bims-proteo Biomed News
on Proteostasis
Issue of 2021–08–01
forty-five papers selected by
Eric Chevet, INSERM
  1. ER-Phagy: A New Regulator of ER Homeostasis.
  2. Ester-linked ubiquitination by HOIL-1 controls immune signalling by shaping the linear ubiquitin landscape.
  3. ATG4s: above and beyond the Atg8-family protein lipidation system.
  4. Conserved and Unique Roles of Chaperone-Dependent E3 Ubiquitin Ligase CHIP in Plants.
  5. Post-ER degradation of misfolded GPI-anchored proteins is linked with microautophagy.
  6. Arabidopsis HIPP proteins regulate endoplasmic reticulum-associated degradation of CKX proteins and cytokinin responses.
  7. Solenoid architecture of HUWE1 contributes to ligase activity and substrate recognition.
  8. Targeting ER-stress in the hepatic tumor microenvironment.
  9. Rewiring of the ubiquitinated proteome determines ageing in C. elegans.
  10. The intrinsic chaperone network of Arabidopsis stem cells confers protection against proteotoxic stress.
  11. SNX27-driven membrane localisation of OTULIN antagonises linear ubiquitination and NF-κB signalling activation.
  12. Cullin 2-RBX1 E3 ligase and USP2 regulate antithrombin ubiquitination and stability.
  13. Stress-primed secretory autophagy promotes extracellular BDNF maturation by enhancing MMP9 secretion.
  14. Antibody toolkit reveals N-terminally ubiquitinated substrates of UBE2W.
  15. CD97 stabilises the immunological synapse between dendritic cells and T cells and is targeted for degradation by the Salmonella effector SteD.
  16. Chemo-proteomics exploration of HDAC degradability by small molecule degraders.
  17. SUMO proteases SENP3 and SENP5 spatiotemporally regulate the kinase activity of Aurora A.
  18. TRIM8 modulates the EWS/FLI oncoprotein to promote survival in Ewing sarcoma.
  19. The integrated stress response is tumorigenic and constitutes a therapeutic liability in KRAS-driven lung cancer.
  20. SNX19 restricts endolysosome motility through contacts with the endoplasmic reticulum.
  21. Activation of the Protein Kinase R-Like Endoplasmic Reticulum Kinase (PERK) Pathway of the Unfolded Protein Response after Experimental Traumatic Brain Injury and Treatment with a PERK Inhibitor.
  22. RTN3 inhibits RIG-I-mediated antiviral responses by impairing TRIM25-mediated K63-linked polyubiquitination.
  23. miR-1 coordinately regulates lysosomal v-ATPase and biogenesis to impact proteotoxicity and muscle function during aging.
  24. The prokaryotic ubiquitin-like protein presents poor cleavage sites for proteasomal degradation.
  25. McsB forms a gated kinase chamber to mark aberrant bacterial proteins for degradation.
  26. ATG7 safeguards human neural integrity.
  27. Paramyxovirus replication induces the Hexosamine Biosynthetic Pathway and Mesenchymal Transition via the IRE1a-XBP1s arm of the Unfolded Protein Response.
  28. Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation.
  29. APC/CFZR-1 regulates centrosomal ZYG-1 to limit centrosome number.
  30. Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity.
  31. THAP1 modulates oligodendrocyte maturation by regulating ECM degradation in lysosomes.
  32. Host autophagy mediates organ wasting and nutrient mobilization for tumor growth.
  33. Ribosome ADP-ribosylation inhibits translation and maintains proteostasis in cancers.
  34. Chop/Ddit3 depletion in β cells alleviates ER stress and corrects hepatic steatosis in mice.
  35. Small molecule inhibition of deubiquitinating enzyme JOSD1 as a novel targeted therapy for leukemias with mutant JAK2.
  36. BARD1 reads H2A lysine 15 ubiquitination to direct homologous recombination.
  37. Sequence requirements of the FFAT-like motif for specific binding to VAP-A are revealed by NMR.
  38. Ufbp1, a Key Player of Ufm1 Conjugation System, Protects Against Ketosis-Induced Liver Injury via Suppressing Smad3 Activation.
  39. Translation reprogramming by eIF3 linked to glioblastoma resistance.
  40. IRE1 and PERK signaling regulates inflammatory responses in a murine model of contact hypersensitivity.
  41. The secreted tyrosine kinase VLK is essential for normal platelet activation and thrombus formation.
  42. Hepatic mTORC1 signaling activates ATF4 as part of its metabolic response to feeding and insulin.
  43. ANXA10 promotes melanoma metastasis by suppressing E3 ligase TRIM41-directed PKD1 degradation.
  44. Inhibition of the unfolded protein response reduces arrhythmic risk after myocardial infarction.
  45. Processing of the ribosomal ubiquitin-like fusion protein FUBI-eS30/FAU is required for 40S maturation and depends on USP36.
  1. Front Cell Dev Biol. 2021 ;9 684526
    ER-Phagy: A New Regulator of ER Homeostasis.
    Ming Yang, Shilu Luo, Xi Wang, Chenrui Li, Jinfei Yang, Xuejing Zhu, Li Xiao, Lin Sun.
      The endoplasmic reticulum (ER) is one of the most important cellular organelles and is essential for cell homeostasis. Upon external stimulation, ER stress induces the unfolded protein response (UPR) and ER-associated degradation (ERAD) to maintain ER homeostasis. However, persistent ER stress can lead to cell damage. ER-phagy is a selective form of autophagy that ensures the timely removal of damaged ER, thereby protecting cells from damage caused by excessive ER stress. As ER-phagy is a newly identified form of autophagy, many receptor-mediated ER-phagy pathways have been discovered in recent years. In this review, we summarize our understanding of the maintenance of ER homeostasis and describe the receptors identified to date. Finally, the relationships between ER-phagy and diseases are also discussed.
    Keywords:  ER-phagy; ERAD; autophagy; endoplasmic reticulum (ER); unfolded protein response (UPR)
    DOI:  https://doi.org/10.3389/fcell.2021.684526
  2. FEBS J. 2021 Jul 28.
    Ester-linked ubiquitination by HOIL-1 controls immune signalling by shaping the linear ubiquitin landscape.
    Jonathan N Pruneda, Rune Busk Damgaard.
      Ester-linked ubiquitination of serine or threonine residues - or even lipids - has emerged as a new regulatory earmark in cell signalling. Petrova et al. (2021) now reveal that ubiquitin esterification by the atypical ubiquitin ligase HOIL-1, a component of the LUBAC complex, is critical for proper formation of linear ubiquitin chains and control of immune signalling in T cells and macrophages. Surprisingly, ester-linked ubiquitination can either promote or inhibit linear ubiquitin conjugation and cytokine production depending on the receptor and immune cell engaged. Comment on: https://doi.org/10.1111/febs.15896.
    Keywords:  HOIL-1; LUBAC; immune signalling; inflammation; ubiquitin
    DOI:  https://doi.org/10.1111/febs.16118
  3. Autophagy. 2021 Jul 25. 1-3
    ATG4s: above and beyond the Atg8-family protein lipidation system.
    Thanh Ngoc Nguyen, Benjamin Scott Padman, Michael Lazarou.
      The sole proteases of the macroautophagy/autophagy machinery, the ATG4s, contribute to autophagosome formation by cleaving Atg8-family protein members (LC3/GABARAPs) which enables Atg8-family protein lipidation and de-lipidation. Our recent work reveals that ATG4s can also promote phagophore growth independently of their protease activity and of Atg8-family proteins. ATG4s and their proximity partners including ARFIP2 and LRBA function to promote trafficking of ATG9A to mitochondria during PINK1-PRKN mitophagy. Through the development of a 3D electron microscopy framework utilizing FIB-SEM and artificial intelligence (termed AIVE: Artificial Intelligence-directed Voxel Extraction), we show that ATG4s promote ER-phagophore contacts during the lipid-transfer phase of autophagosome biogenesis, which requires ATG2B and ATG9A to support phagophore growth. We also discovered that ATG4s are not essential for removal of Atg8-family proteins from autolysosomes, but they can function as deubiquitinase-like enzymes to counteract the conjugation of Atg8-family proteins to other proteins, a process that we have termed ATG8ylation (also known as LC3ylation). These discoveries demonstrate the duality of the ATG4 family in driving autophagosome formation by functioning as both autophagy proteases and trafficking factors, while simultaneously raising questions about the putative roles of ATG8ylation in cell biology.
    Keywords:  ATG4; ATG8; ATG8ylation; PINK1-PRKN mitophagy; Parkinson’s disease; autophagy; de-lipidation; immune disease; mitochondrial dysfunction; ubiquitin-like
    DOI:  https://doi.org/10.1080/15548627.2021.1953263
  4. Front Plant Sci. 2021 ;12 699756
    Conserved and Unique Roles of Chaperone-Dependent E3 Ubiquitin Ligase CHIP in Plants.
    Yan Zhang, Gengshou Xia, Qianggen Zhu.
      Protein quality control (PQC) is essential for maintaining cellular homeostasis by reducing protein misfolding and aggregation. Major PQC mechanisms include protein refolding assisted by molecular chaperones and the degradation of misfolded and aggregated proteins using the proteasome and autophagy. A C-terminus of heat shock protein (Hsp) 70-interacting protein [carboxy-terminal Hsp70-interacting protein (CHIP)] is a chaperone-dependent and U-box-containing E3 ligase. CHIP is a key molecule in PQC by recognizing misfolded proteins through its interacting chaperones and targeting their degradation. CHIP also ubiquitinates native proteins and plays a regulatory role in other cellular processes, including signaling, development, DNA repair, immunity, and aging in metazoans. As a highly conserved ubiquitin ligase, plant CHIP plays an important role in response to a broad spectrum of biotic and abiotic stresses. CHIP protects chloroplasts by coordinating chloroplast PQC both outside and inside the important photosynthetic organelle of plant cells. CHIP also modulates the activity of protein phosphatase 2A (PP2A), a crucial component in a network of plant signaling, including abscisic acid (ABA) signaling. In this review, we discuss the structure, cofactors, activities, and biological function of CHIP with an emphasis on both its conserved and unique roles in PQC, stress responses, and signaling in plants.
    Keywords:  CHIP ubiquitin E3 ligase; chloroplasts; heat shock proteins; molecular chaperones; plant stress responses; protein degradation; protein quality control; ubiquitination
    DOI:  https://doi.org/10.3389/fpls.2021.699756
  5. Curr Biol. 2021 Jul 21. pii: S0960-9822(21)00907-6. [Epub ahead of print]
    Post-ER degradation of misfolded GPI-anchored proteins is linked with microautophagy.
