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Gautam A, Lalande A, Ritter M, Freitas N, Lerolle S, Canus L, Amirache F, Lotteau V, Legros V, Cosset FL, Mathieu C, Boson B. The PACS-2 protein and trafficking motifs in CCHFV Gn and Gc cytoplasmic domains govern CCHFV assembly. Emerg Microbes Infect 2024; 13:2348508. [PMID: 38661085 PMCID: PMC11159592 DOI: 10.1080/22221751.2024.2348508] [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] [Received: 01/25/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024]
Abstract
The Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne bunyavirus that causes high mortality in humans. This enveloped virus harbors two surface glycoproteins (GP), Gn and Gc, that are released by processing of a glycoprotein precursor complex whose maturation takes place in the ER and is completed through the secretion pathway. Here, we characterized the trafficking network exploited by CCHFV GPs during viral assembly, envelopment, and/or egress. We identified membrane trafficking motifs in the cytoplasmic domains (CD) of CCHFV GPs and addressed how they impact these late stages of the viral life cycle using infection and biochemical assays, and confocal microscopy in virus-producing cells. We found that several of the identified CD motifs modulate GP transport through the retrograde trafficking network, impacting envelopment and secretion of infectious particles. Finally, we identified PACS-2 as a crucial host factor contributing to CCHFV GPs trafficking required for assembly and release of viral particles.
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Affiliation(s)
- Anupriya Gautam
- CIRI – Centre International de Recherche en Infectiologie, Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Alexandre Lalande
- CIRI – Centre International de Recherche en Infectiologie, Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Maureen Ritter
- CIRI – Centre International de Recherche en Infectiologie, Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Natalia Freitas
- CIRI – Centre International de Recherche en Infectiologie, Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Solène Lerolle
- CIRI – Centre International de Recherche en Infectiologie, Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Lola Canus
- CIRI – Centre International de Recherche en Infectiologie, Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Fouzia Amirache
- CIRI – Centre International de Recherche en Infectiologie, Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Vincent Legros
- CIRI – Centre International de Recherche en Infectiologie, Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Campus vétérinaire de Lyon, VetAgro Sup, Université de Lyon, Marcy-l’Etoile, France
| | - François-Loïc Cosset
- CIRI – Centre International de Recherche en Infectiologie, Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Cyrille Mathieu
- CIRI – Centre International de Recherche en Infectiologie, Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Bertrand Boson
- CIRI – Centre International de Recherche en Infectiologie, Univ. Lyon, Université Claude Bernard Lyon 1, Lyon, France
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2
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Xiao L, Pi X, Goss AC, El-Baba T, Ehrmann JF, Grinkevich E, Bazua-Valenti S, Padovano V, Alper SL, Carey D, Udeshi ND, Carr SA, Pablo JL, Robinson CV, Greka A, Wu H. Molecular basis of TMED9 oligomerization and entrapment of misfolded protein cargo in the early secretory pathway. SCIENCE ADVANCES 2024; 10:eadp2221. [PMID: 39303030 PMCID: PMC11414720 DOI: 10.1126/sciadv.adp2221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 08/14/2024] [Indexed: 09/22/2024]
Abstract
Intracellular accumulation of misfolded proteins causes serious human proteinopathies. The transmembrane emp24 domain 9 (TMED9) cargo receptor promotes a general mechanism of cytotoxicity by entrapping misfolded protein cargos in the early secretory pathway. However, the molecular basis for this TMED9-mediated cargo retention remains elusive. Here, we report cryo-electron microscopy structures of TMED9, which reveal its unexpected self-oligomerization into octamers, dodecamers, and, by extension, even higher-order oligomers. The TMED9 oligomerization is driven by an intrinsic symmetry mismatch between the trimeric coiled coil domain and the tetrameric transmembrane domain. Using frameshifted Mucin 1 as an example of aggregated disease-related protein cargo, we implicate a mode of direct interaction with the TMED9 luminal Golgi-dynamics domain. The structures suggest and we confirm that TMED9 oligomerization favors the recruitment of coat protein I (COPI), but not COPII coatomers, facilitating retrograde transport and explaining the observed cargo entrapment. Our work thus reveals a molecular basis for TMED9-mediated misfolded protein retention in the early secretory pathway.
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Affiliation(s)
- Le Xiao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Xiong Pi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Alissa C. Goss
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tarick El-Baba
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Julian F. Ehrmann
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Elizabeth Grinkevich
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Silvana Bazua-Valenti
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Seth L. Alper
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Nephrology, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Dominique Carey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Steven A. Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Juan Lorenzo Pablo
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Anna Greka
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
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3
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Yakovleva E, Zhang B. Clinical, Laboratory, Molecular, and Reproductive Aspects of Combined Deficiency of Factors V and VIII. Semin Thromb Hemost 2024. [PMID: 39209292 DOI: 10.1055/s-0044-1789019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Congenital combined deficiency of factor V (FV) and factor VIII (FVIII; F5F8D, OMIM 227300) is a rare hereditary coagulopathy and accounts for approximately 3% of cases of rare coagulation disorders. The prevalence of this disease in the general population is estimated to be 1:1,000,000 and is significantly higher in regions where consanguineous marriages are permitted, such as the Mideast and South Asia. The disease has an autosomal recessive mode of inheritance and therefore occurs with an equal incidence among males and females. Heterozygous mutation carriers usually do not have clinical manifestations. The molecular basis of this disease differs from that of stand-alone congenital deficiencies of FVIII and FV. F5F8D is caused by mutations in either LMAN1 or MCFD2, which encode components of a cargo receptor complex for endoplasmic reticulum to Golgi transport of FV and FVIII, leading to defects in an intracellular transport pathway shared by these two coagulation factors. Congenital combined deficiency of FV and FVIII is characterized by decreased activities of both FV and FVIII in plasma, usually to 5 to 30% of normal. Clinical manifestations in most cases are represented by mild or moderate hemorrhagic syndrome. The simultaneous decreases of two coagulation factors present complications in the diagnosis and management of the disease. In female patients, the disease requires a special approach for family planning, pregnancy management, and parturition. This review summarizes recent progress in clinical, laboratory, and molecular understanding of this disorder.
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Affiliation(s)
- Elena Yakovleva
- Clinical and Diagnostic Department of Hematology and Hemostasis Disorders, National Medical Research Center for Hematology, Novy Zykovsky, Russia
| | - Bin Zhang
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
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Iswanto ABB, Vu MH, Shon JC, Kumar R, Wu S, Kang H, Kim DR, Son GH, Kim WY, Kwak YS, Liu KH, Kim SH, Kim JY. α1-COP modulates plasmodesmata function through sphingolipid enzyme regulation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1639-1657. [PMID: 38888228 DOI: 10.1111/jipb.13711] [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: 09/27/2023] [Accepted: 04/30/2024] [Indexed: 06/20/2024]
Abstract
Callose, a β-1,3-glucan plant cell wall polymer, regulates symplasmic channel size at plasmodesmata (PD) and plays a crucial role in a variety of plant processes. However, elucidating the molecular mechanism of PD callose homeostasis is limited. We screened and identified an Arabidopsis mutant plant with excessive callose deposition at PD and found that the mutated gene was α1-COP, a member of the coat protein I (COPI) coatomer complex. We report that loss of function of α1-COP elevates the callose accumulation at PD by affecting subcellular protein localization of callose degradation enzyme PdBG2. This process is linked to the functions of ERH1, an inositol phosphoryl ceramide synthase, and glucosylceramide synthase through physical interactions with the α1-COP protein. Additionally, the loss of function of α1-COP alters the subcellular localization of ERH1 and GCS proteins, resulting in a reduction of GlcCers and GlcHCers molecules, which are key sphingolipid (SL) species for lipid raft formation. Our findings suggest that α1-COP protein, together with SL modifiers controlling lipid raft compositions, regulates the subcellular localization of GPI-anchored PDBG2 proteins, and hence the callose turnover at PD and symplasmic movement of biomolecules. Our findings provide the first key clue to link the COPI-mediated intracellular trafficking pathway to the callose-mediated intercellular signaling pathway through PD.
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Affiliation(s)
- Arya Bagus Boedi Iswanto
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Minh Huy Vu
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Jong Cheol Shon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 702-701, Korea
| | - Ritesh Kumar
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Shuwei Wu
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Hobin Kang
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Da-Ran Kim
- Departement of Plant Medicine, Gyeongsang National University, Jinju, 52828, Korea
| | - Geon Hui Son
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Woe Yoen Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Youn-Sig Kwak
- Departement of Plant Medicine, Gyeongsang National University, Jinju, 52828, Korea
| | - Kwang Hyeon Liu
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 702-701, Korea
| | - Sang Hee Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
- Division of Life Science, Gyeongsang National University, Jinju, 52828, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
- Division of Life Science, Gyeongsang National University, Jinju, 52828, Korea
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5
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He J, Zhang L. The journey of STING: Guiding immune signaling through membrane trafficking. Cytokine Growth Factor Rev 2024; 78:25-36. [PMID: 39019665 DOI: 10.1016/j.cytogfr.2024.07.003] [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] [Received: 05/09/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/19/2024]
Abstract
Stimulator of Interferon Genes (STING) serves as a pivotal mediator in the innate immune signaling pathway, transducing signals from various DNA receptors and playing a crucial role in natural immune processes. During cellular quiescence, STING protein resides in the endoplasmic reticulum (ER), and its activation typically occurs through the cGAS-STING signaling pathway. Upon activation, STING protein is transported to the Golgi apparatus, thereby initiating downstream signaling cascades. Vesicular transport serves as the primary mechanism for STING protein trafficking between the ER and Golgi apparatus, with COPII mediating anterograde transport from the ER to Golgi apparatus, while COPI is responsible for retrograde transport. Numerous factors influence these transport processes, thereby exerting either promoting or inhibitory effects on STING protein expression. Upon reaching the Golgi apparatus, to prevent over-activation, STING protein is transported to post-Golgi compartments for degradation. In addition to the conventional lysosomal degradation pathway, ESCRT has also been identified as one of the degradation pathways for STING protein. This review summarizes the recent findings on the membrane trafficking pathways of STING, highlighting their contributions to the regulation of cytokine production, the activation of immune cells, and the coordination of immune signaling pathways.
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Affiliation(s)
- Jingyi He
- Department of Infectious Diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China; Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Leiliang Zhang
- Department of Infectious Diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China; Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China.
