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Paddar MA, Wang F, Trosdal ES, Hendrix E, He Y, Salemi M, Mudd M, Jia J, Duque TLA, Javed R, Phinney B, Deretic V. Noncanonical roles of ATG5 and membrane atg8ylation in retromer assembly and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602886. [PMID: 39026874 PMCID: PMC11257513 DOI: 10.1101/2024.07.10.602886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
ATG5 is one of the core autophagy proteins with additional functions such as noncanonical membrane atg8ylation, which among a growing number of biological outputs includes control of tuberculosis in animal models. Here we show that ATG5 associates with retromer's core components VPS26, VPS29 and VPS35 and modulates retromer function. Knockout of ATG5 blocked trafficking of a key glucose transporter sorted by the retromer, GLUT1, to the plasma membrane. Knockouts of other genes essential for membrane atg8ylation, of which ATG5 is a component, affected GLUT1 sorting, indicating that membrane atg8ylation as a process affects retromer function and endosomal sorting. The contribution of membrane atg8ylation to retromer function in GLUT1 sorting was independent of canonical autophagy. These findings expand the scope of membrane atg8ylation to specific sorting processes in the cell dependent on the retromer and its known interactors.
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Affiliation(s)
- Masroor Ahmad Paddar
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Fulong Wang
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Einar S Trosdal
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Emily Hendrix
- Department of Chemistry & Chemical Biology, The University of New Mexico, Albuquerque, NM, USA
| | - Yi He
- Department of Chemistry & Chemical Biology, The University of New Mexico, Albuquerque, NM, USA
| | - Michelle Salemi
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Michal Mudd
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Jingyue Jia
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Thabata L A Duque
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Ruheena Javed
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Brett Phinney
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
- Lead Contact
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2
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Gopaldass N, Chen KE, Collins B, Mayer A. Assembly and fission of tubular carriers mediating protein sorting in endosomes. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00746-8. [PMID: 38886588 DOI: 10.1038/s41580-024-00746-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2024] [Indexed: 06/20/2024]
Abstract
Endosomes are central protein-sorting stations at the crossroads of numerous membrane trafficking pathways in all eukaryotes. They have a key role in protein homeostasis and cellular signalling and are involved in the pathogenesis of numerous diseases. Endosome-associated protein assemblies or coats collect transmembrane cargo proteins and concentrate them into retrieval domains. These domains can extend into tubular carriers, which then pinch off from the endosomal membrane and deliver the cargoes to appropriate subcellular compartments. Here we discuss novel insights into the structure of a number of tubular membrane coats that mediate the recruitment of cargoes into these carriers, focusing on sorting nexin-based coats such as Retromer, Commander and ESCPE-1. We summarize current and emerging views of how selective tubular endosomal carriers form and detach from endosomes by fission, highlighting structural aspects, conceptual challenges and open questions.
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Affiliation(s)
- Navin Gopaldass
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
| | - Kai-En Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Brett Collins
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Andreas Mayer
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
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Pearson GJ, Mears HV, Broncel M, Snijders AP, Bauer DLV, Carlton JG. ER-export and ARFRP1/AP-1-dependent delivery of SARS-CoV-2 Envelope to lysosomes controls late stages of viral replication. SCIENCE ADVANCES 2024; 10:eadl5012. [PMID: 38569033 PMCID: PMC10990277 DOI: 10.1126/sciadv.adl5012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
The β-coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the global COVID-19 pandemic. Coronaviral Envelope (E) proteins are pentameric viroporins that play essential roles in assembly, release, and pathogenesis. We developed a nondisruptive tagging strategy for SARS-CoV-2 E and find that, at steady state, it localizes to the Golgi and to lysosomes. We identify sequences in E, conserved across Coronaviridae, responsible for endoplasmic reticulum-to-Golgi export, and relate this activity to interaction with COP-II via SEC24. Using proximity biotinylation, we identify an ADP ribosylation factor 1/adaptor protein-1 (ARFRP1/AP-1)-dependent pathway allowing Golgi-to-lysosome trafficking of E. We identify sequences in E that bind AP-1, are conserved across β-coronaviruses, and allow E to be trafficked from Golgi to lysosomes. We show that E acts to deacidify lysosomes and, by developing a trans-complementation assay for SARS-CoV-2 structural proteins, that lysosomal delivery of E and its viroporin activity is necessary for efficient viral replication and release.
