Immunology, Phenotype First: How Mutations Have Established New Principles and Pathways in Immunology

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Cassonnet, M. Favre, G. Orth, M. The EVER2 genotype of each of the lines was confirmed by sequencing directly before the experiments. Favre, S. Jablonska, S. Majewski, G.

Autism: New Mutations, Genes, and Pathways

Ramoz, unpublished results. Her first skin lesions were plane warts on the dorsum of the hands that appeared at the age of 7 yrs. The lesions were treated successfully by liquid nitrogen freezing. However at the age of 14 years new extensive skin lesions developed on the dorsum of the hands and feet, as well as on the trunk.

These lesions were much more abundant, some of them larger than typical plane warts. Some of the lesions were confluent with uneven polycystic outlines. The lesions persisted for about 2 years and disappeared after several courses of cryotherapy. Polyclonal T cell lines were generated from PBMC of the 2 patients or healthy controls, as previously described [43]. T cells were restimulated as described every 2 weeks. T cells were used in this study after one stimulation cycle.

Written informed consent was received from all participants. The cells were cultured for 24 h before analysis of EVER protein expression. Free zinc concentration in lymphocytes was measured by flow cytometry as previously described [44]. Briefly, the cells were loaded for 30 min. The zinc concentration was calculated on the basis of the median fluorescence intensity, according to a previously published formula [43].

At the start of the culture or after 3, 6 or 24 h of stimulation, the zinc ionophore pyrithione, Sigma, ref: was added at the indicated concentrations. After 24 h, H 3 -thymidine was added followed by 18 h incubation. Browse Subject Areas? Click through the PLOS taxonomy to find articles in your field. Abstract Human papillomaviruses HPV cause a variety of mucosal and skin lesions ranging from benign proliferations to invasive carcinomas.

Introduction Papillomaviruses are widespread infectious agents, transmitted by sexual or cutaneous contacts. Results and Discussion We first analyzed the expression of EVER genes in a panel of freshly collected murine tissues, and in murine and human lymphocyte subsets.

Download: PPT. Figure 1. Figure 2. Figure 4. Increased cellular zinc concentration in lymphocytes from EVER2-deficient patients. Free Zinc Concentration Measurements Free zinc concentration in lymphocytes was measured by flow cytometry as previously described [44]. Supporting Information. Figure S1.

Figure S2. Figure S3. References 1. J Natl Cancer Inst Monogr 35— View Article Google Scholar 2. J Natl Cancer Inst Monogr 14— View Article Google Scholar 3. J Virol — View Article Google Scholar 4. Microbiol Mol Biol Rev — View Article Google Scholar 5. Immunological and nonimmunological surveillance mechanisms: role in tumor progression. Clin Dermatol — View Article Google Scholar 6. Orth G Genetics of epidermodysplasia verruciformis: Insights into host defense against papillomaviruses.

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Current Topics in Microbiology and Immunology. Springer-Verlag Berlin Heidelberg. J Exp Med 35— J Neurochem — Arch Biochem Biophys — Dermatologica — Br J Dermatol — Haftek M, Jablonska S, Orth G Specific cell-mediated immunity in patients with epidermodysplasia verruciformis and plane warts. J Am Acad Dermatol — Kawai K, Egawa N, Kiyono T, Kanekura T Epidermodysplasia-verruciformis-like eruption associated with gamma-papillomavirus infection in a patient with adult T-cell leukemia.

Dermatology — Lancet — Arch Dermatol — Palmiter RD, Findley SD Cloning and functional characterization of a mammalian zinc transporter that confers resistance to zinc. EMBO J — J Biol Chem — J Immunol — Eide DJ Zinc transporters and the cellular trafficking of zinc. Biochim Biophys Acta — Kaler P, Prasad R Molecular cloning and functional characterization of novel zinc transporter rZip10 Slc39a10 involved in zinc uptake across rat renal brush-border membrane. Finally, are the targets of the cell non-autonomously activated UPRER the same as the targets of the autonomous response, or are different target genes, or different subsets of known UPRER targets, triggered?

The use of model organisms to address these questions, and decipher the mechanisms and signaling pathways involved in UPRER communication, will likely continue to be invaluable. Once these issues are better understood, the possibility that these pathways may be harnessed to combat immunological, metabolic or neurodegenerative diseases, or cancer, will become an exciting prospect.

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Nat Rev Cancer — Mahadevan NR et al Transmission of endoplasmic reticulum stress and pro-inflammation from tumor cells to myeloid cells. Genes Dev — Nakatani Y et al Involvement of endoplasmic reticulum stress in insulin resistance and diabetes. J Biol Chem — Ozcan L et al Endoplasmic reticulum stress plays a central role in development of leptin resistance. Cell Metab — Ozcan U et al Endoplasmic reticulum stress links obesity, insulin action, and type 2 diabetes. Science — Panaretakis T et al Mechanisms of pre-apoptotic calreticulin exposure in immunogenic cell death. Nature — Ron D, Walter P Signal integration in the endoplasmic reticulum unfolded protein response.