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6
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Liang R, Liu K, Li Y, Zhang X, Duan L, Huang M, Sun L, Yuan F, Zhao J, Zhao Y, Zhang G. Adaptive truncation of the S gene in IBV during chicken embryo passaging plays a crucial role in its attenuation. PLoS Pathog 2024; 20:e1012415. [PMID: 39078847 PMCID: PMC11315334 DOI: 10.1371/journal.ppat.1012415] [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: 02/02/2024] [Revised: 08/09/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Like all coronaviruses, infectious bronchitis virus, the causative agent of infectious bronchitis in chickens, exhibits a high mutation rate. Adaptive mutations that arise during the production of live attenuated vaccines against IBV often decrease virulence. The specific impact of these mutations on viral pathogenicity, however, has not been fully elucidated. In this study, we identified a mutation at the 3' end of the S gene in an IBV strain that was serially passaged in chicken embryos, and showed that this mutation resulted in a 9-aa truncation of the cytoplasmic tail (CT) of the S protein. This phenomenon of CT truncation has previously been observed in the production of attenuated vaccines against other coronaviruses such as the porcine epidemic diarrhea virus. We next discovered that the 9-aa truncation in the S protein CT resulted in the loss of the endoplasmic-reticulum-retention signal (KKSV). Rescue experiments with recombinant viruses confirmed that the deletion of the KKSV motif impaired the localization of the S protein to the endoplasmic-reticulum-Golgi intermediate compartment (ERGIC) and increased its expression on the cell surface. This significantly reduced the incorporation of the S protein into viral particles, impaired early subgenomic RNA and protein synthesis, and ultimately reduced viral invasion efficiency in CEK cells. In vivo experiments in chickens confirmed the reduced pathogenicity of the mutant IBV strains. Additionally, we showed that the adaptive mutation altered the TRS-B of ORF3 and impacted the transcriptional regulation of this gene. Our findings underscore the significance of this adaptive mutation in the attenuation of IBV infection and provide a novel strategy for the development of live attenuated IBV vaccines.
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Affiliation(s)
- Rong Liang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Kangchengyin Liu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yingfei Li
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xuehui Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Linqing Duan
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Min Huang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lu Sun
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Fang Yuan
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jing Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ye Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guozhong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
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7
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Dey D, Qing E, He Y, Chen Y, Jennings B, Cohn W, Singh S, Gakhar L, Schnicker NJ, Pierce BG, Whitelegge JP, Doray B, Orban J, Gallagher T, Hasan SS. A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs. Nat Commun 2023; 14:8358. [PMID: 38102143 PMCID: PMC10724246 DOI: 10.1038/s41467-023-44076-3] [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: 01/30/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
The spike (S) protein of SARS-CoV-2 is delivered to the virion assembly site in the ER-Golgi Intermediate Compartment (ERGIC) from both the ER and cis-Golgi in infected cells. However, the relevance and modulatory mechanism of this bidirectional trafficking are unclear. Here, using structure-function analyses, we show that S incorporation into virus-like particles (VLP) and VLP fusogenicity are determined by coatomer-dependent S delivery from the cis-Golgi and restricted by S-coatomer dissociation. Although S mimicry of the host coatomer-binding dibasic motif ensures retrograde trafficking to the ERGIC, avoidance of the host-like C-terminal acidic residue is critical for S-coatomer dissociation and therefore incorporation into virions or export for cell-cell fusion. Because this C-terminal residue is the key determinant of SARS-CoV-2 assembly and fusogenicity, our work provides a framework for the export of S protein encoded in genetic vaccines for surface display and immune activation.
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Affiliation(s)
- Debajit Dey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Yanan He
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
| | - Yihong Chen
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
| | - Benjamin Jennings
- Department of Internal Medicine, Hematology Division, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Whitaker Cohn
- Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Suruchi Singh
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lokesh Gakhar
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Protein and Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- PAQ Therapeutics, Burlington, MA, 01803, USA
| | - Nicholas J Schnicker
- Protein and Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Julian P Whitelegge
- Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Balraj Doray
- Department of Internal Medicine, Hematology Division, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John Orban
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - S Saif Hasan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, Baltimore, MD, 21201, USA.
- Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Rockville, MD, 20850, USA.
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8
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Dey D, Hasan SS. Strategies for rapid production of crystallization quality coatomer WD40 domains. Protein Expr Purif 2023; 212:106358. [PMID: 37625737 PMCID: PMC10529451 DOI: 10.1016/j.pep.2023.106358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
The vesicular secretion of soluble cargo proteins from the endoplasmic reticulum (ER) is accompanied by the export of ER-resident membrane proteins that are co-packaged in secretory vesicles. The cytosolic coatomer protein complex I (COPI) utilizes the N-terminal WD40 domains of α-COPI and β'-COPI subunits to bind these membrane protein "clients" for ER retrieval. These "αWD40" and "β'WD40" domains are structural homologs that demonstrate distinct selectivity for client proteins. However, elucidation of the atomic-level principles of coatomer-client interactions has been challenging due to the tendency of αWD40 domain to undergo aggregation during expression and purification. Here we describe a rapid recombinant production strategy from E. coli, which substantially enhances the quality of the purified αWD40 domain. The αWD40 purification and crystallization are completed within one day, which minimizes aggregation losses and yields a 1.9 Å resolution crystal structure. We demonstrate the versatility of this strategy by applying it to purify the β'WD40 domain, which yields crystal structures in the 1.2-1.3 Å resolution range. As an alternate recombinant production system, we develop a cost-effective strategy for αWD40 production in human Expi293 cells. Finally, we suggest a roadmap to simplify these protocols further, which is of significance for the production of WD40 mutants prone to rapid aggregation. The WD40 production strategies presented here are likely to have broad applications because the WD40 domain represents one of the largest families of biomolecular interaction modules in the eukaryotic proteome and is critical for trafficking of host as well as viral proteins such as the SARS-CoV-2 spike protein.
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Affiliation(s)
- Debajit Dey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - S Saif Hasan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, Baltimore, MD, 21201, USA; Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Rockville, MD, 20850, USA.
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9
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Custer SK, Gilson T, Astroski JW, Nanguneri SR, Iurillo AM, Androphy EJ. COPI coatomer subunit α-COP interacts with the RNA binding protein Nucleolin via a C-terminal dilysine motif. Hum Mol Genet 2023; 32:3263-3275. [PMID: 37658769 PMCID: PMC10656708 DOI: 10.1093/hmg/ddad140] [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: 04/17/2023] [Revised: 08/07/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023] Open
Abstract
The COPI coatomer subunit α-COP has been shown to co-precipitate mRNA in multiple settings, but it was unclear whether the interaction with mRNA was direct or mediated by interaction with an adapter protein. The COPI complex often interacts with proteins via C-terminal dilysine domains. A search for candidate RNA binding proteins with C-terminal dilysine motifs yielded Nucleolin, which terminates in a KKxKxx sequence. This protein was an especially intriguing candidate as it has been identified as an interacting partner for Survival Motor Neuron protein (SMN). Loss of SMN causes the neurodegenerative disease Spinal Muscular Atrophy. We have previously shown that SMN and α-COP interact and co-migrate in axons, and that overexpression of α-COP reduced phenotypic severity in cell culture and animal models of SMA. We show here that in an mRNA independent manner, endogenous Nucleolin co-precipitates endogenous α-COP and ε-COP but not β-COP which may reflect an interaction with the so-called B-subcomplex rather a complete COPI heptamer. The ability of Nucleolin to bind to α-COP requires the presence of the C-terminal KKxKxx domain of Nucleolin. Furthermore, we have generated a point mutant in the WD40 domain of α-COP which eliminates its ability to co-precipitate Nucleolin but does not interfere with precipitation of partners mediated by non-KKxKxx motifs such as the kainate receptor subunit 2. We propose that via interaction between the C-terminal dilysine motif of Nucleolin and the WD40 domain of α-COP, Nucleolin acts an adaptor to allow α-COP to interact with a population of mRNA.
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Affiliation(s)
- Sara K Custer
- Dermatology, Indiana University School of Medicine, 545 Barnhill Drive, Emerson Hall 139, Indianapolis, IN 46202, United States
| | - Timra Gilson
- Dermatology, Indiana University School of Medicine, 545 Barnhill Drive, Emerson Hall 139, Indianapolis, IN 46202, United States
| | - Jacob W Astroski
- Dermatology, Indiana University School of Medicine, 545 Barnhill Drive, Emerson Hall 139, Indianapolis, IN 46202, United States
| | - Siddarth R Nanguneri
- Dermatology, Indiana University School of Medicine, 545 Barnhill Drive, Emerson Hall 139, Indianapolis, IN 46202, United States
| | - Alyssa M Iurillo
- Indiana University School of Medicine, 340 West 10 St, Indianapolis, IN 46202, United States
| | - Elliot J Androphy
- Dermatology, Indiana University School of Medicine, 545 Barnhill Drive, Emerson Hall 139, Indianapolis, IN 46202, United States
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10
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Gurriaran-Rodriguez U, Datzkiw D, Radusky LG, Esper M, Xiao F, Ming H, Fisher S, Rojas MA, De Repentigny Y, Kothary R, Rojas AL, Serrano L, Hierro A, Rudnicki MA. Wnt binding to Coatomer proteins directs secretion on exosomes independently of palmitoylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542914. [PMID: 37398399 PMCID: PMC10312507 DOI: 10.1101/2023.05.30.542914] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Wnt proteins are secreted hydrophobic glycoproteins that act over long distances through poorly understood mechanisms. We discovered that Wnt7a is secreted on extracellular vesicles (EVs) following muscle injury. Structural analysis identified the motif responsible for Wnt7a secretion on EVs that we term the Exosome Binding Peptide (EBP). Addition of the EBP to an unrelated protein directed secretion on EVs. Disruption of palmitoylation, knockdown of WLS, or deletion of the N-terminal signal peptide did not affect Wnt7a secretion on purified EVs. Bio-ID analysis identified Coatomer proteins as candidates responsible for loading Wnt7a onto EVs. The crystal structure of EBP bound to the COPB2 coatomer subunit, the binding thermodynamics, and mutagenesis experiments, together demonstrate that a dilysine motif in the EBP mediates binding to COPB2. Other Wnts contain functionally analogous structural motifs. Mutation of the EBP results in a significant impairment in the ability of Wnt7a to stimulate regeneration, indicating that secretion of Wnt7a on exosomes is critical for normal regeneration in vivo . Our studies have defined the structural mechanism that mediates binding of Wnt7a to exosomes and elucidated the singularity of long-range Wnt signalling.
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11
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Li Y, Yang M, Nan Y, Wang J, Wang S, Cui D, Guo J, He P, Dai W, Zhou S, Zhang Y, Ma W. SARS-CoV-2 spike host cell surface exposure promoted by a COPI sorting inhibitor. Acta Pharm Sin B 2023:S2211-3835(23)00123-5. [PMID: 37360012 PMCID: PMC10110937 DOI: 10.1016/j.apsb.2023.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/26/2023] [Accepted: 04/10/2023] [Indexed: 06/28/2023] Open
Abstract
Via an insufficient coat protein complex I (COPI) retrieval signal, the majority of SARS-CoV-2 spike (S) is resident in host early secretory organelles and a tiny amount is leaked out in cell surface. Only surface-exposed S can be recognized by B cell receptor (BCR) or anti-S therapeutic monoclonal antibodies (mAbs) that is the trigger step for B cell activation after S mRNA vaccination or infected cell clearance by S mAbs. Now, a drug strategy to promote S host surface exposure is absent. Here, we first combined structural and biochemical analysis to characterize S COPI sorting signals. A potent S COPI sorting inhibitor was then invented, evidently capable of promoting S surface exposure and facilitating infected cell clearance by S antibody-dependent cellular cytotoxicity (ADCC). Importantly, with the inhibitor as a probe, we revealed Omicron BA.1 S is less cell surface exposed than prototypes because of a constellation of S folding mutations, possibly corresponding to its ER chaperone association. Our findings not only suggest COPI is a druggable target against COVID-19, but also highlight SARS-CoV-2 evolution mechanism driven by S folding and trafficking mutations.
