bims-unfpre 2019-03-10 papers

bims-unfpre

Biomed News

on Unfolded protein response

Issue of 2019–03–10
twelve papers selected by
Susan Logue, Apoptosis Research Centre

Ufbp1 promotes plasma cell development and ER expansion by modulating distinct branches of UPR.
Merits and pitfalls of conventional and covalent docking in identifying new hydroxyl aryl aldehyde like compounds as human IRE1 inhibitors.
Epigenetic loss of the endoplasmic reticulum-associated degradation inhibitor SVIP induces cancer cell metabolic reprogramming.
Mitochondrial UPR repression during Pseudomonas aeruginosa infection requires the bZIP protein ZIP-3.
Mast Cells Induce Blood Brain Barrier Damage in SCD by Causing Endoplasmic Reticulum Stress in the Endothelium.
Editorial: Stress and Immunity.
The Role of EMC during Membrane Protein Biogenesis.
The E3 ligase Hrd1 stabilizes Tregs by antagonizing inflammatory cytokine-induced ER stress response.
Structural basis for pH-dependent retrieval of ER proteins from the Golgi by the KDEL receptor.
Pharmacological effectors of GRP78 chaperone in cancers.
RGS2 promotes the translation of stress-associated proteins ATF4 and CHOP via its eIF2B-inhibitory domain.
Probing the Global Cellular Responses to Lipotoxicity Caused by Saturated Fatty Acids.

Nat Commun. 2019 Mar 06. 10(1): 1084

Ufbp1 promotes plasma cell development and ER expansion by modulating distinct branches of UPR.

Huabin Zhu, Brinda Bhatt, Sathish Sivaprakasam, Yafei Cai, Siyang Liu, Sai Karthik Kodeboyina, Nikhil Patel, Natasha M Savage, Ashok Sharma, Randal J Kaufman, Honglin Li, Nagendra Singh.

The IRE1α/XBP1 branch of unfolded protein response (UPR) pathway has a critical function in endoplasmic reticulum (ER) expansion in plasma cells via unknown mechanisms; interestingly, another UPR branch, PERK, is suppressed during plasma cell development. Here we show that Ufbp1, a target and cofactor of the ufmylation pathway, promotes plasma cell development by suppressing the activation of PERK. By contrast, the IRE1α/XBP1 axis upregulates the expression of Ufbp1 and ufmylation pathway genes in plasma cells, while Ufbp1 deficiency impairs ER expansion in plasma cells and retards immunoglobulin production. Structure and function analysis suggests that lysine 267 of Ufbp1, the main lysine in Ufbp1 that undergoes ufmylation, is dispensable for the development of plasmablasts, but is required for immunoglobulin production and stimulation of ER expansion in IRE1α-deficient plasmablasts. Thus, Ufbp1 distinctly regulates different branches of UPR pathway to promote plasma cell development and function.

DOI: https://doi.org/10.1038/s41467-019-08908-5
Sci Rep. 2019 Mar 04. 9(1): 3407

Merits and pitfalls of conventional and covalent docking in identifying new hydroxyl aryl aldehyde like compounds as human IRE1 inhibitors.

Antonio Carlesso, Chetan Chintha, Adrienne M Gorman, Afshin Samali, Leif A Eriksson.

IRE1 is an endoplasmic reticulum (ER) bound transmembrane bifunctional kinase and endoribonuclease protein crucial for the unfolded protein response (UPR) signaling pathway. Upon ER stress, IRE1 homodimerizes, oligomerizes and autophosphorylates resulting in endoribonuclease activity responsible for excision of a 26 nucleotide intron from the X-box binding protein 1 (XBP1) mRNA. This unique splicing mechanism results in activation of the XBP1s transcription factor to specifically restore ER stress. Small molecules targeting the reactive lysine residue (Lys907) in IRE1α's RNase domain have been shown to inhibit the cleavage of XBP1 mRNA. Crystal structures of murine IRE1 in complex with covalently bound hydroxyl aryl aldehyde (HAA) inhibitors show that these molecules form hydrophobic interactions with His910 and Phe889, a hydrogen bond with Tyr892 and an indispensable Schiff-base with Lys907. The availability of such data prompted interest in exploring structure-based drug design as a strategy to develop new covalently binding ligands. We extensively evaluated conventional and covalent docking for drug discovery targeting the catalytic site of the RNase domain. The results indicate that neither computational approach is fully successful in the current case, and we highlight herein the potential and limitations of the methods for the design of novel IRE1 RNase binders.

