bims-apauto Biomed News
on Apoptosis and autophagy
Issue of 2023–05–14
nine papers selected by
Su Hyun Lee, Harvard University
  1. Vps13 is required for efficient autophagy in Saccharomyces cerevisiae.
  2. Identifying E3 ligase substrates with quantitative degradation proteomics.
  3. Autophagy-dependent expression of osteopontin and its downstream Stat3 signaling contributes to lymphatic malformation progression to lymphangiosarcoma.
  4. FBXL4 suppresses mitophagy by restricting the accumulation of NIX and BNIP3 mitophagy receptors.
  5. ATG16L1 is equipped with two distinct WIPI2-binding sites to drive autophagy.
  6. Secretory autophagy-promoted cargo exocytosis requires active RAB37.
  7. Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2.
  8. How autophagy, a potential therapeutic target, regulates intestinal inflammation.
  9. TIM23 facilitates PINK1 activation by safeguarding against OMA1-mediated degradation in damaged mitochondria.
  1. Contact (Thousand Oaks). 2022 Jan-Dec;5:5
    Vps13 is required for efficient autophagy in Saccharomyces cerevisiae.
    Yuchen Lei, Xin Wen, Daniel J Klionsky.
      Vps13 is a large, conserved protein that transports lipids between membranes. Its localization at multiple organelle membranes and membrane contact sites suggests its important physiological roles. In addition, the high correlation of mutant VPS13 with certain diseases, especially those involving neurodegeneration, makes this protein of considerable biomedical interest. Taking advantage of the fact that yeasts only have one Vps13 protein, the roles of yeast Vps13 have been well studied. However, whether and how Vps13 functions in macroautophagy/autophagy, a process of degradation of cytoplasmic cargoes, have been elusive questions. In this paper, we investigated the role of Vps13 in both non-selective and selective autophagy and found that this protein participates in non-selective autophagy, reticulophagy and pexophagy, but not mitophagy, and that Vps13 plays a role in the late stage of autophagy.
    Keywords:  Membrane; mitophagy; protein trafficking; stress; vacuole
    DOI:  https://doi.org/10.1177/25152564221136388
  2. Chembiochem. 2023 May 11. e202300108
    Identifying E3 ligase substrates with quantitative degradation proteomics.
    Victoria N Jordan, Alban Ordureau, Heeseon An.
      Controlled protein degradation by the ubiquitinproteasome pathway is critical for almost all cellular processes. E3 ubiquitin ligases are responsible for targeting proteins for ubiquitylation and subsequent proteasomal degradation with spatial and temporal precision. While studies have revealed various E3-substrate pairs involved in distinct biological processes, the complete substrate profiles of individual E3 ligases are largely unknown. Here we report a new approach to identify substrates of an E3 ligase for proteasomal degradation using unnatural amino acid incorporation pulse-chase proteomics (degradomics). Applying this approach, we determine the steadystate substrates of the C - t erminal to L is H (CTLH) E3 ligase, a multicomponent complex with poorly defined substrates. By comparing the proteome degradation profiles of active and inactive CTLH-expressing cells, we successfully identify previously known and new potential substrates of CTLH ligase. Altogether, degradomics can comprehensively identify degradation substrates of an E3 ligase, which can be adapted for other E3 ligases in various cellular contexts.
    Keywords:  Ubiquitin, The Ubiquitin Proteasome System, Protein degradation, Protein half-life, CTLH
    DOI:  https://doi.org/10.1002/cbic.202300108
  3. Autophagy. 2023 May 11.
    Autophagy-dependent expression of osteopontin and its downstream Stat3 signaling contributes to lymphatic malformation progression to lymphangiosarcoma.
    Fuchun Yang, Jun-Lin Guan.
      Lymphatic malformation (LM) is a vascular anomaly from lymphatic endothelial cells (ECs), and a fraction of the patients could progress to the deadly malignant lymphangiosarcoma (LAS). Using genetic tools to delete an essential autophagy gene Rb1cc1/FIP200 or its mutation specifically blocking its autophagy function, we demonstrated that autophagy inhibition abrogated LM progression to LAS although not affecting LM formation in our recently developed mouse model of LAS. Analysis of the mouse models in vivo and vascular tumor cells in vitro showed that autophagy inhibition reduced vascular tumor cell proliferation in vitro and tumorigenicity in vivo without affecting mTORC1 signaling as an oncogenic driver directly. Transcriptional profiling of autophagy-deficient tumor cells and further mechanistic studies revealed a role for osteopontin (OPN) and its downstream Jak/Stat3 signaling in mediating regulation of vascular tumor cells by autophagy. Together, these results support potential new prophylactic strategies to targeting autophagy and/or its downstream OPN expression to prevent progression of the benign LM to the malignant and deadly LAS.
    Keywords:  Lymphangiosarcoma; Osteopontin; RB1CC1/FIP200; Stat3; autophagy; endothelial cells; lymphatic malformation
    DOI:  https://doi.org/10.1080/15548627.2023.2213527
  4. EMBO J. 2023 May 10. e112767
    FBXL4 suppresses mitophagy by restricting the accumulation of NIX and BNIP3 mitophagy receptors.
