bims-proteo Biomed News
on Proteostasis
Issue of 2020‒04‒26
fifty-three papers selected by
Eric Chevet
INSERM
  1. Unfolded Protein Response (UPR) Controls Major Senescence Hallmarks.
  2. Lactogens Reduce Endoplasmic Reticulum Stress-induced Rodent and Human β-cell Death and Diabetes Incidence in Akita Mice.
  3. ATF6 as a Nodal Regulator of Proteostasis in the Heart.
  4. Mesencephalic astrocyte-derived neurotrophic factor is an ER-resident chaperone that protects against reductive stress in the heart.
  5. MYC and the unfolded protein response in cancer: synthetic lethal partners in crime?
  6. The UPR sensor IRE1α and the adenovirus E3-19K glycoprotein sustain persistent and lytic infections.
  7. Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma.
  8. LncRNA GOLGA2P10 is induced by PERK/ATF4/CHOP signaling and protects tumor cells from ER stress-induced apoptosis by regulating Bcl-2 family members.
  9. Osh6 requires Ist2 for localization to the ER-PM contacts and efficient phosphatidylserine transport.
  10. The integrated stress response: From mechanism to disease.
  11. A central role of the endoplasmic reticulum in the cell emerges from its functional contact sites with multiple organelles.
  12. Proteostasis Failure in Neurodegenerative Diseases: Focus on Oxidative Stress.
  13. The Golgi as an Assembly Line to the Autophagosome.
  14. Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis.
  15. Threonine ADP-Ribosylation of Ubiquitin by a Bacterial Effector Family Blocks Host Ubiquitination.
  16. LC3-dependent extracellular vesicle loading and secretion (LDELS).
  17. Loss of VCP/p97 induced by the human cytomegalovirus transmembrane protein pUL50 and its regulation by a small isoform of pUL50.
  18. Starvation and antimetabolic therapy promote cytokine release and recruitment of immune cells.
  19. Squaring the EMC - how promoting membrane protein biogenesis impacts cellular functions and organismal homeostasis.
  20. The Endoplasmic Reticulum Regulates Membraneless Organelles through Contact Sites.
  21. Targeting the inositol-requiring enzyme-1 pathway efficiently reverts Zika virus-induced neurogenesis and spermatogenesis marker perturbations.
  22. TRIM21 and PHLDA3 negatively regulate the crosstalk between the PI3K/AKT pathway and PPP metabolism.
  23. The gene for the lysosomal protein LAMP3 is a direct target of the transcription factor ATF4.
  24. Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex.
  25. Calnexin/Calreticulin and Assays Related to N-Glycoprotein Folding In Vitro.
  26. Serotonin signaling by maternal neurons upon stress ensures progeny survival.
  27. Tissue-specific effects of temperature on proteasome function.
  28. ER arrival sites associate with ER exit sites to create bidirectional transport portals.
  29. TRIC-A shapes oscillatory Ca2+ signals by interaction with STIM1/Orai1 complexes.
  30. MANF Promotes Diabetic Corneal Epithelial Wound Healing and Nerve Regeneration by Attenuating Hyperglycemia-Induced Endoplasmic Reticulum Stress.
  31. COPII components Sar1b and Sar1c play distinct yet interchangeable roles in pollen development.
  32. Spastin mutations impair coordination between lipid droplet dispersion and reticulum.
  33. Post-translational modifications and stress adaptation: the paradigm of FKBP51.
  34. Structural Insight into the Mechanism of N-Linked Glycosylation by Oligosaccharyltransferase.
  35. K6-linked SUMOylation of BAF regulates nuclear integrity and DNA replication in mammalian cells.
  36. Plasticity of nuclear and cytoplasmic stress responses of RNA-binding proteins.
  37. Pathogenic variants of DNAJC12 and evaluation of the encoded co-chaperone as a genetic modifier of hyperphenylalaninemia.
  38. The Proteasome Governs Fungal Morphogenesis via Functional Connections with Hsp90 and cAMP-Protein Kinase A Signaling.
  39. Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells.
  40. Fission and fusion machineries converge at ER contact sites to regulate mitochondrial morphology.
  41. Receptor-mediated endocytosis 8 (RME-8)/DNAJC13 is a novel positive modulator of autophagy and stabilizes cellular protein homeostasis.
  42. MTV proteins unveil ER- and microtubule-associated compartments in the plant vacuolar trafficking pathway.
  43. The switch-like expression of Heme-regulated kinase 1 mediates neuronal proteostasis following proteasome inhibition.
  44. Cathepsin S Regulates Antigen Processing and T Cell Activity in Non-Hodgkin Lymphoma.
  45. The SCFSkp2 ubiquitin ligase complex modulates TRAIL-R2-induced apoptosis by regulating FLIP(L).
  46. Evolution, role in inflammation, and redox control of leaderless secretory proteins.
  47. The gluconeogenic enzyme PCK1 phosphorylates INSIG1/2 for lipogenesis.
  48. The Autophagy-Initiating Kinase ULK1 Controls RIPK1-Mediated Cell Death.
  49. SUMOylation modulates the LIN28A-let-7 signaling pathway in response to cellular stresses in cancer cells.
  50. Gene-edited human stem cell-derived β cells from a patient with monogenic diabetes reverse preexisting diabetes in mice.
  51. Endogenous metabolites promote stress resistance through induction of mitohormesis.
  52. Tollip coordinates Parkin-dependent trafficking of mitochondrial-derived vesicles.
  53. Peptidylprolylisomerases, Protein Folders, or Scaffolders? The Example of FKBP51 and FKBP52.
  1. Trends Biochem Sci. 2020 May;pii: S0968-0004(20)30051-7. [Epub ahead of print]45(5): 371-374
    Unfolded Protein Response (UPR) Controls Major Senescence Hallmarks.
    Corinne Abbadie, Olivier Pluquet.
      Senescence is a complex cellular state, which can be considered as a stress response phenotype. However, the mechanisms through which cells acquire and maintain this phenotype are not fully understood. In this paper, it is argued that the unfolded protein response (UPR) may represent a signalling platform that is associated with the major senescence hallmarks.
    Keywords:  endoplasmic reticulum; proteostasis; secretome, metabolism; senescence; unfolded protein response
    DOI:  https://doi.org/10.1016/j.tibs.2020.02.005
  2. Diabetes. 2020 Apr 24. pii: db190909. [Epub ahead of print]
    Lactogens Reduce Endoplasmic Reticulum Stress-induced Rodent and Human β-cell Death and Diabetes Incidence in Akita Mice.
    Rosemary Li, Nagesha Guthalu Kondegowda, Joanna Filipowska, Rollie F Hampton, Silvia Leblanc, Adolfo Garcia-Ocana, Rupangi C Vasavada.
      Diabetes occurs due to a loss of functional β-cells, resulting from β-cell death and dysfunction. Lactogens protect rodent and human β-cells in vitro and in vivo against triggers of β-cell cytotoxicity relevant to diabetes, many of which converge onto a common pathway, endoplasmic reticulum (ER) stress. However, whether lactogens modulate the ER stress pathway is unknown. This study examines if lactogens can protect β-cells against ER stress and mitigate diabetes incidence in Akita mice, a rodent model of ER stress-induced diabetes, akin to neonatal diabetes in humans. We show that lactogens protect INS1 cells, primary rodent and human β-cells in vitro against two distinct ER stressors, tunicamycin and thapsigargin, through activation of the JAK2/STAT5 pathway. Lactogens mitigate expression of pro-apoptotic molecules in the ER stress pathway that are induced by chronic ER stress in INS1 cells and rodent islets. Transgenic expression of placental lactogen in β-cells of Akita mice drastically reduces the severe hyperglycemia, diabetes incidence, hypoinsulinemia, β-cell death, and loss of β-cell mass observed in Akita littermates. These are the first studies in any cell type demonstrating lactogens modulate the ER stress pathway, causing enhanced β-cell survival and reduced diabetes incidence in the face of chronic ER stress.
    DOI:  https://doi.org/10.2337/db19-0909
  3. Front Physiol. 2020 ;11 267
    ATF6 as a Nodal Regulator of Proteostasis in the Heart.
    Christopher C Glembotski, Adrian Arrieta, Erik A Blackwood, Winston T Stauffer.
      Proteostasis encompasses a homeostatic cellular network in all cells that maintains the integrity of the proteome, which is critical for optimal cellular function. The components of the proteostasis network include protein synthesis, folding, trafficking, and degradation. Cardiac myocytes have a specialized endoplasmic reticulum (ER) called the sarcoplasmic reticulum that is well known for its role in contractile calcium handling. However, less studied is the proteostasis network associated with the ER, which is of particular importance in cardiac myocytes because it ensures the integrity of proteins that are critical for cardiac contraction, e.g., ion channels, as well as proteins necessary for maintaining myocyte viability and interaction with other cell types, e.g., secreted hormones and growth factors. A major aspect of the ER proteostasis network is the ER unfolded protein response (UPR), which is initiated when misfolded proteins in the ER activate a group of three ER transmembrane proteins, one of which is the transcription factor, ATF6. Prior to studies in the heart, ATF6 had been shown in model cell lines to be primarily adaptive, exerting protective effects by inducing genes that encode ER proteins that fortify protein-folding in this organelle, thus establishing the canonical role for ATF6. Subsequent studies in isolated cardiac myocytes and in the myocardium, in vivo, have expanded roles for ATF6 beyond the canonical functions to include the induction of genes that encode proteins outside of the ER that do not have known functions that are obviously related to ER protein-folding. The identification of such non-canonical roles for ATF6, as well as findings that the gene programs induced by ATF6 differ depending on the stimulus, have piqued interest in further research on ATF6 as an adaptive effector in cardiac myocytes, underscoring the therapeutic potential of activating ATF6 in the heart. Moreover, discoveries of small molecule activators of ATF6 that adaptively affect the heart, as well as other organs, in vivo, have expanded the potential for development of ATF6-based therapeutics. This review focuses on the ATF6 arm of the ER UPR and its effects on the proteostasis network in the myocardium.
    Keywords:  ATF6; ER stress; cardiac myocyte; proteostasis; unfolded protein response
    DOI:  https://doi.org/10.3389/fphys.2020.00267
  4. J Biol Chem. 2020 Apr 23. pii: jbc.RA120.013345. [Epub ahead of print]
    Mesencephalic astrocyte-derived neurotrophic factor is an ER-resident chaperone that protects against reductive stress in the heart.
    Adrian Arrieta, Erik A Blackwood, Winston T Stauffer, Michelle Santo Domingo, Alina S Bilal, Donna J Thuerauf, Amber N Pentoney, Cathrine Aivati, Anup V Sarakki, Shirin Doroudgar, Christopher C Glembotski.
      We have previously demonstrated that ischemia/reperfusion (I/R) impairs endoplasmic reticulum (ER)-based protein folding in the heart and thereby activates an unfolded protein response (UPR) sensor and effector, activated transcription factor 6α (ATF6). ATF6 then induces mesencephalic astrocyte-derived neurotrophic factor (MANF), an ER-resident protein with no known structural homologs and unclear ER function. To determine MANF's function in the heart in vivo, here we developed a cardiomyocyte-specific MANF-knockdown mouse model. The MANF knockdown increased cardiac damage after I/R, which was reversed by AAV9-mediated ectopic MANF expression. Mechanistically, MANF knockdown in cultured neonatal rat ventricular myocytes (NRVMs) impaired protein folding in the ER and cardiomyocyte viability during simulated I/R. However, this was not due to MANF-mediated protection from reactive oxygen species generated during reperfusion. Since I/R impairs oxygen-dependent ER protein disulfide formation and such impairment can be caused by reductive stress in the ER, we examined the effects of the reductive ER stressor dithiothreitol (DTT). MANF knockdown in NRVMs increased cell death from DTT-mediated reductive ER stress, but not from non-reductive ER stresses caused by thapsigargin-mediated ER Ca+2 depletion or tunicamycin-mediated inhibition of ER protein glycosylation. In vitro, recombinant MANF exhibited chaperone activity that was dependent on its conserved cysteine residues. Moreover, in cells, MANF bound to a model ER protein exhibiting improper disulfide bond formation during reductive ER stress, but did not bind to this protein during non-reductive ER stress. We conclude that MANF is an ER chaperone that enhances protein folding and myocyte viability during reductive ER stress.