Cell — Singh V, Aballay A Endoplasmic reticulum stress pathway required for immune homeostasis is neurally controlled by arrestin Science — Volchuk A, Ron D The endoplasmic reticulum stress response in the pancreatic beta-cell. Cell Metab — Xu J et al Fibroblast growth factor 21 reverses hepatic steatosis, increases energy expenditure, and improves insulin sensitivity in diet-induced obese mice. Diabetes — Yu L et al Anticipatory activation of the unfolded protein response by epidermal growth factor is required for immediate early gene expression and cell proliferation.

Mol Cell Endocrinol — Abstract The endoplasmic reticulum ER is the primary site for the folding of proteins destined for the membranous compartment and the extracellular space. This elaborate function is coordinated by the unfolded protein response UPR , a stress-activated cellular program that governs proteostasis.

In multicellular organisms, cells have adopted specialized functions, which required functional adaptations of the ER and its UPR. Recently, it has become clear that in immune cells, the UPR has acquired functions that stretch far beyond its original scope. In this review, we will discuss the role of the UPR in the immune system and highlight the plasticity of this signaling cascade throughout immune cell development.

Coordinating an Unfolded Protein Response Janssens e-mail: sophie. Indeed, a disruption of proteostasis has been observed in a number of neurological e. A large set of physiological e. To restore homeostasis, cells activate an ER stress-responsive signaling cascade called the unfolded protein response UPR. Importantly, additional metabolic processes operate at the ER e. These studies underpin the deregulation of the UPR as an inciting event in inflammatory diseases, and uncovered an emerging role of the UPR in regulating immune responses recently reviewed in Janssens et al.

In addition, the UPR has been increasingly implicated in the development of immune cells Iwakoshi et al. In this current review, we questioned how the UPR coordinates the development of the immune system and highlight how this can contribute to disease pathogenesis.

Polypeptide strands entering the ER can be co-translationally N-glycosylated and subsequently bound to the folding chaperones calnexin and calreticulin, to coordinate protein folding and prevent aggregation. A stringent quality control will sense proteins that are not properly folded and prevents their subsequent egress from the ER to the Golgi Tannous et al.

Upon a number of folding iterations, chronically misfolded proteins are translocated back to the cytosol for proteasomal degradation a process called endoplasmic reticulum-associated protein degradation or ERAD. Initially, the UPR aims to restore homeostasis by reducing protein synthesis, enhancing folding capacity, and bolstering ERAD machinery. If unresolved, chronic pathological ER stress drives a pro-apoptotic UPR, although the molecular mechanisms are incompletely understood Tabas and Ron ; Walter and Ron The mode of activation of the UPR sensors is still debated.

The UPR must be carefully tuned to quickly respond to physiological fluctuations in proteostasis, while avoiding unnecessary induction of cell death. Furthermore, crystallization of an Ire1 dimer revealed the presence of a groove predicted to bind misfolded peptide strands Credle et al. The ability of a model unfolded protein to bind to and cluster Ire1 into higher-order protein complexes has led to a unifying concept. In this model, BiP restrains UPR sensor activation by keeping these into inactive monomers while unfolded proteins both sequester BiP and act as direct UPR sensor ligands, inducing oligomerization and activation Kimata et al.

At present, crystal structures of mammalian IRE-1 fail. Although this could represent an alternative conformational state, the direct binding of peptides to mammalian IRE-1 remains a matter of debate reviewed in Gardner et al. In the case of IRE-1 and PERK, studies have illustrated that these sensors also detect alterations in the lipid content of the ER membrane and that the flavonol quercetin can bind and activate IRE-1 through its cytosolic domain Wiseman et al. These observations indicate that the UPR is responsive to a broader set of cues aside of misfolded proteins.

It is a type I membranous protein with a dual function, bearing both a kinase and an endonuclease in its C-terminal domain Sidrauski and Walter XBP1s was found to be essential for driving cell differentiation, tuning cytokine responses, fueling the HIF1 pathway, and regulating. Activation of the UPR initiates both transcriptional and translational processes, resulting in enhanced protein folding machinery, degradation of unfolded proteins, and reduced protein translation. Subsequent cleavage by S1P and S2P proteases releases the cytosolic domain, resulting in a potent transcription factor.

In , Hollien and colleagues revealed a second activity of IRE-1 endonuclease in Drosophilla melanogaster. This alternate function of IRE-1 has been described in other species and appears relevant to cell differentiation, fate regulation, metabolism, and immune responses Coelho and Domingos ; Osorio et al. Although the molecular basis that allows the IRE-1 endonuclease to alternate between the unconventional splicing of XBP1 and the degradation of a broader set of RNAs is still unclear Ghosh et al. Adding an extra layer of complexity, the metazoan IRE-1 kinase also signals independently of its endonuclease activity.

These signaling events connect the UPR to inflammatory and pro-apoptotic pathways Hetz et al. Paradoxically, reduced cap-dependent protein synthesis during ER stress enhances the translation of a number of mRNAs with short upstream open reading. Although restoration of protein translation is crucial for the induction of the UPR machinery and cellular survival, engaging the translational machinery without elimination of the initial ER stress agent can be deleterious, inducing oxidative stress and cell death Novoa et al.

Meanwhile, several additional sensors coordinating the ER stress response have been revealed, putting pressure on the model of a three-pronged UPR. This myriad of threats e. Some of these cells e. In the following section, we will give an overview of the most recent insights on the role of the UPR in the development of the immune system.