    Leticia Lemus, Zrinka Matić, Lihi Gal, Amir Fadel, Maya Schuldiner, Veit Goder.
      Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are membrane-conjugated cell-surface proteins with diverse structural, developmental, and signaling functions and clinical relevance. Typically, after biosynthesis and attachment to the preassembled GPI anchor, GPI-APs rapidly leave the endoplasmic reticulum (ER) and rely on post-ER quality control. Terminally misfolded GPI-APs end up inside the vacuole/lysosome for degradation, but their trafficking itinerary to this organelle and the processes linked to their uptake by the vacuole/lysosome remain uncharacterized. In a yeast mutant that is lacking Pep4, a key vacuolar protease, several misfolded model GPI-APs accumulated in the vacuolar membrane. In the same mutant, macroautophagy and the multi-vesicular body (MVB) pathway were intact, hinting at a hitherto-unknown trafficking pathway for the degradation of misfolded GPI-APs. To unravel it, we used a genome-wide screen coupled to high-throughput fluorescence microscopy and followed the fate of the misfolded GPI-AP: Gas1∗. We found that components of the early secretory and endocytic pathways are involved in its targeting to the vacuole and that vacuolar transporter chaperones (VTCs), with roles in microautophagy, negatively affect the vacuolar uptake of Gas1∗. In support, we demonstrate that Gas1∗ internalizes from vacuolar membranes into membrane-bound intravacuolar vesicles prior to degradation. Our data link post-ER degradation with microautophagy.
    Keywords:  ESCRT machinery; GPI-anchored proteins; Pep4; VTCs; lysosome; microautophagy; post-ER quality control; protein internalization; protein trafficking; vacuolar membrane; vacuolar transporter chaperones; vacuole
    DOI:  https://doi.org/10.1016/j.cub.2021.06.078
  6. Mol Plant. 2021 Jul 24. pii: S1674-2052(21)00303-8. [Epub ahead of print]
    Arabidopsis HIPP proteins regulate endoplasmic reticulum-associated degradation of CKX proteins and cytokinin responses.
    Tianqi Guo, Henriette Weber, Michael C E Niemann, Lisa Theisl, Ondřej Novák, Tomáš Werner.
      Eukaryotic organisms are equipped with quality-control mechanisms that survey protein folding in the endoplasmic reticulum (ER) and remove non-native proteins by ER-associated degradation (ERAD). Recent research has shown that cytokinin-degrading CKX proteins are subjected to ERAD during plant development. The mechanisms of plant ERAD, including the export of substrate proteins from the ER, are not fully understood and the molecular components involved in the ERAD of CKX are unknown. We show that heavy metal-associated isoprenylated plant proteins (HIPP) interact specifically with CKX proteins synthesized in the ER and processed by ERAD. CKX-HIPP protein complexes were detected at the ER as well as in the cytosol, suggesting that the complexes involve retrotranslocated CKX protein species. Altered CKX levels in HIPP-overexpressing and higher-order hipp mutant plants suggest that the studied HIPP proteins control the ERAD of CKX. Deregulation of CKX proteins caused corresponding changes in the cytokinin signaling activity and triggered typical morphological cytokinin responses. Notably, transcriptional repression of HIPP genes by cytokinin indicates a feedback regulatory mechanism of cytokinin homeostasis and signaling responses. Moreover, the loss of HIPP genes constitutively activates the unfolded protein response and compromises the ER stress tolerance, supporting the conclusion that HIPPs represent novel functional components of plant ERAD.
    DOI:  https://doi.org/10.1016/j.molp.2021.07.015
  7. Mol Cell. 2021 Jul 16. pii: S1097-2765(21)00543-8. [Epub ahead of print]
    Solenoid architecture of HUWE1 contributes to ligase activity and substrate recognition.
    Moritz Hunkeler, Cyrus Y Jin, Michelle W Ma, Julie K Monda, Daan Overwijn, Eric J Bennett, Eric S Fischer.
      HECT ubiquitin ligases play essential roles in metazoan development and physiology. The HECT ligase HUWE1 is central to the cellular stress response by mediating degradation of key death or survival factors, including Mcl1, p53, DDIT4, and Myc. Although mutations in HUWE1 and related HECT ligases are widely implicated in human disease, our molecular understanding remains limited. Here we present a comprehensive investigation of full-length HUWE1, deepening our understanding of this class of enzymes. The N-terminal ∼3,900 amino acids of HUWE1 are indispensable for proper ligase function, and our cryo-EM structures of HUWE1 offer a complete molecular picture of this large HECT ubiquitin ligase. HUWE1 forms an alpha solenoid-shaped assembly with a central pore decorated with protein interaction modules. Structures of HUWE1 variants linked to neurodevelopmental disorders as well as of HUWE1 bound to a model substrate link the functions of this essential enzyme to its three-dimensional organization.
    Keywords:  E3; HECT; HUWE1; cryo-EM; modular assembly; protein degradation; ubiquitin; ubiquitin ligase
    DOI:  https://doi.org/10.1016/j.molcel.2021.06.032
  8. FEBS J. 2021 Jul 31.
    Targeting ER-stress in the hepatic tumor microenvironment.
    Nataša Pavlović, Femke Heindryckx.
      Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. It currently ranks as one of the most aggressive and deadly cancers worldwide, with an increasing mortality rate and limited treatment options. An important hallmark of liver pathologies, such as liver fibrosis and HCC, is the accumulation of misfolded and unfolded proteins in the lumen of the endoplasmic reticulum (ER), which induces ER-stress and leads to the activation of the unfolded protein response (UPR). Upon accumulation of misfolded proteins, ER-stress is sensed through three transmembrane proteins, IRE1α, PERK and ATF6, which trigger the UPR to either alleviate ER-stress or induce apoptosis. Increased expression of ER-stress markers has been widely shown to correlate with fibrosis, inflammation, drug resistance and overall HCC aggressiveness, as well as poor patient prognosis. While preclinical in vivo cancer models and in vitro approaches have shown promising results by pharmacologically targeting ER-stress mediators, the major challenge of this therapeutic strategy lies in specifically and effectively targeting ER-stress in HCC. Furthermore, both ER-stress inducers and inhibitors have been shown to ameliorate HCC progression, adding to the complexity of targeting ER-stress players as an anti-cancer strategy. More studies are needed to better understand the dual role and molecular background of ER-stress in HCC, as well as its therapeutic potential for patients with liver cancer.
    Keywords:  ER-stress; fibrosis; hepatocellular carcinoma; tumor microenvironment; unfolded protein response
    DOI:  https://doi.org/10.1111/febs.16145
  9. Nature. 2021 Jul 28.
    Rewiring of the ubiquitinated proteome determines ageing in C. elegans.
    Seda Koyuncu, Rute Loureiro, Hyun Ju Lee, Prerana Wagle, Marcus Krueger, David Vilchez.
      Ageing is driven by a loss of cellular integrity1. Given the major role of ubiquitin modifications in cell function2, here we assess the link between ubiquitination and ageing by quantifying whole-proteome ubiquitin signatures in Caenorhabditis elegans. We find a remodelling of the ubiquitinated proteome during ageing, which is ameliorated by longevity paradigms such as dietary restriction and reduced insulin signalling. Notably, ageing causes a global loss of ubiquitination that is triggered by increased deubiquitinase activity. Because ubiquitination can tag proteins for recognition by the proteasome3, a fundamental question is whether deficits in targeted degradation influence longevity. By integrating data from worms with a defective proteasome, we identify proteasomal targets that accumulate with age owing to decreased ubiquitination and subsequent degradation. Lowering the levels of age-dysregulated proteasome targets prolongs longevity, whereas preventing their degradation shortens lifespan. Among the proteasomal targets, we find the IFB-2 intermediate filament4 and the EPS-8 modulator of RAC signalling5. While increased levels of IFB-2 promote the loss of intestinal integrity and bacterial colonization, upregulation of EPS-8 hyperactivates RAC in muscle and neurons, and leads to alterations in the actin cytoskeleton and protein kinase JNK. In summary, age-related changes in targeted degradation of structural and regulatory proteins across tissues determine longevity.
    DOI:  https://doi.org/10.1038/s41586-021-03781-z
  10. Aging Cell. 2021 Jul 30. e13446
    The intrinsic chaperone network of Arabidopsis stem cells confers protection against proteotoxic stress.
    Ernesto Llamas, Salvador Torres-Montilla, Hyun Ju Lee, María Victoria Barja, Elena Schlimgen, Nick Dunken, Prerana Wagle, Wolfgang Werr, Alga Zuccaro, Manuel Rodríguez-Concepción, David Vilchez.
      The biological purpose of plant stem cells is to maintain themselves while providing new pools of differentiated cells that form organs and rejuvenate or replace damaged tissues. Protein homeostasis or proteostasis is required for cell function and viability. However, the link between proteostasis and plant stem cell identity remains unknown. In contrast to their differentiated counterparts, we find that root stem cells can prevent the accumulation of aggregated proteins even under proteotoxic stress conditions such as heat stress or proteasome inhibition. Notably, root stem cells exhibit enhanced expression of distinct chaperones that maintain proteome integrity. Particularly, intrinsic high levels of the T-complex protein-1 ring complex/chaperonin containing TCP1 (TRiC/CCT) complex determine stem cell maintenance and their remarkable ability to suppress protein aggregation. Overexpression of CCT8, a key activator of TRiC/CCT assembly, is sufficient to ameliorate protein aggregation in differentiated cells and confer resistance to proteotoxic stress in plants. Taken together, our results indicate that enhanced proteostasis mechanisms in stem cells could be an important requirement for plants to persist under extreme environmental conditions and reach extreme long ages. Thus, proteostasis of stem cells can provide insights to design and breed plants tolerant to environmental challenges caused by the climate change.
    Keywords:  chaperones; heat stress; plant stem cells; protein aggregation; protein misfolding; proteostasis
    DOI:  https://doi.org/10.1111/acel.13446
  11. Cell Biosci. 2021 Jul 27. 11(1): 146
    SNX27-driven membrane localisation of OTULIN antagonises linear ubiquitination and NF-κB signalling activation.
    Ruona Shi, Xue Shi, Dajiang Qin, Shibing Tang, Michiel Vermeulen, Xiaofei Zhang.