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Affiliation(s)
- Guy J. Pearson
- Organelle Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- School of Cancer & Pharmaceutical Sciences, King’s College London, Great Maze Pond, London SE1 1UL, UK
| | - Harriet V. Mears
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Malgorzata Broncel
- Proteomic Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P. Snijders
- Proteomic Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David L. V. Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jeremy G. Carlton
- Organelle Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- School of Cancer & Pharmaceutical Sciences, King’s College London, Great Maze Pond, London SE1 1UL, UK
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Walia K, Sharma A, Paul S, Chouhan P, Kumar G, Ringe R, Sharma M, Tuli A. SARS-CoV-2 virulence factor ORF3a blocks lysosome function by modulating TBC1D5-dependent Rab7 GTPase cycle. Nat Commun 2024; 15:2053. [PMID: 38448435 PMCID: PMC10918171 DOI: 10.1038/s41467-024-46417-2] [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: 06/12/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
SARS-CoV-2, the causative agent of COVID-19, uses the host endolysosomal system for entry, replication, and egress. Previous studies have shown that the SARS-CoV-2 virulence factor ORF3a interacts with the lysosomal tethering factor HOPS complex and blocks HOPS-mediated late endosome and autophagosome fusion with lysosomes. Here, we report that SARS-CoV-2 infection leads to hyperactivation of the late endosomal and lysosomal small GTP-binding protein Rab7, which is dependent on ORF3a expression. We also observed Rab7 hyperactivation in naturally occurring ORF3a variants encoded by distinct SARS-CoV-2 variants. We found that ORF3a, in complex with Vps39, sequesters the Rab7 GAP TBC1D5 and displaces Rab7 from this complex. Thus, ORF3a disrupts the GTP hydrolysis cycle of Rab7, which is beneficial for viral production, whereas the Rab7 GDP-locked mutant strongly reduces viral replication. Hyperactivation of Rab7 in ORF3a-expressing cells impaired CI-M6PR retrieval from late endosomes to the trans-Golgi network, disrupting the biosynthetic transport of newly synthesized hydrolases to lysosomes. Furthermore, the tethering of the Rab7- and Arl8b-positive compartments was strikingly reduced upon ORF3a expression. As SARS-CoV-2 egress requires Arl8b, these findings suggest that ORF3a-mediated hyperactivation of Rab7 serves a multitude of functions, including blocking endolysosome formation, interrupting the transport of lysosomal hydrolases, and promoting viral egress.
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Affiliation(s)
- Kshitiz Walia
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Abhishek Sharma
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Sankalita Paul
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Priya Chouhan
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Gaurav Kumar
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Rajesh Ringe
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Mahak Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Amit Tuli
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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Tavares LA, Rodrigues RL, Santos da Costa C, Nascimento JA, Vargas de Carvalho J, Nogueira de Carvalho A, Mardones GA, daSilva LLP. AP-1γ2 is an adaptor protein 1 variant required for endosome-to-Golgi trafficking of the mannose-6-P receptor (CI-MPR) and ATP7B copper transporter. J Biol Chem 2024; 300:105700. [PMID: 38307383 PMCID: PMC10909764 DOI: 10.1016/j.jbc.2024.105700] [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: 07/22/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/04/2024] Open
Abstract
Selective retrograde transport from endosomes back to the trans-Golgi network (TGN) is important for maintaining protein homeostasis, recycling receptors, and returning molecules that were transported to the wrong compartments. Two important transmembrane proteins directed to this pathway are the Cation-Independent Mannose-6-phosphate receptor (CI-MPR) and the ATP7B copper transporter. Among CI-MPR functions is the delivery of acid hydrolases to lysosomes, while ATP7B facilitates the transport of cytosolic copper ions into organelles or the extracellular space. Precise subcellular localization of CI-MPR and ATP7B is essential for the proper functioning of these proteins. This study shows that both CI-MPR and ATP7B interact with a variant of the clathrin adaptor 1 (AP-1) complex that contains a specific isoform of the γ-adaptin subunit called γ2. Through synchronized anterograde trafficking and cell-surface uptake assays, we demonstrated that AP-1γ2 is dispensable for ATP7B and CI-MPR exit from the TGN while being critically required for ATP7B and CI-MPR retrieval from endosomes to the TGN. Moreover, AP-1γ2 depletion leads to the retention of endocytosed CI-MPR in endosomes enriched in retromer complex subunits. These data underscore the importance of AP-1γ2 as a key component in the sorting and trafficking machinery of CI-MPR and ATP7B, highlighting its essential role in the transport of proteins from endosomes.