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Affiliation(s)
- Yiqun Li
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Mingrui Yang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yanan Nan
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Jiaming Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Sanjiao Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Dongxiao Cui
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Jiajian Guo
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Pengfei He
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Wenxin Dai
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Shuqi Zhou
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yue Zhang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Wenfu Ma
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
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12
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Xie B, Guillem C, Date SS, Cohen CI, Jung C, Kendall AK, Best JT, Graham TR, Jackson LP. An interaction between β'-COP and the ArfGAP, Glo3, maintains post-Golgi cargo recycling. J Cell Biol 2023; 222:e202008061. [PMID: 36811888 PMCID: PMC9960064 DOI: 10.1083/jcb.202008061] [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: 08/24/2020] [Revised: 07/14/2022] [Accepted: 01/24/2023] [Indexed: 02/24/2023] Open
Abstract
The essential COPI coat mediates retrieval of transmembrane proteins at the Golgi and endosomes following recruitment by the small GTPase, Arf1. ArfGAP proteins regulate COPI coats, but molecular details for COPI recognition by ArfGAPs remain elusive. Biochemical and biophysical data reveal how β'-COP propeller domains directly engage the yeast ArfGAP, Glo3, with a low micromolar binding affinity. Calorimetry data demonstrate that both β'-COP propeller domains are required to bind Glo3. An acidic patch on β'-COP (D437/D450) interacts with Glo3 lysine residues located within the BoCCS (binding of coatomer, cargo, and SNAREs) region. Targeted point mutations in either Glo3 BoCCS or β'-COP abrogate the interaction in vitro, and loss of the β'-COP/Glo3 interaction drives Ste2 missorting to the vacuole and aberrant Golgi morphology in budding yeast. These data suggest that cells require the β'-COP/Glo3 interaction for cargo recycling via endosomes and the TGN, where β'-COP serves as a molecular platform to coordinate binding to multiple proteins, including Glo3, Arf1, and the COPI F-subcomplex.
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Affiliation(s)
- Boyang Xie
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Clara Guillem
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Swapneeta S. Date
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Cameron I. Cohen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Christian Jung
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Jordan T. Best
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Todd R. Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
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13
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Veeck C, Biedenkopf N, Rohde C, Becker S, Halwe S. Inhibition of Rab1B Impairs Trafficking and Maturation of SARS-CoV-2 Spike Protein. Viruses 2023; 15:824. [PMID: 37112806 PMCID: PMC10145535 DOI: 10.3390/v15040824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/09/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) utilizes cellular trafficking pathways to process its structural proteins and move them to the site of assembly. Nevertheless, the exact process of assembly and subcellular trafficking of SARS-CoV-2 proteins remains largely unknown. Here, we have identified and characterized Rab1B as an important host factor for the trafficking and maturation of the spike protein (S) after synthesis at the endoplasmic reticulum (ER). Using confocal microscopy, we showed that S and Rab1B substantially colocalized in compartments of the early secretory pathway. Co-expression of dominant-negative (DN) Rab1B N121I leads to an aberrant distribution of S into perinuclear spots after ectopic expression and in SARS-CoV-2-infected cells caused by either structural rearrangement of the ERGIC or Golgi or missing interaction between Rab1B and S. Western blot analyses revealed a complete loss of the mature, cleaved S2 subunit in cell lysates and culture supernatants upon co-expression of DN Rab1B N121I. In sum, our studies indicate that Rab1B is an important regulator of trafficking and maturation of SARS-CoV-2 S, which not only improves our understanding of the coronavirus replication cycle but also may have implications for the development of antiviral strategies.
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Affiliation(s)
- Christopher Veeck
- Institute of Virology, Philipps University Marburg, 35043 Marburg, Germany; (C.V.)
| | - Nadine Biedenkopf
- Institute of Virology, Philipps University Marburg, 35043 Marburg, Germany; (C.V.)
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35043 Marburg, Germany
| | - Cornelius Rohde
- Institute of Virology, Philipps University Marburg, 35043 Marburg, Germany; (C.V.)
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35043 Marburg, Germany
| | - Stephan Becker
- Institute of Virology, Philipps University Marburg, 35043 Marburg, Germany; (C.V.)
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35043 Marburg, Germany
| | - Sandro Halwe
- Institute of Virology, Philipps University Marburg, 35043 Marburg, Germany; (C.V.)
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35043 Marburg, Germany
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14
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Taylor RJ, Tagiltsev G, Briggs JAG. The structure of COPI vesicles and regulation of vesicle turnover. FEBS Lett 2023; 597:819-835. [PMID: 36513395 DOI: 10.1002/1873-3468.14560] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
COPI-coated vesicles mediate transport between Golgi stacks and retrograde transport from the Golgi to the endoplasmic reticulum. The COPI coat exists as a stable heptameric complex in the cytosol termed coatomer and is recruited en bloc to the membrane for vesicle formation. Recruitment of COPI onto membranes is mediated by the Arf family of small GTPases, which, in their GTP-bound state, bind both membrane and coatomer. Arf GTPases also influence cargo selection, vesicle scission and vesicle uncoating. Guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs) regulate nucleotide binding by Arf GTPases. To understand the mechanism of COPI-coated vesicle trafficking, it is necessary to characterize the interplay between coatomer and Arf GTPases and their effectors. It is also necessary to understand interactions between coatomer and cargo, cargo adaptors/receptors and tethers facilitating binding to the target membrane. Here, we summarize current knowledge of COPI coat protein structure; we describe how structural and biochemical studies contributed to this knowledge; we review mechanistic insights into COPI vesicle biogenesis and disassembly; and we discuss the potential to answer open questions in the field.
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Affiliation(s)
- Rebecca J Taylor
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Grigory Tagiltsev
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - John A G Briggs
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
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15
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Harwood MC, Woo TT, Takeo Y, DiMaio D, Tsai B. HPV is a cargo for the COPI sorting complex during virus entry. SCIENCE ADVANCES 2023; 9:eadc9830. [PMID: 36662862 PMCID: PMC9858521 DOI: 10.1126/sciadv.adc9830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/20/2022] [Indexed: 05/30/2023]
Abstract
During entry, human papillomavirus (HPV) traffics from the cell surface to the endosome and then to the trans-Golgi network (TGN) and Golgi apparatus. HPV must transit across the TGN/Golgi and exit these compartments to reach the nucleus to cause infection, although how these steps are accomplished is unclear. Combining cellular fractionation, unbiased proteomics, and gene knockdown strategies, we identified the coat protein complex I (COPI), a highly conserved protein complex that facilitates retrograde trafficking of cellular cargos, as a host factor required for HPV infection. Upon TGN/Golgi arrival, the cytoplasmic segment of HPV L2 binds directly to COPI. COPI depletion causes the accumulation of HPV in the TGN/Golgi, resembling the fate of a COPI binding-defective L2 mutant. We propose that the L2-COPI interaction drives HPV trafficking through the TGN and Golgi stacks during virus entry. This shows that an incoming virus is a cargo of the COPI complex.
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Affiliation(s)
- Mara C. Harwood
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tai-Ting Woo
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Yuka Takeo
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
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16
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Roberts BS, Satpute-Krishnan P. The many hats of transmembrane emp24 domain protein TMED9 in secretory pathway homeostasis. Front Cell Dev Biol 2023; 10:1096899. [PMID: 36733337 PMCID: PMC9888432 DOI: 10.3389/fcell.2022.1096899] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
The secretory pathway is an intracellular highway for the vesicular transport of newly synthesized proteins that spans the endoplasmic reticulum (ER), Golgi, lysosomes and the cell surface. A variety of cargo receptors, chaperones, and quality control proteins maintain the smooth flow of cargo along this route. Among these is vesicular transport protein TMED9, which belongs to the p24/transmembrane emp24 domain (TMED) family of proteins, and is expressed across vertebrate species. The TMED family is comprised of structurally-related type I transmembrane proteins with a luminal N-terminal Golgi-dynamics domain, a luminal coiled-coil domain, a transmembrane domain and a short cytosolic C-terminal tail that binds COPI and COPII coat proteins. TMED9, like other members of the TMED family, was first identified as an abundant constituent of the COPI and COPII coated vesicles that mediate traffic between the ER and the Golgi. TMED9 is typically purified in hetero-oligomers together with TMED family members, suggesting that it may function as part of a complex. Recently, TMED family members have been discovered to play various roles in secretory pathway homeostasis including secreted protein processing, quality control and degradation of misfolded proteins, and post-Golgi trafficking. In particular, TMED9 has been implicated in autophagy, lysosomal sorting, viral replication and cancer, which we will discuss in this Mini-Review.
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17
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Hesketh SJ, Mukhopadhyay AG, Nakamura D, Toropova K, Roberts AJ. IFT-A structure reveals carriages for membrane protein transport into cilia. Cell 2022; 185:4971-4985.e16. [PMID: 36462505 DOI: 10.1016/j.cell.2022.11.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 11/09/2022] [Indexed: 12/05/2022]
Abstract
Intraflagellar transport (IFT) trains are massive molecular machines that traffic proteins between cilia and the cell body. Each IFT train is a dynamic polymer of two large complexes (IFT-A and -B) and motor proteins, posing a formidable challenge to mechanistic understanding. Here, we reconstituted the complete human IFT-A complex and obtained its structure using cryo-EM. Combined with AlphaFold prediction and genome-editing studies, our results illuminate how IFT-A polymerizes, interacts with IFT-B, and uses an array of β-propeller and TPR domains to create "carriages" of the IFT train that engage TULP adaptor proteins. We show that IFT-A⋅TULP carriages are essential for cilia localization of diverse membrane proteins, as well as ICK-the key kinase regulating IFT train turnaround. These data establish a structural link between IFT-A's distinct functions, provide a blueprint for IFT-A in the train, and shed light on how IFT evolved from a proto-coatomer ancestor.
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Affiliation(s)
- Sophie J Hesketh
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK
| | - Aakash G Mukhopadhyay
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK
| | - Dai Nakamura
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK
| | - Katerina Toropova
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK.
| | - Anthony J Roberts
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK.
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18
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Solinger JA, Spang A. Sorting of cargo in the tubular endosomal network. Bioessays 2022; 44:e2200158. [DOI: 10.1002/bies.202200158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
Affiliation(s)
| | - Anne Spang
- Biozentrum University of Basel Basel Switzerland
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19
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Cui L, Li H, Xi Y, Hu Q, Liu H, Fan J, Xiang Y, Zhang X, Shui W, Lai Y. Vesicle trafficking and vesicle fusion: mechanisms, biological functions, and their implications for potential disease therapy. MOLECULAR BIOMEDICINE 2022; 3:29. [PMID: 36129576 PMCID: PMC9492833 DOI: 10.1186/s43556-022-00090-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
Intracellular vesicle trafficking is the fundamental process to maintain the homeostasis of membrane-enclosed organelles in eukaryotic cells. These organelles transport cargo from the donor membrane to the target membrane through the cargo containing vesicles. Vesicle trafficking pathway includes vesicle formation from the donor membrane, vesicle transport, and vesicle fusion with the target membrane. Coat protein mediated vesicle formation is a delicate membrane budding process for cargo molecules selection and package into vesicle carriers. Vesicle transport is a dynamic and specific process for the cargo containing vesicles translocation from the donor membrane to the target membrane. This process requires a group of conserved proteins such as Rab GTPases, motor adaptors, and motor proteins to ensure vesicle transport along cytoskeletal track. Soluble N-ethyl-maleimide-sensitive factor (NSF) attachment protein receptors (SNARE)-mediated vesicle fusion is the final process for vesicle unloading the cargo molecules at the target membrane. To ensure vesicle fusion occurring at a defined position and time pattern in eukaryotic cell, multiple fusogenic proteins, such as synaptotagmin (Syt), complexin (Cpx), Munc13, Munc18 and other tethering factors, cooperate together to precisely regulate the process of vesicle fusion. Dysfunctions of the fusogenic proteins in SNARE-mediated vesicle fusion are closely related to many diseases. Recent studies have suggested that stimulated membrane fusion can be manipulated pharmacologically via disruption the interface between the SNARE complex and Ca2+ sensor protein. Here, we summarize recent insights into the molecular mechanisms of vesicle trafficking, and implications for the development of new therapeutics based on the manipulation of vesicle fusion.