DOI: https://doi.org/10.1038/s41598-019-39939-z
JCI Insight. 2019 Mar 07. pii: 125888. [Epub ahead of print]5

Epigenetic loss of the endoplasmic reticulum-associated degradation inhibitor SVIP induces cancer cell metabolic reprogramming.

Pere Llinàs-Arias, Margalida Rosselló-Tortella, Paula Lopez-Serra, Montserrat Pérez-Salvia, Fernando Setién, Silvia Marin, Juan P Muñoz, Alexandra Junza, Jordi Capellades, Maria E Calleja-Cervantes, Humberto J Ferreira, Manuel Castro de Moura, Marina Srbic, Anna Martínez-Cardús, Carolina de la Torre, Alberto Villanueva, Marta Cascante, Oscar Yanes, Antonio Zorzano, Catia Moutinho, Manel Esteller.

  The endoplasmic reticulum (ER) of cancer cells needs to adapt to the enhanced proteotoxic stress associated with the accumulation of unfolded, misfolded and transformation-associated proteins. One way by which tumors thrive in the context of ER stress is by promoting ER-Associated Degradation (ERAD), although the mechanisms are poorly understood. Here, we show that the Small p97/VCP Interacting Protein (SVIP), an endogenous inhibitor of ERAD, undergoes DNA hypermethylation-associated silencing in tumorigenesis to achieve this goal. SVIP exhibits tumor suppressor features and its recovery is associated with increased ER stress and growth inhibition. Proteomic and metabolomic analyses show that cancer cells with epigenetic loss of SVIP are depleted in mitochondrial enzymes and oxidative respiration activity. This phenotype is reverted upon SVIP restoration. The dependence of SVIP hypermethylated cancer cells on aerobic glycolysis and glucose was also associated with sensitivity to an inhibitor of the glucose transporter GLUT1. This could be relevant to the management of tumors carrying SVIP epigenetic loss, because these occur in high-risk patients who manifest poor clinical outcomes. Overall, our study provides insights into how epigenetics helps deal with ER stress and how SVIP epigenetic loss in cancer may be amenable to therapies that target glucose transporters.

Keywords:  Cancer; Epigenetics; Oncology

DOI:  https://doi.org/10.1172/jci.insight.125888
Proc Natl Acad Sci U S A. 2019 Mar 08. pii: 201817259. [Epub ahead of print]

Mitochondrial UPR repression during Pseudomonas aeruginosa infection requires the bZIP protein ZIP-3.

Pan Deng, Nandhitha Uma Naresh, Yunguang Du, Lilian T Lamech, Jun Yu, Lihua Julie Zhu, Read Pukkila-Worley, Cole M Haynes.

  Mitochondria generate most cellular energy and are targeted by multiple pathogens during infection. In turn, metazoans employ surveillance mechanisms such as the mitochondrial unfolded protein response (UPRmt) to detect and respond to mitochondrial dysfunction as an indicator of infection. The UPRmt is an adaptive transcriptional program regulated by the transcription factor ATFS-1, which induces genes that promote mitochondrial recovery and innate immunity. The bacterial pathogen Pseudomonas aeruginosa produces toxins that disrupt oxidative phosphorylation (OXPHOS), resulting in UPRmt activation. Here, we demonstrate that Pseudomonas aeruginosa exploits an intrinsic negative regulatory mechanism mediated by the Caenorhabditis elegans bZIP protein ZIP-3 to repress UPRmt activation. Strikingly, worms lacking zip-3 were impervious to Pseudomonas aeruginosa-mediated UPRmt repression and resistant to infection. Pathogen-secreted phenazines perturbed mitochondrial function and were the primary cause of UPRmt activation, consistent with these molecules being electron shuttles and virulence determinants. Surprisingly, Pseudomonas aeruginosa unable to produce phenazines and thus elicit UPRmt activation were hypertoxic in zip-3-deletion worms. These data emphasize the significance of virulence-mediated UPRmt repression and the potency of the UPRmt as an antibacterial response.