       BACKGROUND: Linear ubiquitination is a novel type of ubiquitination that plays important physiological roles in signalling pathways such as tumour necrosis factor (TNF) signalling. However, little is known about the regulatory mechanisms of linear ubiquitination, except the well-described enzymatic regulators E3 ligase linear ubiquitin chain assembly complex (LUBAC) and deubiquitinase OTULIN.
    RESULTS: Previously, we identified SNX27, a member of the sorting nexin family protein, as a selective linear ubiquitin chain interactor in mass spectrometry-based ubiquitin interaction screening. Here, we demonstrated that the interaction between the linear ubiquitin chain and SNX27 is mediated by the OTULIN. Furthermore, we found that SNX27 inhibits LUBAC-mediated linear ubiquitin chain formation and TNFα-induced signalling activation. Mechanistic studies showed that, upon TNFα stimulation, OTULIN-SNX27 is localised to membrane-associated TNF receptor complex, where OTULIN deubiquitinates the linear polyubiquitin chain that formed by the LUBAC complex. Significantly, chemical inhibition of SNX27-retromer translocation by cholera toxin inhibits OTULIN membrane localization.
    CONCLUSIONS: In conclusion, our study demonstrated that SNX27 inhibits TNFα induced NF-κB signalling activation via facilitating OTULIN to localize to TNF receptor complex.
    Keywords:  Interaction; Linear ubiquitination; Localisation; NF-κB; OTULIN; SNX27
    DOI:  https://doi.org/10.1186/s13578-021-00659-5
  12. FASEB J. 2021 Aug;35(8): e21800
    Cullin 2-RBX1 E3 ligase and USP2 regulate antithrombin ubiquitination and stability.
    Dacai Xu, Jiawen Wu, Jinghong Chen, Liling Jiang, Juan Chen, Wenhao Bao, Xin Chen, Qianqian Yang, Xiaolan Zhang, Leyi Yao, Huabo Su, Jinbao Liu.
      Hemophilia A and B are congenital bleeding disorders caused by a deficiency in pro-coagulant factor VIII or IX that is treated by downregulation of antithrombin. However, the molecular mechanisms that regulate antithrombin expression remain poorly understood. Here, we identified Cullin 2 and USP2 (ubiquitin-specific peptidase-2) as novel regulators of antithrombin expression that act by modulating antithrombin ubiquitination. Inhibition of the proteasome caused accumulation of antithrombin and its ubiquitinated forms in HepG2 and SMMC7721 cells. Notably, inhibition of neddylation with MLN4924 suppressed both ubiquitination and degradation of antithrombin, which is recapitulated by silencing of the neddylation enzymes, NAE1, UBA3, and UBE2M, with small interfering RNA (siRNA). We identified Cullin 2 as the interaction partner of antithrombin, and siRNA-mediated Cullin 2 knockdown reduced antithrombin ubiquitination and increased antithrombin protein. We further found that USP2 interacted with antithrombin and regulated antithrombin expression, showing that overexpression of USP2 inhibits the ubiquitination and proteasomal clearance of antithrombin, whereas pharmacological inhibition or siRNA-mediated knockdown of USP2 downregulates antithrombin. Collectively, these results suggest that Cullin 2 E3 ubiquitin ligase and USP2 coordinately regulate antithrombin ubiquitination and degradation. Thus, targeting Cullin 2 and USP2 could be a potential strategy for treatment of hemophilia.
    Keywords:  coagulation; deubiquitinase; neddylation; ubiquitin
    DOI:  https://doi.org/10.1096/fj.202001146RR
  13. Nat Commun. 2021 Jul 30. 12(1): 4643
    Stress-primed secretory autophagy promotes extracellular BDNF maturation by enhancing MMP9 secretion.
    Silvia Martinelli, Elmira A Anderzhanova, Thomas Bajaj, Svenja Wiechmann, Frederik Dethloff, Katja Weckmann, Daniel E Heinz, Tim Ebert, Jakob Hartmann, Thomas M Geiger, Michael Döngi, Kathrin Hafner, Max L Pöhlmann, Lee Jollans, Alexandra Philipsen, Susanne V Schmidt, Ulrike Schmidt, Giuseppina Maccarrone, Valentin Stein, Felix Hausch, Christoph W Turck, Mathias V Schmidt, Anne-Kathrin Gellner, Bernhard Kuster, Nils C Gassen.
      The stress response is an essential mechanism for maintaining homeostasis, and its disruption is implicated in several psychiatric disorders. On the cellular level, stress activates, among other mechanisms, autophagy that regulates homeostasis through protein degradation and recycling. Secretory autophagy is a recently described pathway in which autophagosomes fuse with the plasma membrane rather than with lysosomes. Here, we demonstrate that glucocorticoid-mediated stress enhances secretory autophagy via the stress-responsive co-chaperone FK506-binding protein 51. We identify the matrix metalloproteinase 9 (MMP9) as one of the proteins secreted in response to stress. Using cellular assays and in vivo microdialysis, we further find that stress-enhanced MMP9 secretion increases the cleavage of pro-brain-derived neurotrophic factor (proBDNF) to its mature form (mBDNF). BDNF is essential for adult synaptic plasticity and its pathway is associated with major depression and posttraumatic stress disorder. These findings unravel a cellular stress adaptation mechanism that bears the potential of opening avenues for the understanding of the pathophysiology of stress-related disorders.
    DOI:  https://doi.org/10.1038/s41467-021-24810-5
  14. Nat Commun. 2021 07 29. 12(1): 4608
    Antibody toolkit reveals N-terminally ubiquitinated substrates of UBE2W.
    Christopher W Davies, Simon E Vidal, Lilian Phu, Jawahar Sudhamsu, Trent B Hinkle, Scott Chan Rosenberg, Frances-Rose Schumacher, Yi Jimmy Zeng, Carsten Schwerdtfeger, Andrew S Peterson, Jennie R Lill, Christopher M Rose, Andrey S Shaw, Ingrid E Wertz, Donald S Kirkpatrick, James T Koerber.
      The ubiquitin conjugating enzyme UBE2W catalyzes non-canonical ubiquitination on the N-termini of proteins, although its substrate repertoire remains unclear. To identify endogenous N-terminally-ubiquitinated substrates, we discover four monoclonal antibodies that selectively recognize tryptic peptides with an N-terminal diglycine remnant, corresponding to sites of N-terminal ubiquitination. Importantly, these antibodies do not recognize isopeptide-linked diglycine (ubiquitin) modifications on lysine. We solve the structure of one such antibody bound to a Gly-Gly-Met peptide to reveal the molecular basis for its selective recognition. We use these antibodies in conjunction with mass spectrometry proteomics to map N-terminal ubiquitination sites on endogenous substrates of UBE2W. These substrates include UCHL1 and UCHL5, where N-terminal ubiquitination distinctly alters deubiquitinase (DUB) activity. This work describes an antibody toolkit for enrichment and global profiling of endogenous N-terminal ubiquitination sites, while revealing functionally relevant substrates of UBE2W.
    DOI:  https://doi.org/10.1038/s41467-021-24669-6
  15. PLoS Pathog. 2021 Jul 27. 17(7): e1009771
    CD97 stabilises the immunological synapse between dendritic cells and T cells and is targeted for degradation by the Salmonella effector SteD.
    Ondrej Cerny, Camilla Godlee, Romina Tocci, Nancy E Cross, Haoran Shi, James C Williamson, Eric Alix, Paul J Lehner, David W Holden.
      The Salmonella enterica effector SteD depletes mature MHC class II (mMHCII) molecules from the surface of infected antigen-presenting cells through ubiquitination of the cytoplasmic tail of the mMHCII β chain. This requires the Nedd4 family HECT E3 ubiquitin ligase Wwp2 and a tumor-suppressing transmembrane protein adaptor Tmem127. Here, through a proteomic screen of dendritic cells, we found that SteD targets the plasma membrane protein CD97 for degradation by a similar mechanism. SteD enhanced ubiquitination of CD97 on K555 and mutation of this residue eliminated the effect of SteD on CD97 surface levels. We showed that CD97 localises to and stabilises the immunological synapse between dendritic cells and T cells. Removal of CD97 by SteD inhibited dendritic cell-T cell interactions and reduced T cell activation, independently of its effect on MHCII. Therefore, SteD suppresses T cell immunity by two distinct processes.
    DOI:  https://doi.org/10.1371/journal.ppat.1009771
  16. Cell Chem Biol. 2021 Jul 15. pii: S2451-9456(21)00312-3. [Epub ahead of print]
    Chemo-proteomics exploration of HDAC degradability by small molecule degraders.
    Yuan Xiong, Katherine A Donovan, Nicholas A Eleuteri, Nadia Kirmani, Hong Yue, Anthony Razov, Noah M Krupnick, Radosław P Nowak, Eric S Fischer.
      Targeted protein degradation refers to the use of small molecules that recruit a ubiquitin ligase to a target protein for ubiquitination and subsequent proteasome-dependent degradation. While degraders have been developed for many targets, key questions regarding degrader development and the consequences of acute pharmacological degradation remain, specifically for targets that exist in obligate multi-protein complexes. Here, we synthesize a pan-histone deacetylase (HDAC) degrader library for the chemo-proteomic exploration of acute degradation of a key class of chromatin-modifying enzymes. Using chemo-proteomics, we not only map the degradability of the zinc-dependent HDAC family identifying leads for targeting HDACs 1-8 and 10 but also explore important aspects of degrading epigenetic enzymes. We discover cell line-driven target specificity and that HDAC degradation often results in collateral loss of HDAC-containing repressive complexes. These findings potentially offer a new mechanism toward controlling chromatin structure, and our resource will facilitate accelerated degrader design and development for HDACs.
    Keywords:  E3 ligase; HDAC; IMiD; PROTAC; collateral degradation; degrader; targeted degradation; ubiquitin
    DOI:  https://doi.org/10.1016/j.chembiol.2021.07.002
  17. J Cell Sci. 2021 07 01. pii: jcs249771. [Epub ahead of print]134(13):
    SUMO proteases SENP3 and SENP5 spatiotemporally regulate the kinase activity of Aurora A.
    Bin Yu, Qiaoyu Lin, Chao Huang, Boyan Zhang, Ying Wang, Qing Jiang, Chuanmao Zhang, Jing Yi.
