1
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Garadi Suresh H, Bonneil E, Albert B, Dominique C, Costanzo M, Pons C, Masinas MPD, Shuteriqi E, Shore D, Henras AK, Thibault P, Boone C, Andrews BJ. K29-linked free polyubiquitin chains affect ribosome biogenesis and direct ribosomal proteins to the intranuclear quality control compartment. Mol Cell 2024:S1097-2765(24)00441-6. [PMID: 38870935 DOI: 10.1016/j.molcel.2024.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 01/25/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs) Ubp2 and Ubp14, and E3 ligases Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the intranuclear quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with ribosomopathies.
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Affiliation(s)
- Harsha Garadi Suresh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Benjamin Albert
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland; Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Carine Dominique
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Myra Paz David Masinas
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Ermira Shuteriqi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - David Shore
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada; Department of Chemistry, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
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2
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Yuan F, Gollapudi S, Day K, Ashby G, Sangani A, Malady B, Wang L, Lafer EM, Huibregtse J, Stachowiak J. Ubiquitin-driven protein condensation initiates clathrin-mediated endocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.21.554139. [PMID: 37662320 PMCID: PMC10473642 DOI: 10.1101/2023.08.21.554139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Clathrin-mediated endocytosis is an essential cellular pathway that enables signaling and recycling of transmembrane proteins and lipids. During endocytosis, dozens of cytosolic proteins come together at the plasma membrane, assembling into a highly interconnected network that drives endocytic vesicle biogenesis. Recently, multiple groups have reported that early endocytic proteins form flexible condensates, which provide a platform for efficient assembly of endocytic vesicles. Given the importance of this network in the dynamics of endocytosis, how might cells regulate its stability? Many receptors and endocytic proteins are ubiquitylated, while early endocytic proteins such as Eps15 contain ubiquitin-interacting motifs. Therefore, we examined the influence of ubiquitin on the stability of the early endocytic protein network. In vitro, we found that recruitment of small amounts of polyubiquitin dramatically increased the stability of Eps15 condensates, suggesting that ubiquitylation could nucleate endocytic assemblies. In live cell imaging experiments, a version of Eps15 that lacked the ubiquitin-interacting motif failed to rescue defects in endocytic initiation created by Eps15 knockout. Furthermore, fusion of Eps15 to a deubiquitylase enzyme destabilized nascent endocytic sites within minutes. In both in vitro and live cell settings, dynamic exchange of Eps15 proteins, a hallmark of liquidlike systems, was modulated by Eps15-Ub interactions. These results collectively suggest that ubiquitylation drives assembly of the flexible protein network responsible for catalyzing endocytic events. More broadly, this work illustrates a biophysical mechanism by which ubiquitylated transmembrane proteins at the plasma membrane could regulate the efficiency of endocytic recycling.
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Shenoy SK, Grimsey NJ, Piper RC. Editorial: Regulation of hormone and growth factor signalling by ubiquitin and ubiquitin-like protein modifications. Front Endocrinol (Lausanne) 2024; 15:1397685. [PMID: 38586453 PMCID: PMC10995326 DOI: 10.3389/fendo.2024.1397685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/09/2024] Open
Affiliation(s)
- Sudha K. Shenoy
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC, United States
- Department of Cell Biology, Duke University Medical Center, Durham, NC, United States
| | - Neil J. Grimsey
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, United States
| | - Robert C. Piper
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, United States
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4
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Bekku Y, Zotter B, You C, Piehler J, Leonard WJ, Salzer JL. Glia trigger endocytic clearance of axonal proteins to promote rodent myelination. Dev Cell 2024; 59:627-644.e10. [PMID: 38309265 PMCID: PMC11089820 DOI: 10.1016/j.devcel.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 09/09/2023] [Accepted: 01/12/2024] [Indexed: 02/05/2024]
Abstract
Axons undergo striking changes in their content and distribution of cell adhesion molecules (CAMs) and ion channels during myelination that underlies the switch from continuous to saltatory conduction. These changes include the removal of a large cohort of uniformly distributed CAMs that mediate initial axon-Schwann cell interactions and their replacement by a subset of CAMs that mediate domain-specific interactions of myelinated fibers. Here, using rodent models, we examine the mechanisms and significance of this removal of axonal CAMs. We show that Schwann cells just prior to myelination locally activate clathrin-mediated endocytosis (CME) in axons, thereby driving clearance of a broad array of axonal CAMs. CAMs engineered to resist endocytosis are persistently expressed along the axon and delay both PNS and CNS myelination. Thus, glia non-autonomously activate CME in axons to downregulate axonal CAMs and presumptively axo-glial adhesion. This promotes the transition from ensheathment to myelination while simultaneously sculpting the formation of axonal domains.
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Affiliation(s)
- Yoko Bekku
- Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA.
| | - Brendan Zotter
- Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA
| | - Changjiang You
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Barbarastr. 11, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Barbarastr. 11, 49076 Osnabrück, Germany
| | - Warren J Leonard
- Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - James L Salzer
- Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA.
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Hämälistö S, Del Valle Batalla F, Yuseff MI, Mattila PK. Endolysosomal vesicles at the center of B cell activation. J Cell Biol 2024; 223:e202307047. [PMID: 38305771 PMCID: PMC10837082 DOI: 10.1083/jcb.202307047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/22/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
The endolysosomal system specializes in degrading cellular components and is crucial to maintaining homeostasis and adapting rapidly to metabolic and environmental cues. Cells of the immune system exploit this network to process antigens or promote cell death by secreting lysosome-related vesicles. In B lymphocytes, lysosomes are harnessed to facilitate the extraction of antigens and to promote their processing into peptides for presentation to T cells, critical steps to mount protective high-affinity antibody responses. Intriguingly, lysosomal vesicles are now considered important signaling units within cells and also display secretory functions by releasing their content to the extracellular space. In this review, we focus on how B cells use pathways involved in the intracellular trafficking, secretion, and function of endolysosomes to promote adaptive immune responses. A basic understanding of such mechanisms poses an interesting frontier for the development of therapeutic strategies in the context of cancer and autoimmune diseases.
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Affiliation(s)
- Saara Hämälistö
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship, University of Turku, Turku, Finland
- Cancer Research Unit and FICAN West Cancer Centre Laboratory, Turku, Finland
| | - Felipe Del Valle Batalla
- Laboratory of Immune Cell Biology, Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María Isabel Yuseff
- Laboratory of Immune Cell Biology, Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pieta K. Mattila
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship, University of Turku, Turku, Finland
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6
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Ueda R, Hashimoto R, Fujii Y, Menezes JCJMDS, Takahashi H, Takeda H, Sawasaki T, Motokawa T, Tokunaga K, Fujita H. Membrane-Associated Ubiquitin Ligase RING Finger Protein 152 Orchestrates Melanogenesis via Tyrosinase Ubiquitination. MEMBRANES 2024; 14:43. [PMID: 38392670 PMCID: PMC10890620 DOI: 10.3390/membranes14020043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/24/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
Lysosomal degradation of tyrosinase, a pivotal enzyme in melanin synthesis, negatively impacts melanogenesis in melanocytes. Nevertheless, the precise molecular mechanisms by which lysosomes target tyrosinase have remained elusive. Here, we identify RING (Really Interesting New Gene) finger protein 152 (RNF152) as a membrane-associated ubiquitin ligase specifically targeting tyrosinase for the first time, utilizing AlphaScreen technology. We observed that modulating RNF152 levels in B16 cells, either via overexpression or siRNA knockdown, resulted in decreased or increased levels of both tyrosinase and melanin, respectively. Notably, RNF152 and tyrosinase co-localized at the trans-Golgi network (TGN). However, upon treatment with lysosomal inhibitors, both proteins appeared in the lysosomes, indicating that tyrosinase undergoes RNF152-mediated lysosomal degradation. Through ubiquitination assays, we found the indispensable roles of both the RING and transmembrane (TM) domains of RNF152 in facilitating tyrosinase ubiquitination. In summary, our findings underscore RNF152 as a tyrosinase-specific ubiquitin ligase essential for regulating melanogenesis in melanocytes.
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Affiliation(s)
- Ryota Ueda
- Faculty of Pharmaceutical Sciences, Nagasaki International University, Sasebo 859-3298, Japan
| | - Rina Hashimoto
- Faculty of Pharmaceutical Sciences, Nagasaki International University, Sasebo 859-3298, Japan
| | - Yuki Fujii
- Faculty of Pharmaceutical Sciences, Nagasaki International University, Sasebo 859-3298, Japan
| | - José C J M D S Menezes
- Faculty of Pharmaceutical Sciences, Nagasaki International University, Sasebo 859-3298, Japan
- Esteem Industries Pvt Ltd., Bicholim 403529, Goa, India
| | | | - Hiroyuki Takeda
- Proteo-Science Center, Ehime University, Matsuyama 790-8577, Japan
| | - Tatsuya Sawasaki
- Proteo-Science Center, Ehime University, Matsuyama 790-8577, Japan
| | - Tomonori Motokawa
- Frontier Research Center, POLA Chemical Industries, Inc., Yokohama 244-0812, Japan
| | - Kenzo Tokunaga
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Hideaki Fujita
- Faculty of Pharmaceutical Sciences, Nagasaki International University, Sasebo 859-3298, Japan
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7
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Altas B, Rhee HJ, Ju A, Solís HC, Karaca S, Winchenbach J, Kaplan-Arabaci O, Schwark M, Ambrozkiewicz MC, Lee C, Spieth L, Wieser GL, Chaugule VK, Majoul I, Hassan MA, Goel R, Wojcik SM, Koganezawa N, Hanamura K, Rotin D, Pichler A, Mitkovski M, de Hoz L, Poulopoulos A, Urlaub H, Jahn O, Saher G, Brose N, Rhee J, Kawabe H. Nedd4-2-dependent regulation of astrocytic Kir4.1 and Connexin43 controls neuronal network activity. J Cell Biol 2024; 223:e201902050. [PMID: 38032389 PMCID: PMC10689203 DOI: 10.1083/jcb.201902050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 10/21/2021] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
Nedd4-2 is an E3 ubiquitin ligase in which missense mutation is related to familial epilepsy, indicating its critical role in regulating neuronal network activity. However, Nedd4-2 substrates involved in neuronal network function have yet to be identified. Using mouse lines lacking Nedd4-1 and Nedd4-2, we identified astrocytic channel proteins inwardly rectifying K+ channel 4.1 (Kir4.1) and Connexin43 as Nedd4-2 substrates. We found that the expression of Kir4.1 and Connexin43 is increased upon conditional deletion of Nedd4-2 in astrocytes, leading to an elevation of astrocytic membrane ion permeability and gap junction activity, with a consequent reduction of γ-oscillatory neuronal network activity. Interestingly, our biochemical data demonstrate that missense mutations found in familial epileptic patients produce gain-of-function of the Nedd4-2 gene product. Our data reveal a process of coordinated astrocytic ion channel proteostasis that controls astrocyte function and astrocyte-dependent neuronal network activity and elucidate a potential mechanism by which aberrant Nedd4-2 function leads to epilepsy.