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Affiliation(s)
- Lucas Alves Tavares
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Roger Luiz Rodrigues
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Cristina Santos da Costa
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Jonas Alburqueque Nascimento
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Julianne Vargas de Carvalho
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Andreia Nogueira de Carvalho
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Gonzalo A Mardones
- Escuela de Medicina, Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
| | - Luis L P daSilva
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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G. Dornan L, C. Simpson J. Rab6-mediated retrograde trafficking from the Golgi: the trouble with tubules. Small GTPases 2023; 14:26-44. [PMID: 37488775 PMCID: PMC10392741 DOI: 10.1080/21541248.2023.2238330] [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: 06/15/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/26/2023] Open
Abstract
Next year marks one-quarter of a century since the discovery of the so-called COPI-independent pathway, which operates between the Golgi apparatus and the endoplasmic reticulum (ER) in eukaryotic cells. Unlike almost all other intracellular trafficking pathways, this pathway is not regulated by the physical accumulation of multisubunit proteinaceous coat molecules, but instead by the small GTPase Rab6. What also sets it apart from other pathways is that the transport carriers themselves often take the form of tubules, rather than conventional vesicles. In this review, we assess the relevant literature that has accumulated to date, in an attempt to provide a concerted description of how this pathway is regulated. We discuss the possible cargo molecules that are carried in this pathway, and the likely mechanism of Rab6 tubule biogenesis, including how the cargo itself may play a critical role. We also provide perspective surrounding the various molecular motors of the kinesin, myosin and dynein families that have been implicated in driving Rab6-coated tubular membranes long distances through the cell prior to delivering their cargo to the ER. Finally, we also raise several important questions that require resolution, if we are to ultimately provide a comprehensive molecular description of how the COPI-independent pathway is controlled.
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Affiliation(s)
- Lucy G. Dornan
- Cell Screening Laboratory, UCD School of Biology & Environmental Science, University College Dublin, Dublin, Ireland
| | - Jeremy C. Simpson
- Cell Screening Laboratory, UCD School of Biology & Environmental Science, University College Dublin, Dublin, Ireland
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7
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Mignani L, Facchinello N, Varinelli M, Massardi E, Tiso N, Ravelli C, Mitola S, Schu P, Monti E, Finazzi D, Borsani G, Zizioli D. Deficiency of AP1 Complex Ap1g1 in Zebrafish Model Led to Perturbation of Neurodevelopment, Female and Male Fertility; New Insight to Understand Adaptinopathies. Int J Mol Sci 2023; 24:ijms24087108. [PMID: 37108275 PMCID: PMC10138411 DOI: 10.3390/ijms24087108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
In vertebrates, two homologous heterotetrameric AP1 complexes regulate the intracellular protein sorting via vesicles. AP-1 complexes are ubiquitously expressed and are composed of four different subunits: γ, β1, μ1 and σ1. Two different complexes are present in eukaryotic cells, AP1G1 (contains γ1 subunit) and AP1G2 (contains γ2 subunit); both are indispensable for development. One additional tissue-specific isoform exists for μ1A, the polarized epithelial cells specific to μ1B; two additional tissue-specific isoforms exist for σ1A: σ1B and σ1C. Both AP1 complexes fulfil specific functions at the trans-Golgi network and endosomes. The use of different animal models demonstrated their crucial role in the development of multicellular organisms and the specification of neuronal and epithelial cells. Ap1g1 (γ1) knockout mice cease development at the blastocyst stage, while Ap1m1 (μ1A) knockouts cease during mid-organogenesis. A growing number of human diseases have been associated with mutations in genes encoding for the subunits of adaptor protein complexes. Recently, a new class of neurocutaneous and neurometabolic disorders affecting intracellular vesicular traffic have been referred to as adaptinopathies. To better understand the functional role of AP1G1 in adaptinopathies, we generated a zebrafish ap1g1 knockout using CRISPR/Cas9 genome editing. Zebrafish ap1g1 knockout embryos cease their development at the blastula stage. Interestingly, heterozygous females and males have reduced fertility and showed morphological alterations in the brain, gonads and intestinal epithelium. An analysis of mRNA profiles of different marker proteins and altered tissue morphologies revealed dysregulated cadherin-mediated cell adhesion. These data demonstrate that the zebrafish model organism enables us to study the molecular details of adaptinopathies and thus also develop treatment strategies.
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Affiliation(s)
- Luca Mignani
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa, 11, 25123 Brescia, Italy
| | - Nicola Facchinello
- Neuroscience Institute, Italian Research Council (CNR), 35131 Padova, Italy
| | - Marco Varinelli
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Elena Massardi
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa, 11, 25123 Brescia, Italy
| | - Natascia Tiso
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Cosetta Ravelli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa, 11, 25123 Brescia, Italy
| | - Stefania Mitola
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa, 11, 25123 Brescia, Italy
- CN3 "Sviluppo di Terapia Genica e Farmaci con Tecnologia ad RNA", 25123 Brescia, Italy
| | - Peter Schu
- Department of Cellular Biochemistry, University Medical Center, Georg-August University, Humboldtallee 23, 37073 Gottingen, Germany
| | - Eugenio Monti
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa, 11, 25123 Brescia, Italy
| | - Dario Finazzi
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa, 11, 25123 Brescia, Italy
- Clinical Chemistry Laboratory, ASST Spedali Civili di Brescia, 25123 Brescia, Italy
| | - Giuseppe Borsani
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa, 11, 25123 Brescia, Italy
| | - Daniela Zizioli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa, 11, 25123 Brescia, Italy
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