    Giang Thanh Nguyen-Dien, Keri-Lyn Kozul, Yi Cui, Brendan Townsend, Prajakta Gosavi Kulkarni, Soo Siang Ooi, Antonio Marzio, Nissa Carrodus, Steven Zuryn, Michele Pagano, Robert G Parton, Michael Lazarou, S Sean Millard, Robert W Taylor, Brett M Collins, Mathew Jk Jones, Julia K Pagan.
      To maintain both mitochondrial quality and quantity, cells selectively remove damaged or excessive mitochondria through mitophagy, which is a specialised form of autophagy. Mitophagy is induced in response to diverse conditions, including hypoxia, cellular differentiation and mitochondrial damage. However, the mechanisms that govern the removal of specific dysfunctional mitochondria under steady-state conditions to fine-tune mitochondrial content are not well understood. Here, we report that SCFFBXL4 , an SKP1/CUL1/F-box protein ubiquitin ligase complex, localises to the mitochondrial outer membrane in unstressed cells and mediates the constitutive ubiquitylation and degradation of the mitophagy receptors NIX and BNIP3 to suppress basal levels of mitophagy. We demonstrate that the pathogenic variants of FBXL4 that cause encephalopathic mtDNA depletion syndrome (MTDPS13) do not efficiently interact with the core SCF ubiquitin ligase machinery or mediate the degradation of NIX and BNIP3. Thus, we reveal a molecular mechanism whereby FBXL4 actively suppresses mitophagy by preventing NIX and BNIP3 accumulation. We propose that the dysregulation of NIX and BNIP3 turnover causes excessive basal mitophagy in FBXL4-associated mtDNA depletion syndrome.
    Keywords:  BNIP3; FBXL4; NIX/BNIP3L; mitochondria; mitophagy
    DOI:  https://doi.org/10.15252/embj.2022112767
  5. Autophagy. 2023 May 10.
    ATG16L1 is equipped with two distinct WIPI2-binding sites to drive autophagy.
    Xinyu Gong, Lifeng Pan.
      The recruitment of ATG12-ATG5-ATG16L1 complex to phagophore mediated by the specific interaction between ATG16L1 and WIPI2, is pivotal to the formation of autophagosomes during macroautophagy. Recently, we reported that ATG16L1 contains two distinct WIPI2-binding sites, the previously reported WIPI2-binding site (WBS1), and the newly identified site (WBS2). By determining the crystal structures of WIPI2 with ATG16L1 WBS1 and WBS2 respectively, we uncovered that, unlike ATG16L1 WBS1, ATG16L1 WBS2 and its binding mechanism to WIPI2 are conserved from yeast to mammals. Using cell-based functional assays, we further demonstrated that the integrity of two WIPI2-binding sites of ATG16L1 is essential for normal autophagic flux. In summary, our study provided mechanistic insights into the interaction of two key autophagic proteins, ATG16L1 and WIPI2, and revealed a dual-binding-site mode adopted by ATG16L1 to associate with WIPI2.
    Keywords:  ATG16L1; Macroautophagy; WIPI2; autophagosome
    DOI:  https://doi.org/10.1080/15548627.2023.2213038
  6. Autophagy. 2023 May 12. 1-2
    Secretory autophagy-promoted cargo exocytosis requires active RAB37.
    Shan-Ying Wu, Yi-Ching Wang, Roberto Zuchini, Kai-Ying Lan, Hsiao-Sheng Liu, Sheng-Hui Lan.
      RAB37 GTPase regulates cargo exocytosis by cycling between an inactive GDP-bound form and an active GTP-bound form. We reveal that RAB37 simultaneously regulates autophagy activation and tissue inhibitor of metalloproteinase 1 (TIMP1) secretion in lung cancer cells under starvation conditions. TIMP1, an inflammatory cytokine, is a known inhibitory molecule of matrix metalloproteinases matrix metalloproteinase 9 and suppresses the mobility of lung cancer cells both in vitro and in vivo through conventional exocytosis under serum-free conditions. Notably, we disclosed that secretory autophagy participates in TIMP1 secretion in a RAB37- and Sec22b-dependent manner. Sec22b, a SNARE family protein, participates in vesicle and membrane fusion of secretory autophagy. Knockdown of Sec22b decreased TIMP1 secretion and cell motility but did not affect cell proliferation under starvation conditions. We confirmed that starvation-activated RAB37 accompanied by Sec22b is essential for secretory autophagy to further enhance TIMP1 exocytosis. We further use an off-label drug amiodarone to demonstrate that autophagy induction facilitates TIMP1 secretion and suppresses the motility and metastasis of lung cancer cells in a RAB37-dependent manner in the lung-to-lung mouse model. In conclusion, we demonstrated that the RAB37 activation plays a pivotal regulatory role in secretory autophagy for TIMP1 secretion in lung cancer.Abbreviations: ATG: autophagy-related gene; GDP: guanosine diphosphate; GTP: guanosine triphosphate; LC3: microtubule-associated protein 1A/1B-light chain 3; SNARE: soluble N-ethylmaleimide-sensitive-factor attachment protein receptor; TIMP1: tissue inhibitor matrix metalloproteinase 1.