The hematopoietic lineage relies on stem cells for the replenishment of aging cells. These stem cells are characterized by their multilineage potential, self-renewal capacity, and longevity. Recently, it has become clear that these properties critically depend on their strict regulation of proteostasis to avoid cellular stresses caused by accumulation of reactive oxygen species ROS or ER stress Rouault-Pierre et al. This resulted in HSC loss and promoted tumor formation Signer et al. Furthermore, human cord blood HSCs were shown to be particularly sensitive to genetically or chemically induced proteotoxic stress in a PERK-dependent manner.

Overexpression of the chaperone Erdj4 in HSCs increased their folding capacity, protected them from ER stress-induced cytotoxicity, and augmented their engraftment rate van Galen et al. These data raise the concept that the stem cell pool maintains clonal integrity by removing stressed and damaged cells, ultimately preventing tumorigenesis Fig. The mechanism of this differential UPR regulation remains largely enigmatic. One study suggested that developmental pluripotency associated 5 dppa5 , highly expressed in long-term stem cells, governs HSC reconstitution capacity through regulation of UPR, mitochondrial respiration, and glycolysis Miharada et al.

Although all aforementioned studies focused on the cell differentiation to granulocytes, translational control and UPR regulation seem to be a conserved feature across hematopoietic lineages as also the macrophage and dendritic cell DC progenitors display higher protein synthesis rates and increased IRE-1 activity compared to HSCs Tavernier SJ et al. The importance of these non-cell autonomous chaperones is further highlighted by in vitro culture studies of HSCs. In culture, HSCs quickly lose their self-renewal capacity and undergo apoptosis, a process that is associated with increased protein synthesis and activation of the UPR Miharada et al.

Although the data on UPR regulation in intestinal stem cells ISCs are scarce, some interesting parallels and differences can be noted. In homeostatic conditions, ISCs are located at the bottom of the crypts, where they generate the rapidly dividing. Both fetus and maternal bile acids BA sustain protein folding in fetal liver stem cells, precluding deleterious PERK activation. In the mononuclear phagocytic branch, CSF-1 ligation induces macrophage differentiation and results in a broad activation of the UPR. Among granulocytes, eosinophils selectively require XBP1 during differentiation.

Correspondingly, eosinophil maturation is associated with enhanced XBP1 splicing. These cells have lost self-renewal capacity and after a number of cycles give rise to the different subtypes of intestinal epithelial cells absorptive cells, Paneth cells, neuroendocrine cells, and goblet cells. These reports suggest that a tight UPR control is essential for stem cell function.

In contrast to HSCs residing in the bone marrow, mucosal stem cells are continuously exposed to a hostile environment with various microbial and inflammatory stresses. The integration of these signals into the UPR pathway might be a possible explanation of these different outcomes. Further research on how the UPR determines these cell responses in these different settings will be instrumental for our understanding how the UPR gives rise to diverging cell fates. Proteostasis seems to be essential in early lymphocyte development. Deletion of BiP in hematopoietic cells induces widespread ER stress and reduces common lymphocyte progenitors in the bone marrow, thymus atrophy, and lymphopenia Wey et al.

Although these results predict that loss of IRE-1 signaling would block B-cell development beyond the pro-B-cell stage or T-cell differentiation in the thymus, mice lacking XBP1 in the hematopoietic lineage do not show obvious signs of lymphopenia Bettigole et al. Indeed, the cytoplasmic domain of IRE-1 but not its enzymatic activity appears required for the rearrangement of the B-cell receptor BCR and B-cell differentiation, in an as-yet poorly understood mechanism Zhang et al.

The terminal differentiation of B cells into immunoglobulin Ig -secreting plasma cells PC requires a fundamental adjustment of the cellular architecture. In particular, the ER needs to expand to cope with the enormous increase in protein secretion. These changes occur in an anticipatory fashion, i. This ensures that the cell is well adapted for its new secretory role Gass et al.

In a series of publications, the molecular basis for this XBP1 dependency was elucidated. Together with BLIMP1, XBP1 sets the stage for terminal differentiation of B cells, including cell growth, enhanced protein synthesis, and expansion of cell organelles such as mitochondria, lysosomes, and the ER Shaffer et al. Future studies should address whether and how IRE-1 inhibitors can be harnessed as potential therapeutics, not only for MM but also for other B-cell malignancies and antibody-driven autoimmune diseases Neubert et al. Although these data collectively give rise to an elegant model of UPR activation in PCs, some outstanding questions remain unanswered.

What drives this early expansion of the folding machinery? Furthermore, PCs generate up to 2ng of antibodies per day Brinkmann and Heusser How can long-lived PCs combine longevity in the bone marrow and this laborious and potentially toxic. This suggests that the anticipatory activation of the UPR by an extracellular signal may be a general mechanism of multiple cell types Pino et al. The tight regulation of key metabolic switches such as mTOR or the UPR is crucial in T-cell development as inappropriate activation of these pathways in quiescent thymocytes results in partial activation, proliferation defects, and enhanced apoptosis Ozcan et al.

Compared to the lymphoid compartment, a similar theme emerges in the development of granulocytes, although with a couple of surprising twists. Granulocyte progenitors display XBP1 splicing in vivo, paralleling the enhanced protein synthesis to underpin granulocyte production Signer et al. Upon overexpression of XBP1s, this cell line exhibits features of granulocyte maturation Kurata et al.