      Precise chromosome segregation is mediated by a well-assembled mitotic spindle, which requires balance of the kinase activity of Aurora A (AurA, also known as AURKA). However, how this kinase activity is regulated remains largely unclear. Here, using in vivo and in vitro assays, we report that conjugation of SUMO2 with AurA at K258 in early mitosis promotes the kinase activity of AurA and facilitates the binding with its activator Bora. Knockdown of the SUMO proteases SENP3 and SENP5 disrupts the deSUMOylation of AurA, leading to increased kinase activity and abnormalities in spindle assembly and chromosome segregation, which could be rescued by suppressing the kinase activity of AurA. Collectively, these results demonstrate that SENP3 and SENP5 deSUMOylate AurA to render spatiotemporal control on its kinase activity in mitosis. This article has an associated First Person interview with the first author of the paper.
    Keywords:  Aurora A; Mitosis; SENP3; SENP5; SUMOylation; Spindle assembly
    DOI:  https://doi.org/10.1242/jcs.249771
  18. Cancer Cell. 2021 Jul 22. pii: S1535-6108(21)00380-9. [Epub ahead of print]
    TRIM8 modulates the EWS/FLI oncoprotein to promote survival in Ewing sarcoma.
    Bo Kyung A Seong, Neekesh V Dharia, Shan Lin, Katherine A Donovan, Shasha Chong, Amanda Robichaud, Amy Conway, Amanda Hamze, Linda Ross, Gabriela Alexe, Biniam Adane, Behnam Nabet, Fleur M Ferguson, Björn Stolte, Emily Jue Wang, Jialin Sun, Xavier Darzacq, Federica Piccioni, Nathanael S Gray, Eric S Fischer, Kimberly Stegmaier.
      Fusion-transcription factors (fusion-TFs) represent a class of driver oncoproteins that are difficult to therapeutically target. Recently, protein degradation has emerged as a strategy to target these challenging oncoproteins. The mechanisms that regulate fusion-TF stability, however, are generally unknown. Using CRISPR-Cas9 screening, we discovered tripartite motif-containing 8 (TRIM8) as an E3 ubiquitin ligase that ubiquitinates and degrades EWS/FLI, a driver fusion-TF in Ewing sarcoma. Moreover, we identified TRIM8 as a selective dependency in Ewing sarcoma compared with >700 other cancer cell lines. Mechanistically, TRIM8 knockout led to an increase in EWS/FLI protein levels that was not tolerated. EWS/FLI acts as a neomorphic substrate for TRIM8, defining the selective nature of the dependency. Our results demonstrate that fusion-TF protein stability is tightly regulated and highlight fusion oncoprotein-specific regulators as selective therapeutic targets. This study provides a tractable strategy to therapeutically exploit oncogene overdose in Ewing sarcoma and potentially other fusion-TF-driven cancers.
    Keywords:  E3 ligases; EWS/FLI; Ewing sarcoma; TRIM8; fusion oncoproteins; neomorphic substrate; oncogene overdose; protein degradation; tumor dependency; ubiquitination
    DOI:  https://doi.org/10.1016/j.ccell.2021.07.003
  19. Nat Commun. 2021 Jul 30. 12(1): 4651
    The integrated stress response is tumorigenic and constitutes a therapeutic liability in KRAS-driven lung cancer.
    Nour Ghaddar, Shuo Wang, Bethany Woodvine, Jothilatha Krishnamoorthy, Vincent van Hoef, Cedric Darini, Urszula Kazimierczak, Nicolas Ah-Son, Helmuth Popper, Myriam Johnson, Leah Officer, Ana Teodósio, Massimo Broggini, Koren K Mann, Maria Hatzoglou, Ivan Topisirovic, Ola Larsson, John Le Quesne, Antonis E Koromilas.
      The integrated stress response (ISR) is an essential stress-support pathway increasingly recognized as a determinant of tumorigenesis. Here we demonstrate that ISR is pivotal in lung adenocarcinoma (LUAD) development, the most common histological type of lung cancer and a leading cause of cancer death worldwide. Increased phosphorylation of the translation initiation factor eIF2 (p-eIF2α), the focal point of ISR, is related to invasiveness, increased growth, and poor outcome in 928 LUAD patients. Dissection of ISR mechanisms in KRAS-driven lung tumorigenesis in mice demonstrated that p-eIF2α causes the translational repression of dual specificity phosphatase 6 (DUSP6), resulting in increased phosphorylation of the extracellular signal-regulated kinase (p-ERK). Treatments with ISR inhibitors, including a memory-enhancing drug with limited toxicity, provides a suitable therapeutic option for KRAS-driven lung cancer insofar as they substantially reduce tumor growth and prolong mouse survival. Our data provide a rationale for the implementation of ISR-based regimens in LUAD treatment.
    DOI:  https://doi.org/10.1038/s41467-021-24661-0
  20. Nat Commun. 2021 07 27. 12(1): 4552
    SNX19 restricts endolysosome motility through contacts with the endoplasmic reticulum.
    Amra Saric, Spencer A Freeman, Chad D Williamson, Michal Jarnik, Carlos M Guardia, Michael S Fernandopulle, David C Gershlick, Juan S Bonifacino.
      The ability of endolysosomal organelles to move within the cytoplasm is essential for the performance of their functions. Long-range movement involves coupling of the endolysosomes to motor proteins that carry them along microtubule tracks. This movement is influenced by interactions with other organelles, but the mechanisms involved are incompletely understood. Herein we show that the sorting nexin SNX19 tethers endolysosomes to the endoplasmic reticulum (ER), decreasing their motility and contributing to their concentration in the perinuclear area of the cell. Tethering depends on two N-terminal transmembrane domains that anchor SNX19 to the ER, and a PX domain that binds to phosphatidylinositol 3-phosphate on the endolysosomal membrane. Two other domains named PXA and PXC negatively regulate the interaction of SNX19 with endolysosomes. These studies thus identify a mechanism for controlling the motility and positioning of endolysosomes that involves tethering to the ER by a sorting nexin.
    DOI:  https://doi.org/10.1038/s41467-021-24709-1
  21. Neurotrauma Rep. 2021 ;2(1): 330-342
    Activation of the Protein Kinase R-Like Endoplasmic Reticulum Kinase (PERK) Pathway of the Unfolded Protein Response after Experimental Traumatic Brain Injury and Treatment with a PERK Inhibitor.
    Rhys D Brady, Stefanie Bird, Mujun Sun, Glenn R Yamakawa, Brendan P Major, Richelle Mychasiuk, Terence J O'Brien, Stuart J McDonald, Sandy R Shultz.
      Neurodegeneration after traumatic brain injury (TBI) is increasingly recognized as a key factor contributing to poor chronic outcomes. Activation (i.e., phosphorylation) of the protein kinase R-like endoplasmic reticulum kinase (PERK) pathway has been implicated in neurodegenerative conditions with pathological similarities to TBI and may be a potential target to improve TBI outcomes. Here, we aimed to determine whether a moderate TBI would induce activation of the PERK pathway and whether treatment with the PERK inhibitor, GSK2606414, would improve TBI recovery. Male mice were administered a lateral fluid percussion injury (FPI) or sham injury and were euthanized at either 2 h, 24 h, or 1 week post-injury (n = 5 per injury group and time point) to assess changes in the PERK pathway. In the injured cortex, there was increased phosphorylated-PERK at 2 h post-FPI and increased phosphorylation of eukaryotic translation initiation factor α at 24 h post-FPI. We next examined the effect of acute treatment with GSK2606414 on pathological and behavioral outcomes at 4 weeks post-injury. Thus, there were a total of four groups: sham + VEH (n = 9); sham + GSK4606414 (n = 10); FPI + VEH (n = 9); and FPI + GSK2606414 (n = 9). GSK2606414 (50 mg/kg) or vehicle treatment was delivered by oral gavage beginning at 30 min post-injury, followed by two further treatments at 12-h increments. There were no significant effects of GSK2606414 on any of the outcomes assessed, which could be attributable to several reasons. For example, activation of PERK may not be a significant contributor to the neurological consequences 4 weeks post-FPI in mice. Further research is required to elucidate the role of the PERK pathway in TBI and whether interventions that target this pathway are beneficial.
    Keywords:  GSK2606414; eukaryotic translation initiation factor α; fluid percussion injury; misfolded proteins; neurodegeneration; protein kinase RNA-like ER kinase
    DOI:  https://doi.org/10.1089/neur.2021.0001
  22. Elife. 2021 Jul 27. pii: e68958. [Epub ahead of print]10
    RTN3 inhibits RIG-I-mediated antiviral responses by impairing TRIM25-mediated K63-linked polyubiquitination.
    Ziwei Yang, Jun Wang, Bailin He, Xiaolin Zhang, Xiaojuan Li, Ersheng Kuang.
      Upon viral RNA recognition, the RIG-I signalosome continuously generates IFNs and cytokines, leading to neutrophil recruitment and inflammation. Thus, attenuation of excessive immune and inflammatory responses is crucial to restore immune homeostasis and prevent unwarranted damage, yet few resolving mediators have been identified. In the present study, we demonstrated that RTN3 is strongly upregulated during RNA viral infection and acts as an inflammation-resolving regulator. Increased RTN3 aggregates on the endoplasmic reticulum and interacts with both TRIM25 and RIG-I, subsequently impairing K63-linked polyubiquitination and resulting in both IRF3 and NF-κB inhibition. Rtn3 overexpression in mice causes an obvious inflammation resolving phenomenon when challenged with VSV, Rtn3-overexpressing mice display significantly decreased neutrophil numbers and inflammatory cell infiltration, which is accompanied by reduced tissue edema in the liver and thinner alveolar interstitium. Taken together, our findings identify RTN3 as a conserved negative regulator of immune and inflammatory responses and provide insights into the negative feedback that maintains immune and inflammatory homeostasis.
    Keywords:  RIG-I; RTN3; TRIM25; antiviral response; cell biology; human; immunology; inflammation; inflammatory resolution; mouse; virus
    DOI:  https://doi.org/10.7554/eLife.68958
  23. Elife. 2021 Jul 27. pii: e66768. [Epub ahead of print]10
    miR-1 coordinately regulates lysosomal v-ATPase and biogenesis to impact proteotoxicity and muscle function during aging.
    Isabelle Schiffer, Birgit Gerisch, Kazuto Kawamura, Raymond Laboy, Jennifer Hewitt, Martin Sebastian Denzel, Marcelo A Mori, Siva Vanapalli, Yidong Shen, Orsolya Symmons, Adam Antebi.