Keywords:  ATFS-1; UPRmt; ZIP-3; immunity; mitochondrial UPR

DOI:  https://doi.org/10.1073/pnas.1817259116
Front Cell Neurosci. 2019 ;13 56

Mast Cells Induce Blood Brain Barrier Damage in SCD by Causing Endoplasmic Reticulum Stress in the Endothelium.

Huy Tran, Aditya Mittal, Varun Sagi, Kathryn Luk, Aithanh Nguyen, Mihir Gupta, Julia Nguyen, Yann Lamarre, Jianxun Lei, Alonso Guedes, Kalpna Gupta.

  Endothelial dysfunction underlies the pathobiology of cerebrovascular disease. Mast cells are located in close proximity to the vasculature, and vasoactive mediators released upon their activation can promote endothelial activation leading to blood brain barrier (BBB) dysfunction. We examined the mechanism of mast cell-induced endothelial activation via endoplasmic reticulum (ER) stress mediated P-selectin expression in a transgenic mouse model of sickle cell disease (SCD), which shows BBB dysfunction. We used mouse brain endothelial cells (mBECs) and mast cells-derived from skin of control and sickle mice to examine the mechanisms involved. Compared to control mouse mast cell conditioned medium (MCCM), mBECs incubated with sickle mouse MCCM showed increased, structural disorganization and swelling of the ER and Golgi, aggregation of ribosomes, ER stress marker proteins, accumulation of galactose-1-phosphate uridyl transferase, mitochondrial dysfunction, reactive oxygen species (ROS) production, P-selectin expression and mBEC permeability. These effects of sickle-MCCM on mBEC were inhibited by Salubrinal, a reducer of ER stress. Histamine levels in the plasma, skin releasate and in mast cells of sickle mice were higher compared to control mice. Compared to control BBB permeability was increased in sickle mice. Treatment of mice with imatinib, Salubrinal, or P-selectin blocking antibody reduced BBB permeability in sickle mice. Mast cells induce endothelial dysfunction via ER stress-mediated P-selectin expression. Mast cell activation contributes to ER stress mediated endothelial P-selectin expression leading to increased endothelial permeability and impairment of BBB. Targeting mast cells and/or ER stress has the potential to ameliorate endothelial dysfunction in SCD and other pathobiologies.

Keywords:  P-selectin; blood brain barrier; endoplasmic reticulum stress; endothelial cell; mast cell; sickle cell disease

DOI:  https://doi.org/10.3389/fncel.2019.00056
Front Immunol. 2019 ;10 245

Editorial: Stress and Immunity.

Yong-Soo Bae, Eui-Cheol Shin, Yoe-Sik Bae, Willem Van Eden.



Keywords:  cell stress; heat shock (stress) proteins; psychological stress; stress protein; unfolded protein response (UPR)

DOI:  https://doi.org/10.3389/fimmu.2019.00245
Trends Cell Biol. 2019 Feb 27. pii: S0962-8924(19)30018-2. [Epub ahead of print]

The Role of EMC during Membrane Protein Biogenesis.

Patrick J Chitwood, Ramanujan S Hegde.

  Ten years ago, high-throughput genetic interaction analyses revealed an abundant and widely conserved protein complex residing in the endoplasmic reticulum (ER) membrane. Dubbed the ER membrane protein complex (EMC), its disruption has since been found to affect wide-ranging processes, including protein trafficking, organelle communication, ER stress, viral maturation, lipid homeostasis, and others. However, its molecular function has remained enigmatic. Recent studies suggest a role for EMC during membrane protein biogenesis. Biochemical reconstitution experiments show that EMC can directly mediate the insertion of transmembrane domains (TMDs) into the lipid bilayer. Given the large proportion of genes encoding membrane proteins, a central role for EMC as a TMD insertion factor can explain its high abundance, wide conservation, and pleiotropic phenotypes.