    Keywords:  RAB37; TIMP1; lung cancer; metastasis; secretory autophagy
    DOI:  https://doi.org/10.1080/15548627.2023.2210446
  7. Nat Commun. 2023 May 12. 14(1): 2730
    Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2.
    Ken Ikeuchi, Nives Ivic, Robert Buschauer, Jingdong Cheng, Thomas Fröhlich, Yoshitaka Matsuo, Otto Berninghausen, Toshifumi Inada, Thomas Becker, Roland Beckmann.
      In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its importance for translation efficiency the exact role and structural basis for this translational reset is poorly understood. Here, structural analysis by cryo-electron microscopy of native and reconstituted Otu2-bound ribosomal complexes reveals that Otu2 engages 40S subunits mainly between ribosome recycling and initiation stages. Otu2 binds to several sites on the intersubunit surface of the 40S that are not occupied by any other 40S-binding factors. This binding mode explains the discrimination against 80S ribosomes via the largely helical N-terminal domain of Otu2 as well as the specificity for mono-ubiquitinated eS7 on 40S. Collectively, this study reveals mechanistic insights into the Otu2-driven deubiquitination steps for translational reset during ribosome recycling/(re)initiation.
    DOI:  https://doi.org/10.1038/s41467-023-38161-w
  8. Front Immunol. 2023 ;14 1087677
    How autophagy, a potential therapeutic target, regulates intestinal inflammation.
    Shuang-Lan Chen, Chun-Meng Li, Wei Li, Qing-Song Liu, Shuang-Yuan Hu, Mao-Yuan Zhao, Dong-Sen Hu, Yan-Wei Hao, Jin-Hao Zeng, Yi Zhang.
      Inflammatory bowel disease (IBD) is a group of disorders that cause chronic inflammation in the intestines, with the primary types including ulcerative colitis and Crohn's disease. The link between autophagy, a catabolic mechanism in which cells clear protein aggregates and damaged organelles, and intestinal health has been widely studied. Experimental animal studies and human clinical studies have revealed that autophagy is pivotal for intestinal homeostasis maintenance, gut ecology regulation and other aspects. However, few articles have summarized and discussed the pathways by which autophagy improves or exacerbates IBD. Here, we review how autophagy alleviates IBD through the specific genes (e.g., ATG16L1, IRGM, NOD2 and LRRK2), crosstalk of multiple phenotypes with autophagy (e.g., Interaction of autophagy with endoplasmic reticulum stress, intestinal antimicrobial defense and apoptosis) and autophagy-associated signaling pathways. Moreover, we briefly discuss the role of autophagy in colorectal cancer and current status of autophagy-based drug research for IBD. It should be emphasized that autophagy has cell-specific and environment-specific effects on the gut. One of the problems of IBD research is to understand how autophagy plays a role in intestinal tract under specific environmental factors. A better understanding of the mechanism of autophagy in the occurrence and progression of IBD will provide references for the development of therapeutic drugs and disease management for IBD in the future.
    Keywords:  autophagy; autophagy-associated gene; endoplasmic reticulum stress; inflammatory bowel disease; intestinal microflora; signaling pathway
    DOI:  https://doi.org/10.3389/fimmu.2023.1087677
  9. Cell Rep. 2023 Apr 30. pii: S2211-1247(23)00465-5. [Epub ahead of print] 112454
    TIM23 facilitates PINK1 activation by safeguarding against OMA1-mediated degradation in damaged mitochondria.
    Shiori Akabane, Kiyona Watanabe, Hidetaka Kosako, Shun-Ichi Yamashita, Kohei Nishino, Masahiro Kato, Shiori Sekine, Tomotake Kanki, Noriyuki Matsuda, Toshiya Endo, Toshihiko Oka.
      PINK1 is activated by autophosphorylation and forms a high-molecular-weight complex, thereby initiating the selective removal of damaged mitochondria by autophagy. Other than translocase of the outer mitochondrial membrane complexes, members of PINK1-containing protein complexes remain obscure. By mass spectrometric analysis of PINK1 co-immunoprecipitates, we identify the inner membrane protein TIM23 as a component of the PINK1 complex. TIM23 downregulation decreases PINK1 levels and significantly delays autophosphorylation, indicating that TIM23 promotes PINK1 accumulation in response to depolarization. Moreover, inactivation of the mitochondrial protease OMA1 not only enhances PINK1 accumulation but also represses the reduction in PINK1 levels induced by TIM23 downregulation, suggesting that TIM23 facilitates PINK1 activation by safeguarding against degradation by OMA1. Indeed, deficiencies of pathogenic PINK1 mutants that fail to interact with TIM23 are partially restored by OMA1 inactivation. These findings indicate that TIM23 plays a distinct role in activating mitochondrial autophagy by protecting PINK1.
    Keywords:  CP: Cell biology; OMA1; PINK1; TIM23; mitochondrial quality control
    DOI:  https://doi.org/10.1016/j.celrep.2023.112454
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