    Keywords:  cardiomyocyte; chaperone; endoplasmic reticulum stress (ER stress); heart function; ischemia; ischemia/reperfusion; mesencephalic astrocyte derived neurotrophic factor; protein folding; reductive stress
    DOI:  https://doi.org/10.1074/jbc.RA120.013345
  5. EMBO Mol Med. 2020 Apr 20. e11845
    MYC and the unfolded protein response in cancer: synthetic lethal partners in crime?
    Tingting Zhang, Ningning Li, Chaoyang Sun, Yang Jin, Xia Sheng.
      The transcription factors of the MYC family play pivotal roles in the initiation and progression of human cancers. High oncogenic level of MYC invades low-affinity sites and enhancer sequences, which subsequently alters the transcriptome, causes metabolic imbalance, and induces stress response. The endoplasmic reticulum (ER) not only plays a central role in maintaining proteostasis, but also contributes to other key biological processes, including Ca2+ metabolism and the synthesis of lipids and glucose. Stress conditions, such as shortage in glucose or oxygen and disruption of Ca2+ homeostasis, may perturb proteostasis and induce the unfolded protein response (UPR), which either restores homeostasis or triggers cell death. Crucial roles of ER stress and UPR signaling have been implicated in various cancers, from oncogenesis to treatment response. Here, we summarize the current knowledge on the interaction between MYC and UPR signaling, and its contribution to cancer development. We also discuss the potential of targeting key UPR signaling nodes as novel synthetic lethal strategies in MYC-driven cancers.
    Keywords:   MYC ; UPR ; ER stress; cancer; synthetic lethality
    DOI:  https://doi.org/10.15252/emmm.201911845
  6. Nat Commun. 2020 Apr 24. 11(1): 1997
    The UPR sensor IRE1α and the adenovirus E3-19K glycoprotein sustain persistent and lytic infections.
    Vibhu Prasad, Maarit Suomalainen, Yllza Jasiqi, Silvio Hemmi, Patrick Hearing, Louise Hosie, Hans-Gerhard Burgert, Urs F Greber.
      Persistent viruses cause chronic disease, and threaten the lives of immunosuppressed individuals. Here, we elucidate a mechanism supporting the persistence of human adenovirus (AdV), a virus that can kill immunosuppressed patients. Cell biological analyses, genetics and chemical interference demonstrate that one of five AdV membrane proteins, the E3-19K glycoprotein specifically triggers the unfolded protein response (UPR) sensor IRE1α in the endoplasmic reticulum (ER), but not other UPR sensors, such as protein kinase R-like ER kinase (PERK) and activating transcription factor 6 (ATF6). The E3-19K lumenal domain activates the IRE1α nuclease, which initiates mRNA splicing of X-box binding protein-1 (XBP1). XBP1s binds to the viral E1A-enhancer/promoter sequence, and boosts E1A transcription, E3-19K levels and lytic infection. Inhibition of IRE1α nuclease interrupts the five components feedforward loop, E1A, E3-19K, IRE1α, XBP1s, E1A enhancer/promoter. This loop sustains persistent infection in the presence of the immune activator interferon, and lytic infection in the absence of interferon.
    DOI:  https://doi.org/10.1038/s41467-020-15844-2
  7. Nat Commun. 2020 Apr 22. 11(1): 1931
    Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma.
    Hector H Huang, Ian D Ferguson, Alexis M Thornton, Prabhakar Bastola, Christine Lam, Yu-Hsiu T Lin, Priya Choudhry, Margarette C Mariano, Makeba D Marcoulis, Chin Fen Teo, Julia Malato, Paul J Phojanakong, Thomas G Martin, Jeffrey L Wolf, Sandy W Wong, Nina Shah, Byron Hann, Angela N Brooks, Arun P Wiita.
      Enhancing the efficacy of proteasome inhibitors (PI) is a central goal in myeloma therapy. We proposed that signaling-level responses after PI may reveal new mechanisms of action that can be therapeutically exploited. Unbiased phosphoproteomics after treatment with the PI carfilzomib surprisingly demonstrates the most prominent phosphorylation changes on splicing related proteins. Spliceosome modulation is invisible to RNA or protein abundance alone. Transcriptome analysis after PI demonstrates broad-scale intron retention, suggestive of spliceosome interference, as well as specific alternative splicing of protein homeostasis machinery components. These findings lead us to evaluate direct spliceosome inhibition in myeloma, which synergizes with carfilzomib and shows potent anti-tumor activity. Functional genomics and exome sequencing further support the spliceosome as a specific vulnerability in myeloma. Our results propose splicing interference as an unrecognized modality of PI mechanism, reveal additional modes of spliceosome modulation, and suggest spliceosome targeting as a promising therapeutic strategy in myeloma.
    DOI:  https://doi.org/10.1038/s41467-020-15521-4
  8. Cell Death Dis. 2020 Apr 24. 11(4): 276
    LncRNA GOLGA2P10 is induced by PERK/ATF4/CHOP signaling and protects tumor cells from ER stress-induced apoptosis by regulating Bcl-2 family members.
    Meng-Zhi Wu, Tao Fu, Jin-Xi Chen, Ying-Ying Lin, Jin-E Yang, Shi-Mei Zhuang.
      Elevated endoplasmic reticulum (ER) stress is frequently observed in cancers, whereas sustained ER stress may trigger apoptosis. How cancer cells escape from ER stress-induced apoptosis remain unclear. Here, we found that a pseudogene-derived lncRNA, Golgin A2 pseudogene 10 (GOLGA2P10), was frequently upregulated in HCC tissues and significantly elevated in hepatoma cells treated with ER stress inducers, such as tunicamycin and thapsigargin. Higher GOLGA2P10 level was correlated with shorter recurrence-free survival of HCC patients. Upon ER stress, CHOP directly bound to the promoter of GOLGA2P10 and induced its transcription via the PERK/ATF4/CHOP pathway. Interestingly, the ER stress inducer-stimulated apoptosis was promoted by silencing GOLGA2P10 but was antagonized by overexpressing GOLGA2P10. Both gain- and loss-of-function analyses disclosed that GOLGA2P10 increased BCL-xL protein level, promoted BAD phosphorylation, and conferred tumor cells with resistance to ER stress-induced apoptosis. Moreover, BCL-xL overexpression or BAD knockdown abrogated the apoptosis-promoting effect of GOLGA2P10 silencing. Consistently, the Ser75Ala mutation in BAD, which caused phosphorylation-resistance, further enhanced the promoting effect of BAD in tunicamycin-induced apoptosis. These results suggest that ER stress induces GOLGA2P10 transcription through the PERK/ATF4/CHOP pathway, and upregulation of GOLGA2P10 protects tumor cells from the cytotoxic effect of persistent ER stress in tumor microenvironment by regulating Bcl-2 family members, which highlight GOLGA2P10 as a potential target for anticancer therapy.
    DOI:  https://doi.org/10.1038/s41419-020-2469-1
  9. J Cell Sci. 2020 Apr 23. pii: jcs.243733. [Epub ahead of print]
    Osh6 requires Ist2 for localization to the ER-PM contacts and efficient phosphatidylserine transport.
    Juan Martín D'Ambrosio, Véronique Albanèse, Nicolas-Frédéric Lipp, Lucile Fleuriot, Delphine Debayle, Guillaume Drin, Alenka Čopič.
      Osh6 and Osh7 are lipid transfer proteins (LTPs) that move phosphatidylserine (PS) from the endoplasmic reticulum (ER) to the plasma membrane (PM). High PS level at the PM is key for many cellular functions. Intriguingly, Osh6/7 localize to ER-PM contact sites, although they lack membrane-targeting motifs, in contrast to multidomain LTPs that both bridge membranes and convey lipids. We show that Osh6 localization to contact sites depends on its interaction with the cytosolic tail of the ER-PM tether Ist2, a homologue of TMEM16 proteins. We identify a motif in the Ist2 tail, conserved in yeasts, as the Osh6-binding region, and we map an Ist2-binding surface on Osh6. Mutations in the Ist2 tail phenocopy osh6Δ osh7Δ deletion: they decrease cellular PS levels, and block PS transport to the PM. Our study unveils an unexpected partnership between a TMEM16-like protein and a soluble LTP, which together mediate lipid transport at contact sites.
    Keywords:  Budding yeast; Lipid homeostasis; Lipid transfer protein; Membrane contact sites; Phosphatidylserine; TMEM16
    DOI:  https://doi.org/10.1242/jcs.243733
  10. Science. 2020 Apr 24. pii: eaat5314. [Epub ahead of print]368(6489):
    The integrated stress response: From mechanism to disease.
    Mauro Costa-Mattioli, Peter Walter.
      Protein quality control is essential for the proper function of cells and the organisms that they make up. The resulting loss of proteostasis, the processes by which the health of the cell's proteins is monitored and maintained at homeostasis, is associated with a wide range of age-related human diseases. Here, we highlight how the integrated stress response (ISR), a central signaling network that responds to proteostasis defects by tuning protein synthesis rates, impedes the formation of long-term memory. In addition, we address how dysregulated ISR signaling contributes to the pathogenesis of complex diseases, including cognitive disorders, neurodegeneration, cancer, diabetes, and metabolic disorders. The development of tools through which the ISR can be modulated promises to uncover new avenues to diminish pathologies resulting from it for clinical benefit.
    DOI:  https://doi.org/10.1126/science.aat5314
  11. Cell Mol Life Sci. 2020 Apr 20.
    A central role of the endoplasmic reticulum in the cell emerges from its functional contact sites with multiple organelles.
    Celso Almeida, Margarida D Amaral.
      Early eukaryotic cells emerged from the compartmentalization of metabolic processes into specific organelles through the development of an endomembrane system (ES), a precursor of the endoplasmic reticulum (ER), which was essential for their survival. Recently, substantial evidence emerged on how organelles communicate among themselves and with the plasma membrane (PM) through contact sites (CSs). From these studies, the ER-the largest single structure in eukaryotic cells-emerges as a central player communicating with all organelles to coordinate cell functions and respond to external stimuli to maintain cellular homeostasis. Herein we review the functional insights into the ER-CSs with other organelles in a physiological perspective. We hypothesize that, in addition to the primitive role by the ES in the appearance of proto-eukaryotes, its successor-the ER-emerges as the key coordinator of inter-organelle/PM communication. The ER thus appears to be the 'maestro' driving eukaryotic cell evolution by incorporating new functions/organelles, while remaining the real coordinator overarching cellular functions and orchestrating them with the external milieu.
    Keywords:  Endosymbiosis; Lysosomes; Mitochondria; Organellar functions; Organelle disorders; Organelle interactions
    DOI:  https://doi.org/10.1007/s00018-020-03523-w
  12. Oxid Med Cell Longev. 2020 ;2020 5497046
    Proteostasis Failure in Neurodegenerative Diseases: Focus on Oxidative Stress.
    Annika Höhn, Antonella Tramutola, Roberta Cascella.