Keywords:  endoplasmic reticulum; membrane insertion; protein biogenesis; translocation

DOI:  https://doi.org/10.1016/j.tcb.2019.01.007
JCI Insight. 2019 Mar 07. pii: 121887. [Epub ahead of print]4(5):

The E3 ligase Hrd1 stabilizes Tregs by antagonizing inflammatory cytokine-induced ER stress response.

Yuanming Xu, Johanna Melo-Cardenas, Yana Zhang, Isabella Gau, Juncheng Wei, Elena Montauti, Yusi Zhang, Beixue Gao, Hongjian Jin, Zhaolin Sun, Sang-Myeong Lee, Deyu Fang.

  Treg differentiation, maintenance, and function are controlled by the transcription factor FoxP3, which can be destabilized under inflammatory or other pathological conditions. Tregs can be destabilized under inflammatory or other pathological conditions, but the underlying mechanisms are not fully defined. Herein, we show that inflammatory cytokines induce ER stress response, which destabilizes Tregs by suppressing FoxP3 expression, suggesting a critical role of the ER stress response in maintaining Treg stability. Indeed, genetic deletion of Hrd1, an E3 ligase critical in suppressing the ER stress response, leads to elevated expression of ER stress-responsive genes in Treg and largely diminishes Treg suppressive functions under inflammatory condition. Mice with Treg-specific ablation of Hrd1 displayed massive multiorgan lymphocyte infiltration, body weight loss, and the development of severe small intestine inflammation with aging. At the molecular level, the deletion of Hrd1 led to the activation of both the ER stress sensor IRE1α and its downstream MAPK p38. Pharmacological suppression of IRE1α kinase, but not its endoribonuclease activity, diminished the elevated p38 activation and fully rescued the stability of Hrd1-null Tregs. Taken together, our studies reveal ER stress response as a previously unappreciated mechanism underlying Treg instability and that Hrd1 is crucial for maintaining Treg stability and functions through suppressing the IRE1α-mediated ER stress response.

Keywords:  Immunology; Molecular biology; T cells; Ubiquitin-proteosome system

DOI:  https://doi.org/10.1172/jci.insight.121887
Science. 2019 Mar 08. 363(6431): 1103-1107

Structural basis for pH-dependent retrieval of ER proteins from the Golgi by the KDEL receptor.

Philipp Bräuer, Joanne L Parker, Andreas Gerondopoulos, Iwan Zimmermann, Markus A Seeger, Francis A Barr, Simon Newstead.

Selective export and retrieval of proteins between the endoplasmic reticulum (ER) and Golgi apparatus is indispensable for eukaryotic cell function. An essential step in the retrieval of ER luminal proteins from the Golgi is the pH-dependent recognition of a carboxyl-terminal Lys-Asp-Glu-Leu (KDEL) signal by the KDEL receptor. Here, we present crystal structures of the chicken KDEL receptor in the apo ER state, KDEL-bound Golgi state, and in complex with an antagonistic synthetic nanobody (sybody). These structures show a transporter-like architecture that undergoes conformational changes upon KDEL binding and reveal a pH-dependent interaction network crucial for recognition of the carboxyl terminus of the KDEL signal. Complementary in vitro binding and in vivo cell localization data explain how these features create a pH-dependent retrieval system in the secretory pathway.

DOI: https://doi.org/10.1126/science.aaw2859
Biochem Pharmacol. 2019 Mar 01. pii: S0006-2952(19)30086-3. [Epub ahead of print]

Pharmacological effectors of GRP78 chaperone in cancers.

Christian Bailly, Michael J Waring.

  The protein chaperone GRP78 is a master regulator of endoplasmic reticulum (ER) functions and is frequently over-expressed at the surface of cancer cells where it contributes to chemo-resistance. It represents a well-studied ER stress marker but an under-explored target for new drug development. This review aims to untangle the structural and functional diversity of GRP78 modulators, covering over 130 natural products, synthetic molecules, specific peptides and monoclonal antibodies that target GRP78. Several approaches to promote or to incapacitate GRP78 are presented, including the use of oligonucleotides and specific cell-delivery peptides often conjugated to cytotoxic payloads to design GRP78-targeted therapeutics. A repertoire of drugs that turn on/off GRP78 is exposed, including molecules which bind directly to GRP78, principally to its ATP site. There exist many options to regulate positively or negatively the expression of the chaperone, or to interfere with its cellular trafficking. This review provides a molecular cartography of GRP78 pharmacological effectors and adds weight to the notion that GRP78 repressors could represent promising anticancer therapeutics, notably as regards limiting chemo-resistance of cancer cells. The potential of GRP78-targeting drugs in other therapeutic modalities is also evoked.