Remarkably, the absence of XBP1 in vivo cripples eosinophil differentiation without noteworthy defects in the neutrophil and basophil lineages Bettigole et al. In this report, the authors found that the absence of XBP1 resulted into enhanced apoptosis of eosinophil progenitors and a developmental block with. The prolonged PERK activation might then drive the subsequent demise of the eosinophil-committed cells Bettigole et al. Furthermore, activation of both neutrophils and basophils during inflammation induces the secretion of a large amount of inflammatory agents, putting a heavy burden on the ER.

The relative contribution of XBP1 during these conditions to the functional properties of granulocytes remains to be elucidated. Considered as a separate branch in the immune system, the mononuclear phagocytic system MPS is comprised of macrophages, monocytes, and DCs Yona and Gordon As a distinct lineage, these cells originate from early committed progenitors and have specialized but pleiotropic functionalities Naik et al.

Whereas monocytes are considered as a quiescent pool of BM residing and circulating cells that can be quickly recruited in the advent of inflammation, macrophages and DCs are tissue-resident cells Guilliams et al. DCs are short-lived and continuously replenished from a pool of BM-derived precursors called pre-DCs.

In contrast, most macrophages develop from yolk sac-derived embryonic precursors and acquire functionalities beyond the classical immune functions, including tissue homeostasis regulation Ginhoux and Jung Furthermore, these cells did not survive ex vivo culture and displayed enhanced cleavage of caspases, a hallmark of apoptosis. Despite reduced CD11c expression in cDC1s, a consequence of the degradation of Itgb2 mRNA, terminally differentiated splenic DCs are present in appropriate numbers and phenotypically normal. Reminiscent of differentiation of B cells into PCs, monocytes increase overall cell size, number of organelles, and protein synthesis upon differentiation into macrophages.

Macrophages are plastic cells, and it has been suggested that UPR activation polarizes macrophages toward a M2 phenotype, promoting cholesterol uptake and development into foam cells upon exposition to cholesterol Oh et al. This UPR-mediated death of foam cells is associated with plaque instability and disease progression Thorp et al.

In particular inflammatory settings, monocytes can also acquire most of the phenotypical and functional characteristics of DCs Plantinga et al. The subsequent intracellular lipid oxidation by ROS generates reactive byproducts shown to generate ER stress. The ensuing XBP1 activation upregulates triglyceride biosynthetic genes e. Indeed, silencing of XBP1 in tumor phagocytes enhances protective T-cell immune responses and host survival Cubillos-Ruiz et al. The contribution of the UPR in tissue-resident macrophage development remains largely unchartered territory, mediated in part by the embryonic origin of these cells.

This research area is ripe for investigation and is bound to reveal unexpected roles in macrophage development and function. Mucosal cells are our foremost barrier, separating tissues such as lung and intestinal parenchym from the luminal content and commensal flora. Among these, Paneth cells and goblet cells are considered professional secretory cells and are an integral part of the innate immune system Hosomi et al.

A thick layer of mucus, which retains antimicrobial products in its framework and forms a physical barrier against environmental threats, lines the intestinal mucosa. Mucus is composed of mucins, large O-glycosylated proteins that are secreted by the goblet cells as polymers Allen et al. The posttranslational processing of these proteins requires an elaborate secretory system to handle this workload, and a physiological UPR activation is crucial for the optimal functioning of goblet cells. For example, goblet cells of mice carrying missense mutations in the Muc2 gene the Winnie and Eeyore mice retain intracellular MUC2 precursor aggregates and suffer from ER stress and enhanced apoptosis Heazlewood et al.

As such, it is of no surprise that the UPR has been implicated in the correct development of the goblet cell. Similarly, OASIS is activated by regulated intramembranous proteolysis during the terminal differentiation of the goblet cell, which is associated with UPR activation. Paneth cells are essential to maintain mucosal integrity and regulate the microbial populations by the production of large amounts of antimicrobial products such as defensins, phospholipase A2, and lysozyme.

Differentiation, proliferation, antimicrobial peptide secretion, and survival of Paneth cells rely on various components of the UPR. In the absence of AGR2, the Paneth cell population expands beyond the base of the crypts into the villi of the small intestine Zhao et al. It remains to be determined whether the direct loss of AGR2 or the indirect effects of UPR activation are accountable for the enhanced Paneth cell proliferation Zhao et al. Loss of XBP1 dramatically reduces the number of Paneth cells with the few remaining cells demonstrating a disorganized ER, hypomorphic granule formation, and displaying signs of ER stress, autophagy induction, and apoptosis Kaser et al.

Except for OASIS, all of the above mutants acquire spontaneous intestinal inflammation or are more susceptible to gastrointestinal infections and experimental models of inflammatory bowel disease IBD. Compared to these mutant mice, mice devoid of Paneth cells or lacking MUC2 in goblet cells display a reduced penetrance of spontaneous inflammatory disease.

This indicates that the ensuing ER stress response in these genetically manipulated mice, rather than the sole loss of function of the IECs, contributes to disease induction and progression Garabedian et al. In this model, IECs integrate a number of cues derived from the intestinal lumen e. In the Winnie mice, IL and corticosteroids limit intestinal inflammation and the anti-inflammatory properties of these molecules partly rely on their capacity to enhance ERAD machinery and optimize MUC2 production Hasnain et al.