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20
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Shi Y, Luo Z, You J. Subcellular delivery of lipid nanoparticles to endoplasmic reticulum and mitochondria. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1803. [PMID: 35441489 DOI: 10.1002/wnan.1803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/23/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Primarily responsible for the biogenesis and metabolism of biomolecules, endoplasmic reticulum (ER) and mitochondria are gradually becoming the targets of therapeutic modulation, whose physiological activities and pathological manifestations determine the functional capacity and even the survival of cells. Drug delivery systems with specific physicochemical properties (passive targeting), or modified by small molecular compounds, polypeptides, and biomembranes demonstrating tropism for ER and mitochondria (active targeting) are able to reduce the nonselective accumulation of drugs, enhancing efficacy while reducing side effects. Lipid nanoparticles feature high biocompatibility, diverse cargo loading, and flexible structure modification, which are frequently used for subcellular organelle-targeted delivery of therapeutics. However, there is still a lack of systematic understanding of lipid nanoparticle-based ER and mitochondria targeting. Herein, we review the pathological significance of drug selectively delivered to the ER and mitochondria. We also summarize the molecular basis and application prospects of lipid nanoparticle-based ER and mitochondria targeting strategies, which may provide guidance for the prevention and treatment of associated diseases and disorders. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Biology-Inspired Nanomaterials > Lipid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Diagnostic Tools > In Vivo Nanodiagnostics and Imaging.
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Affiliation(s)
- Yingying Shi
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhenyu Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jian You
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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21
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Date SS, Xu P, Hepowit NL, Diab NS, Best J, Xie B, Du J, Strieter ER, Jackson LP, MacGurn JA, Graham TR. Ubiquitination drives COPI priming and Golgi SNARE localization. eLife 2022; 11:e80911. [PMID: 35904239 PMCID: PMC9374436 DOI: 10.7554/elife.80911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022] Open
Abstract
Deciphering mechanisms controlling SNARE localization within the Golgi complex is crucial to understanding protein trafficking patterns within the secretory pathway. SNAREs are also thought to prime coatomer protein I (COPI) assembly to ensure incorporation of these essential cargoes into vesicles, but the regulation of these events is poorly understood. Here, we report roles for ubiquitin recognition by COPI in SNARE trafficking and in stabilizing interactions between Arf, COPI, and Golgi SNAREs in Saccharomyces cerevisiae. The ability of COPI to bind ubiquitin, but not the dilysine motif, through its N-terminal WD repeat domain of β'-COP or through an unrelated ubiquitin-binding domain is essential for the proper localization of Golgi SNAREs Bet1 and Gos1. We find that COPI, the ArfGAP Glo3, and multiple Golgi SNAREs are ubiquitinated. Notably, the binding of Arf and COPI to Gos1 is markedly enhanced by ubiquitination of these components. Glo3 is proposed to prime COPI-SNARE interactions; however, Glo3 is not enriched in the ubiquitin-stabilized SNARE-Arf-COPI complex but is instead enriched with COPI complexes that lack SNAREs. These results support a new model for how posttranslational modifications drive COPI priming events crucial for Golgi SNARE localization.
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Affiliation(s)
- Swapneeta S Date
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
| | - Peng Xu
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
| | - Nathaniel L Hepowit
- Department of Cell and Developmental Biology, Vanderbilt UniversityNashvilleUnited States
| | - Nicholas S Diab
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
| | - Jordan Best
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
| | - Boyang Xie
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
| | - Jiale Du
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Lauren P Jackson
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
| | - Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt UniversityNashvilleUnited States
| | - Todd R Graham
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
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22
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Infectious Bronchitis Coronavirus: Genome Evolution in Vaccinated and Non-Vaccinated SPF Chickens. Viruses 2022; 14:v14071392. [PMID: 35891373 PMCID: PMC9319055 DOI: 10.3390/v14071392] [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: 04/27/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 12/04/2022] Open
Abstract
Infectious Bronchitis virus (IBV) continues to cause significant economic losses for the chicken industry despite the use of many live IBV vaccines around the world. Several authors have suggested that vaccine-induced partial protection may contribute to the emergence of new IBV strains. In order to study this hypothesis, three passages of a challenge IBV were made in SPF chickens sham inoculated or vaccinated at day of age using a live vaccine heterologous to the challenge virus. All birds that were challenged with vaccine heterologous virus were positive for viral RNA. NGS analysis of viral RNA in the unvaccinated group showed a rapid selection of seven genetic variants, finally modifying the consensus genome of the viral population. Among them, five were non-synonymous, modifying one position in NSP 8, one in NSP 13, and three in the Spike protein. In the vaccinated group, one genetic variant was selected over the three passages. This synonymous modification was absent from the unvaccinated group. Under these conditions, the genome population of an IBV challenge virus evolved rapidly in both heterologous vaccinated and non-vaccinated birds, while the genetic changes that were selected and the locations of these were very different between the two groups.
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23
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Regulation of protein secretion through chemical regulation of endoplasmic reticulum retention signal cleavage. Nat Commun 2022; 13:1323. [PMID: 35260576 PMCID: PMC8904541 DOI: 10.1038/s41467-022-28971-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/23/2022] [Indexed: 12/12/2022] Open
Abstract
Secreted proteins, such as hormones or cytokines, are key mediators in multicellular organisms. Response of protein secretion based on transcriptional control is rather slow, as it requires transcription, translation and transport from the endoplasmic reticulum (ER) to the plasma membrane via the conventional protein secretion (CPS) pathway. An alternative regulation to provide faster response would be valuable. Here we present two genetically encoded orthogonal regulatory secretion systems, which rely on the retention of pre-synthesized proteins on the ER membrane (membER, released by a cytosolic protease) or inside the ER lumen (lumER, released by an ER-luminal protease), respectively, and their release by the chemical signal-regulated proteolytic removal of an ER-retention signal, without triggering ER stress due to protein aggregates. Design of orthogonal chemically-regulated split proteases enables the combination of signals into logic functions. Its application was demonstrated on a chemically regulated therapeutic protein secretion and regulated membrane translocation of a chimeric antigen receptor (CAR) targeting cancer antigen. Regulation of the ER escape represents a platform for the design of fast-responsive and tightly-controlled modular and scalable protein secretion system for mammalian cells. Secreted proteins, such as hormones or cytokines, are key mediators in multicellular organisms. Here the authors present two genetically encoded orthogonal regulatory secretion systems that enables inducible protein release and construction of logic gates.
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24
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Differential Involvement of Arabidopsis β’-COP Isoforms in Plant Development. Cells 2022; 11:cells11060938. [PMID: 35326389 PMCID: PMC8946003 DOI: 10.3390/cells11060938] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 11/20/2022] Open
Abstract
Coat protein I (COPI) is necessary for intra-Golgi transport and retrograde transport from the Golgi apparatus back to the endoplasmic reticulum. The key component of the COPI coat is the coatomer complex, which is composed of seven subunits (α/β/β’/γ/δ/ε/ζ) and is recruited en bloc from the cytosol onto Golgi membranes. In mammals and yeast, α- and β’-COP WD40 domains mediate cargo-selective interactions with dilysine motifs present in canonical cargoes of COPI vesicles. In contrast to mammals and yeast, three isoforms of β’-COP (β’1-3-COP) have been identified in Arabidopsis. To understand the role of Arabidopsis β’-COP isoforms in plant biology, we have identified and characterized loss-of-function mutants of the three isoforms, and double mutants were also generated. We have found that the trafficking of a canonical dilysine cargo (the p24 family protein p24δ5) is affected in β’-COP double mutants. By western blot analysis, it is also shown that protein levels of α-COP are reduced in the β’-COP double mutants. Although none of the single mutants showed an obvious growth defect, double mutants showed different growth phenotypes. The double mutant analysis suggests that, under standard growth conditions, β’1-COP can compensate for the loss of both β’2-COP and β’3-COP and may have a prominent role during seedling development.
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25
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Protease-controlled secretion and display of intercellular signals. Nat Commun 2022; 13:912. [PMID: 35177637 PMCID: PMC8854555 DOI: 10.1038/s41467-022-28623-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
To program intercellular communication for biomedicine, it is crucial to regulate the secretion and surface display of signaling proteins. If such regulations are at the protein level, there are additional advantages, including compact delivery and direct interactions with endogenous signaling pathways. Here we create a modular, generalizable design called Retained Endoplasmic Cleavable Secretion (RELEASE), with engineered proteins retained in the endoplasmic reticulum and displayed/secreted in response to specific proteases. The design allows functional regulation of multiple synthetic and natural proteins by synthetic protease circuits to realize diverse signal processing capabilities, including logic operation and threshold tuning. By linking RELEASE to additional sensing and processing circuits, we can achieve elevated protein secretion in response to "undruggable" oncogene KRAS mutants. RELEASE should enable the local, programmable delivery of intercellular cues for a broad variety of fields such as neurobiology, cancer immunotherapy and cell transplantation.
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26
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Dey D, Singh S, Khan S, Martin M, Schnicker NJ, Gakhar L, Pierce BG, Hasan SS. An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking. Commun Biol 2022; 5:115. [PMID: 35136165 PMCID: PMC8825798 DOI: 10.1038/s42003-022-03063-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/19/2022] [Indexed: 12/23/2022] Open
Abstract
β-Coronaviruses such as SARS-CoV-2 hijack coatomer protein-I (COPI) for spike protein retrograde trafficking to the progeny assembly site in endoplasmic reticulum-Golgi intermediate compartment (ERGIC). However, limited residue-level details are available into how the spike interacts with COPI. Here we identify an extended COPI binding motif in the spike that encompasses the canonical K-x-H dibasic sequence. This motif demonstrates selectivity for αCOPI subunit. Guided by an in silico analysis of dibasic motifs in the human proteome, we employ mutagenesis and binding assays to show that the spike motif terminal residues are critical modulators of complex dissociation, which is essential for spike release in ERGIC. αCOPI residues critical for spike motif binding are elucidated by mutagenesis and crystallography and found to be conserved in the zoonotic reservoirs, bats, pangolins, camels, and in humans. Collectively, our investigation on the spike motif identifies key COPI binding determinants with implications for retrograde trafficking. The cytosolic tail of β-coronavirus spike proteins contains dibasic motifs that must be able to bind to the host’s coatomer protein-I (COPI) for trafficking and be released for viral assembly in the ER-Golgi intermediate compartment. The critical residues in both the spike cytosolic tail and COPI are identified that modulate the association-dissociation kinetics.