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Affiliation(s)
- Bekir Altas
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- International Max Planck Research School and the Göttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences, Göttingen, Germany
- The Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, PhD Program Systems Neuroscience, University of Göttingen, Göttingen, Germany
- Department of Pharmacology and Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Hong-Jun Rhee
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Anes Ju
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- The Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, PhD Program Systems Neuroscience, University of Göttingen, Göttingen, Germany
| | - Hugo Cruces Solís
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- International Max Planck Research School and the Göttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences, Göttingen, Germany
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Samir Karaca
- International Max Planck Research School and the Göttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jan Winchenbach
- The Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, PhD Program Systems Neuroscience, University of Göttingen, Göttingen, Germany
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Oykum Kaplan-Arabaci
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- The Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, PhD Program Molecular Physiology of the Brain, University of Göttingen, Göttingen, Germany
| | - Manuela Schwark
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Mateusz C. Ambrozkiewicz
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- International Max Planck Research School and the Göttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences, Göttingen, Germany
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - ChungKu Lee
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Lena Spieth
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Georg L. Wieser
- City Campus Light Microscopy Facility, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Viduth K. Chaugule
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Irina Majoul
- Institute of Biology, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
| | - Mohamed A. Hassan
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Egypt
| | - Rashi Goel
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sonja M. Wojcik
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Noriko Koganezawa
- Department of Pharmacology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kenji Hanamura
- Department of Pharmacology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Daniela Rotin
- The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Miso Mitkovski
- City Campus Light Microscopy Facility, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Livia de Hoz
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Alexandros Poulopoulos
- Department of Pharmacology and Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
| | - Olaf Jahn
- Department of Molecular Neurobiology, Neuroproteomics Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Psychiatry and Psychotherapy, Translational Neuroproteomics Group, University Medical Center Göttingen, Göttingen, Germany
| | - Gesine Saher
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - JeongSeop Rhee
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Hiroshi Kawabe
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Pharmacology, Gunma University Graduate School of Medicine, Maebashi, Japan
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe, Japan
- Department of Gerontology, Laboratory of Molecular Life Science, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
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8
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Tey PY, Dufner A, Knobeloch KP, Pruneda JN, Clague MJ, Urbé S. Rapid turnover of CTLA4 is associated with a complex architecture of reversible ubiquitylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573735. [PMID: 38260548 PMCID: PMC10802369 DOI: 10.1101/2023.12.31.573735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The immune checkpoint regulator CTLA4 is an unusually short-lived membrane protein. Here we show that its lysosomal degradation is dependent on ubiquitylation at Lysine residues 203 and 213. Inhibition of the v-ATPase partially restores CTLA4 levels following cycloheximide treatment, but also reveals a fraction that is secreted in exosomes. The endosomal deubiquitylase, USP8, interacts with CTLA4 and its loss enhances CTLA4 ubiquitylation in cancer cells, mouse CD4+ T cells and in cancer cell-derived exosomes. Depletion of the USP8 adapter protein, HD-PTP, but not ESCRT-0 recapitulates this cellular phenotype, but shows distinct properties vis-à-vis exosome incorporation. Re-expression of wild-type USP8, but neither a catalytically inactive, nor a localization-compromised ΔMIT domain mutant can rescue delayed degradation of CTLA4, or counteract its accumulation in clustered endosomes. UbiCRest analysis of CTLA4-associated ubiquitin chain linkages identifies a complex mixture of conventional Lys63- and more unusual Lys27- and Lys29-linked polyubiquitin chains that may underly the rapidity of protein turnover.
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Affiliation(s)
- Pei Yee Tey
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 3BX, UK
| | - Almut Dufner
- Institute of Neuropathology, Medical Faculty, University of Freiburg, 79106 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Medical Faculty, University of Freiburg, 79106 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michael J. Clague
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 3BX, UK
| | - Sylvie Urbé
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 3BX, UK
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9
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Pizzoni A, Zhang X, Altschuler DL. From membrane to nucleus: A three-wave hypothesis of cAMP signaling. J Biol Chem 2024; 300:105497. [PMID: 38016514 PMCID: PMC10788541 DOI: 10.1016/j.jbc.2023.105497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/30/2023] Open
Abstract
For many decades, our understanding of G protein-coupled receptor (GPCR) activity and cyclic AMP (cAMP) signaling was limited exclusively to the plasma membrane. However, a growing body of evidence has challenged this view by introducing the concept of endocytosis-dependent GPCR signaling. This emerging paradigm emphasizes not only the sustained production of cAMP but also its precise subcellular localization, thus transforming our understanding of the spatiotemporal organization of this process. Starting from this alternative point of view, our recent work sheds light on the role of an endocytosis-dependent calcium release from the endoplasmic reticulum in the control of nuclear cAMP levels. This is achieved through the activation of local soluble adenylyl cyclase, which in turn regulates the activation of local protein kinase A (PKA) and downstream transcriptional events. In this review, we explore the dynamic evolution of research on cyclic AMP signaling, including the findings that led us to formulate the novel three-wave hypothesis. We delve into how we abandoned the paradigm of cAMP generation limited to the plasma membrane and the changing perspectives on the rate-limiting step in nuclear PKA activation.
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Affiliation(s)
- Alejandro Pizzoni
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Xuefeng Zhang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel L Altschuler
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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10
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Kalodimou K, Stapountzi M, Vüllings N, Seib E, Klein T, Delidakis C. Separable Roles for Neur and Ubiquitin in Delta Signalling in the Drosophila CNS Lineages. Cells 2023; 12:2833. [PMID: 38132160 PMCID: PMC10741450 DOI: 10.3390/cells12242833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
The execution of a Notch signal at the plasma membrane relies on the mechanical force exerted onto Notch by its ligand. It has been appreciated that the DSL ligands need to collaborate with a ubiquitin (Ub) ligase, either Neuralized or Mindbomb1, in order to exert this pulling force, but the role of ubiquitylation per se is uncertain. Regarding the Delta-Neur pair, it is documented that neither the Neur catalytic domain nor the Delta intracellular lysines (putative Ub acceptors) are needed for activity. Here, we present a dissection of the Delta activity using the Delta-Notch-dependent expression of Hey in newborn Drosophila neurons as a sensitive in vivo assay. We show that the Delta-Neur interaction per se, rather than ubiquitylation, is needed for activity, pointing to the existence of a Delta-Neur signaling complex. The Neur catalytic domain, although not strictly needed, greatly improves Delta-Neur complex functionality when the Delta lysines are mutated, suggesting that the ubiquitylation of some component of the complex, other than Delta, can enhance signaling. Since Hey expression is sensitive to the perturbation of endocytosis, we propose that the Delta-Neur complex triggers a force-generating endocytosis event that activates Notch in the adjacent cell.
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Affiliation(s)
- Konstantina Kalodimou
- Department of Biology, University of Crete, 700 13 Heraklion, Greece;
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 700 13 Heraklion, Greece;
| | - Margarita Stapountzi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 700 13 Heraklion, Greece;
| | - Nicole Vüllings
- Institute of Genetics, Heinrich-Heine-Universitaet Duesseldorf, 40225 Duesseldorf, Germany
| | - Ekaterina Seib
- Institute of Genetics, Heinrich-Heine-Universitaet Duesseldorf, 40225 Duesseldorf, Germany
| | - Thomas Klein
- Institute of Genetics, Heinrich-Heine-Universitaet Duesseldorf, 40225 Duesseldorf, Germany
| | - Christos Delidakis
- Department of Biology, University of Crete, 700 13 Heraklion, Greece;
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 700 13 Heraklion, Greece;
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11
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De Meyer A, Grones P, Van Damme D. How will I recognize you? Insights into endocytic cargo recognition in plants. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102429. [PMID: 37523901 DOI: 10.1016/j.pbi.2023.102429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 06/15/2023] [Accepted: 07/02/2023] [Indexed: 08/02/2023]
Abstract
The plasma membrane (PM) houses a wide variety of proteins, facilitating interactions between the cell and its surroundings. Perception of external stimuli leads to selective internalization of membrane proteins via endocytosis. A multitude of endocytic signals affect protein internalization; however, their coordination and the exact mechanism of their recognition still remain elusive. In this review, we summarized the up-to-date knowledge of different internalization signals in PM cargo proteins and their involvement during protein trafficking.
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Affiliation(s)
- Andreas De Meyer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Peter Grones
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Daniel Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium.
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12
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Suresh HG, Bonneil E, Albert B, Dominique C, Costanzo M, Pons C, David Masinas MP, Shuteriqi E, Shore D, Henras AK, Thibault P, Boone C, Andrews BJ. K29-linked unanchored polyubiquitin chains disrupt ribosome biogenesis and direct ribosomal proteins to the Intranuclear Quality control compartment (INQ). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539259. [PMID: 37205480 PMCID: PMC10187189 DOI: 10.1101/2023.05.03.539259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with Ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs), Ubp2 and Ubp14, and E3 ligases, Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the Ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the Intranuclear Quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with Ribosomopathies.
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13
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Shinde SR, Mick DU, Aoki E, Rodrigues RB, Gygi SP, Nachury MV. The ancestral ESCRT protein TOM1L2 selects ubiquitinated cargoes for retrieval from cilia. Dev Cell 2023; 58:677-693.e9. [PMID: 37019113 PMCID: PMC10133032 DOI: 10.1016/j.devcel.2023.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/19/2022] [Accepted: 03/07/2023] [Indexed: 04/07/2023]
Abstract
Many G protein-coupled receptors (GPCRs) reside within cilia of mammalian cells and must undergo regulated exit from cilia for the appropriate transduction of signals such as hedgehog morphogens. Lysine 63-linked ubiquitin (UbK63) chains mark GPCRs for regulated removal from cilia, but the molecular basis of UbK63 recognition inside cilia remains elusive. Here, we show that the BBSome-the trafficking complex in charge of retrieving GPCRs from cilia-engages the ancestral endosomal sorting factor target of Myb1-like 2 (TOM1L2) to recognize UbK63 chains within cilia of human and mouse cells. TOM1L2 directly binds to UbK63 chains and the BBSome, and targeted disruption of the TOM1L2/BBSome interaction results in the accumulation of TOM1L2, ubiquitin, and the GPCRs SSTR3, Smoothened, and GPR161 inside cilia. Furthermore, the single-cell alga Chlamydomonas also requires its TOM1L2 ortholog in order to clear ubiquitinated proteins from cilia. We conclude that TOM1L2 broadly enables the retrieval of UbK63-tagged proteins by the ciliary trafficking machinery.
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Affiliation(s)
- Swapnil Rohidas Shinde
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David U Mick
- Center of Human and Molecular Biology and Center for Molecular Signaling, Department of Medical Biochemistry and Molecular Biology, Saarland University School of Medicine, Homburg, Germany
| | - Erika Aoki
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rachel B Rodrigues
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Maxence V Nachury
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143, USA.