At present, we have only caught a glimpse of this physiological regulation and our current models of UPR regulation fail to offer a satisfying explanation excellently reviewed in Rutkowski and Hegde This is beautifully demonstrated during the development and activation of the immune system. In the earliest steps of development, long-term stem cells rely on PERK to prevent proteotoxic stress and preserve a healthy niche. This seems to be conserved for the lymphoid, granulocytic, and mononuclear phagocytic lineage but also for intestinal cells Zhang et al. Activation of the UPR in immune cells has been reported in a wide array of diseases reviewed in Hasnain et al.

Given the crucial nature of the UPR in immune cell development, careful use of these therapeutics will be mandatory and future research should aim to dissect the detrimental proinflammatory signals from the physiological branches. Mol Cell — Nature — Annu Rev Biochem — J Biol Chem — Antioxid Redox Signal — Eur J Immunol. J Clin Invest — Nat Cell Biol — Nat Immunol — Cell Immunol — Inflamm Bowel Dis — Gastroenterology — :e6. EMBO J — Cancer Cell — Nucleic Acids Res — PLoS Pathog 8:e Front Genet Cell 1— J Exp Med.

Nat Genet — Eur J Immunol — Mucosal Immunol — Cold Spring Harbor Perspect Biol 5:a Science — Nat Publishing Group — Nat Publishing Group. Nat Rev Immunol — Mol Immunol — Mol Biol Cell — Harding HP, Zhang Y, Zeng H et al An integrated stress response regulates amino acid metabolism and resistance to oxidative stress.

Topic Categories | IMMUNOLOGY ™

Immunol Cell Biol — Gastroenterology — :e9. PLoS Med 5:e Cell Rep — Nat Med — Cold Spring Harbor Perspect Biol. J Cell Biol — Curr Opin Gastroenterol — J Exp Med — FEBS Lett — Nat Rev Mol Cell Biol — Kharabi Masouleh B, Geng H, Hurtz C et al Mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia. Elife 1:e Genes Cells — Annu Rev Cell Dev Biol — EMBO Rep. Cell Death Dis 2:e Cell Stress Chaperones — Trends Biochem Sci. Annu Rev Immunol — Miharada K, Sigurdsson V, Karlsson S Dppa5 improves hematopoietic stem cell activity by reducing endoplasmic reticulum stress.

Blood — Cell Death Differ — Mol Cell Biol — Semin Immunopathol. Nat Immunol. Proc Nat Acad Sci — PLoS Biol 8:e Immunity — Immunity — Reavie L, Gatta Della G, Crusio K et al Regulation of hematopoietic stem cell differentiation by a single ubiquitin ligase-substrate complex. Gut — Dev Cell — Shkoda A, Ruiz PA, Daniel H et al Interleukin blocked endoplasmic reticulum stress in intestinal epithelial cells: impact on chronic inflammation.

YGAST — Sigurdsson V, Takei H, Soboleva S et al Bile acids protect expanding hematopoietic stem cells from unfolded protein stress in fetal liver. Stem Cell — M Tabas I, Ron D Integrating the mechanisms of apoptosis induced by endoplasmic reticulum stress. Semin Cell Dev Biol — J Immunol — PLoS Genet e Wang M, Kaufman RJ Protein misfolding in the endoplasmic reticulum as a conduit to human disease.

Dev Cell — Mol Cell — Yona S, Gordon S From the reticuloendothelial to mononuclear phagocyte system—the unaccounted years. Front Immunol Dev Biol — Semin Immunopathol — Moreover, the dynamic and complex membranous structures constituting the ER allow the formation of contact sites with other organelles and structures, including among others the mitochondria and the plasma membrane PM. The contact sites that the ER form with mitochondria is a hot topic in research, and the nature of the so-called mitochondria-associated membranes MAMs is continuously evolving.

The MAMs harness the main functions of both organelles to form a specialized subcompartment at the interface of the ER and mitochondria. MAMs are also believed to be the master regulators of mitochondrial shape and motility, and to form a crucial site for autophagosome assembly. Not surprisingly, MAMs have been shown to be a hot spot for the transfer of stress signals from the ER to mitochondria, most notably under the conditions of loss of ER proteostasis, by engaging the unfolded protein response UPR.

In this chapter after an introduction on ER biology and ER stress, we will review the emerging and key signaling roles of the MAMs, which have a root in cellular processes and signaling cascades coordinated by the ER. Agostinis kuleuven. However, importantly, the ER is the main subcellular organelle dedicated to protein folding and secretion, and constitutes the location where the synthesis of at least a third of the total proteome takes place.

The ER is a plastic and dynamic organelle at the center of a tight communication network with other subcellular organelles and compartments. In the following subchapters, the main biological and morphological characteristics of this organelle will be discussed.

Igor Kramnik, M.D., Ph.D.

At the morphological level, the ER can be divided into two distinct but interconnected entities, namely the nuclear ER and the peripheral ER. At the morphological level, ribosomes stud the outer RER membrane, and its compartments tend to organize in a series of flattened sheets. Proteins moving into the secretory pathway or destined to be incorporated in the plasma membrane PM will be translated by these ribosomes and co-translationally inserted into the ER lumen. The SER can easily be distinguished by its vast tubular network spanning the length and breadth of the cell Voeltz et al.