      Muscle function relies on the precise architecture of dynamic contractile elements, which must be fine-tuned to maintain motility throughout life. Muscle is also plastic, and remodeled in response to stress, growth, neural and metabolic inputs. The conserved muscle-enriched microRNA, miR-1, regulates distinct aspects of muscle development, but whether it plays a role during aging is unknown. Here we investigated Caenorhabditis elegans miR-1 in muscle function in response to proteostatic stress. mir-1 deletion improved mid-life muscle motility, pharyngeal pumping, and organismal longevity upon polyQ35 proteotoxic challenge. We identified multiple vacuolar ATPase subunits as subject to miR-1 control, and the regulatory subunit vha-13/ATP6V1A as a direct target downregulated via its 3'UTR to mediate miR-1 physiology. miR-1 further regulates nuclear localization of lysosomal biogenesis factor HLH-30/TFEB and lysosomal acidification. Our studies reveal that miR-1 coordinately regulates lysosomal v-ATPase and biogenesis to impact muscle function and health during aging.
    Keywords:  C. elegans; genetics; genomics; lysosomal v-ATPase; miR-1; polyglutamine; proteostasis; vha-13
    DOI:  https://doi.org/10.7554/eLife.66768
  24. Cell Rep. 2021 Jul 27. pii: S2211-1247(21)00845-7. [Epub ahead of print]36(4): 109428
    The prokaryotic ubiquitin-like protein presents poor cleavage sites for proteasomal degradation.
    Erez Zerbib, Shai Schlussel, Nir Hecht, Noy Bagdadi, Jerry Eichler, Eyal Gur.
      In an event reminiscent of eukaryotic ubiquitination, the bacterial prokaryotic ubiquitin-like protein (Pup)-proteasome system (PPS) marks target proteins for proteasomal degradation by covalently attaching Pup, the bacterial tagging molecule. Yet, ubiquitin is released from its conjugated target following proteasome binding, whereas Pup enters the proteasome and remains conjugated to the target. Here, we report that although Pup can be degraded by the bacterial proteasome, it lacks favorable 20S core particle (CP) cleavage sites and is thus a very poor 20S CP substrate. Reconstituting the PPS in vitro, we demonstrate that during pupylated protein degradation, Pup can escape unharmed and remain conjugated to a target-derived degradation fragment. Removal of this degradation fragment by Dop, a depupylase, facilitates Pup recycling and re-conjugation to a new target. This study thus offers a mechanistic model for Pup recycling and demonstrates how a lack of protein susceptibility to proteasome-mediated cleavage can play a mechanistic role in a biological system.
    Keywords:  AAA+; Dop; Mpa; Pup; proteasome; proteolysis
    DOI:  https://doi.org/10.1016/j.celrep.2021.109428
  25. Elife. 2021 Jul 30. pii: e63505. [Epub ahead of print]10
    McsB forms a gated kinase chamber to mark aberrant bacterial proteins for degradation.
    Bence Hajdusits, Marcin J Suskiewicz, Nikolas Hundt, Anton Meinhart, Robert Kurzbauer, Julia Leodolter, Philipp Kukura, Tim Clausen.
      In Gram-positive bacteria, the McsB protein arginine kinase is central to protein quality control, labelling aberrant molecules for degradation by the ClpCP protease. Despite its importance for stress response and pathogenicity, it is still elusive how the bacterial degradation labelling is regulated. Here, we delineate the mechanism how McsB targets aberrant proteins during stress conditions. Structural data reveal a self-compartmentalized kinase, in which the active sites are sequestered in a molecular cage. The 'closed' octamer interconverts with other oligomers in a phosphorylation-dependent manner and, contrary to these 'open' forms, preferentially labels unfolded proteins. In vivo data show that heat-shock triggers accumulation of higher-order oligomers, of which the octameric McsB is essential for surviving stress situations. The interconversion of open and closed oligomers represents a distinct regulatory mechanism of a degradation labeler, allowing the McsB kinase to adapt its potentially dangerous enzyme function to the needs of the bacterial cell.
    Keywords:  B. subtilis; biochemistry; chemical biology; molecular biophysics; structural biology
    DOI:  https://doi.org/10.7554/eLife.63505
  26. Autophagy. 2021 Jul 27. 1-3
    ATG7 safeguards human neural integrity.
    Jack J Collier, Monika Oláhová, Thomas G McWilliams, Robert W Taylor.
      ATG7 drives macroautophagy, hereafter "autophagy", by generating ATG12-ATG5 conjugates and lipidating Atg8 homologs including LC3. A pioneering body of work has defined the requirement of ATG7 for survival in mice and shown that neural-specific atg7 deletion causes neurodegeneration, but it has not been ascertained whether human life is compatible with ATG7 dysfunction. Recently, we defined the importance of ATG7 in human physiology by identifying twelve patients from five families harboring pathogenic, biallelic ATG7 variants causing a neurodevelopmental disorder. Patient fibroblasts show undetectable or severely diminished ATG7 protein levels, and biochemical assessment via autophagic flux and long-lived protein degradation assays demonstrated that attenuated autophagy underpins the pathology. Confirming the pathogenicity of patient variants, mouse cells expressing mutated ATG7 are unable to rescue LC3/Atg8 lipidation to wild-type levels. Our work defines mutated ATG7 as an important cause of human neurological disease and expands our understanding of autophagy in longevity and human health. We demonstrated that in certain circumstances, human survival with relatively mild phenotypes is possible even with undetectable levels of a nonredundant core autophagy protein.
    Keywords:  Autophagy; atg7; cell biology; disease; macroautophagy; molecular genetics; neurodegeneration
    DOI:  https://doi.org/10.1080/15548627.2021.1953267
  27. Am J Physiol Lung Cell Mol Physiol. 2021 07 28.
    Paramyxovirus replication induces the Hexosamine Biosynthetic Pathway and Mesenchymal Transition via the IRE1a-XBP1s arm of the Unfolded Protein Response.
    Dianhua Qiao, Melissa Skibba, Xiaofang Xu, Roberto P Garofalo, Yingxin Zhao, Allan R Brasier.
      The paramyoxviridae, Respiratory Syncytial Virus (RSV) and murine respirovirus are enveloped, negative-sense RNA viruses that are the etiological agents of vertebrate respiratory tract infections (LRTIs). We observe RSV infection in human small airway epithelial cells induces accumulation of glycosylated proteins within the ER, increased Glutamine-Fructose-6-Phosphate Transaminases (GFPT1/2), and accumulation of UDP-N-acetylglucosamine, indicating activation of the hexosamine biosynthetic pathway (HBP). RSV infection induces rapid formation of spliced X-box binding protein 1 (XBP1s) and processing of activating transcription factor 6 (ATF6). Using pathway selective inhibitors and shRNA silencing, we find that the inositol requiring enzyme (IRE1a)-XBP1 arm of the UPR is required not only for activation of the HBP, but also for expression of mesenchymal transition (EMT) through the Snail family transcriptional repressor 1 (SNAI1), ECM-remodeling proteins fibronectin (FN1) and matrix metalloproteinase 9 (MMP9). Probing RSV-induced open chromatin domains by ChIP, we find XBP1 binds and recruits RNA Polymerase II to the IL6, SNAI1 and MMP9 promoters and the intragenic super-enhancer of GFPT2. The UPR is sustained through RSV by an autoregulatory loop where XBP1 enhances Pol II binding to its own promoter. Similarly, we investigated the effects of murine respirovirus infection its natural host (mouse). Murine respirovirus induces mucosal growth factor response, EMT and the indicators of ECM remodeling in an IRE1α-dependent manner, which persists after viral clearance. These data suggest that IRE1a-XBP1s arm of the UPR pathway is responsible for paramyxovirus-induced metabolic adaptation and mucosal remodeling via EMT and ECM secretion.
    Keywords:  N glycosylation; Unfolded protein response; epithelial mesenchymal transition; hexosamine biosynthetic pathway; paramyxovirus
    DOI:  https://doi.org/10.1152/ajplung.00127.2021
  28. Nature. 2021 Jul 28.
    Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation.
    Qi Hu, Maria Victoria Botuyan, Debiao Zhao, Gaofeng Cui, Elie Mer, Georges Mer.
      The BRCA1-BARD1 tumour suppressor is an E3 ubiquitin ligase necessary for the repair of DNA double-strand breaks by homologous recombination1-10. The BRCA1-BARD1 complex localizes to damaged chromatin after DNA replication and catalyses the ubiquitylation of histone H2A and other cellular targets11-14. The molecular bases for the recruitment to double-strand breaks and target recognition of BRCA1-BARD1 remain unknown. Here we use cryo-electron microscopy to show that the ankyrin repeat and tandem BRCT domains in BARD1 adopt a compact fold and bind to nucleosomal histones, DNA and monoubiquitin attached to H2A amino-terminal K13 or K15, two signals known to be specific for double-strand breaks15,16. We further show that RING domains17 in BRCA1-BARD1 orient an E2 ubiquitin-conjugating enzyme atop the nucleosome in a dynamic conformation, primed for ubiquitin transfer to the flexible carboxy-terminal tails of H2A and variant H2AX. Our work reveals a regulatory crosstalk in which recognition of monoubiquitin by BRCA1-BARD1 at the N terminus of H2A blocks the formation of polyubiquitin chains and cooperatively promotes ubiquitylation at the C terminus of H2A. These findings elucidate the mechanisms of BRCA1-BARD1 chromatin recruitment and ubiquitylation specificity, highlight key functions of BARD1 in both processes and explain how BRCA1-BARD1 promotes homologous recombination by opposing the DNA repair protein 53BP1 in post-replicative chromatin18-22. These data provide a structural framework to evaluate BARD1 variants and help to identify mutations that drive the development of cancer.
    DOI:  https://doi.org/10.1038/s41586-021-03716-8
  29. J Cell Sci. 2021 Jul 15. pii: jcs253088. [Epub ahead of print]134(14):
    APC/CFZR-1 regulates centrosomal ZYG-1 to limit centrosome number.
    Jeffrey C Medley, Joseph R DiPanni, Luke Schira, Blake M Shaffou, Brandon M Sebou, Mi Hye Song.