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14
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Lai YT, Sasamura T, Kuroda J, Maeda R, Nakamura M, Hatori R, Ishibashi T, Taniguchi K, Ooike M, Taguchi T, Nakazawa N, Hozumi S, Okumura T, Aigaki T, Inaki M, Matsuno K. The Drosophila AWP1 ortholog Doctor No regulates JAK/STAT signaling for left-right asymmetry in the gut by promoting receptor endocytosis. Development 2023; 150:293490. [PMID: 36861793 PMCID: PMC10112927 DOI: 10.1242/dev.201224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 02/09/2023] [Indexed: 03/03/2023]
Abstract
Many organs of Drosophila show stereotypical left-right (LR) asymmetry; however, the underlying mechanisms remain elusive. Here, we have identified an evolutionarily conserved ubiquitin-binding protein, AWP1/Doctor No (Drn), as a factor required for LR asymmetry in the embryonic anterior gut. We found that drn is essential in the circular visceral muscle cells of the midgut for JAK/STAT signaling, which contributes to the first known cue for anterior gut lateralization via LR asymmetric nuclear rearrangement. Embryos homozygous for drn and lacking its maternal contribution showed phenotypes similar to those with depleted JAK/STAT signaling, suggesting that Drn is a general component of JAK/STAT signaling. Absence of Drn resulted in specific accumulation of Domeless (Dome), the receptor for ligands in the JAK/STAT signaling pathway, in intracellular compartments, including ubiquitylated cargos. Dome colocalized with Drn in wild-type Drosophila. These results suggest that Drn is required for the endocytic trafficking of Dome, which is a crucial step for activation of JAK/STAT signaling and the subsequent degradation of Dome. The roles of AWP1/Drn in activating JAK/STAT signaling and in LR asymmetric development may be conserved in various organisms.
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Affiliation(s)
- Yi-Ting Lai
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takeshi Sasamura
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Junpei Kuroda
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Reo Maeda
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Mitsutoshi Nakamura
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Ryo Hatori
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Tomoki Ishibashi
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kiichiro Taniguchi
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Masashi Ooike
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Tomohiro Taguchi
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Naotaka Nakazawa
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Shunya Hozumi
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takashi Okumura
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Toshiro Aigaki
- Department of Biological Science, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo 192-0397, Japan
| | - Mikiko Inaki
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kenji Matsuno
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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15
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Wang L, Klionsky DJ, Shen HM. The emerging mechanisms and functions of microautophagy. Nat Rev Mol Cell Biol 2023; 24:186-203. [PMID: 36097284 DOI: 10.1038/s41580-022-00529-z] [Citation(s) in RCA: 105] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2022] [Indexed: 02/08/2023]
Abstract
'Autophagy' refers to an evolutionarily conserved process through which cellular contents, such as damaged organelles and protein aggregates, are delivered to lysosomes for degradation. Different forms of autophagy have been described on the basis of the nature of the cargoes and the means used to deliver them to lysosomes. At present, the prevailing categories of autophagy in mammalian cells are macroautophagy, microautophagy and chaperone-mediated autophagy. The molecular mechanisms and biological functions of macroautophagy and chaperone-mediated autophagy have been extensively studied, but microautophagy has received much less attention. In recent years, there has been a growth in research on microautophagy, first in yeast and then in mammalian cells. Here we review this form of autophagy, focusing on selective forms of microautophagy. We also discuss the upstream regulatory mechanisms, the crosstalk between macroautophagy and microautophagy, and the functional implications of microautophagy in diseases such as cancer and neurodegenerative disorders in humans. Future research into microautophagy will provide opportunities to develop novel interventional strategies for autophagy- and lysosome-related diseases.
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Affiliation(s)
- Liming Wang
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Han-Ming Shen
- Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau, China. .,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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16
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Nguyen NH, Brodsky JL. The cellular pathways that maintain the quality control and transport of diverse potassium channels. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194908. [PMID: 36638864 PMCID: PMC9908860 DOI: 10.1016/j.bbagrm.2023.194908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Potassium channels are multi-subunit transmembrane proteins that permit the selective passage of potassium and play fundamental roles in physiological processes, such as action potentials in the nervous system and organismal salt and water homeostasis, which is mediated by the kidney. Like all ion channels, newly translated potassium channels enter the endoplasmic reticulum (ER) and undergo the error-prone process of acquiring post-translational modifications, folding into their native conformations, assembling with other subunits, and trafficking through the secretory pathway to reach their final destinations, most commonly the plasma membrane. Disruptions in these processes can result in detrimental consequences, including various human diseases. Thus, multiple quality control checkpoints evolved to guide potassium channels through the secretory pathway and clear potentially toxic, aggregation-prone misfolded species. We will summarize current knowledge on the mechanisms underlying potassium channel quality control in the secretory pathway, highlight diseases associated with channel misfolding, and suggest potential therapeutic routes.
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Affiliation(s)
- Nga H Nguyen
- Department of Biological Sciences, University of Pittsburgh, A320 Langley Hall, Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, A320 Langley Hall, Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA.
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17
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McGoldrick P, Lau A, You Z, Durcan TM, Robertson J. Loss of C9orf72 perturbs the Ran-GTPase gradient and nucleocytoplasmic transport, generating compositionally diverse Importin β-1 granules. Cell Rep 2023; 42:112134. [PMID: 36821445 DOI: 10.1016/j.celrep.2023.112134] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/05/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
A hexanucleotide (GGGGCC)n repeat expansion in C9orf72 causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), eliciting toxic effects through generation of RNA foci, dipeptide repeat proteins, and/or loss of C9orf72 protein. Defects in nucleocytoplasmic transport (NCT) have been implicated as a pathogenic mechanism underlying repeat expansion toxicity. Here, we show that loss of C9orf72 disrupts the Ran-GTPase gradient and NCT in vitro and in vivo. NCT disruption in vivo is enhanced by the presence of compositionally different types of cytoplasmic Importin β-1 granule that exhibit neuronal subtype-specific properties. We show that the abundance of Importin β-1 granules is increased in the context of C9orf72 deficiency, disrupting interactions with nuclear pore complex proteins. These granules appear to associate with the nuclear envelope and are co-immunoreactive for G3BP1 and K63-ubiquitin. These findings link loss of C9orf72 protein to gain-of-function mechanisms and defects in NCT.
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Affiliation(s)
- Philip McGoldrick
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada.
| | - Agnes Lau
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Zhipeng You
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada
| | - Thomas M Durcan
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada; Department of Laboratory Medicine and Pathobiology, 27 King's College Circle, Toronto, ON M5S 1A1, Canada.
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18
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Berlin I, Sapmaz A, Stévenin V, Neefjes J. Ubiquitin and its relatives as wizards of the endolysosomal system. J Cell Sci 2023; 136:288517. [PMID: 36825571 PMCID: PMC10022685 DOI: 10.1242/jcs.260101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The endolysosomal system comprises a dynamic constellation of vesicles working together to sense and interpret environmental cues and facilitate homeostasis. Integrating extracellular information with the internal affairs of the cell requires endosomes and lysosomes to be proficient in decision-making: fusion or fission; recycling or degradation; fast transport or contacts with other organelles. To effectively discriminate between these options, the endolysosomal system employs complex regulatory strategies that crucially rely on reversible post-translational modifications (PTMs) with ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. The cycle of conjugation, recognition and removal of different Ub- and Ubl-modified states informs cellular protein stability and behavior at spatial and temporal resolution and is thus well suited to finetune macromolecular complex assembly and function on endolysosomal membranes. Here, we discuss how ubiquitylation (also known as ubiquitination) and its biochemical relatives orchestrate endocytic traffic and designate cargo fate, influence membrane identity transitions and support formation of membrane contact sites (MCSs). Finally, we explore the opportunistic hijacking of Ub and Ubl modification cascades by intracellular bacteria that remodel host trafficking pathways to invade and prosper inside cells.
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Affiliation(s)
- Ilana Berlin
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Aysegul Sapmaz
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Virginie Stévenin
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Jacques Neefjes
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
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19
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Pedrosa AG, Francisco T, Rodrigues TA, Ferreira MJ, van der Heden van Noort GJ, Azevedo JE. The Extraction Mechanism of Monoubiquitinated PEX5 from the Peroxisomal Membrane. J Mol Biol 2023; 435:167896. [PMID: 36442669 DOI: 10.1016/j.jmb.2022.167896] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
The AAA ATPases PEX1•PEX6 extract PEX5, the peroxisomal protein shuttling receptor, from the peroxisomal membrane so that a new protein transport cycle can start. Extraction requires ubiquitination of PEX5 at residue 11 and involves a threading mechanism, but how exactly this occurs is unclear. We used a cell-free in vitro system and a variety of engineered PEX5 and ubiquitin molecules to challenge the extraction machinery. We show that PEX5 modified with a single ubiquitin is a substrate for extraction and extend previous findings proposing that neither the N- nor the C-terminus of PEX5 are required for extraction. Chimeric PEX5 molecules possessing a branched polypeptide structure at their C-terminal domains can still be extracted from the peroxisomal membrane thus suggesting that the extraction machinery can thread more than one polypeptide chain simultaneously. Importantly, we found that the PEX5-linked monoubiquitin is unfolded at a pre-extraction stage and, accordingly, an intra-molecularly cross-linked ubiquitin blocked extraction when conjugated to residue 11 of PEX5. Collectively, our data suggest that the PEX5-linked monoubiquitin is the extraction initiator and that the complete ubiquitin-PEX5 conjugate is threaded by PEX1•PEX6.
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Affiliation(s)
- Ana G Pedrosa
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Tânia Francisco
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Tony A Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Maria J Ferreira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Gerbrand J van der Heden van Noort
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Jorge E Azevedo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
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20
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Lalnunthangi A, Dakpa G, Tiwari S. Multifunctional role of the ubiquitin proteasome pathway in phagocytosis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 194:179-217. [PMID: 36631192 DOI: 10.1016/bs.pmbts.2022.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Phagocytosis is a specialized form of endocytosis where large cells and particles (>0.5μm) are engulfed by the phagocytic cells, and ultimately digested in the phagolysosomes. This process not only eliminates unwanted particles and pathogens from the extracellular sources, but also eliminates apoptotic cells within the body, and is critical for maintenance of tissue homeostasis. It is believed that both endocytosis and phagocytosis share common pathways after particle internalization, but specialized features and differences between these two routes of internalization are also likely. The recruitment and removal of each protein/particle during the maturation of endocytic/phagocytic vesicles has to be tightly regulated to ensure their timely action. Ubiquitin proteasome pathway (UPP), degrades unwanted proteins by post-translational modification of proteins with chains of conserved protein Ubiquitin (Ub), with subsequent recognition of Ub chains by the 26S proteasomes and substrate degradation by this protease. This pathway utilizes different Ub linkages to modify proteins to regulate protein-protein interaction, localization, and activity. Due to its vast number of targets, it is involved in many cellular pathways, including phagocytosis. This chapters describes the basic steps and signaling in phagocytosis and different roles that UPP plays at multiple steps in regulating phagocytosis directly, or through its interaction with other phagosomal proteins. How aberrations in UPP function affect phagocytosis and their association with human diseases, and how pathogens exploit this pathway for their own benefit is also discussed.