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Affiliation(s)
- Debajit Dey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Suruchi Singh
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Saif Khan
- Protein and Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA
| | - Matthew Martin
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.,University of Pittsburgh Kenneth P. Dietrich School of Arts and Sciences, Pittsburgh, PA, USA
| | - Nicholas J Schnicker
- Protein and Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Lokesh Gakhar
- Protein and Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,PAQ Therapeutics, Cambridge, MA, USA
| | - Brian G Pierce
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - S Saif Hasan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA. .,University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA. .,Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Rockville, MD, USA.
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27
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Degrandmaison J, Grisé O, Parent JL, Gendron L. Differential barcoding of opioid receptors trafficking. J Neurosci Res 2021; 100:99-128. [PMID: 34559903 DOI: 10.1002/jnr.24949] [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: 11/26/2020] [Revised: 07/25/2021] [Accepted: 08/05/2021] [Indexed: 11/09/2022]
Abstract
Over the past several years, studies have highlighted the δ-opioid receptor (DOPr) as a promising therapeutic target for chronic pain management. While exhibiting milder undesired effects than most currently prescribed opioids, its specific agonists elicit effective analgesic responses in numerous animal models of chronic pain, including inflammatory, neuropathic, diabetic, and cancer-related pain. However, as compared with the extensively studied μ-opioid receptor, the molecular mechanisms governing its trafficking remain elusive. Recent advances have denoted several significant particularities in the regulation of DOPr intracellular routing, setting it apart from the other members of the opioid receptor family. Although they share high homology, each opioid receptor subtype displays specific amino acid patterns potentially involved in the regulation of its trafficking. These precise motifs or "barcodes" are selectively recognized by regulatory proteins and therefore dictate several aspects of the itinerary of a receptor, including its anterograde transport, internalization, recycling, and degradation. With a specific focus on the regulation of DOPr trafficking, this review will discuss previously reported, as well as potential novel trafficking barcodes within the opioid and nociceptin/orphanin FQ opioid peptide receptors, and their impact in determining distinct interactomes and physiological responses.
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Affiliation(s)
- Jade Degrandmaison
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Institut de Pharmacologie de Sherbrooke, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Quebec Network of Junior Pain Investigators, QC, Canada
| | - Olivier Grisé
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Institut de Pharmacologie de Sherbrooke, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Luc Parent
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Institut de Pharmacologie de Sherbrooke, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Louis Gendron
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Institut de Pharmacologie de Sherbrooke, Centre de Recherche du CHUS, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Quebec Pain Research Network, QC, Canada
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28
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Sequences in the cytoplasmic tail of SARS-CoV-2 Spike facilitate expression at the cell surface and syncytia formation. Nat Commun 2021; 12:5333. [PMID: 34504087 PMCID: PMC8429659 DOI: 10.1038/s41467-021-25589-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023] Open
Abstract
The Spike (S) protein of SARS-CoV-2 binds ACE2 to direct fusion with host cells. S comprises a large external domain, a transmembrane domain, and a short cytoplasmic tail. Understanding the intracellular trafficking of S is relevant to SARS-CoV-2 infection, and to vaccines expressing full-length S from mRNA or adenovirus vectors. Here we report a proteomic screen for cellular factors that interact with the cytoplasmic tail of S. We confirm interactions with the COPI and COPII vesicle coats, ERM family actin regulators, and the WIPI3 autophagy component. The COPII binding site promotes exit from the endoplasmic reticulum, and although binding to COPI should retain S in the early Golgi where viral budding occurs, there is a suboptimal histidine residue in the recognition motif. As a result, S leaks to the surface where it accumulates and can direct the formation of multinucleate syncytia. Thus, the trafficking signals in the tail of S indicate that syncytia play a role in the SARS-CoV-2 lifecycle.
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29
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Bainter W, Platt CD, Park SY, Stafstrom K, Wallace JG, Peters ZT, Massaad MJ, Becuwe M, Salinas SA, Jones J, Beaussant-Cohen S, Jaber F, Yang JS, Walther TC, Orange JS, Rao C, Rakoff-Nahoum S, Tsokos M, Naseem SUR, Al-Tamemi S, Chou J, Hsu VW, Geha RS. Combined immunodeficiency due to a mutation in the γ1 subunit of the coat protein I complex. J Clin Invest 2021; 131:140494. [PMID: 33529166 DOI: 10.1172/jci140494] [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: 05/26/2020] [Accepted: 11/25/2020] [Indexed: 12/14/2022] Open
Abstract
The coat protein I (COPI) complex mediates retrograde trafficking from the Golgi to the endoplasmic reticulum (ER). Five siblings with persistent bacterial and viral infections and defective humoral and cellular immunity had a homozygous p.K652E mutation in the γ1 subunit of COPI (γ1-COP). The mutation disrupts COPI binding to the KDEL receptor and impairs the retrieval of KDEL-bearing chaperones from the Golgi to the ER. Homozygous Copg1K652E mice had increased ER stress in activated T and B cells, poor antibody responses, and normal numbers of T cells that proliferated normally, but underwent increased apoptosis upon activation. Exposure of the mutants to pet store mice caused weight loss, lymphopenia, and defective T cell proliferation that recapitulated the findings in the patients. The ER stress-relieving agent tauroursodeoxycholic acid corrected the immune defects of the mutants and reversed the phenotype they acquired following exposure to pet store mice. This study establishes the role of γ1-COP in the ER retrieval of KDEL-bearing chaperones and thereby the importance of ER homeostasis in adaptive immunity.
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Affiliation(s)
- Wayne Bainter
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Craig D Platt
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Seung-Yeol Park
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Kelsey Stafstrom
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jacqueline G Wallace
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Zachary T Peters
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michel J Massaad
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michel Becuwe
- Department of Genetics and Complex Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sandra Andrea Salinas
- Division of Immunogenetics, Department of Pediatrics, Morgan Stanley Children's Hospital of New York Presbyterian, Columbia University Irving Medical Center, New York, New York, USA
| | - Jennifer Jones
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sarah Beaussant-Cohen
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Faris Jaber
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jia-Shu Yang
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tobias C Walther
- Department of Genetics and Complex Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jordan S Orange
- Division of Immunogenetics, Department of Pediatrics, Morgan Stanley Children's Hospital of New York Presbyterian, Columbia University Irving Medical Center, New York, New York, USA
| | - Chitong Rao
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Seth Rakoff-Nahoum
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Maria Tsokos
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Salem Al-Tamemi
- Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman
| | - Janet Chou
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Victor W Hsu
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Raif S Geha
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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30
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Lujan P, Campelo F. Should I stay or should I go? Golgi membrane spatial organization for protein sorting and retention. Arch Biochem Biophys 2021; 707:108921. [PMID: 34038703 DOI: 10.1016/j.abb.2021.108921] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/12/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022]
Abstract
The Golgi complex is the membrane-bound organelle that lies at the center of the secretory pathway. Its main functions are to maintain cellular lipid homeostasis, to orchestrate protein processing and maturation, and to mediate protein sorting and export. These functions are not independent of one another, and they all require that the membranes of the Golgi complex have a well-defined biochemical composition. Importantly, a finely-regulated spatiotemporal organization of the Golgi membrane components is essential for the correct performance of the organelle. In here, we review our current mechanistic and molecular understanding of how Golgi membranes are spatially organized in the lateral and axial directions to fulfill their functions. In particular, we highlight the current evidence and proposed models of intra-Golgi transport, as well as the known mechanisms for the retention of Golgi residents and for the sorting and export of transmembrane cargo proteins. Despite the controversies, conflicting evidence, clashes between models, and technical limitations, the field has moved forward and we have gained extensive knowledge in this fascinating topic. However, there are still many important questions that remain to be completely answered. We hope that this review will help boost future investigations on these issues.
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Affiliation(s)
- Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860, Barcelona, Spain.
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860, Barcelona, Spain.
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31
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Mosquera JV, Bacher MC, Priess JR. Nuclear lipid droplets and nuclear damage in Caenorhabditis elegans. PLoS Genet 2021; 17:e1009602. [PMID: 34133414 PMCID: PMC8208577 DOI: 10.1371/journal.pgen.1009602] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/14/2021] [Indexed: 01/01/2023] Open
Abstract
Fat stored in the form of lipid droplets has long been considered a defining characteristic of cytoplasm. However, recent studies have shown that nuclear lipid droplets occur in multiple cells and tissues, including in human patients with fatty liver disease. The function(s) of stored fat in the nucleus has not been determined, and it is possible that nuclear fat is beneficial in some situations. Conversely, nuclear lipid droplets might instead be deleterious by disrupting nuclear organization or triggering aggregation of hydrophobic proteins. We show here that nuclear lipid droplets occur normally in C. elegans intestinal cells and germ cells, but appear to be associated with damage only in the intestine. Lipid droplets in intestinal nuclei can be associated with novel bundles of microfilaments (nuclear actin) and membrane tubules that might have roles in damage repair. To increase the normal, low frequency of nuclear lipid droplets in wild-type animals, we used a forward genetic screen to isolate mutants with abnormally large or abundant nuclear lipid droplets. Genetic analysis and cloning of three such mutants showed that the genes encode the lipid regulator SEIP-1/seipin, the inner nuclear membrane protein NEMP-1/Nemp1/TMEM194A, and a component of COPI vesicles called COPA-1/α-COP. We present several lines of evidence that the nuclear lipid droplet phenotype of copa-1 mutants results from a defect in retrieving mislocalized membrane proteins that normally reside in the endoplasmic reticulum. The seip-1 mutant causes most germ cells to have nuclear lipid droplets, the largest of which occupy more than a third of the nuclear volume. Nevertheless, the nuclear lipid droplets do not trigger apoptosis, and the germ cells differentiate into gametes that produce viable, healthy progeny. Thus, our results suggest that nuclear lipid droplets are detrimental to intestinal nuclei, but have no obvious deleterious effect on germ nuclei.
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Affiliation(s)
| | - Meghan C. Bacher
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - James R. Priess
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
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32
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Abstract
The Golgi complex plays a central role in protein secretion by regulating cargo sorting and trafficking. As these processes are of functional importance to cell polarity, motility, growth, and division, there is considerable interest in achieving a comprehensive understanding of Golgi complex biology. However, the unique stack structure of this organelle has been a major hurdle to our understanding of how proteins are secreted through the Golgi apparatus. Herein, we summarize available relevant research to gain an understanding of protein secretion via the Golgi complex. This includes the molecular mechanisms of intra-Golgi trafficking and cargo export in the trans-Golgi network. Moreover, we review recent insights on signaling pathways regulated by the Golgi complex and their physiological significance.