      Aberrant centrosome numbers are associated with human cancers. The levels of centrosome regulators positively correlate with centrosome number. Thus, tight control of centrosome protein levels is critical. In Caenorhabditis elegans, the anaphase-promoting complex/cyclosome and its co-activator FZR-1 (APC/CFZR-1), a ubiquitin ligase, negatively regulates centrosome assembly through SAS-5 degradation. In this study, we report the C. elegans ZYG-1 (Plk4 in humans) as a potential substrate of APC/CFZR-1. Inhibiting APC/CFZR-1 or mutating a ZYG-1 destruction (D)-box leads to elevated ZYG-1 levels at centrosomes, restoring bipolar spindles and embryonic viability to zyg-1 mutants, suggesting that APC/CFZR-1 influences centrosomal ZYG-1 via the D-box motif. We also show the Slimb/βTrCP-binding (SB) motif is critical for ZYG-1 degradation, substantiating a conserved mechanism by which ZYG-1/Plk4 stability is regulated by the SKP1-CUL1-F-box (Slimb/βTrCP)-protein complex (SCFSlimb/βTrCP)-dependent proteolysis via the conserved SB motif in C. elegans. Furthermore, we show that co-mutating ZYG-1 SB and D-box motifs stabilizes ZYG-1 in an additive manner, suggesting that the APC/CFZR-1 and SCFSlimb/βTrCP ubiquitin ligases function cooperatively for timely ZYG-1 destruction in C. elegans embryos where ZYG-1 activity remains at threshold level to ensure normal centrosome number.
    Keywords:   C. elegans ; APC/C; Centrosome; FZR-1; Proteolysis; ZYG-1
    DOI:  https://doi.org/10.1242/jcs.253088
  30. Elife. 2021 Jul 29. pii: e68336. [Epub ahead of print]10
    Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity.
    Stephen M Blazie, Seika Takayanagi-Kiya, Katherine M McCulloch, Yishi Jin.
      The translation initiation complex eIF3 imparts specialized functions to regulate protein expression. However, understanding of eIF3 activities in neurons remains limited despite widespread dysregulation of eIF3 subunits in neurological disorders. Here, we report a selective role of the C. elegans RNA-binding subunit EIF-3.G in shaping the neuronal protein landscape. We identify a missense mutation in the conserved Zinc-Finger (ZF) of EIF-3.G that acts in a gain-of-function manner to dampen neuronal hyperexcitation. Using neuron type-specific seCLIP, we systematically mapped EIF-3.G-mRNA interactions and identified EIF-3.G occupancy on GC-rich 5'UTRs of a select set of mRNAs enriched in activity-dependent functions. We demonstrate that the ZF mutation in EIF-3.G alters translation in a 5'UTR dependent manner. Our study reveals an in vivo mechanism for eIF3 in governing neuronal protein levels to control neuronal activity states and offers insights into how eIF3 dysregulation contributes to neuronal disorders.
    Keywords:  C. elegans; genetics; genomics
    DOI:  https://doi.org/10.7554/eLife.68336
  31. Proc Natl Acad Sci U S A. 2021 Aug 03. pii: e2100862118. [Epub ahead of print]118(31):
    THAP1 modulates oligodendrocyte maturation by regulating ECM degradation in lysosomes.
    Dhananjay Yellajoshyula, Samuel S Pappas, Abigail E Rogers, Biswa Choudhury, Xylena Reed, Jinhui Ding, Mark R Cookson, Vikram G Shakkottai, Roman J Giger, William T Dauer.
      Mechanisms controlling myelination during central nervous system (CNS) maturation play a pivotal role in the development and refinement of CNS circuits. The transcription factor THAP1 is essential for timing the inception of myelination during CNS maturation through a cell-autonomous role in the oligodendrocyte lineage. Here, we demonstrate that THAP1 modulates the extracellular matrix (ECM) composition by regulating glycosaminoglycan (GAG) catabolism within oligodendrocyte progenitor cells (OPCs). Thap1 -/- OPCs accumulate and secrete excess GAGs, inhibiting their maturation through an autoinhibitory mechanism. THAP1 controls GAG metabolism by binding to and regulating the GusB gene encoding β-glucuronidase, a GAG-catabolic lysosomal enzyme. Applying GAG-degrading enzymes or overexpressing β-glucuronidase rescues Thap1 -/- OL maturation deficits in vitro and in vivo. Our studies establish lysosomal GAG catabolism within OPCs as a critical mechanism regulating oligodendrocyte development.
    Keywords:  CNS myelination; extracellular matrix; neurodevelopmental disease
    DOI:  https://doi.org/10.1073/pnas.2100862118
  32. EMBO J. 2021 Jul 26. e107336
    Host autophagy mediates organ wasting and nutrient mobilization for tumor growth.
    Rojyar Khezri, Petter Holland, Todd Andrew Schoborg, Ifat Abramovich, Szabolcs Takáts, Caroline Dillard, Ashish Jain, Fergal O'Farrell, Sebastian Wolfgang Schultz, William M Hagopian, Eduardo Martin Quintana, Rachel Ng, Nadja Sandra Katheder, Mohammed Mahidur Rahman, José Gerardo Teles Reis, Andreas Brech, Heinrich Jasper, Nasser M Rusan, Anne Hope Jahren, Eyal Gottlieb, Tor Erik Rusten.
      During tumor growth-when nutrient and anabolic demands are high-autophagy supports tumor metabolism and growth through lysosomal organelle turnover and nutrient recycling. Ras-driven tumors additionally invoke non-autonomous autophagy in the microenvironment to support tumor growth, in part through transfer of amino acids. Here we uncover a third critical role of autophagy in mediating systemic organ wasting and nutrient mobilization for tumor growth using a well-characterized malignant tumor model in Drosophila melanogaster. Micro-computed X-ray tomography and metabolic profiling reveal that RasV12 ; scrib-/- tumors grow 10-fold in volume, while systemic organ wasting unfolds with progressive muscle atrophy, loss of body mass, -motility, -feeding, and eventually death. Tissue wasting is found to be mediated by autophagy and results in host mobilization of amino acids and sugars into circulation. Natural abundance Carbon 13 tracing demonstrates that tumor biomass is increasingly derived from host tissues as a nutrient source as wasting progresses. We conclude that host autophagy mediates organ wasting and nutrient mobilization that is utilized for tumor growth.
    Keywords:   Drosophila ; autophagy; cancer cachexia; muscle; tumor; wasting
    DOI:  https://doi.org/10.15252/embj.2020107336
  33. Cell. 2021 Jul 19. pii: S0092-8674(21)00831-X. [Epub ahead of print]
    Ribosome ADP-ribosylation inhibits translation and maintains proteostasis in cancers.
    Sridevi Challa, Beman R Khulpateea, Tulip Nandu, Cristel V Camacho, Keun W Ryu, Hao Chen, Yan Peng, Jayanthi S Lea, W Lee Kraus.
      Defects in translation lead to changes in the expression of proteins that can serve as drivers of cancer formation. Here, we show that cytosolic NAD+ synthesis plays an essential role in ovarian cancer by regulating translation and maintaining protein homeostasis. Expression of NMNAT-2, a cytosolic NAD+ synthase, is highly upregulated in ovarian cancers. NMNAT-2 supports the catalytic activity of the mono(ADP-ribosyl) transferase (MART) PARP-16, which mono(ADP-ribosyl)ates (MARylates) ribosomal proteins. Depletion of NMNAT-2 or PARP-16 leads to inhibition of MARylation, increased polysome association and enhanced translation of specific mRNAs, aggregation of their translated protein products, and reduced growth of ovarian cancer cells. Furthermore, MARylation of the ribosomal proteins, such as RPL24 d RPS6, inhibits polysome assembly by stabilizing eIF6 binding to ribosomes. Collectively, our results demonstrate that ribosome MARylation promotes protein homeostasis in cancers by fine-tuning the levels of protein synthesis and preventing toxic protein aggregation.
    Keywords:  ADP-ribosylation; MARylation; NAD(+); NAD(+) sensor; NAD(+) synthesis; NMNAT-2; PARP-16; cancer; mRNA translation; mono(ADP-ribose); mono(ADP-ribosyl)ation; ovarian cancer; protein aggregation; protein synthesis; ribosomes; translation
    DOI:  https://doi.org/10.1016/j.cell.2021.07.005
  34. Sci Transl Med. 2021 Jul 28. pii: eaba9796. [Epub ahead of print]13(604):
    Chop/Ddit3 depletion in β cells alleviates ER stress and corrects hepatic steatosis in mice.
    Jing Yong, Vishal S Parekh, Shannon M Reilly, Jonamani Nayak, Zhouji Chen, Cynthia Lebeaupin, Insook Jang, Jiangwei Zhang, Thazha P Prakash, Hong Sun, Sue Murray, Shuling Guo, Julio E Ayala, Leslie S Satin, Alan R Saltiel, Randal J Kaufman.
      Type 2 diabetes (T2D) is a metabolic disorder characterized by hyperglycemia, hyperinsulinemia, and insulin resistance (IR). During the early phase of T2D, insulin synthesis and secretion by pancreatic β cells is enhanced, which can lead to proinsulin misfolding that aggravates endoplasmic reticulum (ER) protein homeostasis in β cells. Moreover, increased circulating insulin may contribute to fatty liver disease. Medical interventions aimed at alleviating ER stress in β cells while maintaining optimal insulin secretion are therefore an attractive therapeutic strategy for T2D. Previously, we demonstrated that germline Chop gene deletion preserved β cells in high-fat diet (HFD)-fed mice and in leptin receptor-deficient db/db mice. In the current study, we further investigated whether targeting Chop/Ddit3 specifically in murine β cells conferred therapeutic benefits. First, we showed that Chop deletion in β cells alleviated β cell ER stress and delayed glucose-stimulated insulin secretion (GSIS) in HFD-fed mice. Second, β cell-specific Chop deletion prevented liver steatosis and hepatomegaly in aged HFD-fed mice without affecting basal glucose homeostasis. Third, we provide mechanistic evidence that Chop depletion reduces ER Ca2+ buffering capacity and modulates glucose-induced islet Ca2+ oscillations, leading to transcriptional changes of ER chaperone profile ("ER remodeling"). Last, we demonstrated that a GLP1-conjugated Chop antisense oligonucleotide strategy recapitulated the reduction in liver triglycerides and pancreatic insulin content. In summary, our results demonstrate that Chop depletion in β cells provides a therapeutic strategy to alleviate dysregulated insulin secretion and consequent fatty liver disease in T2D.
    DOI:  https://doi.org/10.1126/scitranslmed.aba9796
  35. Leukemia. 2021 Jul 29.
    Small molecule inhibition of deubiquitinating enzyme JOSD1 as a novel targeted therapy for leukemias with mutant JAK2.