Despite these distinct differences, the entire ER is connected and forms one continuous network, allowing biomolecules like proteins to travel between different compartments. A characteristic of ER tubules is their high membrane curvatures, a requirement to form tubules. In contrast, overexpression of these proteins leads to long, unbranched tubules.

In line, overexpression of climp63 leads to the formation of ER sheets Shibata et al. Cells that produce steroid hormones, such as adrenal cortex cells, or cells that mainly detoxify xenobiotics like liver cells , will have substantially more SER.

As it will be discussed later Sect. Besides forming morphologically distinct structures, as described briefly above, the ER also coordinates a variety of biosynthetic and signaling functions. Proper protein folding is not only a crucial process to maintain homeostasis, but also a highly complex process, requiring the assistance of many folding enzymes and a specialized oxidizing environment Dinner et al. Important processes include N-linked glycosylation, where N-linked glycans are attached to Asn residues on the polypeptide by oligosaccharyltransferases. Terminal failure in protein folding or in oligomer assembly results in ER-associated protein degradation ERAD , in which non-native conformers are retrotranslocated to the cytosol and degraded by the 26S proteasome McCracken and Brodsky In mammalian cells, glycerophospholipids constitute the largest class of lipids.

The ER plays a central role in the synthesis of glycerophospholipids through the presence of multiple enzymes that catalyze the production of the most important lipid species. Phosphatidylethanolamine PE , the second most abundant phospholipid, is produced either at the ER, or at the inner mitochondrial membrane through two distinct pathways.

The third major phospholipid produced in the ER is phosphatidylserine PS , which is produced by exchanging the polar head group of PE or PC for serine. The enzymes responsible for this conversion, PS synthase 1 and 2, are present in the subcompartment of the ER, the mitochondria-associated membranes MAMs , which will be discussed in detail later Vance The ER is thus a balanced organelle that requires a tight homeostasis to perform its functions, of which protein folding is one of the most important.

Perturbation in this homeostasis will lead to a condition termed ER stress, in which the ER protein folding machinery can no longer cope with the influx of newly synthesized proteins, leading to their accumulation Malhotra and Kaufman ; Ron and Walter ER stress is set off by various intracellular and extracellular insults, which alter the protein folding capacity of the ER.

Perturbation of ER homeostasis activates an evolutionarily conserved stress response, collectively called the unfolded protein response or UPR. The following is a brief description of the major signaling arms of the UPR and the emerging role this adaptive response plays in certain pathological conditions. When these mechanisms are inadequate to restore homeostasis in the ER, the UPR switches to promote a cell death program, which in higher vertebrates is most likely activated in order to protect the host organism from an accumulation of dysfunctional cells.

These transmembrane proteins contain a luminal domain, which functions as a sensor of the ER folding capacity, and a cytosolic effector domain that provides a signaling bridge connecting the ER to other cellular compartments. In unstressed cells, the luminal domain of the transmembrane receptors is bound to BiP. BiP belongs to the heat-shock protein HSP 70 class of molecular chaperones and can form complexes with heterologous proteins that are processed through the ER. AMPylated BiP loses its ability to bind to nascent unfolded proteins, in a rapid process that matches fluctuating protein load with ER folding capacity Preissler et al.

Furthermore, BiP cycles between oligomeric and. Upon ER stress, and the accumulation of unfolded proteins, BiP releases its inhibitory binding of the three ER stress proteins and activates them. Activated ATF6 will migrate toward the Golgi, to be cleaved, and will become a transcription factor. IRE1, when activated, will dimerize, which will activate its mRNase activity. XBP-1 will then act as a transcription factor. Paradoxically, this translation stop will upregulate the transcription factor ATF4. This upregulation of chaperones goes hand in hand with the induction of ERAD and autophagy pathways, in order to clear terminally misfolded proteins.

Furthermore, lipid synthesis will be increased in order for the ER to physically expand. Combined, these responses are geared to increase cell survival and re-establish ER proteostasis. On accumulation of unfolded proteins, which promotes a dramatic increase in the luminal pool of monomeric BiP, BiP is. Recently, ER protein overload has been shown to be alleviated by the secretory pathway, through a newly described mechanism, whereby unfolded glycosylphosphatidylinositol GPI -anchored proteins are exported via the Golgi apparatus to the PM for subsequent endocytosis and lysosome degradation Noack and Molinari Other lysosomal degradative pathways contribute to the cytosolic removal of misfolded proteins.

In line with this, autophagy has been shown to play an important cytoprotective role in restoring ER proteostasis under conditions of ER stress Ogata et al. ATF4 promotes cell survival through the induction of several genes involved in restoring ER homeostasis. This leads to the upregulation of proteins mainly involved in cellular redox homeostasis, such as glutathione-S-transferase GST and heme-oxygenase HO The limited proteolysis of ATF6 releases the transcription factor domain into the cytosol and allows its migration into the nucleus, where it binds DNA and activates gene expression.

IRE1 autophosphorylation stimulates its endonuclease activity and, unlike PERK, does not result in the propagation of a phosphorylation cascade. The main UPR pathways are shown schematically in Fig. However, in the event that this response is inadequate and loss of ER proteostasis persists, the UPR promotes cell death, which occurs primarily, although not exclusively, through apoptosis Jager et al. It was long thought that this process would allow the resumption of physiological protein folding after the resolving of ER stress, but new reports have indicated that under severe ER stress, this would lead to an increased burden on the ER and oxidative stress, promoting apoptosis Han et al.

