingdoms. In this study we have characterized AtSDF2 as crucial component of the UPR in Arabidopsis thaliana. Using a combination of biochemical and cell biological methods, we demonstrate that SDF2 is induced in response to ER stress conditions causing the accumulation of unfolded proteins. Transgenic reporter plants confirmed induction of SDF2 during ER stress. Under normal growth conditions SDF2 is highly expressed in fast growing, differentiating cells and meristematic tissues. The increased production of SDF2 due to ER stress and in tissues that require enhanced protein biosynthesis and secretion, and its association with the ER membrane qualifies SDF2 as a downstream target of the UPR. Determination of the SDF2 three-dimensional crystal structure at 1.95 Å resolution revealed the typical β-trefoil fold with potential carbohydrate binding sites. Hence, SDF2 might be involved in the quality control of glycoproteins. Arabidopsis sdf2 mutants display strong defects and morphological phenotypes during seedling development specifically under ER stress conditions, thus establishing that SDF2-type proteins play a key role in the UPR.     

A Combined Approach of Quantitative Interaction Proteomics and Live-cell Imaging Reveals a Regulatory Role for Endoplasmic Reticulum (ER) Reticulon Homology Proteins in Peroxisome Biogenesis

Peroxisome biogenesis initiates at the endoplasmic reticulum (ER) and maturation allows for the formation of metabolically active organelles. Yet, peroxisomes can also multiply by growth and division. Several proteins, called peroxins, are known to participate in these processes but little is known about their organization to orchestrate peroxisome proliferation. Here, we demonstrate that regulation of peroxisome proliferation relies on the integrity of the tubular ER network. Using a dual track SILAC-based quantitative interaction proteomics approach, we established a comprehensive network of stable as well as transient interactions of the peroxin Pex30p, an integral membrane protein. Through association with merely ER resident proteins, in particular with proteins containing a reticulon homology domain, and with other peroxins, Pex30p designates peroxisome contact sites at ER subdomains. We show that Pex30p traffics through the ER and segregates in punctae to which peroxisomes specifically append, and we ascertain its transient interaction with all subunits of the COPI coatomer complex suggesting the involvement of a vesicle-mediated transport. We establish that the membrane protein Pex30p facilitates the connection of peroxisomes to the ER. Taken together, our data indicate that Pex30p-containing protein complexes act as focal points from which peroxisomes can form and that the tubular ER architecture organized by the reticulon homology proteins Rtn1p, Rtn2p and Yop1p controls this process.All nucleated cells contain essential round-shaped organelles called peroxisomes, whose function is mainly associated with lipid metabolism (1). Depending on the cellular requirements, the size, number, and protein content of these single membrane-bound organelles can vary widely. Although peroxisomes are dispensable for unicellular species such as yeasts, they are essential for the development of multicellular organisms (2, 3). In human, mutations in PEX genes lead to defects in peroxisome function or formation and are associated with the development of lethal pathologies (4). These PEX genes code for proteins, called peroxins, which are involved in peroxisome assembly and maintenance (5).Two major routes seem to lead to peroxisome formation, namely, de novo biogenesis and growth/division of pre-existing peroxisomes. The division pathway operates with proteins of the Pex11 family and requires fission factors shared with mitochondria (6). Studies in yeast and mammalian cells revealed that through the action of the protein Pex3p peroxisome precursors can also originate from the endoplasmic reticulum (ER)¹ and, via import of membrane and matrix proteins, mature into fully functional organelles (7, 8). Furthermore, several peroxisomal membrane proteins were shown to migrate to peroxisomes via the ER (7, 9, 10). The molecular mechanism underlying the biogenic pathway of peroxisome formation has not been clarified so far. Recent data based on cell-free vesicle-budding reactions, however, demonstrated that several peroxisomal proteins traffic from the ER to peroxisomes in a COPII vesicle-independent manner (11). These observations point to the existence of vesicular events to mediate the transport of peroxisomal membrane proteins from the ER. In fact, analysis of secretory mutant yeast cells already suggest that part of the ER-associated secretory machinery is involved in peroxisome biogenesis (12).The de novo biogenesis of peroxisomes and the growth/division pathways are usually seen as independent routes; however, these events may be coordinated and, thus, intimately linked. Indeed, peroxisomes need to acquire membrane components to proliferate and it has been proposed that their binding to the cell cortex or to the cytoskeleton allows their partitioning and segregation during cell division (13–15).Among the proteins required for assembly of peroxisomes, the membrane proteins Pex23p and Pex24p play essential roles in the yeast Yarrowia lipolytica (16, 17). Homologs of these two proteins in Saccharomyces cerevisiae are Pex30p, Pex31p, and Pex32p, all containing at least one transmembrane domain and a dysferlin domain as common structural motifs, as well as Pex28p and Pex29p. In S. cerevisiae, these proteins seem to negatively control peroxisomal size and number (18, 19). Interestingly, Pex30p seems to exhibit species-specific differences in the regulation of peroxisome proliferation. While the lack of Pex30p in S. cerevisiae leads to an increase in the number of normal-sized peroxisomes (18), in Pichia pastoris its absence correlates with the appearance of fewer and clustered peroxisomes (20). Although peroxisomes are highly versatile organelles, under given conditions their total number per cell remains fairly constant owing to the delicate balance of proliferation, inheritance and degradation (21, 22). The question is: what are the molecular mechanisms responsible for the spatiotemporal organization of these events?Here, we present data obtained from a dual approach based on quantitative interaction proteomics using stable isotope labeling with amino acids in cell culture (SILAC) (23, 24) and live-cell imaging, revealing for the first time the dynamic interaction network around Pex30p and its function in the organization of ER-to-peroxisome membrane associations. We report the existence of a macromolecular membrane protein complex that acts as a hub for the regulation of peroxisome proliferation and movement. Our data suggest a direct role for the tubular cortical ER and the reticulon homology proteins Rtn1p, Rtn2p, and Yop1p in the regulation of peroxisome biogenesis. Furthermore, as an initially cortical-ER localized protein that interacts with reticulon homology proteins, Pex30p is shown in this work to establish contacts between ER tubules and peroxisomes and to specifically traffic through the ER. In summary, our data reveal a central role for Pex30p in the formation of ER-to-peroxisomes associations that appear to be involved in the coordination of peroxisome biogenesis and maintenance.     