      Protein homeostasis or proteostasis is an essential balance of cellular protein levels mediated through an extensive network of biochemical pathways that regulate different steps of the protein quality control, from the synthesis to the degradation. All proteins in a cell continuously turn over, contributing to development, differentiation, and aging. Due to the multiple interactions and connections of proteostasis pathways, exposure to stress conditions may cause various types of protein damage, altering cellular homeostasis and disrupting the entire network with additional cellular stress. Furthermore, protein misfolding and/or alterations during protein synthesis results in inactive or toxic proteins, which may overload the degradation mechanisms. The maintenance of a balanced proteome, preventing the formation of impaired proteins, is accomplished by two major catabolic routes: the ubiquitin proteasomal system (UPS) and the autophagy-lysosomal system. The proteostasis network is particularly important in nondividing, long-lived cells, such as neurons, as its failure is implicated with the development of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. These neurological disorders share common risk factors such as aging, oxidative stress, environmental stress, and protein dysfunction, all of which alter cellular proteostasis, suggesting that general mechanisms controlling proteostasis may underlay the etiology of these diseases. In this review, we describe the major pathways of cellular proteostasis and discuss how their disruption contributes to the onset and progression of neurodegenerative diseases, focusing on the role of oxidative stress.
    DOI:  https://doi.org/10.1155/2020/5497046
  13. Trends Biochem Sci. 2020 Apr 16. pii: S0968-0004(20)30087-6. [Epub ahead of print]
    The Golgi as an Assembly Line to the Autophagosome.
    Stefano De Tito, Javier H Hervás, Alexander R van Vliet, Sharon A Tooze.
      Autophagy is traditionally depicted as a signaling cascade that culminates in the formation of an autophagosome that degrades cellular cargo. However, recent studies have identified myriad pathways and cellular organelles underlying the autophagy process, be it as signaling platforms or through the contribution of proteins and lipids. The Golgi complex is recognized as being a central transport hub in the cell, with a critical role in endocytic trafficking and endoplasmic reticulum (ER) to plasma membrane (PM) transport. However, the Golgi is also an important site of key autophagy regulators, including the protein autophagy-related (ATG)-9A and the lipid, phosphatidylinositol-4-phosphate [PI(4)P]. In this review, we highlight the central function of this organelle in autophagy as a transport hub supplying various components of autophagosome formation.
    Keywords:  ATG9A; BAR domain; Golgi complex; PI(4)P; adaptor complexes; autophagy
    DOI:  https://doi.org/10.1016/j.tibs.2020.03.010
  14. Nat Commun. 2020 Apr 21. 11(1): 1920
    Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis.
    Tatsuya Tsukui, Kai-Hui Sun, Joseph B Wetter, John R Wilson-Kanamori, Lisa A Hazelwood, Neil C Henderson, Taylor S Adams, Jonas C Schupp, Sergio D Poli, Ivan O Rosas, Naftali Kaminski, Michael A Matthay, Paul J Wolters, Dean Sheppard.
      Collagen-producing cells maintain the complex architecture of the lung and drive pathologic scarring in pulmonary fibrosis. Here we perform single-cell RNA-sequencing to identify all collagen-producing cells in normal and fibrotic lungs. We characterize multiple collagen-producing subpopulations with distinct anatomical localizations in different compartments of murine lungs. One subpopulation, characterized by expression of Cthrc1 (collagen triple helix repeat containing 1), emerges in fibrotic lungs and expresses the highest levels of collagens. Single-cell RNA-sequencing of human lungs, including those from idiopathic pulmonary fibrosis and scleroderma patients, demonstrate similar heterogeneity and CTHRC1-expressing fibroblasts present uniquely in fibrotic lungs. Immunostaining and in situ hybridization show that these cells are concentrated within fibroblastic foci. We purify collagen-producing subpopulations and find disease-relevant phenotypes of Cthrc1-expressing fibroblasts in in vitro and adoptive transfer experiments. Our atlas of collagen-producing cells provides a roadmap for studying the roles of these unique populations in homeostasis and pathologic fibrosis.
    DOI:  https://doi.org/10.1038/s41467-020-15647-5
  15. Mol Cell. 2020 Apr 02. pii: S1097-2765(20)30164-7. [Epub ahead of print]
    Threonine ADP-Ribosylation of Ubiquitin by a Bacterial Effector Family Blocks Host Ubiquitination.
    Fujie Yan, Chunfeng Huang, Xiaofei Wang, Jiaxing Tan, Sen Cheng, Muyang Wan, Zhao Wang, Shuangyu Wang, Shuhui Luo, Arong Li, Xing Guo, Mingguang Feng, Xiaoyun Liu, Yongqun Zhu, Yan Zhou.
      Ubiquitination is essential for numerous eukaryotic cellular processes. Here, we show that the type III effector CteC from Chromobacterium violaceum functions as an adenosine diphosphate (ADP)-ribosyltransferase that specifically modifies ubiquitin via threonine ADP-ribosylation on residue T66. The covalent modification prevents the transfer of ubiquitin from ubiquitin-activating enzyme E1 to ubiquitin-conjugating enzyme E2, which inhibits subsequent ubiquitin activation by E2 and E3 enzymes in the ubiquitination cascade and leads to the shutdown of polyubiquitin synthesis in host cells. This unique modification also causes dysfunction of polyubiquitin chains in cells, thereby blocking host ubiquitin signaling. The disruption of host ubiquitination by CteC plays a crucial role in C. violaceum colonization in mice during infection. CteC represents a family of effector proteins in pathogens of hosts from different kingdoms. All the members of this family specifically ADP-ribosylate ubiquitin. The action of CteC reveals a new mechanism for interfering with host ubiquitination by pathogens.
    Keywords:  ADP-ribosylation; Chromobacterium violaceum; NF-κB; bacterial pathogens; effector protein; polyubiquitin chain; posttranslational modification; type III secretion system; ubiquitin; ubiquitination
    DOI:  https://doi.org/10.1016/j.molcel.2020.03.016
  16. Autophagy. 2020 Apr 24. 1-2
    LC3-dependent extracellular vesicle loading and secretion (LDELS).
    Andrew M Leidal, Jayanta Debnath.
      Accumulating evidence implicates various autophagy-related (ATG) proteins in cellular secretion. Recently, we identified a new secretory autophagy pathway in which components of LC3 conjugation machinery specify the incorporation of RNA binding proteins (RBPs) and small non-coding RNAs into extracellular vesicles (EVs), resulting in their secretion outside of cells. We term this process LC3-Dependent EV Loading and Secretion (LDELS). Importantly, LDELS is distinct from classical macroautophagy/autophagy because it requires components of the LC3 conjugation machinery, but not other ATGs involved in autophagosome formation. Because EVs have emerged as mediators of intracellular communication, our results provide new insight into how the autophagy machinery may influence the non-cell autonomous exchange of information between cells.
    Keywords:  Extracellular vesicles; RNA-binding proteins; autophagy; exosomes
    DOI:  https://doi.org/10.1080/15548627.2020.1756557
  17. J Virol. 2020 Apr 22. pii: JVI.00110-20. [Epub ahead of print]
    Loss of VCP/p97 induced by the human cytomegalovirus transmembrane protein pUL50 and its regulation by a small isoform of pUL50.
    Myoung Kyu Lee, Seokhwan Hyeon, Jin-Hyun Ahn.
      The human cytomegalovirus (HCMV) UL50 gene encodes a transmembrane protein, pUL50, which acts as a core component of the nuclear egress complex (NEC) for nucleocapsids. Recently, pUL50 has been shown to have NEC-independent activities; downregulation of IRE1 to repress the unfolded protein response and degradation of UBE1L to inhibit the protein ISG15 modification pathway. Here, we demonstrate that a 26-kDa N-terminal truncated isoform of pUL50 (UL50-p26) is expressed from an internal methionine at amino acid position 199, and regulates the activity of pUL50 to induce loss of valosin-containing protein (VCP/p97). UL50(M199V) mutant virus expressing pUL50(M199V) but not UL50-p26 showed delayed growth at low multiplicity of infection. There was also delayed accumulation of viral immediate-early (IE) 2 protein in the mutant virus, and this correlated with reduced expression of VCP/p97, which promotes IE2 expression. Infection with mutant virus did not significantly alter ISGylation levels. In transient expression assays, pUL50 induced VCP/p97 loss post-transcriptionally, and this was dependent on the presence of its transmembrane domain. By contrast, UL50-p26 did not destabilize VCP/p97 but rather inhibited pUL50-mediated VCP/p97 loss and the associated major IE gene suppression. Both pUL50 and UL50-p26 interacted with VCP/p97, although UL50-p26 did so more weakly than pUL50. UL50-p26 interacted with pUL50, and this interaction was much stronger than the pUL50 self-interaction. Furthermore, UL50-p26 was able to interfere with the pUL50-VCP/p97 interaction. Our study newly identifies UL50-p26 expression during HCMV infection and suggests a regulatory role for UL50-p26 in blocking pUL50-mediated VCP/p97 loss by associating with pUL50.IMPORTANCE Targeting the endoplasmic reticulum (ER) by viral proteins may affect ER-associated protein homeostasis. During human cytomegalovirus (HCMV) infection, pUL50 targets the ER through its transmembrane domain and moves to the inner nuclear membrane (INM) to form the nuclear egress complex (NEC), which facilitates capsid transport from the nucleus to the cytoplasm. Here, we demonstrate that pUL50 induces loss of valosin-containing protein (VCP/p97), which promotes the expression of viral major immediate-early gene products, in a manner dependent on its membrane targeting, but a small isoform of pUL50 is expressed to negatively regulate this pUL50 activity. This study reports a new NEC-independent function of pUL50 and highlights the fine regulation of pUL50 activity by a smaller isoform for efficient viral growth.
    DOI:  https://doi.org/10.1128/JVI.00110-20
  18. Proc Natl Acad Sci U S A. 2020 Apr 20. pii: 201913707. [Epub ahead of print]
    Starvation and antimetabolic therapy promote cytokine release and recruitment of immune cells.
    Franziska Püschel, Francesca Favaro, Jaime Redondo-Pedraza, Estefanía Lucendo, Raffaella Iurlaro, Sandrine Marchetti, Blanca Majem, Eric Eldering, Ernest Nadal, Jean-Ehrland Ricci, Eric Chevet, Cristina Muñoz-Pinedo.
      Cellular starvation is typically a consequence of tissue injury that disrupts the local blood supply but can also occur where cell populations outgrow the local vasculature, as observed in solid tumors. Cells react to nutrient deprivation by adapting their metabolism, or, if starvation is prolonged, it can result in cell death. Cell starvation also triggers adaptive responses, like angiogenesis, that promote tissue reorganization and repair, but other adaptive responses and their mediators are still poorly characterized. To explore this issue, we analyzed secretomes from glucose-deprived cells, which revealed up-regulation of multiple cytokines and chemokines, including IL-6 and IL-8, in response to starvation stress. Starvation-induced cytokines were cell type-dependent, and they were also released from primary epithelial cells. Most cytokines were up-regulated in a manner dependent on NF-κB and the transcription factor of the integrated stress response ATF4, which bound directly to the IL-8 promoter. Furthermore, glutamine deprivation, as well as the antimetabolic drugs 2-deoxyglucose and metformin, also promoted the release of IL-6 and IL-8. Finally, some of the factors released from starved cells induced chemotaxis of B cells, macrophages, and neutrophils, suggesting that nutrient deprivation in the tumor environment can serve as an initiator of tumor inflammation.
    Keywords:  cancer immunity; cancer metabolism; cytokines; glucose
    DOI:  https://doi.org/10.1073/pnas.1913707117
  19. J Cell Sci. 2020 Apr 24. pii: jcs243519. [Epub ahead of print]133(8):
    Squaring the EMC - how promoting membrane protein biogenesis impacts cellular functions and organismal homeostasis.
    Norbert Volkmar, John C Christianson.