Keywords:  GRP78; anticancer drugs; cancer; chaperone; monoclonal antibodies; natural products

DOI:  https://doi.org/10.1016/j.bcp.2019.02.038
Cell Signal. 2019 Feb 28. pii: S0898-6568(19)30036-1. [Epub ahead of print]

RGS2 promotes the translation of stress-associated proteins ATF4 and CHOP via its eIF2B-inhibitory domain.

Chang-Hui Wang, Peter Chidiac.

  Regulator of G protein signaling 2 (RGS2) is upregulated by multiple forms of stress and can augment translational attenuation associated with the phosphorylation of the initiation factor eIF2, a hallmark of several stress-induced coping mechanisms. Under stress-induced translational inhibition, key factors, such as ATF4, are selectively expressed via alternative translation mechanisms. These factors are known to regulate molecular switches that control cell fate by regulating pro-survival and pro-apoptotic signals. The molecular mechanisms that balance these opposing responses to stresses are unclear. The present results suggest that RGS2 may be an important regulatory component in the cellular stress response through its translational control abilities. Previously, we have shown that RGS2 can interact with the translation initiation factor, eIF2B, and inhibit de novo protein synthesis. Here, we demonstrate that the expression of either full length RGS2 or its eIF2B-interacting domain (RGS2eb) significantly increases levels of ATF4 and CHOP, both of which are linked to stress-induced apoptosis. Furthermore, we show that these effects are translationally regulated and independent of eIF2 phosphorylation. The present results thus point to a novel function of RGS2 in the stress response directly related to its ability to reduce global protein synthesis.

Keywords:  ATF4; CHOP; Cell stress response; Eukaryotic initiation factor 2 (eIF2); Regulator of G protein signaling 2 (RGS2); Translation

DOI:  https://doi.org/10.1016/j.cellsig.2019.02.007
Mol Cell. 2019 Feb 26. pii: S1097-2765(19)30056-5. [Epub ahead of print]

Probing the Global Cellular Responses to Lipotoxicity Caused by Saturated Fatty Acids.

Manuele Piccolis, Laura M Bond, Martin Kampmann, Pamela Pulimeno, Chandramohan Chitraju, Christina B K Jayson, Laura P Vaites, Sebastian Boland, Zon Weng Lai, Katlyn R Gabriel, Shane D Elliott, Joao A Paulo, J Wade Harper, Jonathan S Weissman, Tobias C Walther, Robert V Farese.

  Excessive levels of saturated fatty acids are toxic to cells, although the basis for this lipotoxicity remains incompletely understood. Here, we analyzed the transcriptome, lipidome, and genetic interactions of human leukemia cells exposed to palmitate. Palmitate treatment increased saturated glycerolipids, accompanied by a transcriptional stress response, including upregulation of the endoplasmic reticulum (ER) stress response. A comprehensive genome-wide short hairpin RNA (shRNA) screen identified >350 genes modulating lipotoxicity. Among previously unknown genetic modifiers of lipotoxicity, depletion of RNF213, a putative ubiquitin ligase mutated in Moyamoya vascular disease, protected cells from lipotoxicity. On a broader level, integration of our comprehensive datasets revealed that changes in di-saturated glycerolipids, but not other lipid classes, are central to lipotoxicity in this model. Consistent with this, inhibition of ER-localized glycerol-3-phosphate acyltransferase activity protected from all aspects of lipotoxicity. Identification of genes modulating the response to saturated fatty acids may reveal novel therapeutic strategies for treating metabolic diseases linked to lipotoxicity.

Keywords:  Moyamoya disease; glycerolipid; lipotoxicity; palmitate; saturated fatty acid

DOI:  https://doi.org/10.1016/j.molcel.2019.01.036