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Affiliation(s)
| | | | - Swati Tiwari
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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21
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Asimaki E, Petriukov K, Renz C, Meister C, Ulrich HD. Fast friends - Ubiquitin-like modifiers as engineered fusion partners. Semin Cell Dev Biol 2022; 132:132-145. [PMID: 34840080 PMCID: PMC9703124 DOI: 10.1016/j.semcdb.2021.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022]
Abstract
Ubiquitin and its relatives are major players in many biological pathways, and a variety of experimental tools based on biological chemistry or protein engineering is available for their manipulation. One popular approach is the use of linear fusions between the modifier and a protein of interest. Such artificial constructs can facilitate the understanding of the role of ubiquitin in biological processes and can be exploited to control protein stability, interactions and degradation. Here we summarize the basic design considerations and discuss the advantages as well as limitations associated with their use. Finally, we will refer to several published case studies highlighting the principles of how they provide insight into pathways ranging from membrane protein trafficking to the control of epigenetic modifications.
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22
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Low JJW, Sulaiman SA, Johdi NA, Abu N. Immunomodulatory effects of extracellular vesicles in glioblastoma. Front Cell Dev Biol 2022; 10:996805. [DOI: 10.3389/fcell.2022.996805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022] Open
Abstract
Glioblastoma (GB) is a type of brain cancer that can be considered aggressive. Glioblastoma treatment has significant challenges due to the immune privilege site of the brain and the presentation of an immunosuppressive tumor microenvironment. Extracellular vesicles (EVs) are cell-secreted nanosized vesicles that engage in intercellular communication via delivery of cargo that may cause downstream effects such as tumor progression and recipient cell modulation. Although the roles of extracellular vesicles in cancer progression are well documented, their immunomodulatory effects are less defined. Herein, we focus on glioblastoma and explain the immunomodulatory effects of extracellular vesicles secreted by both tumor and immune cells in detail. The tumor to immune cells, immune cells to the tumor, and intra-immune cells extracellular vesicles crosstalks are involved in various immunomodulatory effects. This includes the promotion of immunosuppressive phenotypes, apoptosis, and inactivation of immune cell subtypes, which affects the central nervous system and peripheral immune system response, aiding in its survival and progression in the brain.
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Lee BH, Tebaldi G, Pritchard SM, Nicola AV. Host Cell Neddylation Facilitates Alphaherpesvirus Entry in a Virus-Specific and Cell-Dependent Manner. Microbiol Spectr 2022; 10:e0311422. [PMID: 36173301 PMCID: PMC9603186 DOI: 10.1128/spectrum.03114-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/13/2022] [Indexed: 01/04/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) commandeers the host cell proteasome at several steps of its replication cycle, including entry. Here we demonstrate that HSV-2, pseudorabies virus (PRV), and bovine herpesvirus 1 (BoHV-1) entry are blocked by bortezomib, a proteasome inhibitor that is an FDA-approved cancer drug. Proteasome-dependent entry of HSV-1 is thought to be ubiquitin-independent. To interrogate further the proteasomal mechanism of entry, we determined the involvement of the ubiquitin-like molecule NEDD8 and the neddylation cascade in alphaherpesvirus entry and infection. MLN4924 is a small-molecule inhibitor of neddylation that binds directly to the NEDD8-activating enzyme. Cell treatment with MLN4924 inhibited plaque formation and infectivity by HSV-1, PRV, and BoHV-1 at noncytotoxic concentrations. Thus, the neddylation pathway is broadly important for alphaherpesvirus infection. However, the neddylation inhibitor had little effect on entry of the veterinary viruses but had a significant inhibitory effect on entry of HSV-1 and HSV-2 into seven different cell types. Washout experiments indicated that MLN4924's effect on viral entry was reversible. A time-of-addition assay suggested that the drug was acting on an early step in the entry process. Small interfering RNA (siRNA) knockdown of NEDD8 significantly inhibited HSV entry. In probing the neddylation-dependent step in entry, we found that MLN4924 dramatically blocked endocytic uptake of HSV from the plasma membrane by >90%. In contrast, the rate of HSV entry into cells that support direct fusion of HSV with the cell surface was unaffected by MLN4924. Interestingly, proteasome activity was less important for the endocytic internalization of HSV from the cell surface. The results suggest that the NEDD8 cascade is critical for the internalization step of HSV entry. IMPORTANCE Alphaherpesviruses are ubiquitous pathogens of humans and veterinary species that cause lifelong latent infections and significant morbidity and mortality. Host cell neddylation is important for cell homeostasis and for the infection of many viruses, including HSV-1, HSV-2, PRV, and BoHV-1. Inhibition of neddylation by a pharmacologic inhibitor or siRNA blocked HSV infection at the entry step. Specifically, the NEDD8 pathway was critically important for HSV-1 internalization from the cell surface by an endocytosis mechanism. The results expand our limited understanding of cellular processes that mediate HSV internalization. To our knowledge, this is the first demonstration of a function for the neddylation cascade in virus entry.
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Affiliation(s)
- Becky H. Lee
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Giulia Tebaldi
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Suzanne M. Pritchard
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Anthony V. Nicola
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
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Wu B, Wang Q, Shi X, Jiang M. Targeting Endocytosis and Cell Communications in the Tumor Immune Microenvironment. Cell Commun Signal 2022; 20:161. [PMID: 36258231 PMCID: PMC9578241 DOI: 10.1186/s12964-022-00968-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/23/2022] [Indexed: 01/18/2023] Open
Abstract
The existence of multiple endocytic pathways is well known, and their exact biological effects in tumors have been intensively investigated. Endocytosis can affect the connection between tumor cells and determine the fate of tumor cells. Many relationships between endocytosis and tumor cells have been elucidated, but the mechanism of endocytosis between different types of cells in tumors needs to be explored in greater depth. Endocytic receptors sense the environment and are induced by specific ligands to trigger communication between tumor and immune cells. Crosstalk in the tumor microenvironment can occur through direct contact between cell adhesion molecules or indirectly through exosomes. So a better understanding of the endocytic pathways that control cell adhesion molecules and function is expected to lead to new candidates for cancer treatment. In additional, tumor-derived exosomes may changes immune cell function, which may be a key role for tumors to evade immune detection and response. The overall understanding of exosomes through endocytosis is also expected to bring new candidates for therapeutic regulation of tumor immune microenvironment. In this case, endocytic pathways coordinate cell adhesion molecules and exosomes and can be used as targets in the tumor immune microenvironment for cancer treatment. Video Abstract
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25
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Kazan JM, Pollato-Blanco A, Lukacs GL, Pause A. Measuring EGFR plasma membrane density, stability, internalization, and recycling in alive adherent cells by cell surface ELISA. STAR Protoc 2022; 3:101475. [PMID: 35755125 PMCID: PMC9213824 DOI: 10.1016/j.xpro.2022.101475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Jalal M Kazan
- Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; Biochemistry Department, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Ariadna Pollato-Blanco
- Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; Biochemistry Department, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Gergely L Lukacs
- Physiology Department, McGill University, Montreal, QC H3G 1Y6, Canada.
| | - Arnim Pause
- Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; Biochemistry Department, McGill University, Montreal, QC H3G 1Y6, Canada.
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Heterotropic roles of divalent cations in the establishment of allostery and affinity maturation of integrin αXβ2. Cell Rep 2022; 40:111254. [PMID: 36001965 PMCID: PMC9440770 DOI: 10.1016/j.celrep.2022.111254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 05/23/2022] [Accepted: 08/02/2022] [Indexed: 11/21/2022] Open
Abstract
Allosteric activation and silencing of leukocyte β2-integrins transpire through cation-dependent structural changes, which mediate integrin biosynthesis and recycling, and are essential to designing leukocyte-specific drugs. Stepwise addition of Mg2+ reveals two mutually coupled events for the αXβ2 ligand-binding domain-the αX I-domain-corresponding to allostery establishment and affinity maturation. Electrostatic alterations in the Mg2+-binding site establish long-range couplings, leading to both pH- and Mg2+-occupancy-dependent biphasic stability change in the αX I-domain fold. The ligand-binding sensorgrams show composite affinity events for the αX I-domain accounting for the multiplicity of the αX I-domain conformational states existing in the solution. On cell surfaces, increasing Mg2+ concentration enhanced adhesiveness of αXβ2. This work highlights how intrinsically flexible pH- and cation-sensitive architecture endows a unique dynamic continuum to the αI-domain structure on the intact integrin, thereby revealing the importance of allostery establishment and affinity maturation in both extracellular and intracellular integrin events.
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2-deoxyglucose transiently inhibits yeast AMPK signaling and triggers glucose transporter endocytosis, potentiating the drug toxicity. PLoS Genet 2022; 18:e1010169. [PMID: 35951639 PMCID: PMC9398028 DOI: 10.1371/journal.pgen.1010169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/23/2022] [Accepted: 07/20/2022] [Indexed: 11/19/2022] Open
Abstract
2-deoxyglucose is a glucose analog that impacts many aspects of cellular physiology. After its uptake and its phosphorylation into 2-deoxyglucose-6-phosphate (2DG6P), it interferes with several metabolic pathways including glycolysis and protein N-glycosylation. Despite this systemic effect, resistance can arise through strategies that are only partially understood. In yeast, 2DG resistance is often associated with mutations causing increased activity of the yeast 5’-AMP activated protein kinase (AMPK), Snf1. Here we focus on the contribution of a Snf1 substrate in 2DG resistance, namely the alpha-arrestin Rod1 involved in nutrient transporter endocytosis. We report that 2DG triggers the endocytosis of many plasma membrane proteins, mostly in a Rod1-dependent manner. Rod1 participates in 2DG-induced endocytosis because 2DG, following its phosphorylation by hexokinase Hxk2, triggers changes in Rod1 post-translational modifications and promotes its function in endocytosis. Mechanistically, this is explained by a transient, 2DG-induced inactivation of Snf1/AMPK by protein phosphatase 1 (PP1). We show that 2DG-induced endocytosis is detrimental to cells, and the lack of Rod1 counteracts this process by stabilizing glucose transporters at the plasma membrane. This facilitates glucose uptake, which may help override the metabolic blockade caused by 2DG, and 2DG export—thus terminating the process of 2DG detoxification. Altogether, these results shed a new light on the regulation of AMPK signaling in yeast and highlight a remarkable strategy to bypass 2DG toxicity involving glucose transporter regulation.
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Desai D, Londhe R, Chandane M, Kulkarni S. Altered HIV-1 Viral Copy Number and Gene Expression Profiles of Peripheral (CEM CCR5+) and Mucosal (A3R5.7) T Cell Lines Co-Infected with HSV-2 In Vitro. Viruses 2022; 14:v14081715. [PMID: 36016337 PMCID: PMC9413683 DOI: 10.3390/v14081715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 01/27/2023] Open
Abstract
Co-infecting pathogens have been speculated to influence Human Immunodeficiency Virus (HIV) disease progression. Herpes Simplex Virus Type-2 (HSV-2), another sexually transmitted pathogen, is commonly observed in individuals with HIV-1. Some clinical studies have observed an increase in HIV-1 viral copy number in HSV-2 co-infected individuals. In vitro studies have also demonstrated an increase in the expression of HIV-1 co-receptors on immune cells infected with HSV-2. Although both the viruses show distinctive persistent infection, the influence of HSV-2 on HIV-1 is poorly understood. Here we present a comparative analysis of primary CD4+ T-cells and four different T-cell lines (PM-1, CEM CCR5+, MOLT4 CCR5+, and A3R5.7) to assess the influence of HSV-2 co-infection on HIV-1 replication in vitro. Cell lines indicating significant changes in HIV-1 viral copy number [CEM CCR5+ (0.61 Log10), A3R5.7 (0.78 Log10)] were further evaluated for the infectivity of HIV-1 virions and the changes in gene expression profiles of HSV-2/HIV-1 co-infected and mono-infected cells, which were further confirmed by qPCR. Significant changes in NUP, MED, and VPS mRNA expression were observed in the gene expression profiles in co-infected CEM CCR5+ and A3R5.7 cells. In both cell lines, it was observed that the WNT signaling, PI3 kinase, apoptosis, and T-cell activation pathways were negatively affected in co-infected cells. The data suggest that HSV-2 infection of T-cells may influence the expression of genes that have been previously shown to affect HIV-1 replication in vitro. This idea needs to be explored further to identify anti-viral targets for HSV-2 and HIV-1.