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Affiliation(s)
- Kunyou Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Sungeun Ju
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
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33
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Jennings BC, Kornfeld S, Doray B. A weak COPI binding motif in the cytoplasmic tail of SARS-CoV-2 spike glycoprotein is necessary for its cleavage, glycosylation, and localization. FEBS Lett 2021; 595:1758-1767. [PMID: 33991349 PMCID: PMC8209879 DOI: 10.1002/1873-3468.14109] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 11/11/2022]
Abstract
The SARS-CoV-2 spike glycoprotein (spike) mediates viral entry by binding ACE2 receptors on host cell surfaces. Spike glycan processing and cleavage, which occur in the Golgi network, are important for fusion at the plasma membrane, promoting both virion infectivity and cell-to-cell viral spreading. We show that a KxHxx motif in the cytosolic tail of spike weakly binds the COPβ' subunit of COPI coatomer, which facilitates some recycling of spike within the Golgi, while releasing the remainder to the cell surface. Although histidine (KxHxx) has been proposed to be equivalent to lysine within di-lysine endoplasmic reticulum (ER) retrieval sequences, we show that histidine-to-lysine substitution (KxKxx) retains spike at the ER and prevents glycan processing, protease cleavage, and transport to the plasma membrane.
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Affiliation(s)
- Benjamin C Jennings
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Stuart Kornfeld
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Balraj Doray
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
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34
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Taguchi T, Mukai K, Takaya E, Shindo R. STING Operation at the ER/Golgi Interface. Front Immunol 2021; 12:646304. [PMID: 34012437 PMCID: PMC8126659 DOI: 10.3389/fimmu.2021.646304] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 04/21/2021] [Indexed: 11/16/2022] Open
Abstract
DNA is present in the nucleus and mitochondria of eukaryotic cells. There are, however, certain instances in which DNA emerges in the cytosol. The two major sources of cytosolic DNA are self DNA that is leaked out from the nucleus or mitochondria, and non-self DNA from DNA viruses. The cytosolic DNA triggers the host immune response. Recent studies have identified two key molecules, cyclic GMP-AMP (cGAMP) synthase (cGAS) and stimulator of interferon genes (STING) in this immune response. STING is an endoplasmic reticulum (ER) protein. After STING binding to cGAMP, STING exits the ER and translocates to the Golgi, where STING triggers the type I interferon- and proinflammatory responses through the activation of interferon regulatory factor 3 (IRF3) and nuclear factor-kappa B (NF-κB). STING also activates other cellular responses including cell senescence, autophagy, and cell death. In this review, we focus on emerging issues regarding the regulation of STING by membrane traffic, with a particular focus on the retrograde membrane traffic from the Golgi to the ER. The retrograde membrane traffic is recently shown by us and others to be critical for silencing the STING signaling pathway and the defect in this traffic underlies the pathogenesis of the COPA syndrome, a monogenic autoinflammatory disease caused by missense mutations of coatomer protein complex subunit α (COP-α).
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Affiliation(s)
- Tomohiko Taguchi
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.,AMED-PRIME, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Kojiro Mukai
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Eiko Takaya
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ruri Shindo
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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35
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Sánchez-Simarro J, Bernat-Silvestre C, Aniento F, Marcote MJ. ß-COP mutants show specific high sensitivity to chloride ions. PLANT SIGNALING & BEHAVIOR 2021; 16:1858629. [PMID: 33432878 PMCID: PMC7889185 DOI: 10.1080/15592324.2020.1858629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Coat Protein I (COPI) consists of a complex (coatomer) formed by seven subunits (α-, β-, β'-, γ-, δ-, ε-, and ζ-COP) that is recruited to Golgi membranes to form vesicles that shuttle from the Golgi apparatus to the ER and between Golgi stacks. Recently, it has been described that loss of function mutants of the two Arabidopsis β-COP genes, β1-COP and β2-COP, showed increased sensitivity to salt stress (NaCl). Using a mixture of either Na+ or Cl- salts, we have now found that β-COP mutants are specifically and highly sensitive to chloride ions.
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Affiliation(s)
- Judit Sánchez-Simarro
- Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universitat de Valencia
| | - César Bernat-Silvestre
- Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universitat de Valencia
| | - Fernando Aniento
- Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universitat de Valencia
| | - María Jesús Marcote
- Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universitat de Valencia
- CONTACT María Jesús Marcote Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED)
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Laborenz J, Bykov YS, Knöringer K, Räschle M, Filker S, Prescianotto-Baschong C, Spang A, Tatsuta T, Langer T, Storchová Z, Schuldiner M, Herrmann JM. The ER protein Ema19 facilitates the degradation of nonimported mitochondrial precursor proteins. Mol Biol Cell 2021; 32:664-674. [PMID: 33596095 PMCID: PMC8108515 DOI: 10.1091/mbc.e20-11-0748] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
For the biogenesis of mitochondria, hundreds of proteins need to be targeted from the cytosol into the various compartments of this organelle. The intramitochondrial targeting routes these proteins take to reach their respective location in the organelle are well understood. However, the early targeting processes, from cytosolic ribosomes to the membrane of the organelle, are still largely unknown. In this study, we present evidence that an integral membrane protein of the endoplasmic reticulum (ER), Ema19, plays a role in this process. Mutants lacking Ema19 show an increased stability of mitochondrial precursor proteins, indicating that Ema19 promotes the proteolytic degradation of nonproductive precursors. The deletion of Ema19 improves the growth of respiration-deficient cells, suggesting that Ema19-mediated degradation can compete with productive protein import into mitochondria. Ema19 is the yeast representative of a conserved protein family. The human Ema19 homologue is known as sigma 2 receptor or TMEM97. Though its molecular function is not known, previous studies suggested a role of the sigma 2 receptor as a quality control factor in the ER, compatible with our observations about Ema19. More globally, our data provide an additional demonstration of the important role of the ER in mitochondrial protein targeting.
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Affiliation(s)
- Janina Laborenz
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Yury S Bykov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Sabine Filker
- Molecular Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | | | - Anne Spang
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Takashi Tatsuta
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Thomas Langer
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Zuzana Storchová
- Molecular Genetics, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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The conserved autoimmune-disease risk gene TMEM39A regulates lysosome dynamics. Proc Natl Acad Sci U S A 2021; 118:2011379118. [PMID: 33531362 DOI: 10.1073/pnas.2011379118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
TMEM39A encodes an evolutionarily conserved transmembrane protein and carries single-nucleotide polymorphisms associated with increased risk of major human autoimmune diseases, including multiple sclerosis. The exact cellular function of TMEM39A remains not well understood. Here, we report that TMEM-39, the sole Caenorhabditis elegans (C. elegans) ortholog of TMEM39A, regulates lysosome distribution and accumulation. Elimination of tmem-39 leads to lysosome tubularization and reduced lysosome mobility, as well as accumulation of the lysosome-associated membrane protein LMP-1. In mammalian cells, loss of TMEM39A leads to redistribution of lysosomes from the perinuclear region to cell periphery. Mechanistically, TMEM39A interacts with the dynein intermediate light chain DYNC1I2 to maintain proper lysosome distribution. Deficiency of tmem-39 or the DYNC1I2 homolog in C. elegans impairs mTOR signaling and activates the downstream TFEB-like transcription factor HLH-30. We propose evolutionarily conserved roles of TMEM39 family proteins in regulating lysosome distribution and lysosome-associated signaling, dysfunction of which in humans may underlie aspects of autoimmune diseases.
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Frémond ML, Crow YJ. STING-Mediated Lung Inflammation and Beyond. J Clin Immunol 2021; 41:501-514. [PMID: 33532887 DOI: 10.1007/s10875-021-00974-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/18/2021] [Indexed: 02/07/2023]
Abstract
Mendelian autoinflammatory diseases characterized by constitutive activation of the type I interferon pathway, the so-called type I interferonopathies, constitute a rapidly expanding group of inborn errors of immunity. Among the type I interferonopathies, STING-associated vasculopathy with onset in infancy (SAVI) and COPA syndrome were described in the last 6 years, both manifesting a major inflammatory lung component associated with significant morbidity and increased mortality. There is striking clinical and histopathological overlap between SAVI and COPA syndrome, although distinct features are also present. Of note, there is a remarkably high frequency of clinical non-penetrance among individuals harboring pathogenic COPA mutations. SAVI is caused by, principally heterozygous, gain-of-function mutations in STING1 (previously referred to as TMEM173) encoding STING, a key adaptor of the interferon signaling pathway induced by DNA. COPA syndrome results from heterozygous dominant-negative mutations in the coatomer protein subunit alpha, forming part of a complex involved in intracellular cargo protein transport between the Golgi and the endoplasmic reticulum (ER). Of importance, a role for COPA in regulating the trafficking of STING, an ER-resident protein which translocates to the Golgi during the process of its activation, was recently defined, thereby possibly explaining some aspects of the phenotypic overlap between SAVI and COPA syndrome. Here, we review the expanding phenotype of these diseases, highlighting common as well as specific features, and recent advances in our understanding of STING biology that have informed therapeutic decision-making in both conditions. Beyond these rare Mendelian disorders, DNA sensing through STING is likely relevant to the pathology of several diseases associated with lung inflammation, including systemic lupus erythematosus, dermatomyositis, environmental toxin exposure, and viral infection.
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Affiliation(s)
- Marie-Louise Frémond
- Université de Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, 24 boulevard du Montparnasse, F-75015, Paris, France. .,Paediatric Haematology-Immunology and Rheumatology Unit, AP-HP, Necker Hospital, F-75015, Paris, France.
| | - Yanick J Crow
- Université de Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, 24 boulevard du Montparnasse, F-75015, Paris, France.,Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh, UK
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Mukai K, Ogawa E, Uematsu R, Kuchitsu Y, Kiku F, Uemura T, Waguri S, Suzuki T, Dohmae N, Arai H, Shum AK, Taguchi T. Homeostatic regulation of STING by retrograde membrane traffic to the ER. Nat Commun 2021; 12:61. [PMID: 33397928 PMCID: PMC7782846 DOI: 10.1038/s41467-020-20234-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/20/2020] [Indexed: 01/04/2023] Open
Abstract
Coat protein complex I (COP-I) mediates the retrograde transport from the Golgi apparatus to the endoplasmic reticulum (ER). Mutation of the COPA gene, encoding one of the COP-I subunits (α-COP), causes an immune dysregulatory disease known as COPA syndrome. The molecular mechanism by which the impaired retrograde transport results in autoinflammation remains poorly understood. Here we report that STING, an innate immunity protein, is a cargo of the retrograde membrane transport. In the presence of the disease-causative α-COP variants, STING cannot be retrieved back to the ER from the Golgi. The forced Golgi residency of STING results in the cGAS-independent and palmitoylation-dependent activation of the STING downstream signaling pathway. Surf4, a protein that circulates between the ER/ ER-Golgi intermediate compartment/ Golgi, binds STING and α-COP, and mediates the retrograde transport of STING to the ER. The STING/Surf4/α-COP complex is disrupted in the presence of the disease-causative α-COP variant. We also find that the STING ligand cGAMP impairs the formation of the STING/Surf4/α-COP complex. Our results suggest a homeostatic regulation of STING at the resting state by retrograde membrane traffic and provide insights into the pathogenesis of COPA syndrome. COPA regulates Golgi to ER transport, and mutations lead to autoinflammation and disease through poorly understood mechanisms. Here, the authors show that disease-causing COPA variants prevent STING transport from the Golgi to the ER, leading to cGAS-independent activation of the STING pathway.