A Plasma Membrane-Type Ca2+-ATPase of 120 Kilodaltons on the Endoplasmic Reticulum from Carrot (Daucus carota) Cells (Properties of the Phosphorylated Intermediate)

Cytosolic Ca2+ levels are regulated in part by Ca2+-pumping ATPases that export Ca2+ from the cytoplasm; however, the types and properties of Ca2+ pumps in plants are not well understood. We have characterized the kinetic properties of a 120-kD phosphoenzyme (PE) intermediate formed during the reaction cycle of a Ca2+-ATPase from suspension-cultured carrot (Daucus carota) cells. Only one Ca2+-dependent phosphoprotein was formed when carrot membrane vesicles were incubated with [[gamma]-32P]ATP (W.L. Hsieh, W.S. Pierce, and H. Sze [1991] Plant Physiol 97: 1535-1544). Formation of this 120-kD phosphoprotein was inhibited by vanadate, enhanced by La3+, and decreased by hydroxylamine, confirming its identification as an intermediate of a phosphorylated-type Ca2+-translocating ATPase. The 120-kD Ca2+-ATPase was most abundant in endoplasmic reticulum-enriched fractions, in which the Ca2+-ATPase was estimated to be 0.1% of membrane protein. Direct quantitation of Ca2+-dependent phosphoprotein was used to examine the kinetics of PE formation. PE formation exhibited a Km for Ca2+ of 1 to 2 [mu]M and a Km for ATP of 67 nM. Relative affinities of substrates, determined by competition experiments, were 0.075 [mu]M for ATP, 1 [mu]M for ADP, 100 [mu]M for ITP, and 250 [mu]M for GTP. Thapsigargin and cyclopiazonic acid, specific inhibitors of animal sarcoplasmic/endoplasmic reticulum Ca2+-ATPase, had no effect on PE formation; erythrosin B inhibited with 50% inhibition at <0.1 [mu]M. Calmodulin (1 [mu]M) stimulated PE formation by 25%. The results indicate that the carrot 120-kD Ca2+-ATPase is similar but not identical to animal plasma membrane-type Ca2+- ATPase and yet is located on endomembranes, such as the endoplasmic reticulum. This type of Ca2+ pump may reside on the cortical endoplasmic reticulum, which is thought to play a major role in anchoring the cytoskeleton and in facilitating secretion.