bims-unfpre Biomed News
on Unfolded protein response
Issue of 2019–11–10
seven papers selected by
Susan Logue, University of Manitoba
  1. UPR proteins IRE1 and PERK switch BiP from chaperone to ER stress sensor.
  2. Methods to Detect Endoplasmic Reticulum Stress and Apoptosis in Diabetic Nephropathy.
  3. Sterile activation of invariant natural killer T cells by ER-stressed antigen-presenting cells.
  4. ESCRT-III-driven piecemeal micro-ER-phagy remodels the ER during recovery from ER stress.
  5. Effect of Kinase Inhibiting RNase Attenuator (KIRA) Compounds on the Formation of Face-to-Face Dimers of Inositol-Requiring Enzyme 1: Insights from Computational Modeling.
  6. The UFMylation System in Proteostasis and Beyond.
  7. The Role of MicroRNAs on Endoplasmic Reticulum Stress in Myocardial Ischemia and Cardiac Hypertrophy.
  1. Nat Struct Mol Biol. 2019 Nov 06.
    UPR proteins IRE1 and PERK switch BiP from chaperone to ER stress sensor.
    Megan C Kopp, Natacha Larburu, Vinoth Durairaj, Christopher J Adams, Maruf M U Ali.
      BiP is a major endoplasmic reticulum (ER) chaperone and is suggested to act as primary sensor in the activation of the unfolded protein response (UPR). How BiP operates as a molecular chaperone and as an ER stress sensor is unknown. Here, by reconstituting components of human UPR, ER stress and BiP chaperone systems, we discover that the interaction of BiP with the luminal domains of UPR proteins IRE1 and PERK switch BiP from its chaperone cycle into an ER stress sensor cycle by preventing the binding of its co-chaperones, with loss of ATPase stimulation. Furthermore, misfolded protein-dependent dissociation of BiP from IRE1 is primed by ATP but not ADP. Our data elucidate a previously unidentified mechanistic cycle of BiP function that explains its ability to act as an Hsp70 chaperone and ER stress sensor.
    DOI:  https://doi.org/10.1038/s41594-019-0324-9
  2. Methods Mol Biol. 2020 ;2067 153-173
    Methods to Detect Endoplasmic Reticulum Stress and Apoptosis in Diabetic Nephropathy.
    Khurrum Shahzad, Sanchita Ghosh, Akash Mathew, Berend Isermann.
      A variety of pathophysiological cellular dysfunctions stress the endoplasmic reticulum (ER), promoting an accumulation of unfolded proteins in the ER lumen. The latter is sensed by intrinsic ER transmembrane proteins: IRE1α (inositol-requiring protein-1α), PERK (protein kinase RNA (PKR)-like ER kinase), and ATF6 (activating transcription factor 6) which when activated trigger the unfolded protein response (UPR), which includes an inhibition of protein translation while inducing specific transcription factors that induce genes aiming to relieve the ER stress response. Collectively, this reduces the burden of unfolded proteins within the ER, eventually restoring ER homeostasis and thus promoting cell survival and adaptation. However, under unresolvable ER stress conditions, the UPR promotes cell death. Diabetic nephropathy (dNP), a leading cause of end-stage renal disease in industrialized countries, is mechanistically closely linked with ER stress and renal cell death. Here, we describe methods (both in vivo and in vitro) for monitoring ER stress, UPR signaling, and cell death in renal cells by analyzing proteins and protein-protein interactions serving as markers of ER stress or cell death. These methods include visualization of interactions of UPR regulators by proximity ligation assay on renal tissue and cells and methods to detect cell death based on DNA fragmentation or fluorochrome substrates for caspases. We include two selected in vivo models to manipulate ER stress regulators and thus the UPR in murine models of dNP. Collectively, these analyses allow assessment of the activation of ER stress-induced signaling pathways and cell death in dNP and manipulation of the UPR in vivo, enabling researchers to probe for causality.