The tight interplay between ATP consumption, mainly involving mitochondria and ER stress, will be discussed in more detail below.

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IRE1 has a dual role in promoting cell death, relying on its scaffolding function and mRNase activity. JNK activation is important in ER stress-induced apoptosis, although the exact mechanism is not entirely clear Hetz ; Urano et al. Moreover, JNK activation can also modulate autophagy, through the phosphorylation of Bcl2, which in turn triggers the activation of Beclin 1 Wei et al.

IRE1 is also able to induce cell death through its mRNase activity. While the cleavage of XBP-1 is considered to be a pro-survival response, leading to the upregulation of various chaperones and pro-survival factors Moenner et al. The cleaved miRNAs include miR, miRa, miR, and miRb, which have been reported to suppress the expression of certain pro-death and pro-inflammatory mediators, such as caspase 2 and thioredoxin-interacting protein TXNIP , a modulator of the nucleotide-binding oligomerization domain NOD -like receptor family 3 NLRP3 inflammasome Maurel et al.

The different morphologies that the ER plastically adopts couple structural changes to distinct functions, which are exerted and modulated by the formation of contact sites with other organelles and the PM. Among these, the most studied are the ER—mitochondria contact sites, also termed mitochondria-associated membranes MAMs , but also ER-PM contact sites are becoming a much studied and hot topic. A tight physical relationship between the mitochondria and ER had already been suggested many decades ago by pioneering electron microscopic observations done by John Ruby and co-workers, who discovered a potential connection between the ER membrane and the mitochondrial outer membrane in Ruby et al.

The functional characterization of the MAMs did not come up to speed until the turn of the millennium, the work of Rizzuto and co-workers being a major driving force Rizzuto et al. It was at this time that the Vance lab followed up its initial discovery by investigating the role of the MAMs in lipid homeostasis in liver cells of the rat Shiao et al. Soon it became clear that the MAMs provide more than just a protein link between the two organelles; rather, they allow a functional transit of metabolites and signaling molecules between the ER and mitochondria, with implications in cell fate decisions.

At the present time, even this claim seems to underestimate the true role of MAMs, and a growing number of studies are appearing involving this little piece of the puzzle of the cell in a vast cascade of crucial homeostatic functions both in the cell and outside of it.

Here, focus will be mainly on the molecular components of the MAMs and their role in the regulation of ER stress. Just like both organelles that they physically link, MAMs should not be interpreted as static bridges linking mitochondria and ER. In contrast, MAMs seem very flexible and entail a specialized set of proteins, which are able to support a multitude of signaling components in accordance with the needs of the cell. Recent research has uncovered two novel protein tethers that can function as linkers between the ER and. Despite MFN2 being one of the best studied MAM-resident proteins, some controversy has recently arisen concerning its exact role in the ER—mitochondria contact sites.

Initial studies, which have since been reproduced, have indicated that MFN2 acts as a physical tether between the two organelles by homotypic and heterotypic with MFN1 interactions Naon et al. However, some recent studies have, however, shown the opposite effect that MFN2 might act as an inhibitor of close ER—mitochondria apposition Filadi et al.

Future studies will have to clear out these discrepancies. As already discussed briefly above, proper protein folding is not only a crucial process to maintain homeostasis, it is also highly complex, requiring the assistance of many folding enzymes and a specialized oxidized environment Dinner et al. This cER formation goes along with the appearance of thin tubules making close contact with the plasma membrane of the cell Shen et al.

PTP opening in turn induces mitochondrial swelling and OMM rupture, with the consequent release of caspase-activating factors and apoptosis induction Kroemer et al. The study of Iwasawa et al. This suggests that a tight association between ER and mitochondria is required for this mechanism of Bapmediated apoptosis. Additionally, it has also become clear that not only do the targeting and sorting mechanisms modulate MAMs functionality, and also the length of the connections linking the ER and mitochondria is important to determine their effect on each organelle Csordas et al.

Elegant work done in the laboratory of Hajnoczky by using electron tomography and expression of synthetic linkers, addressed the issue of the relevance of a proper ER—mitochondria distance. These authors found that the ER and mitochondria are juxtaposed through trypsin-sensitive domains thus proteinaceous in nature , which are approximately 10 nm at the smooth ER and 25 nm at the rough ER Csordas et al.

In contrast loosening without disrupting these ER—mitochondrial contact sites stimulated mitochondrial respiration and ATP production Csordas et al. As mentioned above, the ER is also the prime site for lipid synthesis and is the central hub around which all lipids are formed. Initially phosphatidylserine PS is formed in a subdomain of the ER and further transported to the mitochondria where it is imported in the IMM and becomes a substrate for PS decarboxylase 1, resulting in the synthesis of PE. Upon closer inspection however, the vital location for the synthesis and shuttling of all these lipids resides in the MAMs Voelker Additionally, the transport of PS to the mitochondria has even been shown to constitute the rate-limiting step in the synthesis of PE in the mitochondria Voelker In line with.