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29
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Dao TP, Yang Y, Presti MF, Cosgrove MS, Hopkins JB, Ma W, Loh SN, Castañeda CA. Mechanistic insights into enhancement or inhibition of phase separation by different polyubiquitin chains. EMBO Rep 2022; 23:e55056. [PMID: 35762418 PMCID: PMC9346500 DOI: 10.15252/embr.202255056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 12/03/2022] Open
Abstract
Ubiquitin‐binding shuttle UBQLN2 mediates crosstalk between proteasomal degradation and autophagy, likely via interactions with K48‐ and K63‐linked polyubiquitin chains, respectively. UBQLN2 comprises self‐associating regions that drive its homotypic liquid–liquid phase separation (LLPS). Specific interactions between one of these regions and ubiquitin inhibit UBQLN2 LLPS. Here, we show that, unlike ubiquitin, the effects of multivalent polyubiquitin chains on UBQLN2 LLPS are highly dependent on chain types. Specifically, K11‐Ub4 and K48‐Ub4 chains generally inhibit UBQLN2 LLPS, whereas K63‐Ub4, M1‐Ub4 chains, and a designed tetrameric ubiquitin construct significantly enhance LLPS. We demonstrate that these opposing effects stem from differences in chain conformations but not in affinities between chains and UBQLN2. Chains with extended conformations and increased accessibility to the ubiquitin‐binding surface promote UBQLN2 LLPS by enabling a switch between homotypic to partially heterotypic LLPS that is driven by both UBQLN2 self‐interactions and interactions between multiple UBQLN2 units with each polyubiquitin chain. Our study provides mechanistic insights into how the structural and conformational properties of polyubiquitin chains contribute to heterotypic LLPS with ubiquitin‐binding shuttles and adaptors.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
| | - Yiran Yang
- Department of Chemistry Syracuse University Syracuse NY USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Weikang Ma
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Carlos A Castañeda
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
- Interdisciplinary Neuroscience Program Syracuse University Syracuse NY USA
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30
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Ghilarducci K, Cabana VC, Harake A, Cappadocia L, Lussier MP. Membrane Targeting and GTPase Activity of Rab7 Are Required for Its Ubiquitination by RNF167. Int J Mol Sci 2022; 23:ijms23147847. [PMID: 35887194 PMCID: PMC9319455 DOI: 10.3390/ijms23147847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 11/30/2022] Open
Abstract
Rab7 is a GTPase that controls late endosome and lysosome trafficking. Recent studies have demonstrated that Rab7 is ubiquitinated, a post-translational modification mediated by an enzymatic cascade. To date, only one ubiquitin E3 ligase and one deubiquitinase have been identified in regulating Rab7 ubiquitination. Here, we report that RNF167, a transmembrane endolysosomal ubiquitin ligase, can ubiquitinate Rab7. Using immunoprecipitation and in vitro ubiquitination assays, we demonstrate that Rab7 is a direct substrate of RNF167. Subcellular fractionation indicates that RNF167 activity maintains Rab7′s membrane localization. Epifluorescence microscopy in HeLa cells shows that Rab7-positive vesicles are larger under conditions enabling Rab7 ubiquitination by RNF167. Characterization of its ubiquitination reveals that Rab7 must be in its GTP-bound active form for membrane anchoring and, thus, accessible for RNF167-mediated ubiquitin attachment. Cellular distribution analyses of lysosome marker Lamp1 show that vesicle positioning is independent of Rab7 and RNF167 expression and that Rab7 endosomal localization is not affected by RNF167 knockdown. However, both Rab7 and RNF167 depletion affect each other’s lysosomal localization. Finally, this study demonstrates that the RNF167-mediated ubiquitination of Rab7 GTPase is impaired by variants of Charcot–Marie–Tooth Type 2B disease. This study identified RNF167 as a new ubiquitin ligase for Rab7 while expanding our knowledge of the mechanisms underlying the ubiquitination of Rab7.
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Affiliation(s)
- Kim Ghilarducci
- Département de Chimie, Université du Québec à Montréal, Montréal, QC H2X 2J6, Canada; (K.G.); (V.C.C.); (A.H.); (L.C.)
- Centre d’Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada
| | - Valérie C. Cabana
- Département de Chimie, Université du Québec à Montréal, Montréal, QC H2X 2J6, Canada; (K.G.); (V.C.C.); (A.H.); (L.C.)
- Centre d’Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada
| | - Ali Harake
- Département de Chimie, Université du Québec à Montréal, Montréal, QC H2X 2J6, Canada; (K.G.); (V.C.C.); (A.H.); (L.C.)
- Centre d’Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada
| | - Laurent Cappadocia
- Département de Chimie, Université du Québec à Montréal, Montréal, QC H2X 2J6, Canada; (K.G.); (V.C.C.); (A.H.); (L.C.)
- Centre d’Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada
| | - Marc P. Lussier
- Département de Chimie, Université du Québec à Montréal, Montréal, QC H2X 2J6, Canada; (K.G.); (V.C.C.); (A.H.); (L.C.)
- Centre d’Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada
- Correspondence: ; Tel.: +1-514-987-3000 (ext. 5591); Fax: +1-514-987-4054
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31
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Vasconcelos-Cardoso M, Batista-Almeida D, Rios-Barros LV, Castro-Gomes T, Girao H. Cellular and molecular mechanisms underlying plasma membrane functionality and integrity. J Cell Sci 2022; 135:275922. [PMID: 35801807 DOI: 10.1242/jcs.259806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plasma membrane not only protects the cell from the extracellular environment, acting as a selective barrier, but also regulates cellular events that originate at the cell surface, playing a key role in various biological processes that are essential for the preservation of cell homeostasis. Therefore, elucidation of the mechanisms involved in the maintenance of plasma membrane integrity and functionality is of utmost importance. Cells have developed mechanisms to ensure the quality of proteins that inhabit the cell surface, as well as strategies to cope with injuries inflicted to the plasma membrane. Defects in these mechanisms can lead to the development or onset of several diseases. Despite the importance of these processes, a comprehensive and holistic perspective of plasma membrane quality control is still lacking. To tackle this gap, in this Review, we provide a thorough overview of the mechanisms underlying the identification and targeting of membrane proteins that are to be removed from the cell surface, as well as the membrane repair mechanisms triggered in both physiological and pathological conditions. A better understanding of the mechanisms underlying protein quality control at the plasma membrane can reveal promising and unanticipated targets for the development of innovative therapeutic approaches.
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Affiliation(s)
- Maria Vasconcelos-Cardoso
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
| | - Daniela Batista-Almeida
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
| | - Laura Valeria Rios-Barros
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901, Brazil
| | - Thiago Castro-Gomes
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901, Brazil
| | - Henrique Girao
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
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32
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Duncan ED, Han KJ, Trout MA, Prekeris R. Ubiquitylation by Rab40b/Cul5 regulates Rap2 localization and activity during cell migration. J Cell Biol 2022; 221:213068. [PMID: 35293963 PMCID: PMC8931537 DOI: 10.1083/jcb.202107114] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/08/2021] [Accepted: 02/01/2022] [Indexed: 02/07/2023] Open
Abstract
Cell migration is a complex process that involves coordinated changes in membrane transport and actin cytoskeleton dynamics. Ras-like small monomeric GTPases, such as Rap2, play a key role in regulating actin cytoskeleton dynamics and cell adhesions. However, how Rap2 function, localization, and activation are regulated during cell migration is not fully understood. We previously identified the small GTPase Rab40b as a regulator of breast cancer cell migration. Rab40b contains a suppressor of cytokine signaling (SOCS) box, which facilitates binding to Cullin5, a known E3 ubiquitin ligase component responsible for protein ubiquitylation. In this study, we show that the Rab40b/Cullin5 complex ubiquitylates Rap2. Importantly, we demonstrate that ubiquitylation regulates Rap2 activation as well as recycling of Rap2 from the endolysosomal compartment to the lamellipodia of migrating breast cancer cells. Based on these data, we propose that Rab40b/Cullin5 ubiquitylates and regulates Rap2-dependent actin dynamics at the leading edge, a process that is required for breast cancer cell migration and invasion.
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Affiliation(s)
- Emily D Duncan
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ke-Jun Han
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Margaret A Trout
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
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Aisenberg WH, McCray BA, Sullivan JM, Diehl E, DeVine LR, Alevy J, Bagnell AM, Carr P, Donohue JK, Goretzki B, Cole RN, Hellmich UA, Sumner CJ. Multiubiquitination of TRPV4 reduces channel activity independent of surface localization. J Biol Chem 2022; 298:101826. [PMID: 35300980 PMCID: PMC9010760 DOI: 10.1016/j.jbc.2022.101826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Ubiquitin (Ub)-mediated regulation of plasmalemmal ion channel activity canonically occurs via stimulation of endocytosis. Whether ubiquitination can modulate channel activity by alternative mechanisms remains unknown. Here, we show that the transient receptor potential vanilloid 4 (TRPV4) cation channel is multiubiquitinated within its cytosolic N-terminal and C-terminal intrinsically disordered regions (IDRs). Mutagenizing select lysine residues to block ubiquitination of the N-terminal but not C-terminal IDR resulted in a marked elevation of TRPV4-mediated intracellular calcium influx, without increasing cell surface expression levels. Conversely, enhancing TRPV4 ubiquitination via expression of an E3 Ub ligase reduced TRPV4 channel activity but did not decrease plasma membrane abundance. These results demonstrate Ub-dependent regulation of TRPV4 channel function independent of effects on plasma membrane localization. Consistent with ubiquitination playing a key negative modulatory role of the channel, gain-of-function neuropathy-causing mutations in the TRPV4 gene led to reduced channel ubiquitination in both cellular and Drosophila models of TRPV4 neuropathy, whereas increasing mutant TRPV4 ubiquitination partially suppressed channel overactivity. Together, these data reveal a novel mechanism via which ubiquitination of an intracellular flexible IDR domain modulates ion channel function independently of endocytic trafficking and identify a contributory role for this pathway in the dysregulation of TRPV4 channel activity by neuropathy-causing mutations.