      Integral membrane proteins play key functional roles at organelles and the plasma membrane, necessitating their efficient and accurate biogenesis to ensure appropriate targeting and activity. The endoplasmic reticulum membrane protein complex (EMC) has recently emerged as an important eukaryotic complex for biogenesis of integral membrane proteins by promoting insertion and stability of atypical and sub-optimal transmembrane domains (TMDs). Although confirmed as a bona fide complex almost a decade ago, light is just now being shed on the mechanism and selectivity underlying the cellular responsibilities of the EMC. In this Review, we revisit the myriad of functions attributed the EMC through the lens of these new mechanistic insights, to address questions of the cellular and organismal roles the EMC has evolved to undertake.
    Keywords:  EMC; Membrane protein; Protein folding; Protein quality control
    DOI:  https://doi.org/10.1242/jcs.243519
  20. Biochemistry. 2020 Apr 23.
    The Endoplasmic Reticulum Regulates Membraneless Organelles through Contact Sites.
    Shoken Lee, Shirin Bahmanyar.
      
    DOI:  https://doi.org/10.1021/acs.biochem.0c00232
  21. ACS Infect Dis. 2020 Apr 24.
    Targeting the inositol-requiring enzyme-1 pathway efficiently reverts Zika virus-induced neurogenesis and spermatogenesis marker perturbations.
    Hin Chu, Terrence Yuen, Kenn K H Chik, Shuofeng Yuan, Huiping Shuai, Zijiao Zou, Yixin Wang, Zheng Zhu, Dong Yang, Vincent K M Poon, Chris C S Chan, Jie Zhou, Feifei Yin, Kin-Hang Kok, Kwok-Yung Yuen, Jasper Fuk-Woo Chan.
      Zika virus (ZIKV) is an emerging flavivirus that may be associated with congenital anomalies in infected fetuses and severe neurological and genital tract complications in infected adults. Currently, antiviral treatments to revert these ZIKV-induced complications are lacking. ZIKV infection has recently been suggested to upregulate the host unfolded protein response, which may contribute to the congenital neurological anomalies. Extending from these findings, we thoroughly investigated ZIKV-induced unfolded protein response using a combination of neuronal cell line, induced pluripotent stem cells-derived human neuronal stem and progenitor cells, and an interferon receptor-deficient A129 mouse model. Our results revealed a critical contribution of the inositol-requiring enzyme-1 (IRE1) arm of the unfolded protein response to ZIKV-induced neurological and testicular complications. Importantly, inhibiting IRE1 signaling pathway activation with KIRA6 (Kinase-Inhibiting RNAse Attenuator 6), a selective small molecule IRE1 inhibitor that promotes cell survival, potently reverted the ZIKV-induced perturbations of the key gene expressions associated with neurogenesis and spermatogenesis in vitro and in vivo, highlighting the potential of IRE1 inhibition as a novel host-targeting antiviral strategy in combating against ZIKV-induced neurological and testicular pathologies.
    DOI:  https://doi.org/10.1021/acsinfecdis.9b00526
  22. Nat Commun. 2020 Apr 20. 11(1): 1880
    TRIM21 and PHLDA3 negatively regulate the crosstalk between the PI3K/AKT pathway and PPP metabolism.
    Jie Cheng, Yan Huang, Xiaohui Zhang, Yue Yu, Shumin Wu, Jing Jiao, Linh Tran, Wanru Zhang, Ran Liu, Liuzhen Zhang, Mei Wang, Mengyao Wang, Wenyu Yan, Yilin Wu, Fangtao Chi, Peng Jiang, Xinxiang Zhang, Hong Wu.
      PI3K/AKT signaling is known to regulate cancer metabolism, but whether metabolic feedback regulates the PI3K/AKT pathway is unclear. Here, we demonstrate the important reciprocal crosstalk between the PI3K/AKT signal and pentose phosphate pathway (PPP) branching metabolic pathways. PI3K/AKT activation stabilizes G6PD, the rate-limiting enzyme of the PPP, by inhibiting the newly identified E3 ligase TIRM21 and promotes the PPP. PPP metabolites, in turn, reinforce AKT activation and further promote cancer metabolic reprogramming by blocking the expression of the AKT inhibitor PHLDA3. Knockout of TRIM21 or PHLDA3 promotes crosstalk and cell proliferation. Importantly, PTEN null human cancer cells and in vivo murine models are sensitive to anti-PPP treatments, suggesting the importance of the PPP in maintaining AKT activation even in the presence of a constitutively activated PI3K pathway. Our study suggests that blockade of this reciprocal crosstalk mechanism may have a therapeutic benefit for cancers with PTEN loss or PI3K/AKT activation.
    DOI:  https://doi.org/10.1038/s41467-020-15819-3
  23. J Biol Chem. 2020 Apr 20. pii: jbc.RA119.011864. [Epub ahead of print]
    The gene for the lysosomal protein LAMP3 is a direct target of the transcription factor ATF4.
    Thomas D Burton, Anthony O Fedele, Jianling Xie, Lauren Sandeman, Christopher G Proud.
      Autophagy and lysosomal activities play a key role in the cell by initiating and carrying out the degradation of misfolded proteins. Transcription factor EB (TFEB) functions as a master controller of lysosomal biogenesis and function during lysosomal stress, controlling most, but, importantly, not all lysosomal genes. Here, we sought to better understand the regulation of lysosomal genes whose expression does not appear to be controlled by TFEB. Sixteen of these genes were screened for transactivation in response to diverse cellular insults. mRNA levels for lysosomal-associated membrane protein 3 (LAMP3), a gene that is highly up-regulated in many forms of cancer, including breast and cervical cancers, were significantly increased during the integrated stress response (ISR), which occurs in eukaryotic cells in response to accumulation of unfolded and misfolded proteins. Of note, results from siRNA-mediated knockdown of activating transcription factor 4 (ATF4) and overexpression of exogenous ATF4 cDNA, indicated that ATF4 up-regulates LAMP3 mRNA levels. Finally, ChIP assays verified an ATF4-binding site in the LAMP3 gene promoter, and a dual luciferase assay confirmedthat this ATF4-binding site is indeed required for transcriptional up-regulation of LAMP3 These results reveal that ATF4 directly regulates LAMP3, representing the first identification of a gene for a lysosomal component whose expression is directly controlled by ATF4. This finding may provide a key link between stresses such as accumulation of unfolded proteins and modulation of autophagy, which removes them.
    Keywords:  activating transcription factor 4 (ATF4); autophagy; cell stress; eukaryotic initiation factor 2 (eIF2); lysosomal-associated membrane protein 3 (LAMP3); lysosome; mammalian target of rapamycin complex 1 (mTORC1); protein misfolding; transcription factor EB (TFEB); unfolded protein response (UPR)
    DOI:  https://doi.org/10.1074/jbc.RA119.011864
  24. Science. 2020 Apr 24. pii: eaaz2449. [Epub ahead of print]368(6489):
    Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex.
    Xudong Wu, Marc Siggel, Sergey Ovchinnikov, Wei Mi, Vladimir Svetlov, Evgeny Nudler, Maofu Liao, Gerhard Hummer, Tom A Rapoport.
      Misfolded luminal endoplasmic reticulum (ER) proteins undergo ER-associated degradation (ERAD-L): They are retrotranslocated into the cytosol, polyubiquitinated, and degraded by the proteasome. ERAD-L is mediated by the Hrd1 complex (composed of Hrd1, Hrd3, Der1, Usa1, and Yos9), but the mechanism of retrotranslocation remains mysterious. Here, we report a structure of the active Hrd1 complex, as determined by cryo-electron microscopy analysis of two subcomplexes. Hrd3 and Yos9 jointly create a luminal binding site that recognizes glycosylated substrates. Hrd1 and the rhomboid-like Der1 protein form two "half-channels" with cytosolic and luminal cavities, respectively, and lateral gates facing one another in a thinned membrane region. These structures, along with crosslinking and molecular dynamics simulation results, suggest how a polypeptide loop of an ERAD-L substrate moves through the ER membrane.
    DOI:  https://doi.org/10.1126/science.aaz2449
  25. Methods Mol Biol. 2020 ;2132 295-308
    Calnexin/Calreticulin and Assays Related to N-Glycoprotein Folding In Vitro.
    Yoshito Ihara, Midori Ikezaki, Maki Takatani, Yukishige Ito.
      Calnexin (CNX) and calreticulin (CRT) are ER-resident lectin-like molecular chaperones involved in the quality control of secretory or membrane glycoproteins. They can exert molecular chaperone functions via specific binding to the early processing intermediates of Glc1Man9GlcNAc2 oligosaccharides of N-glycoproteins. CNX and CRT have similar N-terminal luminal domains and share the same jelly roll tertiary structure as legume lectins. In addition to the lectin-like interactions, CNX and CRT also suppress the aggregation of non-glycosylated substrates through interaction with hydrophobic peptide parts, suggesting a general chaperone function in glycan-dependent and glycan-independent manners. This chapter describes the isolation and purification of CRT produced in a bacterial expression system. We also introduce in vitro assays to estimate the molecular chaperone functions of CRT via the interaction with monoglucosylated N-glycans using Jack bean α-mannosidase as a target substrate. These assays are valuable in assessing quality control events related to the CNX/CRT chaperone cycle and lectin functions.
    Keywords:  Aggregation; Calnexin; Calreticulin; Chaperone; Endoplasmic reticulum; N-glycan; α-Mannosidase
    DOI:  https://doi.org/10.1007/978-1-0716-0430-4_29
  26. Elife. 2020 Apr 23. pii: e55246. [Epub ahead of print]9
    Serotonin signaling by maternal neurons upon stress ensures progeny survival.
    Srijit Das, Felicia K Ooi, Johnny Cruz Corchado, Leah C Fuller, Joshua A Weiner, Veena Prahlad.
      Germ cells are vulnerable to stress. Therefore, how organisms protect their future progeny from damage in a fluctuating environment is a fundamental question in biology. We show that in Caenorhabditis elegans, serotonin released by maternal neurons during stress ensures the viability and stress resilience of future offspring. Serotonin acts through a signal transduction pathway conserved between C. elegans and mammalian cells to enable the transcription factor HSF1 to alter chromatin in soon-to-be fertilized germ cells by recruiting the histone chaperone FACT, displacing histones, and initiating protective gene expression. Without serotonin release by maternal neurons, FACT is not recruited by HSF1 in germ cells, transcription occurs but is delayed, and progeny of stressed C. elegans mothers fail to complete development. These studies uncover a novel mechanism by which stress sensing by neurons is coupled to transcription response times of germ cells to protect future offspring.
    Keywords:  cell biology
    DOI:  https://doi.org/10.7554/eLife.55246
  27. Cell Stress Chaperones. 2020 Apr 18.
    Tissue-specific effects of temperature on proteasome function.
    Johanna Pispa, Olli Matilainen, Carina I Holmberg.
      Variation in ambient growth temperature can cause changes in normal animal physiology and cellular functions such as control of protein homeostasis. A key mechanism for maintaining proteostasis is the selective degradation of polyubiquitinated proteins, mediated by the ubiquitin-proteasome system (UPS). It is still largely unsolved how temperature changes affect the UPS at the organismal level. Caenorhabditis elegans nematodes are normally bred at 20 °C, but for some experimental conditions, 25 °C is often used. We studied the effect of 25 °C on C. elegans UPS by measuring proteasome activity and polyubiquitinated proteins both in vitro in whole animal lysates and in vivo in tissue-specific transgenic reporter strains. Our results show that an ambient temperature shift from 20 to 25 °C increases the UPS activity in the intestine, but not in the body wall muscle tissue, where a concomitant accumulation of polyubiquitinated proteins occurs. These changes in the UPS activity and levels of polyubiquitinated proteins were not detectable in whole animal lysates. The exposure of transgenic animals to 25 °C also induced ER stress reporter fluorescence, but not the fluorescence of a heat shock responsive reporter, albeit detection of a mild induction in hsp-16.2 mRNA levels. In conclusion, C. elegans exhibits tissue-specific responses of the UPS as an organismal strategy to cope with a rise in ambient temperature.