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Affiliation(s)
- Kojiro Mukai
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Emari Ogawa
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Rei Uematsu
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Yoshihiko Kuchitsu
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Fumika Kiku
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Takefumi Uemura
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Hiroyuki Arai
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Anthony K Shum
- Department of Medicine, Division of Pulmonary and Critical Care, University of California San Francisco, San Francisco, CA, USA
| | - Tomohiko Taguchi
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
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DeNies MS, Smrcka AV, Schnell S, Liu AP. β-arrestin mediates communication between plasma membrane and intracellular GPCRs to regulate signaling. Commun Biol 2020; 3:789. [PMID: 33339901 PMCID: PMC7749148 DOI: 10.1038/s42003-020-01510-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/16/2020] [Indexed: 01/14/2023] Open
Abstract
It has become increasingly apparent that G protein-coupled receptor (GPCR) localization is a master regulator of cell signaling. However, the molecular mechanisms involved in this process are not well understood. To date, observations of intracellular GPCR activation can be organized into two categories: a dependence on OCT3 cationic channel-permeable ligands or the necessity of endocytic trafficking. Using CXC chemokine receptor 4 (CXCR4) as a model, we identified a third mechanism of intracellular GPCR signaling. We show that independent of membrane permeable ligands and endocytosis, upon stimulation, plasma membrane and internal pools of CXCR4 are post-translationally modified and collectively regulate EGR1 transcription. We found that β-arrestin-1 (arrestin 2) is necessary to mediate communication between plasma membrane and internal pools of CXCR4. Notably, these observations may explain that while CXCR4 overexpression is highly correlated with cancer metastasis and mortality, plasma membrane localization is not. Together these data support a model where a small initial pool of plasma membrane-localized GPCRs are capable of activating internal receptor-dependent signaling events. DeNies et al. identify a new mechanism of intracellular GPCR signalling. Using CXC chemokine receptor 4 (CXCR4) as a model, they show that upon stimulation with receptor agonists that not only plasma membrane-localized receptors, but also intracellular CXCR4 molecules are post-translationally modified and regulate transcription. This study suggests that a small pool of plasma membrane-localized GPCRs can activate internal receptor-dependent signaling, and that β-arrestin-1 mediates this activation.
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Affiliation(s)
- Maxwell S DeNies
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Alan V Smrcka
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Santiago Schnell
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA.,Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Allen P Liu
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA. .,Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA. .,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA. .,Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
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Wang Y, Xie G, Li M, Du J, Wang M. COPB2 gene silencing inhibits colorectal cancer cell proliferation and induces apoptosis via the JNK/c-Jun signaling pathway. PLoS One 2020; 15:e0240106. [PMID: 33211699 PMCID: PMC7676692 DOI: 10.1371/journal.pone.0240106] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/18/2020] [Indexed: 12/13/2022] Open
Abstract
Objectives Colorectal cancer (CRC) is one of the most common malignant human tumors. It is associated with high morbidity and mortality rates. In recent years, tumor gene therapy has emerged as a promising new approach for colorectal cancer therapy. Herein, we identify and analyze the role of COPB2 (coatomer protein complex, subunit beta 2) in proliferation and apoptosis of CRC cells. Methods To investigate the role of COPB2 in the proliferation and apoptosis of CRC cells, a shCOPB2 vector and a shCtrl vector were constructed for transfection into RKO and HCT116 cells. Cells proliferation was subsequently measured via cell counting kit-8 (CCK8) assay and Celigo cell counting assay. Apoptosis was measured via flow cytometry. The activity level of Caspase 3/7 was measured. Finally, the level of several JNK/c-Jun apoptosis pathway-related proteins were measured to characterize the mechanism of apoptosis. Results Our results showed that the proliferation rate was decreased and the apoptosis rate was increased in shCOPB2-treated RKO and HCT116 cells compared to those in controls. After the silencing of COPB2, JNK/c-Jun signal pathway activation was increased, the expression levels of apoptosis pathway-related proteins, such as Bad, p53 and Caspase 3, were also increased. Conclusion COPB2 gene silencing can inhibit RKO and HCT116 cells proliferation and induce apoptosis via the JNK/c-Jun signaling pathway.
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Affiliation(s)
- Yan Wang
- Gansu Provincial Hospital, Lanzhou, Gansu, China
- Institute of Pathology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, China
- * E-mail:
| | - Guangmei Xie
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou, Gansu, China
| | - Min Li
- Institute of Pathology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Juan Du
- Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Min Wang
- Institute of Pathology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, China
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Abstract
Two studies published in this issue of JEM, by Lepelley et al. (https://doi.org/10.1084/jem.20200600) and Deng et al. (https://doi.org/10.1084/jem.20201045), and two additional manuscripts by Mukai et al. (https://doi.org/10.1101/2020.05.20.107664 Preprint v1) and Steiner et al. (https://doi.org/10.1101/2020.07.09.194399 Preprint v1) demonstrate that COPA syndrome-associated high interferon titers are linked to mutations in COPA preventing STING's retrieval from the Golgi back to the ER and thereby causing chronic immune activation.
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Affiliation(s)
- Sophie Rivara
- Global Health Institute, Swiss Federal Institute of Technology Lausanne, Lausanne, Switzerland
| | - Andrea Ablasser
- Global Health Institute, Swiss Federal Institute of Technology Lausanne, Lausanne, Switzerland
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Lepelley A, Martin-Niclós MJ, Le Bihan M, Marsh JA, Uggenti C, Rice GI, Bondet V, Duffy D, Hertzog J, Rehwinkel J, Amselem S, Boulisfane-El Khalifi S, Brennan M, Carter E, Chatenoud L, Chhun S, Coulomb l’Hermine A, Depp M, Legendre M, Mackenzie KJ, Marey J, McDougall C, McKenzie KJ, Molina TJ, Neven B, Seabra L, Thumerelle C, Wislez M, Nathan N, Manel N, Crow YJ, Frémond ML. Mutations in COPA lead to abnormal trafficking of STING to the Golgi and interferon signaling. J Exp Med 2020; 217:e20200600. [PMID: 32725128 PMCID: PMC7596811 DOI: 10.1084/jem.20200600] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/04/2020] [Accepted: 07/06/2020] [Indexed: 01/01/2023] Open
Abstract
Heterozygous missense mutations in coatomer protein subunit α, COPA, cause a syndrome overlapping clinically with type I IFN-mediated disease due to gain-of-function in STING, a key adaptor of IFN signaling. Recently, increased levels of IFN-stimulated genes (ISGs) were described in COPA syndrome. However, the link between COPA mutations and IFN signaling is unknown. We observed elevated levels of ISGs and IFN-α in blood of symptomatic COPA patients. In vitro, both overexpression of mutant COPA and silencing of COPA induced STING-dependent IFN signaling. We detected an interaction between COPA and STING, and mutant COPA was associated with an accumulation of ER-resident STING at the Golgi. Given the known role of the coatomer protein complex I, we speculate that loss of COPA function leads to enhanced type I IFN signaling due to a failure of Golgi-to-ER STING retrieval. These data highlight the importance of the ER-Golgi axis in the control of autoinflammation and inform therapeutic strategies in COPA syndrome.
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Affiliation(s)
- Alice Lepelley
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, Paris, France
| | | | - Melvin Le Bihan
- Immunity and Cancer Department, Institut Curie, Paris-Sciences-et-Lettres Research University, Institut National de la Santé et de la Recherche Médicale U932, Paris, France
| | - Joseph A. Marsh
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Carolina Uggenti
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Gillian I. Rice
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Vincent Bondet
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
- Institut National de la Santé et de la Recherche Médicale U1223, Paris, France
| | - Darragh Duffy
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
- Institut National de la Santé et de la Recherche Médicale U1223, Paris, France
| | - Jonny Hertzog
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Serge Amselem
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale/UMRS_933, Trousseau University Hospital, Paris, France
- Genetics Department, Trousseau University Hospital, Assistance Publique–Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Siham Boulisfane-El Khalifi
- Emergency, Infectious Disease and Pediatric Rheumatology Department, Centre Hospitalier Régional Universitaire Lille, University of Lille, Lille, France
| | - Mary Brennan
- Department of Paediatric Rheumatology, Royal Hospital for Sick Children, Edinburgh, UK
| | - Edwin Carter
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Lucienne Chatenoud
- Paris Descartes University, Université de Paris, Sorbonne-Paris-Cité, Paris, France
- Laboratory of Immunology, Hôpital Necker-Enfants Malades, Assistance Publique–Hôpitaux de Paris, Centre-Université de Paris, Paris, France
- Institut Necker-Enfants Malades, Centre National de la Recherche Scientifique UMR8253, Institut National de la Santé et de la Recherche Médicale UMR1151, Team Immunoregulation and Immunopathology, Paris, France
| | - Stéphanie Chhun
- Paris Descartes University, Université de Paris, Sorbonne-Paris-Cité, Paris, France
- Laboratory of Immunology, Hôpital Necker-Enfants Malades, Assistance Publique–Hôpitaux de Paris, Centre-Université de Paris, Paris, France
- Institut Necker-Enfants Malades, Centre National de la Recherche Scientifique UMR8253, Institut National de la Santé et de la Recherche Médicale UMR1151, Team Immunoregulation and Immunopathology, Paris, France
| | - Aurore Coulomb l’Hermine
- Pathology Department, Trousseau University Hospital, Assistance Publique–Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Marine Depp
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Marie Legendre
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale/UMRS_933, Trousseau University Hospital, Paris, France
- Genetics Department, Trousseau University Hospital, Assistance Publique–Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Karen J. Mackenzie
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Jonathan Marey
- Pneumology Department, Cochin Hospital, Assistance Publique–Hôpitaux de Paris, Centre-Université de Paris, Paris, France
| | - Catherine McDougall
- Department of Paediatric Respiratory Medicine, Royal Hospital for Sick Children, Edinburgh, UK
| | - Kathryn J. McKenzie
- Paediatric Pathology Department, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Thierry Jo Molina
- Paris Descartes University, Université de Paris, Sorbonne-Paris-Cité, Paris, France
- Pathology Department, Hôpital Necker-Enfants Malades, Assistance Publique–Hôpitaux de Paris, Centre-Université de Paris, Paris, France
| | - Bénédicte Neven
- Paris Descartes University, Université de Paris, Sorbonne-Paris-Cité, Paris, France
- Pediatric Hematology-Immunology and Rheumatology Department, Hôpital Necker-Enfants Malades, Assistance Publique–Hôpitaux de Paris, Centre-Université de Paris, Paris, France
- Institut National de la Santé et de la Recherche Médicale UMR 1163, Laboratory of Immunogenetics of Paediatric Autoimmunity, Imagine Institute, Paris, France
| | - Luis Seabra
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, Paris, France
| | - Caroline Thumerelle
- Pediatric Pneumology Department, Hôpital Jeanne de Flandre, Centre Hospitalier Régional Universitaire Lille, Lille, France
| | - Marie Wislez
- Pneumology Department, Cochin Hospital, Assistance Publique–Hôpitaux de Paris, Centre-Université de Paris, Paris, France
- Cordeliers Research Center, Université Paris Descartes, Université de Paris, UMRS1138 Inflammation, Complement and Cancer Team, Paris, France
| | - Nadia Nathan
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale/UMRS_933, Trousseau University Hospital, Paris, France
- Pediatric Pulmonology Department and Reference Center for Rare Lung Disease RespiRare, Trousseau University Hospital, Assistance Publique–Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Nicolas Manel
- Immunity and Cancer Department, Institut Curie, Paris-Sciences-et-Lettres Research University, Institut National de la Santé et de la Recherche Médicale U932, Paris, France
| | - Yanick J. Crow
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, Paris, France
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Marie-Louise Frémond
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, Paris, France
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Frémond ML, Nathan N. COPA syndrome, 5 years after: Where are we? Joint Bone Spine 2020; 88:105070. [PMID: 32919065 DOI: 10.1016/j.jbspin.2020.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 09/02/2020] [Indexed: 01/01/2023]
Abstract
Heterozygous missense mutations in COPA, encoding coatomer protein subunit alpha (COPA), cause an interferonopathy mainly associating lung, joint and kidney involvement. This rare autoinflammatory disease is characterised by variable expression and a remarkably high frequency of clinical non-penetrance. Lung features, predominantly chronic diffuse alveolar haemorrhage (DAH), are observed in almost patients and can result in end-stage respiratory insufficiency. The initially described phenotype was broadened to include isolated DAH or lupus nephritis. Rare manifestations reminiscent of other monogenic interferonopathies occur. This indicates the need for careful clinical evaluation in patients with suspicion or diagnosis of COPA syndrome. Considering the dominant inheritance model and the highly variable phenotype, ranging from severe multi-organic disorder to non-penetrance, a careful family screening is recommended. New insights in disease pathogenesis have linked COPA mutations to STING-mediated interferon signalling. Beside a variable efficacy of 'classical' immunosuppressive drugs, Janus kinase (JAK) inhibitors constitute a promising treatment in COPA syndrome, and further targeted therapies are awaited.