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Affiliation(s)
- William H Aisenberg
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brett A McCray
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jeremy M Sullivan
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erika Diehl
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Lauren R DeVine
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jonathan Alevy
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anna M Bagnell
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Patrice Carr
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jack K Donohue
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Benedikt Goretzki
- Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence 'Balance of the Microverse', Friedrich-Schiller-Universität, Jena, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, Frankfurt am Main, Germany
| | - Robert N Cole
- Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence 'Balance of the Microverse', Friedrich-Schiller-Universität, Jena, Germany
| | - Ute A Hellmich
- Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence 'Balance of the Microverse', Friedrich-Schiller-Universität, Jena, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, Frankfurt am Main, Germany
| | - Charlotte J Sumner
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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Bowman RW, Jordahl EM, Davis S, Hedayati S, Barsouk H, Ozbaki-Yagan N, Chiang A, Li Y, O’Donnell AF. TORC1 Signaling Controls the Stability and Function of α-Arrestins Aly1 and Aly2. Biomolecules 2022; 12:biom12040533. [PMID: 35454122 PMCID: PMC9031309 DOI: 10.3390/biom12040533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
Nutrient supply dictates cell signaling changes, which in turn regulate membrane protein trafficking. To better exploit nutrients, cells relocalize membrane transporters via selective protein trafficking. Key in this reshuffling are the α-arrestins, selective protein trafficking adaptors conserved from yeast to man. α-Arrestins bind membrane proteins, controlling the ubiquitination and endocytosis of many transporters. To prevent the spurious removal of membrane proteins, α-arrestin-mediated endocytosis is kept in check through phospho-inhibition. This phospho-regulation is complex, with up to 87 phospho-sites on a single α-arrestin and many kinases/phosphatases targeting α-arrestins. To better define the signaling pathways controlling paralogous α-arrestins, Aly1 and Aly2, we screened the kinase and phosphatase deletion (KinDel) library, which is an array of all non-essential kinase and phosphatase yeast deletion strains, for modifiers of Aly-mediated phenotypes. We identified many Aly regulators, but focused our studies on the TORC1 kinase, a master regulator of nutrient signaling across eukaryotes. We found that TORC1 and its signaling effectors, the Sit4 protein phosphatase and Npr1 kinase, regulate the phosphorylation and stability of Alys. When Sit4 is lost, Alys are hyperphosphorylated and destabilized in an Npr1-dependent manner. These findings add new dimensions to our understanding of TORC1 regulation of α-arrestins and have important ramifications for cellular metabolism.
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Affiliation(s)
- Ray W. Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.W.B.II); (E.M.J.); (S.D.); (S.H.); (H.B.); (N.O.-Y.); (A.C.)
| | - Eric M. Jordahl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.W.B.II); (E.M.J.); (S.D.); (S.H.); (H.B.); (N.O.-Y.); (A.C.)
| | - Sydnie Davis
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.W.B.II); (E.M.J.); (S.D.); (S.H.); (H.B.); (N.O.-Y.); (A.C.)
| | - Stefanie Hedayati
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.W.B.II); (E.M.J.); (S.D.); (S.H.); (H.B.); (N.O.-Y.); (A.C.)
| | - Hannah Barsouk
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.W.B.II); (E.M.J.); (S.D.); (S.H.); (H.B.); (N.O.-Y.); (A.C.)
| | - Nejla Ozbaki-Yagan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.W.B.II); (E.M.J.); (S.D.); (S.H.); (H.B.); (N.O.-Y.); (A.C.)
| | - Annette Chiang
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.W.B.II); (E.M.J.); (S.D.); (S.H.); (H.B.); (N.O.-Y.); (A.C.)
| | - Yang Li
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA;
| | - Allyson F. O’Donnell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.W.B.II); (E.M.J.); (S.D.); (S.H.); (H.B.); (N.O.-Y.); (A.C.)
- Correspondence: ; Tel.: +1-412-648-4270
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Ubiquitination of the ubiquitin-binding machinery: how early ESCRT components are controlled. Essays Biochem 2022; 66:169-177. [PMID: 35352804 PMCID: PMC9400068 DOI: 10.1042/ebc20210042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/04/2022] [Accepted: 03/16/2022] [Indexed: 12/22/2022]
Abstract
To be able to quickly and accurately respond to the environment, cells need to tightly control the amount and localization of plasma membrane proteins. The post-translation modification by the protein modifier ubiquitin is the key signal for guiding membrane-associated cargo to the lysosome/vacuole for their degradation. The machinery responsible for such sorting contains several subunits that function as ubiquitin receptors, many of which are themselves subjected to ubiquitination. This review will focus on what is currently known about the modulation of the machinery itself by ubiquitination and how this might affect its function with a special emphasis on current findings from the plant field.
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36
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Li J, Hochstrasser M. Selective microautophagy of proteasomes is initiated by ESCRT-0 and is promoted by proteasome ubiquitylation. J Cell Sci 2022; 135:274460. [PMID: 35099016 PMCID: PMC8919337 DOI: 10.1242/jcs.259393] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/20/2022] [Indexed: 01/18/2023] Open
Abstract
The proteasome is central to proteolysis by the ubiquitin-proteasome system under normal growth conditions but is itself degraded through macroautophagy under nutrient stress. A recently described AMP-activated protein kinase (AMPK)-regulated endosomal sorting complex required for transport (ESCRT)-dependent microautophagy pathway also regulates proteasome trafficking and degradation in low-glucose conditions in yeast. Aberrant proteasomes are more prone to microautophagy, suggesting the ESCRT system fine-tunes proteasome quality control under low-glucose stress. Here, we uncover additional features of the selective microautophagy of proteasomes in budding yeast. Genetic or pharmacological induction of aberrant proteasomes is associated with increased mono- or oligo-ubiquitylation of proteasome components, which appears to be recognized by ESCRT-0. AMPK controls this pathway in part by regulating the trafficking of ESCRT-0 to the vacuole surface, which also leads to degradation of the Vps27 subunit of ESCRT-0. The Rsp5 ubiquitin ligase contributes to proteasome subunit ubiquitylation, and multiple ubiquitin-binding elements in Vps27 are involved in their recognition. We propose that ESCRT-0 at the vacuole surface recognizes ubiquitylated proteasomes and initiates their microautophagic elimination during glucose depletion. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Jianhui Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA,Author for correspondence ()
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37
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Wang T, Woodman P, Humphrey SJ, Petersen J. Environmental control of Pub1 (NEDD4 family E3 ligase) in Schizosaccharomyces pombe is regulated by TORC2 and Gsk3. Life Sci Alliance 2022; 5:5/5/e202101082. [PMID: 35121625 PMCID: PMC8817228 DOI: 10.26508/lsa.202101082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
The NEDD4 family E3 ligase Pub1 is regulated by the nutrient environment, TORC2, and Gsk3 signalling pathway to control the level of amino acid transporters on the plasma membrane and thus nutrient uptake. Cells respond to changing nutrient environments by adjusting the abundance of surface nutrient transporters and receptors. This can be achieved by modulating ubiquitin-dependent endocytosis, which in part is regulated by the NEDD4 family of E3 ligases. Here we report novel regulation of Pub1, a fission yeast Schizosaccharomyces pombe member of the NEDD4-family of E3 ligases. We show that nitrogen stress inhibits Pub1 function, thereby increasing the abundance of the amino acid transporter Aat1 at the plasma membrane and enhancing sensitivity to the toxic arginine analogue canavanine. We show that TOR complex 2 (TORC2) signalling negatively regulates Pub1, thus TORC2 mutants under nutrient stress have decreased Aat1 at the plasma membrane and are resistant to canavanine. Inhibition of TORC2 signalling increases Pub1 phosphorylation, and this is dependent on Gsk3 activity. Addition of the Tor inhibitor Torin1 increases phosphorylation of Pub1 at serine 199 (S199) by 2.5-fold, and Pub1 protein levels in S199A phospho-ablated mutants are reduced. S199 is conserved in NEDD4 and is located immediately upstream of a WW domain required for protein interaction. Together, we describe how the major TORC2 nutrient-sensing signalling network regulates environmental control of Pub1 to modulate the abundance of nutrient transporters.
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Affiliation(s)
- Tingting Wang
- Flinders Health and Medical Research Institute, Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, Australia
| | - Philip Woodman
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Sean J Humphrey
- Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia
| | - Janni Petersen
- Flinders Health and Medical Research Institute, Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, Australia
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38
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Priya A, Datta S. Monitoring Endosomal Cargo Retrieval to the Trans-Golgi Network by Microscopic and Biochemical Approaches. Methods Mol Biol 2022; 2473:213-236. [PMID: 35819769 DOI: 10.1007/978-1-0716-2209-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The endosomal recycling pathway plays a crucial role in diverse physiologically important biological processes such as cell-to-cell signaling, nutrient uptake, immune response, and autophagy. A selective subset of these recycling cargoes, mostly transmembrane proteins, is retrieved from endosomes to the trans-Golgi network (TGN) by a retrograde transport process. Endosome-to-TGN retrograde trafficking is crucial for maintaining cellular homeostasis and signaling by preventing proteins and lipids from degradation in the lysosome. Many of the membrane sorting machinery, such as the retromer complex and sorting nexins (SNXs) are involved in endosomal retrieval and recycling of various transmembrane proteins. Recent technological advances in the resolution of light microscopy and unbiased analytical approaches in quantitative image analysis enable us to explore and understand the regulation of membrane trafficking pathways in greater detail. In this chapter, we describe quantitative imaging-based methods for analyzing the roles of proteins involved in the retrograde trafficking in retromer dependent or independent fashion, using cation-independent mannose-6-phosphate receptor (CIM6PR) as an example.
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Affiliation(s)
- Amulya Priya
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France.
| | - Sunando Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
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Pashkova N, Gakhar L, Yu L, Schnicker NJ, Minard AY, Winistorfer S, Johnson IE, Piper RC. ANTH domains within CALM, HIP1R, and Sla2 recognize ubiquitin internalization signals. eLife 2021; 10:72583. [PMID: 34821552 PMCID: PMC8648300 DOI: 10.7554/elife.72583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Attachment of ubiquitin (Ub) to cell surface proteins serves as a signal for internalization via clathrin-mediated endocytosis (CME). How ubiquitinated membrane proteins engage the internalization apparatus remains unclear. The internalization apparatus contains proteins such as Epsin and Eps15, which bind Ub, potentially acting as adaptors for Ub-based internalization signals. Here, we show that additional components of the endocytic machinery including CALM, HIP1R, and Sla2 bind Ub via their N-terminal ANTH domain, a domain belonging to the superfamily of ENTH and VHS domains. Structural studies revealed that Ub binds with µM affinity to a unique C-terminal region within the ANTH domain not found in ENTH domains. Functional studies showed that combined loss of Ub-binding by ANTH-domain proteins and other Ub-binding domains within the yeast internalization apparatus caused defects in the Ub-dependent internalization of the GPCR Ste2 that was engineered to rely exclusively on Ub as an internalization signal. In contrast, these mutations had no effect on the internalization of Ste2 engineered to use an alternate Ub-independent internalization signal. These studies define new components of the internalization machinery that work collectively with Epsin and Eps15 to specify recognition of Ub as an internalization signal.