In the mitochondria cholesterol is further converted into pregnenolone, which is then transported back to the ER via the MAMs to be further converted to other steroids. The MAMs have long been known as a lipid raft-like structure, highly enriched in cholesterol Hayashi and Fujimoto Furthermore, altering cholesterol levels itself has been shown to modulate the ER—mitochondrial connections.

In line with this, when cholesterol is depleted from the cell, an increased association of the ER with mitochondria is observed, likely as a mechanism to improve MAMs functionality and re-establish cholesterol synthesis Fujimoto et al. Another indication of the importance of cholesterol synthesis at the MAMs is the presence of caveolin-1 Cav-1 at these ER—mitochondria subdomains.

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Therefore, regulation of lipid shuttling at the MAMs has clear implications for mitochondrial lipid composition, mitochondrial metabolism and apoptotic signaling. Furthermore, the observations that mice lacking PS decarboxylase display aberrantly shaped mitochondria, showing a fragmented network Steenbergen et al.

Earlier research had already shown that the closely related oxysterol-binding proteins OSBP were responsible for cholesterol—phosphatidylinositol 4-phosphate PI4P countertransport between the ER membrane and the Golgi Rysman et al. The connection between the ER and mitochondria is becoming one of the major factors in controlling the dynamic changes in shape and motility of these two organelles.

Similar to the ER, mitochondria are commonly organized in long tubular networks and are very dynamic organelles. Mitochondria are constantly fusing, fragmenting and branching, dictated by the various impulses which include metabolic stimuli, general calcium buffering needs or different cellular stresses.

Accumulating data highlight an important role for the MAMs in the coordination of ER and mitochondria shape and dynamics. Indeed, some of the proteins involved in mitochondrial motion along microtubules, i. Important regulators of mitochondrial movement are the Miro proteins Miro 1 and 2. Miro 1 and 2 are located at the OMM, where they are anchored through a short C-terminal domain. Miro 1 and 2 enable mitochondrial movement by anchoring mitochondria to the cytoskeleton Saotome et al.

As mentioned earlier, the yeast ortholog of Miro, Gem1, has been shown to have an impact on the size and number of the ER—mitochondria encounter structure ERMES connecting both organelles, and to affect the phospholipid homeostasis. Kornmann et al. These stress conditions, which can lead to an increased production of reactive oxygen species, are able to compromise mitochondrial membrane potential and cause disturbances in the mitochondrial function, leading to excessive fragmentation. The major player in this process though is believed to be the highly conserved dynamin-related protein 1 drp1.

Drp1 works by forming a spiral oligomer in a GTP-dependent manner through intra- and intermolecular interactions. Drp1, by oligomerizing in this manner, is believed to provide the required mechanochemical force that is needed to induce division of the outer and inner mitochondrial membranes Ingerman et al. This action induced local fragmentation and recruitment of Drp1. This interplay between tubular ER and mitochondria strongly hints at involvement of the MAMs in mitochondrial division. For a schematic depiction of the MAMs, please see Fig. Here, the various important functions and signaling roles of the MAMs are shown.

Autophagy regulation, initiated by the relocation of syntaxin 17 Stx17 which then proceeds to recruit ATG14L, p, Vps34, and Beclin1 comprising the phosphoinositide 3-kinase, PI3 K, complex , is also shown. One of the most energy-demanding processes in the cell is the proper folding of de novo synthesized proteins. As it has been described previously, there is a tight link between the ATP produced in the mitochondria, and the demand of the stressed ER. The tightening of the ER—mitochondria contact sites under ER stress conditions points to a role in favoring a temporary increase in the intracellular ATP pool.

This increased ATP is required to meet the demands of the increased amount of ER chaperones, newly expressed through the pro-survival ER stress transcriptional machinery, during the early adaptive phases of ER stress. As mentioned previously, when ER stress is persistent or too severe for the UPR to resolve, UPR pathways will switch and turn on a pro-apoptotic signal, eventually causing apoptotic cell death Ron and Walter ; Schroder and Kaufman ; Verfaillie et al.

This higher expression of Parkin did not alleviate ER stress itself but prevented additional mitochondrial fragmentation and loss of ATP production as a result of ER stress Bouman et al. This was highlighted in a follow-up study, where it was shown that increasing Parkin levels caused tighter functional and physical ER— mitochondrial coupling Cali et al.

Also, whether other members of the UPR are localized to or have a signaling or tethering role at the ER—mitochondria contact sites still remains to be investigated. Further implicating ER—mitochondria contact sites to ER stress and UPR and other cellular stresses , several reports have indicated that the MAMs play a central role in the initiation of autophagy and the formation of the autophagosome Hamasaki et al.

Autophagy is the main pathway for the removal, degradation, and recycling of intracellular components through lysosomal degradation. These include superfluous or damaged organelles and proteins Shintani and Klionsky Although autophagy is constitutively active at a basal level to preserve homeostasis, this catabolic process is typically stimulated when the cells perceive the lack of nutrients or in conditions where organellar functionality or proteostasis is compromised Yorimitsu and Klionsky ; He and Klionsky Consistent with this, the stress conditions which lead to ER stress and UPR activation are also able to induce the autophagic machinery.

In this context, autophagy is initiated to aid in the disposal of terminally misfolded proteins and to relieve the folding burden on the ER, and can be induced by PERK-ATF4-mediated transcriptional upregulation of selected autophagy genes Yorimitsu et al.