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Affiliation(s)
- Marie-Louise Frémond
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, 24, boulevard du Montparnasse, 75015 Paris, France.
| | - Nadia Nathan
- Pediatric Pulmonology Department and Reference center for rare lung disease RespiRare, Trousseau University Hospital, AP-HP, Sorbonne Université, Paris, France; Sorbonne Université, Inserm/UMRS_933, Trousseau University Hospital, Paris, France
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Chiasson MA, Rollins NJ, Stephany JJ, Sitko KA, Matreyek KA, Verby M, Sun S, Roth FP, DeSloover D, Marks DS, Rettie AE, Fowler DM. Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. eLife 2020; 9:e58026. [PMID: 32870157 PMCID: PMC7462613 DOI: 10.7554/elife.58026] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 01/05/2023] Open
Abstract
Vitamin K epoxide reductase (VKOR) drives the vitamin K cycle, activating vitamin K-dependent blood clotting factors. VKOR is also the target of the widely used anticoagulant drug, warfarin. Despite VKOR's pivotal role in coagulation, its structure and active site remain poorly understood. In addition, VKOR variants can cause vitamin K-dependent clotting factor deficiency or alter warfarin response. Here, we used multiplexed, sequencing-based assays to measure the effects of 2,695 VKOR missense variants on abundance and 697 variants on activity in cultured human cells. The large-scale functional data, along with an evolutionary coupling analysis, supports a four transmembrane domain topology, with variants in transmembrane domains exhibiting strongly deleterious effects on abundance and activity. Functionally constrained regions of the protein define the active site, and we find that, of four conserved cysteines putatively critical for function, only three are absolutely required. Finally, 25% of human VKOR missense variants show reduced abundance or activity, possibly conferring warfarin sensitivity or causing disease.
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Affiliation(s)
- Melissa A Chiasson
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Nathan J Rollins
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
| | - Jason J Stephany
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Katherine A Sitko
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Kenneth A Matreyek
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Marta Verby
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Song Sun
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Frederick P Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | | | - Debora S Marks
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of WashingtonSeattleUnited States
| | - Douglas M Fowler
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Department of Bioengineering, University of WashingtonSeattleUnited States
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46
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Wu F, de Boer R, Krikken AM, Akşit A, Bordin N, Devos DP, van der Klei IJ. Pex24 and Pex32 are required to tether peroxisomes to the ER for organelle biogenesis, positioning and segregation in yeast. J Cell Sci 2020; 133:jcs246983. [PMID: 32665322 DOI: 10.1242/jcs.246983] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022] Open
Abstract
The yeast Hansenula polymorpha contains four members of the Pex23 family of peroxins, which characteristically contain a DysF domain. Here we show that all four H. polymorpha Pex23 family proteins localize to the endoplasmic reticulum (ER). Pex24 and Pex32, but not Pex23 and Pex29, predominantly accumulate at peroxisome-ER contacts. Upon deletion of PEX24 or PEX32 - and to a much lesser extent, of PEX23 or PEX29 - peroxisome-ER contacts are lost, concomitant with defects in peroxisomal matrix protein import, membrane growth, and organelle proliferation, positioning and segregation. These defects are suppressed by the introduction of an artificial peroxisome-ER tether, indicating that Pex24 and Pex32 contribute to tethering of peroxisomes to the ER. Accumulation of Pex32 at these contact sites is lost in cells lacking the peroxisomal membrane protein Pex11, in conjunction with disruption of the contacts. This indicates that Pex11 contributes to Pex32-dependent peroxisome-ER contact formation. The absence of Pex32 has no major effect on pre-peroxisomal vesicles that occur in pex3 atg1 deletion cells.
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Affiliation(s)
- Fei Wu
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9300CC Groningen, The Netherlands
| | - Rinse de Boer
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9300CC Groningen, The Netherlands
| | - Arjen M Krikken
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9300CC Groningen, The Netherlands
| | - Arman Akşit
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9300CC Groningen, The Netherlands
| | - Nicola Bordin
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Carretera de Utrera, Km.1, Seville 41013, Spain
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Carretera de Utrera, Km.1, Seville 41013, Spain
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9300CC Groningen, The Netherlands
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47
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Keiser KJ, Barlowe C. Molecular dissection of the Erv41-Erv46 retrograde receptor reveals a conserved cysteine-rich region in Erv46 required for retrieval activity. Mol Biol Cell 2019; 31:209-220. [PMID: 31825724 PMCID: PMC7001479 DOI: 10.1091/mbc.e19-08-0484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Erv41-Erv46 complex is a conserved retrograde cargo receptor that retrieves ER resident proteins from Golgi compartments in a pH-dependent manner. Here we functionally dissect the Erv46 subunit and define an approximately 60 residue cysteine-rich region that is unique to the Erv46 family of proteins. This cysteine-rich region contains two vicinal cysteine pairs in CXXC and CCXXC configurations that are each required for retrieval activity in cells. Mutation of the individual cysteine residues produced stable Erv46 proteins that were partially reduced and form mixed-disulfide species on nonreducing gels. Conserved hydrophobic amino acids within the cysteine-rich region of Erv46 were also required for retrieval function in cells. In vitro binding experiments showed that this hydrophobic patch is required for direct cargo binding. Surprisingly, the Erv46 cysteine mutants continued to bind cargo in cell-free assays and produced an increased level of Erv46-cargo complexes in cell extracts suggesting that disulfide linkages in the cysteine-rich region perform a role in releasing bound cargo. On the basis of these findings, we propose that both pH and redox environments regulate cargo binding to a hydrophobic site within the cysteine-rich region of Erv46.
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Affiliation(s)
- Kristofer J Keiser
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Charles Barlowe
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
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48
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Travis SM, Kokona B, Fairman R, Hughson FM. Roles of singleton tryptophan motifs in COPI coat stability and vesicle tethering. Proc Natl Acad Sci U S A 2019; 116:24031-24040. [PMID: 31712447 PMCID: PMC6883825 DOI: 10.1073/pnas.1909697116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Coat protein I (COPI)-coated vesicles mediate retrograde transport from the Golgi to the endoplasmic reticulum (ER), as well as transport within the Golgi. Major progress has been made in defining the structure of COPI coats, in vitro and in vivo, at resolutions as high as 9 Å. Nevertheless, important questions remain unanswered, including what specific interactions stabilize COPI coats, how COPI vesicles recognize their target membranes, and how coat disassembly is coordinated with vesicle fusion and cargo delivery. Here, we use X-ray crystallography to identify a conserved site on the COPI subunit α-COP that binds to flexible, acidic sequences containing a single tryptophan residue. One such sequence, found within α-COP itself, mediates α-COP homo-oligomerization. Another such sequence is contained within the lasso of the ER-resident Dsl1 complex, where it helps mediate the tethering of Golgi-derived COPI vesicles at the ER membrane. Together, our findings suggest that α-COP homo-oligomerization plays a key role in COPI coat stability, with potential implications for the coordination of vesicle tethering, uncoating, and fusion.
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Affiliation(s)
- Sophie M Travis
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, PA 19041
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, PA 19041
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49
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Ludlam WG, Aoba T, Cuéllar J, Bueno-Carrasco MT, Makaju A, Moody JD, Franklin S, Valpuesta JM, Willardson BM. Molecular architecture of the Bardet-Biedl syndrome protein 2-7-9 subcomplex. J Biol Chem 2019; 294:16385-16399. [PMID: 31530639 DOI: 10.1074/jbc.ra119.010150] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/10/2019] [Indexed: 02/04/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is a genetic disorder characterized by malfunctions in primary cilia resulting from mutations that disrupt the function of the BBSome, an 8-subunit complex that plays an important role in protein transport in primary cilia. To better understand the molecular basis of BBS, here we used an integrative structural modeling approach consisting of EM and chemical cross-linking coupled with MS analyses, to analyze the structure of a BBSome 2-7-9 subcomplex consisting of three homologous BBS proteins, BBS2, BBS7, and BBS9. The resulting molecular model revealed an overall structure that resembles a flattened triangle. We found that within this structure, BBS2 and BBS7 form a tight dimer through a coiled-coil interaction and that BBS9 associates with the dimer via an interaction with the α-helical domain of BBS2. Interestingly, a BBS-associated mutation of BBS2 (R632P) is located in its α-helical domain at the interface between BBS2 and BBS9, and binding experiments indicated that this mutation disrupts the BBS2-BBS9 interaction. This finding suggests that BBSome assembly is disrupted by the R632P substitution, providing molecular insights that may explain the etiology of BBS in individuals harboring this mutation.
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Affiliation(s)
- W Grant Ludlam
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602
| | - Takuma Aoba
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602
| | - Jorge Cuéllar
- Centro Nacional de Biotecnología (CNB-CSIC), Campus de la Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - M Teresa Bueno-Carrasco
- Centro Nacional de Biotecnología (CNB-CSIC), Campus de la Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Aman Makaju
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112
| | - James D Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602
| | - Sarah Franklin
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112
| | - José M Valpuesta
- Centro Nacional de Biotecnología (CNB-CSIC), Campus de la Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Barry M Willardson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602
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50
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Abstract
Protein coats are supramolecular complexes that assemble on the cytosolic face of membranes to promote cargo sorting and transport carrier formation in the endomembrane system of eukaryotic cells. Several types of protein coats have been described, including COPI, COPII, AP-1, AP-2, AP-3, AP-4, AP-5, and retromer, which operate at different stages of the endomembrane system. Defects in these coats impair specific transport pathways, compromising the function and viability of the cells. In humans, mutations in subunits of these coats cause various congenital diseases that are collectively referred to as coatopathies. In this article, we review the fundamental properties of protein coats and the diseases that result from mutation of their constituent subunits.
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Affiliation(s)
- Esteban C Dell'Angelica
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Juan S Bonifacino
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland 20892, USA;
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