    Keywords:  Ambient temperature; Caenorhabditis elegans; Stress; Tissue specificity; Ubiquitin-proteasome system (UPS)
    DOI:  https://doi.org/10.1007/s12192-020-01107-y
  28. J Cell Biol. 2020 Apr 06. pii: e201902114. [Epub ahead of print]219(4):
    ER arrival sites associate with ER exit sites to create bidirectional transport portals.
    Sudeshna Roy Chowdhury, Chumki Bhattacharjee, Jason C Casler, Bhawik Kumar Jain, Benjamin S Glick, Dibyendu Bhattacharyya.
      COPI vesicles mediate Golgi-to-ER recycling, but COPI vesicle arrival sites at the ER have been poorly defined. We explored this issue using the yeast Pichia pastoris. ER arrival sites (ERAS) can be visualized by labeling COPI vesicle tethers such as Tip20. Our results place ERAS at the periphery of COPII-labeled ER export sites (ERES). The dynamics of ERES and ERAS are indistinguishable, indicating that these structures are tightly coupled. Displacement or degradation of Tip20 does not alter ERES organization, whereas displacement or degradation of either COPII or COPI components disrupts ERAS organization. We infer that Golgi compartments form at ERES and then produce COPI vesicles to generate ERAS. As a result, ERES and ERAS are functionally linked to create bidirectional transport portals at the ER-Golgi interface. COPI vesicles likely become tethered while they bud, thereby promoting efficient retrograde transport. In mammalian cells, the Tip20 homologue RINT1 associates with ERES, indicating possible conservation of the link between ERES and ERAS.
    DOI:  https://doi.org/10.1083/jcb.201902114
  29. PLoS Biol. 2020 Apr 24. 18(4): e3000700
    TRIC-A shapes oscillatory Ca2+ signals by interaction with STIM1/Orai1 complexes.
    Niroj Shrestha, Bernadett Bacsa, Hwei Ling Ong, Susanne Scheruebel, Helmut Bischof, Roland Malli, Indu Suresh Ambudkar, Klaus Groschner.
      Trimeric intracellular cation (TRIC) channels have been proposed to modulate Ca2+ release from the endoplasmic reticulum (ER) and determine oscillatory Ca2+ signals. Here, we report that TRIC-A-mediated amplitude and frequency modulation of ryanodine receptor 2 (RyR2)-mediated Ca2+ oscillations and inositol 1,4,5-triphosphate receptor (IP3R)-induced cytosolic signals is based on attenuating store-operated Ca2+ entry (SOCE). Further, TRIC-A-dependent delay in ER Ca2+ store refilling contributes to shaping the pattern of Ca2+ oscillations. Upon ER Ca2+ depletion, TRIC-A clusters with stromal interaction molecule 1 (STIM1) and Ca2+-release-activated Ca2+ channel 1 (Orai1) within ER-plasma membrane (PM) junctions and impairs assembly of the STIM1/Orai1 complex, causing a decrease in Orai1-mediated Ca2+ current and SOCE. Together, our findings demonstrate that TRIC-A is a negative regulator of STIM1/Orai1 function. Thus, aberrant SOCE could contribute to muscle disorders associated with loss of TRIC-A.
    DOI:  https://doi.org/10.1371/journal.pbio.3000700
  30. Diabetes. 2020 Apr 20. pii: db190835. [Epub ahead of print]
    MANF Promotes Diabetic Corneal Epithelial Wound Healing and Nerve Regeneration by Attenuating Hyperglycemia-Induced Endoplasmic Reticulum Stress.
    Xiaochuan Wang, Weina Li, Qingjun Zhou, Jing Li, Xiaolei Wang, Jing Zhang, Dewei Li, Xia Qi, Ting Liu, Xiaowen Zhao, Suxia Li, Lingling Yang, Lixin Xie.
      Mesencephalic astrocyte-derived neurotrophic factor (MANF) is a neurotrophic factor widely expressed in mammalian tissues, and it exerts critical protective effects on neurons and other cell types in various disease models, such as those for diabetes. However, to date, the expression and roles of MANF in the cornea, with or without diabetic keratopathy (DK), remain unclear. Here, we demonstrate that MANF is abundantly expressed in normal corneal epithelial cells; however, MANF expression was significantly reduced in both unwounded and wounded corneal epithelium in streptozotocin-induced type 1 diabetic C57BL/6 mice. Recombinant human MANF significantly promoted normal and diabetic corneal epithelial wound healing and nerve regeneration. Furthermore, MANF inhibited hyperglycemia-induced endoplasmic reticulum (ER) stress and ER stress-mediated apoptosis. Attenuation of ER stress with 4-phenylbutyric acid (4-PBA) also ameliorated corneal epithelial closure and nerve regeneration. However, the beneficial effects of MANF and 4-PBA were abolished by an Akt inhibitor and Akt-specific small interfering RNA (siRNA). Finally, we reveal that the subconjunctival injection of MANF-specific siRNA prevents corneal epithelial wound healing and nerve regeneration. Our results provide important evidence that hyperglycemia-suppressed MANF expression may contribute to delayed corneal epithelial wound healing and impaired nerve regeneration by increasing ER stress, and MANF may be a useful therapeutic modality for treating DK.
    DOI:  https://doi.org/10.2337/db19-0835
  31. Plant Physiol. 2020 Apr 23. pii: pp.00159.2020. [Epub ahead of print]
    COPII components Sar1b and Sar1c play distinct yet interchangeable roles in pollen development.
    Xin Liang, Shan-Wei Li, Li-Min Gong, Sha Li, Yan Zhang.
      The development of pollen is a pre-requisite for double fertilization in angiosperms. COPII mediates anterograde transport of vesicles from the endoplasmic reticulum to Golgi. Components of the COPII complex have been reported to regulate either sporophytic or gametophytic control of pollen development. The Arabidopsis genome encodes five Sar1 isoforms, the small GTPases essential for COPII formation. By using a dominant negative (DN) approach, Sar1 isoforms were proposed to have distinct cargo specificity despite their sequence similarity. Here, we examined the function of three Sar1 isoforms through analysis of CRISPR/Cas9-generated mutants. We report that functional loss of Sar1b caused malfunction of tapetum, leading to male sterility. Ectopic expression of Sar1c could compensate for Sar1b loss-of-function in sporophytic control of pollen development, suggesting that they are interchangeable. Functional distinction between Sar1b and Sar1c may have resulted from their different gene transcription levels based on expression analyses. On the other hand, Sar1b and Sar1c redundantly mediate male gametophytic development such that the sar1b;sar1c microspores aborted at anther developmental stage 10. The study uncovers the role of Sar1 isoforms in both sporophytic and gametophytic control of pollen development. It also suggests that distinct function of Sar1 isoforms may be caused by their distinct transcription programs.
    DOI:  https://doi.org/10.1104/pp.20.00159
  32. PLoS Genet. 2020 Apr;16(4): e1008665
    Spastin mutations impair coordination between lipid droplet dispersion and reticulum.
    Yoan Arribat, Dogan Grepper, Sylviane Lagarrigue, Timothy Qi, Sarah Cohen, Francesca Amati.
      Lipid droplets (LD) are affected in multiple human disorders. These highly dynamic organelles are involved in many cellular roles. While their intracellular dispersion is crucial to ensure their function and other organelles-contact, underlying mechanisms are still unclear. Here we show that Spastin, one of the major proteins involved in Hereditary Spastic Paraplegia (HSP), controls LD dispersion. Spastin depletion in zebrafish affects metabolic properties and organelle dynamics. These functions are ensured by a conserved complex set of splice variants. M1 isoforms determine LD dispersion in the cell by orchestrating endoplasmic reticulum (ER) shape along microtubules (MTs). To further impact LD fate, Spastin modulates transcripts levels and subcellular location of other HSP key players, notably Seipin and REEP1. In pathological conditions, mutations in human Spastin M1 disrupt this mechanism and impacts LD network. Spastin depletion influences not only other key proteins but also modulates specific neutral lipids and phospholipids, revealing an impact on membrane and organelle components. Altogether our results show that Spastin and its partners converge in a common machinery that coordinates LD dispersion and ER shape along MTs. Any alteration of this system results in HSP clinical features and impacts lipids profile, thus opening new avenues for novel biomarkers of HSP.
    DOI:  https://doi.org/10.1371/journal.pgen.1008665
  33. Biochem Soc Trans. 2020 Apr 22. pii: BST20190332. [Epub ahead of print]
    Post-translational modifications and stress adaptation: the paradigm of FKBP51.
    Theo Rein.
      Adaptation to stress is a fundamental requirement to cope with changing environmental conditions that pose a threat to the homeostasis of cells and organisms. Post-translational modifications (PTMs) of proteins represent a possibility to quickly produce proteins with new features demanding relatively little cellular resources. FK506 binding protein (FKBP) 51 is a pivotal stress protein that is involved in the regulation of several executers of PTMs. This mini-review discusses the role of FKBP51 in the function of proteins responsible for setting the phosphorylation, ubiquitination and lipidation of other proteins. Examples include the kinases Akt1, CDK5 and GSK3β, the phosphatases calcineurin, PP2A and PHLPP, and the ubiquitin E3-ligase SKP2. The impact of FKBP51 on PTMs of signal transduction proteins significantly extends the functional versatility of this protein. As a stress-induced protein, FKBP51 uses re-setting of PTMs to relay the effect of stress on various signaling pathways.
    Keywords:  FKBP51; post-translational modification; signal transduction; stress response
    DOI:  https://doi.org/10.1042/BST20190332
  34. Biomolecules. 2020 Apr 17. pii: E624. [Epub ahead of print]10(4):
    Structural Insight into the Mechanism of N-Linked Glycosylation by Oligosaccharyltransferase.
    Smita Mohanty, Bharat P Chaudhary, David Zoetewey.
      Asparagine-linked glycosylation, also known as N-linked glycosylation is an essential and highly conserved post-translational protein modification that occurs in all three domains of life. This modification is essential for specific molecular recognition, protein folding, sorting in the endoplasmic reticulum, cell-cell communication, and stability. Defects in N-linked glycosylation results in a class of inherited diseases known as congenital disorders of glycosylation (CDG). N-linked glycosylation occurs in the endoplasmic reticulum (ER) lumen by a membrane associated enzyme complex called the oligosaccharyltransferase (OST). In the central step of this reaction, an oligosaccharide group is transferred from a lipid-linked dolichol pyrophosphate donor to the acceptor substrate, the side chain of a specific asparagine residue of a newly synthesized protein. The prokaryotic OST enzyme consists of a single polypeptide chain, also known as single subunit OST or ssOST. In contrast, the eukaryotic OST is a complex of multiple non-identical subunits. In this review, we will discuss the biochemical and structural characterization of the prokaryotic, yeast, and mammalian OST enzymes. This review explains the most recent high-resolution structures of OST determined thus far and the mechanistic implication of N-linked glycosylation throughout all domains of life. It has been shown that the ssOST enzyme, AglB protein of the archaeon Archaeoglobus fulgidus, and the PglB protein of the bacterium Campylobactor lari are structurally and functionally similar to the catalytic Stt3 subunit of the eukaryotic OST enzyme complex. Yeast OST enzyme complex contains a single Stt3 subunit, whereas the human OST complex is formed with either STT3A or STT3B, two paralogues of Stt3. Both human OST complexes, OST-A (with STT3A) and OST-B (containing STT3B), are involved in the N-linked glycosylation of proteins in the ER. The cryo-EM structures of both human OST-A and OST-B complexes were reported recently. An acceptor peptide and a donor substrate (dolichylphosphate) were observed to be bound to the OST-B complex whereas only dolichylphosphate was bound to the OST-A complex suggesting disparate affinities of two OST complexes for the acceptor substrates. However, we still lack an understanding of the independent role of each eukaryotic OST subunit in N-linked glycosylation or in the stabilization of the enzyme complex. Discerning the role of each subunit through structure and function studies will potentially reveal the mechanistic details of N-linked glycosylation in higher organisms. Thus, getting an insight into the requirement of multiple non-identical subunits in the N-linked glycosylation process in eukaryotes poses an important future goal.