    Keywords:  Activated protein C; Apoptosis; Cell death; Diabetic nephropathy; Endoplasmic reticulum; Unfolded protein response
    DOI:  https://doi.org/10.1007/978-1-4939-9841-8_12
  3. Proc Natl Acad Sci U S A. 2019 Nov 05. pii: 201910097. [Epub ahead of print]
    Sterile activation of invariant natural killer T cells by ER-stressed antigen-presenting cells.
    Melissa Bedard, Dilip Shrestha, David A Priestman, Yuting Wang, Falk Schneider, Juan D Matute, Shankar S Iyer, Uzi Gileadi, Gennaro Prota, Matheswaran Kandasamy, Natacha Veerapen, Gurdyal Besra, Marco Fritzsche, Sebastian Zeissig, Andrej Shevchenko, John C Christianson, Frances M Platt, Christian Eggeling, Richard S Blumberg, Mariolina Salio, Vincenzo Cerundolo.
      Invariant NKT (iNKT) cells have the unique ability to shape immunity during antitumor immune responses and other forms of sterile and nonsterile inflammation. Recent studies have highlighted a variety of classes of endogenous and pathogen-derived lipid antigens that can trigger iNKT cell activation under sterile and nonsterile conditions. However, the context and mechanisms that drive the presentation of self-lipid antigens in sterile inflammation remain unclear. Here we report that endoplasmic reticulum (ER)-stressed myeloid cells, via signaling events modulated by the protein kinase RNA-like ER kinase (PERK) pathway, increase CD1d-mediated presentation of immunogenic endogenous lipid species, which results in enhanced iNKT cell activation both in vitro and in vivo. In addition, we demonstrate that actin cytoskeletal reorganization during ER stress results in an altered distribution of CD1d on the cell surface, which contributes to enhanced iNKT cell activation. These results define a previously unidentified mechanism that controls iNKT cell activation during sterile inflammation.
    Keywords:  CD1d; ER stress; NKT; cancer
    DOI:  https://doi.org/10.1073/pnas.1910097116
  4. Nat Commun. 2019 Nov 07. 10(1): 5058
    ESCRT-III-driven piecemeal micro-ER-phagy remodels the ER during recovery from ER stress.
    Marisa Loi, Andrea Raimondi, Diego Morone, Maurizio Molinari.
      The endoplasmic reticulum (ER) produces about 40% of the nucleated cell's proteome. ER size and content in molecular chaperones increase upon physiologic and pathologic stresses on activation of unfolded protein responses (UPR). On stress resolution, the mammalian ER is remodeled to pre-stress, physiologic size and function on activation of the LC3-binding activity of the translocon component SEC62. This elicits recov-ER-phagy, i.e., the delivery of the excess ER generated during the phase of stress to endolysosomes (EL) for clearance. Here, ultrastructural and genetic analyses reveal that recov-ER-phagy entails the LC3 lipidation machinery and proceeds via piecemeal micro-ER-phagy, where RAB7/LAMP1-positive EL directly engulf excess ER in processes that rely on the Endosomal Sorting Complex Required for Transport (ESCRT)-III component CHMP4B and the accessory AAA+ ATPase VPS4A. Thus, ESCRT-III-driven micro-ER-phagy emerges as a key catabolic pathway activated to remodel the mammalian ER on recovery from ER stress.
    DOI:  https://doi.org/10.1038/s41467-019-12991-z
  5. Int J Mol Sci. 2019 Nov 06. pii: E5538. [Epub ahead of print]20(22):
    Effect of Kinase Inhibiting RNase Attenuator (KIRA) Compounds on the Formation of Face-to-Face Dimers of Inositol-Requiring Enzyme 1: Insights from Computational Modeling.
    Antonio Carlesso, Chetan Chintha, Adrienne M Gorman, Afshin Samali, Leif A Eriksson.