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Affiliation(s)
- Natalya Pashkova
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Lokesh Gakhar
- Carver College of Medicine Protein Crystallography Core, University of Iowa, Iowa City, United States.,Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, United States
| | - Liping Yu
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, United States.,Carver College of Medicine NMR Core, University of Iowa, Iowa City, United States
| | - Nicholas J Schnicker
- Carver College of Medicine Protein Crystallography Core, University of Iowa, Iowa City, United States
| | - Annabel Y Minard
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Stanley Winistorfer
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Ivan E Johnson
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
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40
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Jenkin KA, Han Y, Lin S, He P, Yun CC. Nedd4-2-dependent Ubiquitination Potentiates the Inhibition of Human NHE3 by Cholera Toxin and Enteropathogenic Escherichia coli. Cell Mol Gastroenterol Hepatol 2021; 13:695-716. [PMID: 34823064 PMCID: PMC8789535 DOI: 10.1016/j.jcmgh.2021.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Diarrhea is one of the most common illnesses and is often caused by bacterial infection. Recently, we have shown that human Na+/H+ exchanger NHE3 (hNHE3), but not non-human NHE3s, interacts with the E3 ubiquitin ligase Nedd4-2. We hypothesize that this property of hNHE3 contributes to the increased severity of diarrhea in humans. METHODS We used humanized mice expressing hNHE3 in the intestine (hNHE3int) to compare the contribution of hNHE3 and mouse NHE3 to diarrhea induced by cholera toxin (CTX) and enteropathogenic Escherichia coli (EPEC). We measured Na+/H+ exchange activity and fluid absorption. The role of Nedd4-2 on hNHE3 activity and ubiquitination was determined by knockdown in Caco-2bbe cells. The effects of protein kinase A (PKA), the primary mediator of CTX-induced diarrhea, on Nedd4-2 and hNHE3 phosphorylation and their interaction were determined. RESULTS The effects of CTX and EPEC were greater in hNHE3int mice than in control wild-type (WT) mice, resulting in greater inhibition of NHE3 activity and increased fluid accumulation in the intestine, the hallmark of diarrhea. Activation of PKA increased ubiquitination of hNHE3 and enhanced interaction of Nedd4-2 with hNHE3 via phosphorylation of Nedd4-2 at S342. S342A mutation mitigated the Nedd4-2-hNHE3 interaction and blocked PKA-induced inhibition of hNHE3. Unlike non-human NHE3s, inhibition of hNHE3 by PKA is independent of NHE3 phosphorylation, suggesting a distinct mechanism of hNHE3 regulation. CONCLUSIONS The effects of CTX and EPEC on hNHE3 are amplified, and the unique properties of hNHE3 may contribute to diarrheal symptoms occurring in humans.
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Affiliation(s)
- Kayte A. Jenkin
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia,School of Science, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Yiran Han
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia,Atlanta VA Medical Center, Decatur, Georgia
| | - Songbai Lin
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia,Atlanta VA Medical Center, Decatur, Georgia
| | - Peijian He
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - C. Chris Yun
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia,Atlanta VA Medical Center, Decatur, Georgia,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia,Correspondence Address correspondence to: Chris Yun, PhD, Division of Digestive Diseases, Emory University School of Medicine, Atlanta, Georgia 30324. fax: (404) 727-5767.
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41
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Welch MA, Jansen LAR, Baro DJ. SUMOylation of the Kv4.2 Ternary Complex Increases Surface Expression and Current Amplitude by Reducing Internalization in HEK 293 Cells. Front Mol Neurosci 2021; 14:757278. [PMID: 34795560 PMCID: PMC8593141 DOI: 10.3389/fnmol.2021.757278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/05/2021] [Indexed: 11/29/2022] Open
Abstract
Kv4 α-subunits exist as ternary complexes (TC) with potassium channel interacting proteins (KChIP) and dipeptidyl peptidase-like proteins (DPLP); multiple ancillary proteins also interact with the α-subunits throughout the channel’s lifetime. Dynamic regulation of Kv4.2 protein interactions adapts the transient potassium current, IA, mediated by Kv4 α-subunits. Small ubiquitin-like modifier (SUMO) is an 11 kD peptide post-translationally added to lysine (K) residues to regulate protein–protein interactions. We previously demonstrated that when expressed in human embryonic kidney (HEK) cells, Kv4.2 can be SUMOylated at two K residues, K437 and K579. SUMOylation at K437 increased surface expression of electrically silent channels while SUMOylation at K579 reduced IA maximal conductance (Gmax) without altering surface expression. KChIP and DPLP subunits are known to modify the pattern of Kv4.2 post-translational decorations and/or their effects. In this study, co-expressing Kv4.2 with KChIP2a and DPP10c altered the effects of enhanced Kv4.2 SUMOylation. First, the effect of enhanced SUMOylation was the same for a TC containing either the wild-type Kv4.2 or the mutant K437R Kv4.2, suggesting that either the experimental manipulation no longer enhanced K437 SUMOylation or K437 SUMOylation no longer influenced Kv4.2 surface expression. Second, instead of decreasing IA Gmax, enhanced SUMOylation at K579 now produced a significant ∼37–70% increase in IA maximum conductance (Gmax) and a significant ∼30–50% increase in Kv4.2g surface expression that was accompanied by a 65% reduction in TC internalization. Blocking clathrin-mediated endocytosis (CME) in HEK cells expressing the Kv4.2 TC mimicked and occluded the effect of SUMO on IA Gmax; however, the amount of Kv4.2 associated with the major adaptor for constitutive CME, adaptor protein 2 (AP2), was not SUMO dependent. Thus, SUMOylation reduced Kv4.2 internalization by acting downstream of Kv4.2 recruitment into clathrin-coated pits. In sum, the two major findings of this study are: SUMOylation of Kv4.2 at K579 regulates TC internalization most likely by promoting channel recycling. Additionally, there is a reciprocity between Kv4.2 SUMOylation and the Kv4.2 interactome such that SUMOylation regulates the interactome and the interactome influences the pattern and effect of SUMOylation.
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Affiliation(s)
- Meghyn A Welch
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | | | - Deborah J Baro
- Department of Biology, Georgia State University, Atlanta, GA, United States.,Neuroscience Institute, Georgia State University, Atlanta, GA, United States
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42
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Kazan JM, Desrochers G, Martin CE, Jeong H, Kharitidi D, Apaja PM, Roldan A, St. Denis N, Gingras AC, Lukacs GL, Pause A. Endofin is required for HD-PTP and ESCRT-0 interdependent endosomal sorting of ubiquitinated transmembrane cargoes. iScience 2021; 24:103274. [PMID: 34761192 PMCID: PMC8567383 DOI: 10.1016/j.isci.2021.103274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/18/2021] [Accepted: 10/12/2021] [Indexed: 11/20/2022] Open
Abstract
Internalized and ubiquitinated signaling receptors are silenced by their intraluminal budding into multivesicular bodies aided by the endosomal sorting complexes required for transport (ESCRT) machinery. HD-PTP, an ESCRT protein, forms complexes with ESCRT-0, -I and -III proteins, and binds to Endofin, a FYVE-domain protein confined to endosomes with poorly understood roles. Using proximity biotinylation, we showed that Endofin forms a complex with ESCRT constituents and Endofin depletion increased integrin α5-and EGF-receptor plasma membrane density and stability by hampering their lysosomal delivery. This coincided with sustained receptor signaling and increased cell migration. Complementation of Endofin- or HD-PTP-depleted cells with wild-type Endofin or HD-PTP, but not with mutants harboring impaired Endofin/HD-PTP association or cytosolic Endofin, restored EGFR lysosomal delivery. Endofin also promoted Hrs indirect interaction with HD-PTP. Jointly, our results indicate that Endofin is required for HD-PTP and ESCRT-0 interdependent sorting of ubiquitinated transmembrane cargoes to ensure efficient receptor desensitization and lysosomal delivery.
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Affiliation(s)
- Jalal M. Kazan
- Goodman Cancer Research Center, McGill University, Montreal, QC H3A 1A3, Canada
- Biochemistry Department, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Guillaume Desrochers
- Goodman Cancer Research Center, McGill University, Montreal, QC H3A 1A3, Canada
- Biochemistry Department, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Claire E. Martin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Hyeonju Jeong
- Goodman Cancer Research Center, McGill University, Montreal, QC H3A 1A3, Canada
- Biochemistry Department, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Dmitri Kharitidi
- Goodman Cancer Research Center, McGill University, Montreal, QC H3A 1A3, Canada
- Biochemistry Department, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Pirjo M. Apaja
- Physiology Department, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Ariel Roldan
- Physiology Department, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Nicole St. Denis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gergely L. Lukacs
- Biochemistry Department, McGill University, Montreal, QC H3G 1Y6, Canada
- Physiology Department, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Arnim Pause
- Goodman Cancer Research Center, McGill University, Montreal, QC H3A 1A3, Canada
- Biochemistry Department, McGill University, Montreal, QC H3G 1Y6, Canada
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Amoiradaki K, Bunting KR, Paine KM, Ayre JE, Hogg K, Laidlaw KME, MacDonald C. The Rpd3-Complex Regulates Expression of Multiple Cell Surface Recycling Factors in Yeast. Int J Mol Sci 2021; 22:12477. [PMID: 34830359 PMCID: PMC8617818 DOI: 10.3390/ijms222212477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
Intracellular trafficking pathways control residency and bioactivity of integral membrane proteins at the cell surface. Upon internalisation, surface cargo proteins can be delivered back to the plasma membrane via endosomal recycling pathways. Recycling is thought to be controlled at the metabolic and transcriptional level, but such mechanisms are not fully understood. In yeast, recycling of surface proteins can be triggered by cargo deubiquitination and a series of molecular factors have been implicated in this trafficking. In this study, we follow up on the observation that many subunits of the Rpd3 lysine deacetylase complex are required for recycling. We validate ten Rpd3-complex subunits in recycling using two distinct assays and developed tools to quantify both. Fluorescently labelled Rpd3 localises to the nucleus and complements recycling defects, which we hypothesised were mediated by modulated expression of Rpd3 target gene(s). Bioinformatics implicated 32 candidates that function downstream of Rpd3, which were over-expressed and assessed for capacity to suppress recycling defects of rpd3∆ cells. This effort yielded three hits: Sit4, Dit1 and Ldb7, which were validated with a lipid dye recycling assay. Additionally, the essential phosphatidylinositol-4-kinase Pik1 was shown to have a role in recycling. We propose recycling is governed by Rpd3 at the transcriptional level via multiple downstream target genes.
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Affiliation(s)
- Konstantina Amoiradaki
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Kate R. Bunting
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Katherine M. Paine
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Josephine E. Ayre
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Karen Hogg
- Imaging and Cytometry Laboratory, Bioscience Technology Facility, University of York, York YO10 5DD, UK;
| | - Kamilla M. E. Laidlaw
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
| | - Chris MacDonald
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK; (K.A.); (K.R.B.); (K.M.P.); (J.E.A.); (K.M.E.L.)