    Keywords:  congenital disorders of glycosylation; cryo-EM structures; human oligosaccharyltransferase; mechanism of N-linked glycosylation; membrane proteins; yeast oligosaccharyltransferase
    DOI:  https://doi.org/10.3390/biom10040624
  35. Proc Natl Acad Sci U S A. 2020 Apr 24. pii: 201912984. [Epub ahead of print]
    K6-linked SUMOylation of BAF regulates nuclear integrity and DNA replication in mammalian cells.
    Qiaoyu Lin, Bin Yu, Xiangyang Wang, Shicong Zhu, Gan Zhao, Mingkang Jia, Fan Huang, Nan Xu, He Ren, Qing Jiang, Chuanmao Zhang.
      Barrier-to-autointegration factor (BAF) is a highly conserved protein in metazoans that has multiple functions during the cell cycle. We found that BAF is SUMOylated at K6, and that this modification is essential for its nuclear localization and function, including nuclear integrity maintenance and DNA replication. K6-linked SUMOylation of BAF promotes binding and interaction with lamin A/C to regulate nuclear integrity. K6-linked SUMOylation of BAF also supports BAF binding to DNA and proliferating cell nuclear antigen and regulates DNA replication. SENP1 and SENP2 catalyze the de-SUMOylation of BAF at K6. Disrupting the SUMOylation and de-SUMOylation cycle of BAF at K6 not only disturbs nuclear integrity, but also induces DNA replication failure. Taken together, our findings demonstrate that SUMOylation at K6 is an important regulatory mechanism that governs the nuclear functions of BAF in mammalian cells.
    Keywords:  SUMOylation; barrier-to-autointegration factor (BAF); cell cycle; lamin A/C; nuclear integrity
    DOI:  https://doi.org/10.1073/pnas.1912984117
  36. Nucleic Acids Res. 2020 Apr 20. pii: gkaa256. [Epub ahead of print]
    Plasticity of nuclear and cytoplasmic stress responses of RNA-binding proteins.
    Michael Backlund, Frank Stein, Mandy Rettel, Thomas Schwarzl, Joel I Perez-Perri, Annika Brosig, Yang Zhou, Gabriele Neu-Yilik, Matthias W Hentze, Andreas E Kulozik.
      Cellular stress causes multifaceted reactions to trigger adaptive responses to environmental cues at all levels of the gene expression pathway. RNA-binding proteins (RBP) are key contributors to stress-induced regulation of RNA fate and function. Here, we uncover the plasticity of the RNA interactome in stressed cells, differentiating between responses in the nucleus and in the cytoplasm. We applied enhanced RNA interactome capture (eRIC) analysis preceded by nucleo-cytoplasmic fractionation following arsenite-induced oxidative stress. The data reveal unexpectedly compartmentalized RNA interactomes and their responses to stress, including differential responses of RBPs in the nucleus versus the cytoplasm, which would have been missed by whole cell analyses.
    DOI:  https://doi.org/10.1093/nar/gkaa256
  37. Hum Mutat. 2020 Apr 25.
    Pathogenic variants of DNAJC12 and evaluation of the encoded co-chaperone as a genetic modifier of hyperphenylalaninemia.
    Diana Gallego, Fátima Leal, Alejandra Gámez, Margarita Castro, Rosa Navarrete, Obdulia Sanchez-Lijarcio, Isidro Vitoria, María Bueno-Delgado, Amaya Belanger-Quintana, Ana Morais, Consuelo Pedrón-Giner, Inmaculada García, Jaume Campistol, Rafael Artuch, Carlos Alcaide, Veronica Cornejo, David Gil, Raquel Yahyaoui, Lourdes R Desviat, Magdalena Ugarte, Aurora Martínez, Belén Pérez.
      Biallelic variants of the gene DNAJC12, which encodes a co-chaperone, were recently described in patients with hyperphenylalaninemia (HPA). This paper reports the retrospective genetic analysis of a cohort of unsolved cases of HPA. Biallelic variants of DNAJC12 were identified in 20 patients (generally neurologically asymptomatic) previously diagnosed with phenylalanine hydroxylase (PAH) deficiency (phenylketonuria, PKU). Further, mutations of DNAJC12 were identified in four carriers of a pathogenic variant of PAH. The genetic spectrum of DNAJC12 in the present patients included four new variants, two intronic changes c.298-2A>C and c.502+1G>C, presumably affecting the splicing process, and two exonic changes c.309G>T (p.Trp103Cys) and c.524G>A (p.Trp175Ter), classified as variants of unknown clinical significance (VUS). The variant p.Trp175Ter was detected in 83% of the mutant alleles, with 14 cases homozygous, and was present in 0.3% of a Spanish control population. Functional analysis indicated a significant reduction in PAH and its activity, reduced TH stability, but no effect on TPH2 stability, classifying the two VUS as pathogenic variants. Additionally, the effect of the overexpression of DNAJC12 on some destabilising PAH mutations was examined and a mutation-specific effect on stabilization was detected suggesting that the proteostasis network could be a genetic modifier of PAH deficiency and a potential target for developing mutation-specific treatments for phenylketonuria. This article is protected by copyright. All rights reserved.
    Keywords:   DNAJC12 ; hyperphenylalaninemia; molecular chaperones; phenylketonuria; proteostasis network
    DOI:  https://doi.org/10.1002/humu.24026
  38. mBio. 2020 Apr 21. pii: e00290-20. [Epub ahead of print]11(2):
    The Proteasome Governs Fungal Morphogenesis via Functional Connections with Hsp90 and cAMP-Protein Kinase A Signaling.
    Saif Hossain, Amanda O Veri, Leah E Cowen.
      Protein homeostasis is critical for proliferation and viability of all organisms. For Candida albicans, protein homeostasis also modulates the transition between yeast and filamentous forms, which is critical for virulence. A key regulator of morphogenesis is the molecular chaperone Hsp90, which mediates proteostasis under physiological and stress conditions. Hsp90 regulates morphogenesis by repressing cyclic AMP-protein kinase A (cAMP-PKA) signaling, such that inhibition of Hsp90 causes filamentation in the absence of an inducing cue. We explored the effect of perturbation of another facet of protein homeostasis and discovered that morphogenesis is also regulated by the proteasome, a large 33-subunit protein complex consisting of a 20S catalytic core and two 19S regulatory particles, which controls degradation of intracellular proteins. We identified a conserved role of the proteasome in morphogenesis as pharmacological inhibition of the proteasome induced filamentation of C. albicans and the related species Candida dubliniensis, Candida tropicalis, Candida krusei, and Candida parapsilosis For C. albicans, genetic depletion of any of 29 subunits of the 19S or 20S particle induced filamentation. Filaments induced by inhibition of either the proteasome or Hsp90 have shared structural characteristics, such as aberrant nuclear content, and shared genetic dependencies, such as intact cAMP-PKA signaling. Consistent with a functional connection between these facets of protein homeostasis that modulate morphogenesis, we observed that proteasome inhibition results in an accumulation of ubiquitinated proteins that overwhelm Hsp90 function, relieving Hsp90-mediated repression of morphogenesis. Together, our findings provide a mechanism whereby interconnected facets of proteostasis regulate C. albicans morphogenesis.IMPORTANCE Fungi cause life-threatening infections and pose a serious threat to human health as there are very few effective antifungal drugs. Candida albicans is a major human fungal pathogen and cause of morbidity and mortality in immunocompromised individuals. A key trait that enables C. albicans virulence is its ability to transition between yeast and filamentous forms. Understanding the mechanisms regulating this virulence trait can facilitate the development of much-needed, novel therapeutic strategies. A key regulator of morphogenesis is the molecular chaperone Hsp90, which is crucial for proteostasis. Here, we expanded our understanding of how proteostasis regulates fungal morphogenesis and identified the proteasome as a repressor of filamentation in C. albicans and related species. Our work suggests that proteasome inhibition overwhelms Hsp90 function, thereby inducing morphogenesis. This work provides a foundation for understanding the role of the proteasome in fungal virulence and offers potential for targeting the proteasome to disarm fungal pathogens.
    Keywords:  Candida ; Hsp90; Ras signaling; fungi; morphogenesis; proteasome
    DOI:  https://doi.org/10.1128/mBio.00290-20
  39. Mol Cell. 2020 Apr 09. pii: S1097-2765(20)30198-2. [Epub ahead of print]
    Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells.
    Benjamin Schumann, Stacy Alyse Malaker, Simon Peter Wisnovsky, Marjoke Froukje Debets, Anthony John Agbay, Daniel Fernandez, Lauren Jan Sarbo Wagner, Liang Lin, Zhen Li, Junwon Choi, Douglas Michael Fox, Jessie Peh, Melissa Anne Gray, Kayvon Pedram, Jennifer Jean Kohler, Milan Mrksich, Carolyn Ruth Bertozzi.
      Studying posttranslational modifications classically relies on experimental strategies that oversimplify the complex biosynthetic machineries of living cells. Protein glycosylation contributes to essential biological processes, but correlating glycan structure, underlying protein, and disease-relevant biosynthetic regulation is currently elusive. Here, we engineer living cells to tag glycans with editable chemical functionalities while providing information on biosynthesis, physiological context, and glycan fine structure. We introduce a non-natural substrate biosynthetic pathway and use engineered glycosyltransferases to incorporate chemically tagged sugars into the cell surface glycome of the living cell. We apply the strategy to a particularly redundant yet disease-relevant human glycosyltransferase family, the polypeptide N-acetylgalactosaminyl transferases. This approach bestows a gain-of-chemical-functionality modification on cells, where the products of individual glycosyltransferases can be selectively characterized or manipulated to understand glycan contribution to major physiological processes.
    Keywords:  O-glycosylation; bioorthogonal; chemical proteomics; glycosyltransferase; isoenzyme; mucin
    DOI:  https://doi.org/10.1016/j.molcel.2020.03.030
  40. J Cell Biol. 2020 Apr 06. pii: e201911122. [Epub ahead of print]219(4):
    Fission and fusion machineries converge at ER contact sites to regulate mitochondrial morphology.
    Robert G Abrisch, Samantha C Gumbin, Brett Taylor Wisniewski, Laura L Lackner, Gia K Voeltz.
      The steady-state morphology of the mitochondrial network is maintained by a balance of constitutive fission and fusion reactions. Disruption of this steady-state morphology results in either a fragmented or elongated network, both of which are associated with altered metabolic states and disease. How the processes of fission and fusion are balanced by the cell is unclear. Here we show that mitochondrial fission and fusion are spatially coordinated at ER membrane contact sites (MCSs). Multiple measures indicate that the mitochondrial fusion machinery, Mitofusins, accumulate at ER MCSs where fusion occurs. Furthermore, fission and fusion machineries colocalize to form hotspots for membrane dynamics at ER MCSs that can persist through sequential events. Because these hotspots can undergo fission and fusion, they have the potential to quickly respond to metabolic cues. Indeed, we discover that ER MCSs define the interface between polarized and depolarized segments of mitochondria and can rescue the membrane potential of damaged mitochondria by ER-associated fusion.