      Inositol-requiring enzyme 1α (IRE1α) is a transmembrane dual kinase/ribonuclease protein involved in propagation of the unfolded protein response (UPR). Inositol-requiring enzyme 1α is currently being explored as a potential drug target due to the growing evidence of its role in variety of disease conditions. Upon activation, IRE1 cleaves X-box binding protein 1 (XBP1) mRNA through its RNase domain. Small molecules targeting the kinase site are known to either increase or decrease RNase activity, but the allosteric relationship between the kinase and RNase domains of IRE1α is poorly understood. Subsets of IRE1 kinase inhibitors (known as "KIRA" compounds) bind to the ATP-binding site and allosterically impede the RNase activity. The KIRA compounds are able to regulate the RNase activity by stabilizing the monomeric form of IRE1α. In the present work, computational analysis, protein-protein and protein-ligand docking studies, and molecular dynamics simulations were applied to different IRE1 dimer systems to provide structural insights into the perturbation of IRE1 dimers by small molecules kinase inhibitors that regulate the RNase activity. By analyzing structural deviations, energetic components, and the number of hydrogen bonds in the interface region, we propose that the KIRA inhibitors act at an early stage of IRE1 activation by interfering with IRE1 face-to-face dimer formation thus disabling the activation of the RNase domain. This work sheds light on the mechanism of action of KIRA compounds and may assist in development of further compounds in, for example, cancer therapeutics. The work also provides information on the sequence of events and protein-protein interactions initiating the unfolded protein response.
    Keywords:  IRE1; KIRA; dimer formation; molecular dynamics simulations; protein–protein docking; unfolded protein response
    DOI:  https://doi.org/10.3390/ijms20225538
  6. Trends Cell Biol. 2019 Nov 05. pii: S0962-8924(19)30163-1. [Epub ahead of print]
    The UFMylation System in Proteostasis and Beyond.
    Yannis Gerakis, Michaela Quintero, Honglin Li, Claudio Hetz.
      Post-translational modifications are at the apex of cellular communication and eventually regulate every aspect of life. The identification of new post-translational modifiers is opening alternative avenues in understanding fundamental cell biology processes and may ultimately provide novel therapeutic opportunities. The ubiquitin-fold modifier 1 (UFM1) is a post-translational modifier discovered a decade ago but its biological significance has remained mostly unknown. The field has recently witnessed an explosion of research uncovering the implications of the pathway to cellular homeostasis in living organisms. We overview recent advances in the function and regulation of the UFM1 pathway, and its implications for cell physiology and disease.
    Keywords:  ER stress; UBL; UFM1; UPR; proteostasis
    DOI:  https://doi.org/10.1016/j.tcb.2019.09.005
  7. Pharmacol Res. 2019 Nov 04. pii: S1043-6618(19)31391-X. [Epub ahead of print] 104516
    The Role of MicroRNAs on Endoplasmic Reticulum Stress in Myocardial Ischemia and Cardiac Hypertrophy.
    Navid Omidkhoda, A Wallace Hayes, Russel Reiter, Gholamreza Karimi.
      The endoplasmic reticulum (ER) is the site of production and folding of secreted, membrane bound and some organelle targeted proteins. Accumulation of misfolded or unfolded proteins in the ER makes cells undergo a stress response known as the unfolded protein response (UPR). UPR is initially protective. However, prolonged and severe ER stress can lead to the induction of apoptosis in stressed cells. Cardiac hypertrophy and myocardial ischemia accounts for substantial morbidity and mortality worldwide. Accumulating evidence suggests that aberrant cardiac cell death caused by ER stress is often associated with structural or functional cardiac abnormalities. MicroRNAs (miRNAs) are a class of small non-coding RNAs that mediate posttranscriptional gene silencing. The miRNAs play important roles in regulating cardiac physiological and pathological events such as hypertrophy, apoptosis, and heart failure. In this review, we discussed the role of microRNAs on Endoplasmic Reticulum Stress in myocardial ischemia and cardiac hypertrophy to demonstrate the relation between microRNAs and the ER in cardiac cells providing potential new treatment strategies and improvement of survival.
    Keywords:  Cardiac hypertrophy; Endoplasmic reticulum stress; MicroRNA; Myocardial ischemia
    DOI:  https://doi.org/10.1016/j.phrs.2019.104516
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