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44
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Parkinson G, Roboti P, Zhang L, Taylor S, Woodman P. His domain protein tyrosine phosphatase and Rabaptin-5 couple endo-lysosomal sorting of EGFR with endosomal maturation. J Cell Sci 2021; 134:272512. [PMID: 34657963 PMCID: PMC8627557 DOI: 10.1242/jcs.259192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/13/2021] [Indexed: 01/20/2023] Open
Abstract
His domain protein tyrosine phosphatase (HD-PTP; also known as PTPN23) collaborates with endosomal sorting complexes required for transport (ESCRTs) to sort endosomal cargo into intralumenal vesicles, forming the multivesicular body (MVB). Completion of MVB sorting is accompanied by maturation of the endosome into a late endosome, an event that requires inactivation of the early endosomal GTPase Rab5 (herein referring to generically to all isoforms). Here, we show that HD-PTP links ESCRT function with endosomal maturation. HD-PTP depletion prevents MVB sorting, while also blocking cargo from exiting Rab5-rich endosomes. HD-PTP-depleted cells contain hyperphosphorylated Rabaptin-5 (also known as RABEP1), a cofactor for the Rab5 guanine nucleotide exchange factor Rabex-5 (also known as RABGEF1), although HD-PTP is unlikely to directly dephosphorylate Rabaptin-5. In addition, HD-PTP-depleted cells exhibit Rabaptin-5-dependent hyperactivation of Rab5. HD-PTP binds directly to Rabaptin-5, between its Rabex-5- and Rab5-binding domains. This binding reaction involves the ESCRT-0/ESCRT-III binding site in HD-PTP, which is competed for by an ESCRT-III peptide. Jointly, these findings indicate that HD-PTP may alternatively scaffold ESCRTs and modulate Rabex-5–Rabaptin-5 activity, thereby helping to coordinate the completion of MVB sorting with endosomal maturation. Summary: Sorting of endocytic cargo to the multivesicular body is accompanied by endosomal maturation. Here, we provide a potential mechanism by which these two processes are linked.
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Affiliation(s)
- Gabrielle Parkinson
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Peristera Roboti
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Ling Zhang
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Sandra Taylor
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Philip Woodman
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
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Pashkova N, Yu L, Schnicker NJ, Tseng CC, Gakhar L, Katzmann DJ, Piper RC. Interactions of ubiquitin and CHMP5 with the V domain of HD-PTP reveals role for regulation of Vps4 ATPase. Mol Biol Cell 2021; 32:ar42. [PMID: 34586919 PMCID: PMC8694081 DOI: 10.1091/mbc.e21-04-0219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The family of Bro1 proteins coordinates the activity of the Endosomal Sorting Complexes Required for Transport (ESCRTs) to mediate a number of membrane remodeling events. These events culminate in membrane scission catalyzed by ESCRT-III, whose polymerization and disassembly is controlled by the AAA-ATPase, Vps4. Bro1-family members Alix and HD-PTP as well as yeast Bro1 have central “V” domains that noncovalently bind Ub and connect ubiquitinated proteins to ESCRT-driven functions such as the incorporation of ubiquitinated membrane proteins into intralumenal vesicles of multivesicular bodies. Recently, it was discovered that the V domain of yeast Bro1 binds the MIT domain of Vps4 to stimulate its ATPase activity. Here we determine the structural basis for how the V domain of human HD-PTP binds ubiquitin. The HD-PTP V domain also binds the MIT domain of Vps4, and ubiquitin binding to the HD-PTP V domain enhances its ability to stimulate Vps4 ATPase activity. Additionally, we found that V domains of both HD-PTP and Bro1 bind CHMP5 and Vps60, respectively, providing another potential molecular mechanism to alter Vps4 activity. These data support a model whereby contacts between ubiquitin, ESCRT-III, and Vps4 by V domains of the Bro1 family may coordinate late events in ESCRT-driven membrane remodeling events.
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Affiliation(s)
- Natalya Pashkova
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242
| | - Liping Yu
- NMR facility, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242.,Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242
| | | | - Chun-Che Tseng
- Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, 55905.,Protein Crystallography Facility, University of Iowa, Iowa City, IA, 52242
| | - Lokesh Gakhar
- Protein Crystallography Facility, University of Iowa, Iowa City, IA, 52242
| | - David J Katzmann
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242
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46
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Rab11-FIP1 and Rab11-FIP5 Regulate pIgR/pIgA Transcytosis through TRIM21-Mediated Polyubiquitination. Int J Mol Sci 2021; 22:ijms221910466. [PMID: 34638806 PMCID: PMC8508952 DOI: 10.3390/ijms221910466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/01/2023] Open
Abstract
Polymeric immunoglobulin receptor (pIgR)-mediated polymeric immunoglobulin A (pIgA) transcytosis across mucosal epithelial cells plays an essential role in mucosal immunity. The general trafficking process has been well investigated, yet the elaborate regulatory mechanisms remain enigmatic. We identified a new pIgR interacting protein, the Rab11 effector Rab11-FIP1. Rab11-FIP1 and Rab11-FIP5 knockdown additively impaired pIgA transcytosis in both polarized and incompletely polarized cells. Moreover, Rab11-FIP1 and Rab11-FIP5 knockdown exhibited more significant inhibitory effects on pIgA transcytosis in incompletely polarized cells than in polarized cells. Interestingly, the trafficking process of pIgA in incompletely polarized cells is distinct from that in polarized cells. In incompletely polarized cells, the endocytic pIgR/pIgA was first transported from the basolateral plasma membrane to the vicinity of the centrosome where Rab11-FIP1 and Rab11-FIP5 bound to it, before the Rab11a-positive endosomes containing pIgR/pIgA, Rab11-FIP1 and Rab11-FIP5 were further transported to the apical plasma membrane via Golgi apparatus. During the trafficking process, TRIM21 mediated the K11-linked polyubiquitination of Rab11-FIP1 and the K6-linked polyubiquitination of Rab11-FIP5 to promote their activation and pIgA transcytosis. This study indicates that polyubiquitinated Rab11-FIP1 and Rab11-FIP5 mediated by TRIM21 cooperatively facilitate pIgA transcytosis and provides new insights into the intracellular trafficking process of pIgA in incompletely polarized cells.
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47
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Ramesh ST, Navyasree KV, Sah S, Ashok AB, Qathoon N, Mohanty S, Swain RK, Umasankar PK. BMP2K phosphorylates AP-2 and regulates clathrin-mediated endocytosis. Traffic 2021; 22:377-396. [PMID: 34480404 DOI: 10.1111/tra.12814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 01/29/2023]
Abstract
Phosphorylation of the central adaptor protein complex, AP-2 is pivotal for clathrin-mediated endocytosis (CME). Here, we uncover the role of an uncharacterized kinase (BMP-2 inducible kinase-BMP2K) in AP-2 phosphorylation. We demonstrate that BMP2K can phosphorylate AP-2 in vitro and in vivo. Functional impairment of BMP2K impedes AP-2 phosphorylation leading to defects in clathrin-coated pit (CCP) morphology and cargo internalization. BMP2K engages AP-2 via its extended C-terminus and this interaction is important for its CCP localization and function. Notably, endogenous BMP2K levels decline upon functional impairment of AP-2 indicating AP-2 dependent BMP2K stabilization in cells. Further, functional inactivation of BMP2K in zebrafish embryos yields gastrulation phenotypes which mirror AP-2 loss-of-function suggesting physiological relevance of BMP2K in vertebrates. Together, our findings propose involvement of a novel kinase in AP-2 phosphorylation and in the operation of CME.
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Affiliation(s)
- Shikha T Ramesh
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.,Centre for Doctoral Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Kolaparamba V Navyasree
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.,Centre for Doctoral Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sneha Sah
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Anjitha B Ashok
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Nishada Qathoon
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | | | | | - Perunthottathu K Umasankar
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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48
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Snyder NA, Silva GM. Deubiquitinating enzymes (DUBs): Regulation, homeostasis, and oxidative stress response. J Biol Chem 2021; 297:101077. [PMID: 34391779 PMCID: PMC8424594 DOI: 10.1016/j.jbc.2021.101077] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Ubiquitin signaling is a conserved, widespread, and dynamic process in which protein substrates are rapidly modified by ubiquitin to impact protein activity, localization, or stability. To regulate this process, deubiquitinating enzymes (DUBs) counter the signal induced by ubiquitin conjugases and ligases by removing ubiquitin from these substrates. Many DUBs selectively regulate physiological pathways employing conserved mechanisms of ubiquitin bond cleavage. DUB activity is highly regulated in dynamic environments through protein-protein interaction, posttranslational modification, and relocalization. The largest family of DUBs, cysteine proteases, are also sensitive to regulation by oxidative stress, as reactive oxygen species (ROS) directly modify the catalytic cysteine required for their enzymatic activity. Current research has implicated DUB activity in human diseases, including various cancers and neurodegenerative disorders. Due to their selectivity and functional roles, DUBs have become important targets for therapeutic development to treat these conditions. This review will discuss the main classes of DUBs and their regulatory mechanisms with a particular focus on DUB redox regulation and its physiological impact during oxidative stress.
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Affiliation(s)
- Nathan A Snyder
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, North Carolina, USA.
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49
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Historical perspective and progress on protein ubiquitination at glutamatergic synapses. Neuropharmacology 2021; 196:108690. [PMID: 34197891 DOI: 10.1016/j.neuropharm.2021.108690] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/07/2021] [Accepted: 06/22/2021] [Indexed: 12/23/2022]
Abstract
Transcription-translation coupling leads to the production of proteins that are key for controlling essential neuronal processes that include neuronal development and changes in synaptic strength. Although these events have been a prevailing theme in neuroscience, the regulation of proteins via posttranslational signaling pathways are equally relevant for these neuronal processes. Ubiquitin is one type of posttranslational modification that covalently attaches to its targets/substrates. Ubiquitination of proteins play a key role in multiple signaling pathways, the predominant being removal of its substrates by a large molecular machine called the proteasome. Here, I review 40 years of progress on ubiquitination in the nervous system at glutamatergic synapses focusing on axon pathfinding, synapse formation, presynaptic release, dendritic spine formation, and regulation of postsynaptic glutamate receptors. Finally, I elucidate emerging themes in ubiquitin biology that may challenge our current understanding of ubiquitin signaling in the nervous system.
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50
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Tada T, Zhang Y, Fujita H, Tokunaga K. MARCH8: the tie that binds to viruses. FEBS J 2021; 289:3642-3654. [PMID: 33993615 DOI: 10.1111/febs.16017] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/23/2021] [Accepted: 05/12/2021] [Indexed: 11/28/2022]
Abstract
Membrane-associated RING-CH (MARCH) family member proteins are RING-finger E3 ubiquitin ligases that are known to downregulate cellular transmembrane proteins. MARCH8 is a novel antiviral factor that inhibits HIV-1 envelope glycoprotein and vesicular stomatitis virus G by downregulating these envelope glycoproteins from the cell surface, resulting in their reduced incorporation into virions. More recently, we have found that MARCH8 reduces viral infectivity via two different mechanisms. Additionally, several groups have reported further antiviral or virus-supportive functions of the MARCH8 protein and its other cellular mechanisms. In this review, we summarize the current knowledge about the molecular mechanisms by which MARCH8 can regulate cellular homeostasis and inhibit and occasionally support enveloped virus infection.
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Affiliation(s)
- Takuya Tada
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Microbiology, NYU School of Medicine, NY, USA
| | - Yanzhao Zhang
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideaki Fujita
- Faculty of Pharmaceutical Sciences, Nagasaki International University, Japan
| | - Kenzo Tokunaga
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
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