    DOI:  https://doi.org/10.1083/jcb.201911122
  41. Cell Mol Life Sci. 2020 Apr 22.
    Receptor-mediated endocytosis 8 (RME-8)/DNAJC13 is a novel positive modulator of autophagy and stabilizes cellular protein homeostasis.
    Anna S Besemer, Joanna Maus, Mirjam D A Ax, Anna Stein, Stella Vo, Christian Freese, Karsten Nalbach, Christian von Hilchen, Ines F Pfalzgraf, Ingrid Koziollek-Drechsler, Beate Silva, Heike Huesmann, Fatima Boukhallouk, Luise Florin, Andreas Kern, Christian Behl, Albrecht M Clement.
      The cellular protein homeostasis (proteostasis) network responds effectively to insults. In a functional screen in C. elegans, we recently identified the gene receptor-mediated endocytosis 8 (rme-8; human ortholog: DNAJC13) as a component of the proteostasis network. Accumulation of aggregation-prone proteins, such as amyloid-β 42 (Aβ), α-synuclein, or mutant Cu/Zn-superoxide dismutase (SOD1), were aggravated upon the knockdown of rme-8/DNAJC13 in C. elegans and in human cell lines, respectively. DNAJC13 is involved in endosomal protein trafficking and associated with the retromer and the WASH complex. As both complexes have been linked to autophagy, we investigated the role of DNAJC13 in this degradative pathway. In knockdown and overexpression experiments, DNAJC13 acts as a positive modulator of autophagy. In contrast, the overexpression of the Parkinson's disease-associated mutant DNAJC13(N855S) did not enhance autophagy. Reduced DNAJC13 levels affected ATG9A localization at and its transport from the recycling endosome. As a consequence, ATG9A co-localization at LC3B-positive puncta under steady-state and autophagy-induced conditions is impaired. These data demonstrate a novel function of RME-8/DNAJC13 in cellular homeostasis by modulating ATG9A trafficking and autophagy.
    Keywords:  ATG9A; Autophagy; C. elegans; DNAJC13; Proteostasis; RME-8; Recycling endosome
    DOI:  https://doi.org/10.1007/s00018-020-03521-y
  42. Proc Natl Acad Sci U S A. 2020 Apr 22. pii: 201919820. [Epub ahead of print]
    MTV proteins unveil ER- and microtubule-associated compartments in the plant vacuolar trafficking pathway.
    María Otilia Delgadillo, Guillermo Ruano, Jan Zouhar, Michael Sauer, Jinbo Shen, Aleksandra Lazarova, Maite Sanmartín, Louis Tung Faat Lai, Cesi Deng, Pengwei Wang, Patrick J Hussey, José Juan Sánchez-Serrano, Liwen Jiang, Enrique Rojo.
      The factors and mechanisms involved in vacuolar transport in plants, and in particular those directing vesicles to their target endomembrane compartment, remain largely unknown. To identify components of the vacuolar trafficking machinery, we searched for Arabidopsis modified transport to the vacuole (mtv) mutants that abnormally secrete the synthetic vacuolar cargo VAC2. We report here on the identification of 17 mtv mutations, corresponding to mutant alleles of MTV2/VSR4, MTV3/PTEN2A MTV7/EREL1, MTV8/ARFC1, MTV9/PUF2, MTV10/VPS3, MTV11/VPS15, MTV12/GRV2, MTV14/GFS10, MTV15/BET11, MTV16/VPS51, MTV17/VPS54, and MTV18/VSR1 Eight of the MTV proteins localize at the interface between the trans-Golgi network (TGN) and the multivesicular bodies (MVBs), supporting that the trafficking step between these compartments is essential for segregating vacuolar proteins from those destined for secretion. Importantly, the GARP tethering complex subunits MTV16/VPS51 and MTV17/VPS54 were found at endoplasmic reticulum (ER)- and microtubule-associated compartments (EMACs). Moreover, MTV16/VPS51 interacts with the motor domain of kinesins, suggesting that, in addition to tethering vesicles, the GARP complex may regulate the motors that transport them. Our findings unveil a previously uncharacterized compartment of the plant vacuolar trafficking pathway and support a role for microtubules and kinesins in GARP-dependent transport of soluble vacuolar cargo in plants.
    Keywords:  microtubules; trafficking; vacuoles
    DOI:  https://doi.org/10.1073/pnas.1919820117
  43. Elife. 2020 Apr 24. pii: e52714. [Epub ahead of print]9
    The switch-like expression of Heme-regulated kinase 1 mediates neuronal proteostasis following proteasome inhibition.
    Beatriz Alvarez-Castelao, Susanne Tom Dieck, Claudia M Fusco, Paul G Donlin-Asp, Julio D Perez, Erin M Schuman.
      We examined the feedback between the major protein degradation pathway, the ubiquitin-proteasome system (UPS), and protein synthesis in rat and mouse neurons. When protein degradation was inhibited, we observed a coordinate dramatic reduction in nascent protein synthesis in neuronal cell bodies and dendrites. The mechanism for translation inhibition involved the phosphorylation of eIF2α, surprisingly mediated by eIF2α kinase 1, or heme-regulated kinase inhibitor (HRI). Under basal conditions, neuronal expression of HRI is barely detectable. Following proteasome inhibition, HRI protein levels increase owing to stabilization of HRI and enhanced translation, likely via the increased availability of tRNAs for its rare codons. Once expressed, HRI is constitutively active in neurons because endogenous heme levels are so low; HRI activity results in eIF2α phosphorylation and the resulting inhibition of translation. These data demonstrate a novel role for HRI in neurons that senses and responds to compromised function of the proteasome to restore proteostasis.
    Keywords:  neuroscience; rat
    DOI:  https://doi.org/10.7554/eLife.52714
  44. Cancer Cell. 2020 Apr 13. pii: S1535-6108(20)30156-2. [Epub ahead of print]
    Cathepsin S Regulates Antigen Processing and T Cell Activity in Non-Hodgkin Lymphoma.
    Elie Dheilly, Elena Battistello, Natalya Katanayeva, Stephanie Sungalee, Justine Michaux, Gerben Duns, Sarah Wehrle, Jessica Sordet-Dessimoz, Marco Mina, Julien Racle, Pedro Farinha, George Coukos, David Gfeller, Anja Mottok, Robert Kridel, Bruno E Correia, Christian Steidl, Michal Bassani-Sternberg, Giovanni Ciriello, Vincent Zoete, Elisa Oricchio.
      Genomic alterations in cancer cells can influence the immune system to favor tumor growth. In non-Hodgkin lymphoma, physiological interactions between B cells and the germinal center microenvironment are coopted to sustain cancer cell proliferation. We found that follicular lymphoma patients harbor a recurrent hotspot mutation targeting tyrosine 132 (Y132D) in cathepsin S (CTSS) that enhances protein activity. CTSS regulates antigen processing and CD4+ and CD8+ T cell-mediated immune responses. Loss of CTSS activity reduces lymphoma growth by limiting communication with CD4+ T follicular helper cells while inducing antigen diversification and activation of CD8+ T cells. Overall, our results suggest that CTSS inhibition has non-redundant therapeutic potential to enhance anti-tumor immune responses in indolent and aggressive lymphomas.
    Keywords:  T cells; antigen presentation; cysteine proteases; germinal centers; immunotherapy; lymphoma
    DOI:  https://doi.org/10.1016/j.ccell.2020.03.016
  45. Cell Death Differ. 2020 Apr 20.
    The SCFSkp2 ubiquitin ligase complex modulates TRAIL-R2-induced apoptosis by regulating FLIP(L).
    Jamie Z Roberts, Caitriona Holohan, Tamas Sessler, Jennifer Fox, Nyree Crawford, Joel S Riley, Hajrah Khawaja, Joanna Majkut, Emma Evergren, Luke M Humphreys, Jennifer Ferris, Catherine Higgins, Margarita Espona-Fiedler, Paul Moynagh, Simon S McDade, Daniel B Longley.
      TRAIL-R2 (DR5) is a clinically-relevant therapeutic target and a key target for immune effector cells. Herein, we identify a novel interaction between TRAIL-R2 and the Skp1-Cullin-1-F-box (SCF) Cullin-Ring E3 Ubiquitin Ligase complex containing Skp2 (SCFSkp2). We find that SCFSkp2 can interact with both TRAIL-R2's pre-ligand association complex (PLAC) and ligand-activated death-inducing signalling complex (DISC). Moreover, Cullin-1 interacts with TRAIL-R2 in its active NEDDylated form. Inhibiting Cullin-1's DISC recruitment using the NEDDylation inhibitor MLN4924 (Pevonedistat) or siRNA increased apoptosis induction in response to TRAIL. This correlated with enhanced levels of the caspase-8 regulator FLIP at the TRAIL-R2 DISC, particularly the long splice form, FLIP(L). We subsequently found that FLIP(L) (but not FLIP(S), caspase-8, nor the other core DISC component FADD) interacts with Cullin-1 and Skp2. Importantly, this interaction is enhanced when FLIP(L) is in its DISC-associated, C-terminally truncated p43-form. Prevention of FLIP(L) processing to its p43-form stabilises the protein, suggesting that by enhancing its interaction with SCFSkp2, cleavage to the p43-form is a critical step in FLIP(L) turnover. In support of this, we found that silencing any of the components of the SCFSkp2 complex inhibits FLIP ubiquitination, while overexpressing Cullin-1/Skp2 enhances its ubiquitination in a NEDDylation-dependent manner. DISC recruitment of TRAF2, previously identified as an E3 ligase for caspase-8 at the DISC, was also enhanced when Cullin-1's recruitment was inhibited, although its interaction with Cullin-1 was found to be mediated indirectly via FLIP(L). Notably, the interaction of p43-FLIP(L) with Cullin-1 disrupts its ability to interact with FADD, caspase-8 and TRAF2. Collectively, our results suggest that processing of FLIP(L) to p43-FLIP(L) at the TRAIL-R2 DISC enhances its interaction with co-localised SCFSkp2, leading to disruption of p43-FLIP(L)'s interactions with other DISC components and promoting its ubiquitination and degradation, thereby modulating TRAIL-R2-mediated apoptosis.
    DOI:  https://doi.org/10.1038/s41418-020-0539-7
  46. J Biol Chem. 2020 Apr 24. pii: jbc.REV119.008907. [Epub ahead of print]
    Evolution, role in inflammation, and redox control of leaderless secretory proteins.
    Roberto Sitia, Anna Rubartelli.
      Members of the interleukin (IL)-1 family are key determinants of inflammation. Despite their role as intercellular mediators, most lack the leader peptide typically required for protein secretion. This lack is a characteristic of dozens of other proteins that are actively and selectively secreted from living cells independently of the classical endoplasmic reticulum-Golgi exocytic route. These proteins, termed leaderless secretory proteins (LLSPs), comprise proteins directly or indirectly involved in inflammation, including cytokines such as IL-1β and IL-18, growth factors such as fibroblast growth factor 2 (FGF2), redox enzymes such as thioredoxin, and proteins most expressed in the brain, some of which participate to the pathogenesis of neurodegenerative disorders. In spite of much effort, motifs that promote LLSP secretion remain to be identified. In this review, we summarize the mechanisms and pathophysiological significance of the unconventional secretory pathways that cells use to release LLSPs. We place special emphasis on redox regulation and inflammation, with focus on IL-1β, which is secreted after processing of its biologically inactive precursor pro-IL-1β in the cytosol. Although LLSP externalization remains poorly understood, some possible mechanisms have emerged. For example, a common feature of LLSP pathways is that they become active in response to stress and that they involve several distinct excretion mechanisms, including direct plasma membrane translocation, lysosome exocytosis, exosome formation, membrane vesiculation, autophagy, and pyroptosis. Further investigations of unconventional secretory pathways for LLSP secretion may shed light on their evolution and could help advance therapeutic avenues for managing pathological conditions such as diseases arising from inflammation.