    Jing Yang, Ellen L Weisberg, Xiaoxi Liu, Robert S Magin, Wai Cheung Chan, Bin Hu, Nathan J Schauer, Shengzhe Zhang, Ilaria Lamberto, Laura Doherty, Chengcheng Meng, Martin Sattler, Lucia Cabal-Hierro, Eric Winer, Richard Stone, Jarrod A Marto, James D Griffin, Sara J Buhrlage.
      Mutations in the Janus Kinase 2 (JAK2) gene resulting in constitutive kinase activation represent the most common genetic event in myeloproliferative neoplasms (MPN), a group of diseases involving overproduction of one or more kinds of blood cells, including red cells, white cells, and platelets. JAK2 kinase inhibitors, such as ruxolitinib, provide clinical benefit, but inhibition of wild-type (wt) JAK2 limits their clinical utility due to toxicity to normal cells, and small molecule inhibition of mutated JAK2 kinase activity can lead to drug resistance. Here, we present a strategy to target mutated JAK2 for degradation, using the cell's intracellular degradation machinery, while sparing non-mutated JAK2. We employed a chemical genetics screen, followed by extensive selectivity profiling and genetic studies, to identify the deubiquitinase (DUB), JOSD1, as a novel regulator of mutant JAK2. JOSD1 interacts with and stabilizes JAK2-V617F, and inactivation of the DUB leads to JAK2-V617F protein degradation by increasing its ubiquitination levels, thereby shortening its protein half-life. Moreover, targeting of JOSD1 leads to the death of JAK2-V617F-positive primary acute myeloid leukemia (AML) cells. These studies provide a novel therapeutic approach to achieving selective targeting of mutated JAK2 signaling in MPN.
    DOI:  https://doi.org/10.1038/s41375-021-01336-9
  36. Nature. 2021 Jul 28.
    BARD1 reads H2A lysine 15 ubiquitination to direct homologous recombination.
    Jordan R Becker, Gillian Clifford, Clara Bonnet, Anja Groth, Marcus D Wilson, J Ross Chapman.
      Protein ubiquitination at sites of DNA double-strand breaks (DSBs) by RNF168 recruits BRCA1 and 53BP11,2, which are mediators of the homologous recombination and non-homologous end joining DSB repair pathways, respectively3. Non-homologous end joining relies on 53BP1 binding directly to ubiquitinated lysine 15 on H2A-type histones (H2AK15ub)4,5 (which is an RNF168-dependent modification6), but how RNF168 promotes BRCA1 recruitment and function remains unclear. Here we identify a tandem BRCT-domain-associated ubiquitin-dependent recruitment motif (BUDR) in BRCA1-associated RING domain protein 1 (BARD1) (the obligate partner protein of BRCA1) that, by engaging H2AK15ub, recruits BRCA1 to DSBs. Disruption of the BUDR of BARD1 compromises homologous recombination and renders cells hypersensitive to PARP inhibition and cisplatin. We further show that BARD1 binds nucleosomes through multivalent interactions: coordinated binding of H2AK15ub and unmethylated H4 lysine 20 by its adjacent BUDR and ankyrin repeat domains, respectively, provides high-affinity recognition of DNA lesions in replicated chromatin and promotes the homologous recombination activities of the BRCA1-BARD1 complex. Finally, our genetic epistasis experiments confirm that the need for BARD1 chromatin-binding activities can be entirely relieved upon deletion of RNF168 or 53BP1. Thus, our results demonstrate that by sensing DNA-damage-dependent and post-replication histone post-translation modification states, BRCA1-BARD1 complexes coordinate the antagonization of the 53BP1 pathway with promotion of homologous recombination, establishing a simple paradigm for the governance of the choice of DSB repair pathway.
    DOI:  https://doi.org/10.1038/s41586-021-03776-w
  37. FEBS Lett. 2021 Jul 27.
    Sequence requirements of the FFAT-like motif for specific binding to VAP-A are revealed by NMR.
    Kyoko Furuita, Marina Hiraoka, Kentaro Hanada, Toshimichi Fujiwara, Chojiro Kojima.
      The endoplasmic reticulum transmembrane protein vesicle-associated membrane protein-associated protein (VAP) plays a central role in the formation and function of membrane contact sites (MCS) through its interactions with proteins. The major sperm protein (MSP) domain of VAP binds to a variety of sequences which are referred to as FFAT-like motifs. In this study, we investigated the interactions of eight peptides containing FFAT-like motifs with the VAP-A MSP domain (VAP-AMSP ) by solution NMR. Six of eight peptides specifically bound to VAP-A. Furthermore, we found that the RNA-dependent RNA polymerase of severe acute respiratory syndrome coronavirus 2 has an FFAT-like motif which specifically binds to VAP-AMSP as well as other FFAT-like motifs. Our results will contribute to the discovery of new VAP interactors.
    Keywords:  FFAT motif; FFAT-like motif; SARS-CoV-2; VAMP-associated protein; protein-protein interaction; solution NMR
    DOI:  https://doi.org/10.1002/1873-3468.14166
  38. Front Cell Dev Biol. 2021 ;9 676789
    Ufbp1, a Key Player of Ufm1 Conjugation System, Protects Against Ketosis-Induced Liver Injury via Suppressing Smad3 Activation.
    Fanghui Chen, Le Sheng, Chenjie Xu, Jun Li, Ilyas Ali, Honglin Li, Yafei Cai.
      The dairy cattle suffer from severe liver dysfunction during the pathogenesis of ketosis. The Ufm1 conjugation system is crucial for liver development and homeostasis. Ufm1 binding protein (Ufbp1) is a putative Ufm1 target and an integral component, but its role in ketosis-induced liver injury is unclear so far. The purpose of this study is to explore the key role of Ufbp1 in liver fibrosis caused by ketosis in vivo and in vitro. Liver tissues were collected from ketotic cows and Ufbp1 conditional knockout (CKO) mice in vivo. However, Ufbp1 -/- mouse embryonic fibroblast cells and Hela cells were used for in vitro validation. Subsequently, various assays were performed to reveal the underlying molecular mechanisms of the Ufbp1 protective effect. In this study, hepatic fibrosis, endoplasmic reticulum (ER) stress, and apoptosis were reported in the liver of ketotic cows, fibrotic markers (alpha-smooth muscle actin, Collagen1) and ER stress markers (glucose-regulated protein 78, CEBP homologous protein) were upregulated remarkably, and the apoptosis-related genes (Bcl2, Bax) were in line with expectations. Interestingly, Ufbp1 expression was almost disappeared, and Smad2/Smad3 protein was largely phosphorylated in the liver of ketotic cows, but Ufbp1 deletion caused Smad3 phosphorylation apparently, rather than Smad2, and elevated ER stress was observed in the CKO mice model. At the cellular level, Ufbp1 deficiency led to serious fibrotic and ER stress response, Smad3 was activated by phosphorylation significantly and then was translocated into the nucleus, whereas p-Smad2 was largely unaffected in embryonic fibroblast cells. Ufbp1 overexpression obviously suppressed Smad3 phosphorylation in Hela cells. Ufbp1 was found to be in full combination with Smad3 using endogenous immunoprecipitation. Taken together, our findings suggest that downregulation or ablation of Ufbp1 leads to Smad3 activation, elevated ER stress, and hepatocyte apoptosis, which in turn causes liver fibrosis. Ufbp1 plays a protective role in ketosis-induced liver injury.
    Keywords:  ER stress; Smad3 activation; Ufbp1; hepatic fibrosis; ketosis
    DOI:  https://doi.org/10.3389/fcell.2021.676789
  39. NAR Cancer. 2020 Sep;2(3): zcaa020
    Translation reprogramming by eIF3 linked to glioblastoma resistance.
    Juliette Bertorello, Julie Sesen, Julia Gilhodes, Solène Evrard, Monique Courtade-Saïdi, Meera Augustus, Emmanuelle Uro-Coste, Christine Toulas, Elizabeth Cohen-Jonathan Moyal, Catherine Seva, Erik Dassi, Anne Cammas, Nicolas Skuli, Stefania Millevoi.
      Intrinsic resistance to current therapies, leading to dismal clinical outcomes, is a hallmark of glioblastoma multiforme (GBM), the most common and aggressive brain tumor. Understanding the underlying mechanisms of such malignancy is, therefore, an urgent medical need. Deregulation of the protein translation machinery has been shown to contribute to cancer initiation and progression, in part by driving selective translational control of specific mRNA transcripts involved in distinct cancer cell behaviors. Here, we focus on eIF3, a multimeric complex with a known role in the initiation of translation and that is frequently deregulated in cancer. Our results show that the deregulated expression of eIF3e, the e subunit of eIF3, in specific GBM regions could impinge on selective protein synthesis impacting the GBM outcome. In particular, eIF3e restricts the expression of proteins involved in the response to cellular stress and increases the expression of key functional regulators of cell stemness. Such a translation program can therefore serve as a double-edged sword promoting GBM tumor growth and resistance to radiation.
    DOI:  https://doi.org/10.1093/narcan/zcaa020
  40. Allergy. 2021 Jul 27.
    IRE1 and PERK signaling regulates inflammatory responses in a murine model of contact hypersensitivity.
    Fabian Gendrisch, Lukas Völkel, Melanie Fluck, Petya Apostolova, Robert Zeiser, Thilo Jakob, Stefan F Martin, Philipp R Esser.
       BACKGROUND: Contact sensitizers may interfere with correct protein folding. Generation of un-/misfolded proteins can activate the IRE-1 or PERK-signaling pathways initiating the unfolded protein response (UPR) and thereby determine inflammatory immune responses. We have analyzed the effect of sensitizers with different potencies on the induction of UPR activation/inhibition and the subsequent generation of a pro-inflammatory micromilieu in vitro as well as the effect of UPR modulation on the inflammatory response in the murine contact hypersensitivity (CHS) in vivo.
    METHODS: Semi-quantitative and quantitative PCR, fluorescence microscopy, ELISA, NF-κB activation and translocation assays, DC/keratinocyte co-culture assay, FACS and in vivo CHS experiments were performed.
    RESULTS: Sensitizers and irritants activate IRE-1 and PERK in murine and human keratinocytes. Synergistic effects occur after combination of different weak sensitizers / addition of irritants. Moreover, tolerogenic dinitrothiocyanobenzene can be converted into a strong sensitizer by pre-activation of the UPR. Blocking UPR signaling results in decreased NF-κB activation and cytokine production in keratinocytes and in activation marker downregulation in a HaCaT/THP-1 co-culture. Interestingly, not only systemic but also topical application of UPR inhibitors abrogates CHS responses in vivo.