    Keywords:  Cryopyrin Associated Periodic Syndromes; gasdermin D; inflammation; innate immunity; interleukin 1 (IL-1); leaderless secretory proteins; lysosome; misfolding; monocyte; oxidation-reduction (redox); reactive oxygen species (ROS); secretion; stress; toll-like receptor (TLR); unconventional secretion
    DOI:  https://doi.org/10.1074/jbc.REV119.008907
  47. Nature. 2020 Apr;580(7804): 530-535
    The gluconeogenic enzyme PCK1 phosphorylates INSIG1/2 for lipogenesis.
    Daqian Xu, Zheng Wang, Yan Xia, Fei Shao, Weiya Xia, Yongkun Wei, Xinjian Li, Xu Qian, Jong-Ho Lee, Linyong Du, Yanhua Zheng, Guishuai Lv, Jia-Shiun Leu, Hongyang Wang, Dongming Xing, Tingbo Liang, Mien-Chie Hung, Zhimin Lu.
      Cancer cells increase lipogenesis for their proliferation and the activation of sterol regulatory element-binding proteins (SREBPs) has a central role in this process. SREBPs are inhibited by a complex composed of INSIG proteins, SREBP cleavage-activating protein (SCAP) and sterols in the endoplasmic reticulum. Regulation of the interaction between INSIG proteins and SCAP by sterol levels is critical for the dissociation of the SCAP-SREBP complex from the endoplasmic reticulum and the activation of SREBPs1,2. However, whether this protein interaction is regulated by a mechanism other than the abundance of sterol-and in particular, whether oncogenic signalling has a role-is unclear. Here we show that activated AKT in human hepatocellular carcinoma (HCC) cells phosphorylates cytosolic phosphoenolpyruvate carboxykinase 1 (PCK1), the rate-limiting enzyme in gluconeogenesis, at Ser90. Phosphorylated PCK1 translocates to the endoplasmic reticulum, where it uses GTP as a phosphate donor to phosphorylate INSIG1 at Ser207 and INSIG2 at Ser151. This phosphorylation reduces the binding of sterols to INSIG1 and INSIG2 and disrupts the interaction between INSIG proteins and SCAP, leading to the translocation of the SCAP-SREBP complex to the Golgi apparatus, the activation of SREBP proteins (SREBP1 or SREBP2) and the transcription of downstream lipogenesis-related genes, proliferation of tumour cells, and tumorigenesis in mice. In addition, phosphorylation of PCK1 at Ser90, INSIG1 at Ser207 and INSIG2 at Ser151 is not only positively correlated with the nuclear accumulation of SREBP1 in samples from patients with HCC, but also associated with poor HCC prognosis. Our findings highlight the importance of the protein kinase activity of PCK1 in the activation of SREBPs, lipogenesis and the development of HCC.
    DOI:  https://doi.org/10.1038/s41586-020-2183-2
  48. Cell Rep. 2020 Apr 21. pii: S2211-1247(20)30457-5. [Epub ahead of print]31(3): 107547
    The Autophagy-Initiating Kinase ULK1 Controls RIPK1-Mediated Cell Death.
    Wenxian Wu, Xiaojing Wang, Niklas Berleth, Jana Deitersen, Nora Wallot-Hieke, Philip Böhler, David Schlütermann, Fabian Stuhldreier, Jan Cox, Katharina Schmitz, Sabine Seggewiß, Christoph Peter, Gary Kasof, Anja Stefanski, Kai Stühler, Astrid Tschapek, Axel Gödecke, Björn Stork.
      Autophagy, apoptosis, and necroptosis are stress responses governing the ultimate fate of a cell. However, the crosstalk between these cellular stress responses is not entirely understood. Especially, it is not clear whether the autophagy-initiating kinase ULK1 and the cell-death-regulating kinase RIPK1 are involved in this potential crosstalk. Here, we identify RIPK1 as a substrate of ULK1. ULK1-dependent phosphorylation of RIPK1 reduces complex IIb/necrosome assembly and tumor necrosis factor (TNF)-induced cell death, whereas deprivation of ULK1 enhances TNF-induced cell death. We observe that ULK1 phosphorylates multiple sites of RIPK1, but it appears that especially phosphorylation of S357 within the intermediate domain of RIPK1 mediates this cell-death-inhibiting effect. We propose that ULK1 is a regulator of RIPK1-mediated cell death.
    Keywords:  MLKL; RIPK1; RIPK3; TNF; ULK1; autophagy; complex I; complex II; necroptosis; necrosome
    DOI:  https://doi.org/10.1016/j.celrep.2020.107547
  49. Mol Oncol. 2020 Apr 25.
    SUMOylation modulates the LIN28A-let-7 signaling pathway in response to cellular stresses in cancer cells.
    Jinzhuo Dou, Hailong Zhang, Ran Chen, Zimei Shu, Haihua Yuan, Xian Zhao, Yanli Wang, Jian Huang, Aiwu Zhou, Jianxiu Yu.
      LIN28A is a conserved RNA-binding protein that inhibits the biogenesis of let-7 microRNAs, thus promoting cancer progression. However, mechanisms underlying the activation of the LIN28A-let-7 signaling pathway remain poorly understood. Here, we show that LIN28A is SUMOylated in vivo and in vitro at K15, which is increased by hypoxia but reduced by chemotherapy drugs such as Cisplatin and Paclitaxel. SUMOylation of LIN28A aggravates its inhibition of let-7 maturation, resulting in a stark reduction of let-7, which promotes cancer cell proliferation, migration, invasion, and tumor growth in vivo. Mechanistically, SUMOylation of LIN28A increases its binding affinity with the precursor let-7 (pre-let-7), which subsequently enhances LIN28A-mediated recruitment of terminal uridylyltransferase (TUTase) TUT4 and simultaneously blocks DICER processing of pre-let-7, thereby reducing mature let-7 production. These effects are abolished in SUMOylation-deficient mutant LIN28A-K15R. In summary, these findings shed light on a novel mechanism by which SUMOylation could regulate the LIN28A-let-7 pathway in response to cellular stress in cancer cells.
    Keywords:  LIN28A; SUMOylation; binding affinity to precursor let-7; cancer progression; let-7 biogenesis; stresses
    DOI:  https://doi.org/10.1002/1878-0261.12694
  50. Sci Transl Med. 2020 Apr 22. pii: eaax9106. [Epub ahead of print]12(540):
    Gene-edited human stem cell-derived β cells from a patient with monogenic diabetes reverse preexisting diabetes in mice.
    Kristina G Maxwell, Punn Augsornworawat, Leonardo Velazco-Cruz, Michelle H Kim, Rie Asada, Nathaniel J Hogrebe, Shuntaro Morikawa, Fumihiko Urano, Jeffrey R Millman.
      Differentiation of insulin-producing pancreatic β cells from induced pluripotent stem cells (iPSCs) derived from patients with diabetes promises to provide autologous cells for diabetes cell replacement therapy. However, current approaches produce patient iPSC-derived β (SC-β) cells with poor function in vitro and in vivo. Here, we used CRISPR-Cas9 to correct a diabetes-causing pathogenic variant in Wolfram syndrome 1 (WFS1) in iPSCs derived from a patient with Wolfram syndrome (WS). After differentiation to β cells with our recent six-stage differentiation strategy, corrected WS SC-β cells performed robust dynamic insulin secretion in vitro in response to glucose and reversed preexisting streptozocin-induced diabetes after transplantation into mice. Single-cell transcriptomics showed that corrected SC-β cells displayed increased insulin and decreased expression of genes associated with endoplasmic reticulum stress. CRISPR-Cas9 correction of a diabetes-inducing gene variant thus allows for robust differentiation of autologous SC-β cells that can reverse severe diabetes in an animal model.
    DOI:  https://doi.org/10.1126/scitranslmed.aax9106
  51. EMBO Rep. 2020 Apr 23. e50340
    Endogenous metabolites promote stress resistance through induction of mitohormesis.
    Fabian Fischer, Michael Ristow.
      Interventions and small molecules, which promote formation of reactive oxygen species (ROS), have repeatedly been shown to increase stress resistance and lifespan of different model organisms. These phenotypes occur only in response to low concentrations of ROS, while higher concentrations exert opposing effects. This non-linear or hormetic dose-response relationship has been termed mitohormesis, since ROS are mainly generated within the mitochondrial compartment. A report by Matsumura et al in this issue of EMBO Reports now demonstrates that an endogenously formed metabolite, namely N-acetyl-L-tyrosine (NAT), is instrumental in promoting cellular and organismal resilience by inducing mitohormetic mechanisms, likely in an evolutionarily conserved manner [1].
    DOI:  https://doi.org/10.15252/embr.202050340
  52. EMBO J. 2020 Apr 20. e102539
    Tollip coordinates Parkin-dependent trafficking of mitochondrial-derived vesicles.
    Thomas A Ryan, Elliott O Phillips, Charlotte L Collier, Alice Jb Robinson, Daniel Routledge, Rebecca E Wood, Emelia A Assar, David A Tumbarello.
      Multiple mitochondrial quality control pathways exist to maintain the health of mitochondria and ensure cell homeostasis. Here, we investigate the role of the endosomal adaptor Tollip during the mitochondrial stress response and identify its interaction and colocalisation with the Parkinson's disease-associated E3 ubiquitin ligase Parkin. The interaction between Tollip and Parkin is dependent on the ubiquitin-binding CUE domain of Tollip, but independent of Tom1 and mitophagy. Interestingly, this interaction is independent of Parkin mitochondrial recruitment and ligase activity but requires an intact ubiquitin-like (UBL) domain. Importantly, Tollip regulates Parkin-dependent endosomal trafficking of a discrete subset of mitochondrial-derived vesicles (MDVs) to facilitate delivery to lysosomes. Retromer function and an interaction with Tom1 allow Tollip to facilitate late endosome/lysosome trafficking in response to mitochondrial stress. We find that upregulation of TOM20-positive MDVs upon mitochondrial stress requires Tollip interaction with ubiquitin, endosomal membranes and Tom1 to ensure their trafficking to the lysosomes. Thus, we conclude that Tollip, via an association with Parkin, is an essential coordinator to sort damaged mitochondrial-derived cargo to the lysosomes.
    Keywords:  Parkinson's disease; lysosome; membrane trafficking; mitochondria; vesicle transport
    DOI:  https://doi.org/10.15252/embj.2019102539
  53. Bioessays. 2020 Apr 22. e1900250
    Peptidylprolylisomerases, Protein Folders, or Scaffolders? The Example of FKBP51 and FKBP52.
    Theo Rein.
      Peptidylprolyl-isomerases (PPIases) comprise of the protein families of FK506 binding proteins (FKBPs), cyclophilins, and parvulins. Their common feature is their ability to expedite the transition of peptidylprolyl bonds between the cis and the trans conformation. Thus, it seemed highly plausible that PPIase enzymatic activity is crucial for protein folding. However, this has been difficult to prove over the decades since their discovery. In parallel, more and more studies have discovered scaffolding functions of PPIases. This essay discusses the hypothesis that PPIase enzymatic activity might be the consequence of binding to peptidylprolyl protein motifs. The main focus of this paper is the large immunophilins FKBP51 and FKBP52, but other PPIases such as cyclophilin A and Pin1 are also described. From the hypothesis, it follows that the PPIase activity of these proteins might be less relevant, if at all, than the organization of protein complexes through versatile protein binding. Also see the video abstract here https://youtu.be/A33la0dx5LE.
    Keywords:  FKBP5; FKBP51; FKBP52; Peptidylprolylisomerases; chaperones
    DOI:  https://doi.org/10.1002/bies.201900250
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