    CONCLUSION: These observations highlight an important role of the UPR in determination of the inflammatory response in vitro and in vivo further underlining the importance of tissue stress- and damage responses in the development of ACD and provide mechanistically based concepts as a basis for the development of new therapeutic approaches to treat allergic contact dermatitis.
    Keywords:  Allergic contact dermatitis; Contact hypersensitivity; Inflammation; Unfolded protein response
    DOI:  https://doi.org/10.1111/all.15024
  41. Blood. 2021 Jul 30. pii: blood.2020010342. [Epub ahead of print]
    The secreted tyrosine kinase VLK is essential for normal platelet activation and thrombus formation.
    Leila Denise Revollo, Glenn Merrill-Skoloff, Karen De Ceunynck, James R Dilks, Shihui Guo, Mattia Renato Bordoli, Christian G Peters, Leila Noetzli, Andreia Marina Ionescu, Vicki Rosen, Joseph E Italiano, Malcolm Whitman, Robert Flaumenhaft.
      Tyrosine phosphorylation of extracellular proteins is observed in cell cultures and in vivo, but little is known about the functional roles of tyrosine phosphorylation of extracellular proteins. Vertebrate Lonesome Kinase (VLK) is a broadly expressed secretory pathway tyrosine kinase present in platelet ɑ-granules. It is released from platelets upon activation and phosphorylates substrates extracellularly. Its role in platelet function, however, has not been previously studied. In human platelets, we identified phosphorylated tyrosines mapped to luminal or extracellular domains of transmembrane and secreted proteins implicated in the regulation of platelet activation. To determine the role of VLK in extracellular tyrosine phosphorylation and platelet function, we generated mice with a megakaryocyte/platelet-specific deficiency of VLK. Platelets from these mice are normal in abundance and morphology, but have significant changes in function both in vitro and in vivo. Resting and thrombin-stimulated VLK-deficient platelets demonstrate a significant decrease of several tyrosine phosphobands. Functional testing of VLK-deficient platelets shows decreased PAR4- and collagen-mediated platelet aggregation, but normal responses to ADP. Dense granule and a-granule release are reduced in these platelets. Furthermore, VLK-deficient platelets exhibit decreased PAR4-mediated Akt (S473) and Erk1/2 (T202/Y204) phosphorylation, indicating altered proximal signaling. In vivo, mice lacking VLK in megakaryocytes/platelets demonstrate strongly reduced platelet accumulation and fibrin formation following laser-injury of cremaster arterioles compared to controls, but normal bleeding times. These studies demonstrate that the secretory pathway tyrosine kinase VLK is critical for stimulus-dependent platelet activation and thrombus formation, providing the first evidence that a secreted protein kinase is required for normal platelet function.
    DOI:  https://doi.org/10.1182/blood.2020010342
  42. Mol Metab. 2021 Jul 22. pii: S2212-8778(21)00156-3. [Epub ahead of print] 101309
    Hepatic mTORC1 signaling activates ATF4 as part of its metabolic response to feeding and insulin.
    Vanessa Byles, Yann Cormerais, Krystle Kalafut, Victor Barrera, James E Hughes Hallett, Shannan Ho Sui, John M Asara, Christopher M Adams, Gerta Hoxhaj, Issam Ben-Sahra, Brendan D Manning.
       OBJECTIVE: The mechanistic target of rapamycin complex 1 (mTORC1) is dynamically regulated by fasting and feeding cycles in the liver to promote protein and lipid synthesis while suppressing autophagy. However, beyond these functions, the metabolic response of the liver to feeding and insulin signaling orchestrated by mTORC1 remains poorly defined. Here, we determine whether ATF4, a stress responsive transcription factor recently found to be independently regulated by mTORC1 signaling in proliferating cells, is responsive to hepatic mTORC1 signaling to alter hepatocyte metabolism.
    METHODS: ATF4 protein levels and expression of canonical gene targets were analyzed in the liver following fasting and physiological feeding in the presence or absence of the mTORC1 inhibitor rapamycin. Primary hepatocytes from wild-type or liver-specific Atf4 knockout (LAtf4KO) mice were used to characterize the effects of insulin-stimulated mTORC1-ATF4 function on hepatocyte gene expression and metabolism. Both unbiased steady-state metabolomics and stable-isotope tracing methods were employed to define mTORC1 and ATF4-dependent metabolic changes. RNA-sequencing was used to determine global changes in feeding-induced transcripts in the livers of wild-type versus LAtf4KO mice.
    RESULTS: We demonstrate that ATF4 and its metabolic gene targets are stimulated by mTORC1 signaling in the liver in response to feeding and in a hepatocyte-intrinsic manner by insulin. While we demonstrate that de novo purine and pyrimidine synthesis is stimulated by insulin through mTORC1 signaling in primary hepatocytes, this regulation was independent of ATF4. Metabolomics and metabolite tracing studies revealed that insulin-mTORC1-ATF4 signaling stimulates pathways of non-essential amino acid synthesis in primary hepatocytes, including those of alanine, aspartate, methionine, and cysteine, but not serine.
    CONCLUSION: The results demonstrate that ATF4 is a novel metabolic effector of mTORC1 in liver, extending the molecular consequences of feeding and insulin-induced mTORC1 signaling in this key metabolic tissue to the control of amino acid metabolism.
    Keywords:  ATF4; feeding; insulin; liver; mTORC1; methionine metabolism
    DOI:  https://doi.org/10.1016/j.molmet.2021.101309
  43. Cancer Lett. 2021 Jul 26. pii: S0304-3835(21)00360-8. [Epub ahead of print]
    ANXA10 promotes melanoma metastasis by suppressing E3 ligase TRIM41-directed PKD1 degradation.
    Xuerui Zhang, Zhaoqing Hu, Xinran Wang, Lin Li, Banghui Zhu, Xiaolei Lin, Jing Zhang, Zichun Hua.
      Melanoma is a highly metastatic cancer that requires effective and targeted curative therapy. Annexin A10 (ANXA10), a member of the annexin family, is a calcium- and phospholipid-binding protein. Considerable evidence indicates that ANXA10 is involved in tumour progression, but little is known about its role in melanoma development. In this study, we find that ANXA10 expression is significantly upregulated, and correlates with melanoma progression. ANXA10 knockout profoundly reduces cell migration and the metastatic activity of melanoma. In addition, ANXA10 knockout induces the N- to E-cadherin switch by upregulating SMAD6, an inhibitory SMAD in the TGF-β/SMAD pathway. The negative regulation of SMAD6 by ANXA10 is dependent on PKD1. ANXA10 interacts with PKD1 and inhibits E3 ligase TRIM41-targeted PKD1 degradation. In B16F10 melanoma cells, protein levels of ANXA10 and PKD1 are inversely correlated with SMAD6 level, but correlated with cell migration. Interestingly, ANXA10 and SMAD6 levels are inversely correlated in clinical samples of melanoma progression. Our findings suggest that the ANXA10-PKD1-SMAD6 axis is a new target for therapeutic strategies against melanoma metastasis.
    Keywords:  ANXA10; Cadherin switch; Melanoma metastasis; PKD1; SMAD6
    DOI:  https://doi.org/10.1016/j.canlet.2021.07.033
  44. J Clin Invest. 2021 Jul 29. pii: 147836. [Epub ahead of print]
    Inhibition of the unfolded protein response reduces arrhythmic risk after myocardial infarction.
    Man Liu, Hong Liu, Preethy Parthiban, Gyeoung-Jin Kang, Guangbin Shi, Feng Feng, Anyu Zhou, Lianzhi Gu, Courtney Karnopp, Elena G Tolkacheva, Samuel C Dudley.
      Ischemic cardiomyopathy is associated with an increased risk of sudden death, activation of the unfolded protein response (UPR), and reductions in multiple cardiac ion channels. When activated, the protein kinase-like ER kinase (PERK) branch of the UPR reduces protein translation and abundance. We hypothesized that PERK inhibition could prevent ion channel downregulation and reduce arrhythmic risk after myocardial infarct (MI). MI induced by coronary artery ligation resulted in mice exhibited reduced ion channel levels, ventricular tachycardia (VT), and prolonged corrected intervals between the Q and T waves of the ECGs (QTc). Protein levels of major cardiac ion channels were decreased. MI cardiomyocytes showed significantly prolonged action potential duration and decreased maximum upstroke velocity. Cardiac-specific PERK knockout (PERKKO) reduced electrical remodeling in response to MI with shortened QTc intervals, less VT episodes, and higher survival rates (P<0.05 vs. MI). Pharmacological PERK inhibition had similar effects. In conclusion, activated PERK during MI contributed to arrhythmic risk by downregulation of select cardiac ion channels. PERK inhibition prevented these changes and reduced arrhythmic risk. These results suggest that ion channel downregulation during MI is a fundamental arrhythmic mechanism and maintaining ion channel levels is antiarrhythmic.
    Keywords:  Arrhythmias; Cardiology; Cell stress; Ion channels
    DOI:  https://doi.org/10.1172/JCI147836
  45. Elife. 2021 Jul 28. pii: e70560. [Epub ahead of print]10
    Processing of the ribosomal ubiquitin-like fusion protein FUBI-eS30/FAU is required for 40S maturation and depends on USP36.
    Jasmin van den Heuvel, Caroline Ashiono, Ludovic C Gillet, Kerstin Dörner, Emanuel Wyler, Ivo Zemp, Ulrike Kutay.
      In humans and other holozoan organisms, the ribosomal protein eS30 is synthesized as a fusion protein with the ubiquitin-like protein FUBI. However, FUBI is not part of the mature 40S ribosomal subunit and cleaved off by an as-of-yet unidentified protease. How FUBI-eS30 processing is coordinated with 40S subunit maturation is unknown. To study the mechanism and importance of FUBI-eS30 processing, we expressed non-cleavable mutants in human cells, which affected late steps of cytoplasmic 40S maturation, including the maturation of 18S rRNA and recycling of late-acting ribosome biogenesis factors. Differential affinity purification of wild-type and non-cleavable FUBI-eS30 mutants identified the deubiquitinase USP36 as a candidate FUBI-eS30 processing enzyme. Depletion of USP36 by RNAi or CRISPRi indeed impaired FUBI-eS30 processing and moreover, purified USP36 cut FUBI-eS30 in vitro. Together, these data demonstrate the functional importance of FUBI-eS30 cleavage and identify USP36 as a novel protease involved in this process.
    Keywords:  biochemistry; cell biology; chemical biology; human
    DOI:  https://doi.org/10.7554/eLife.70560
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