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Bare Y, Defourny K, Bretou M, Van Niel G, Nolte-'t Hoen E, Gaudin R. The endoplasmic reticulum as a cradle for virus and extracellular vesicle secretion. Trends Cell Biol 2025; 35:282-293. [PMID: 39730274 DOI: 10.1016/j.tcb.2024.11.008] [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: 08/23/2024] [Revised: 11/08/2024] [Accepted: 11/25/2024] [Indexed: 12/29/2024]
Abstract
Extracellular vesicles (EVs) are small membranous carriers of protein, lipid, and nucleic acid cargoes and play a key role in intercellular communication. Recent work has revealed the previously under-recognized participation of endoplasmic reticulum (ER)-associated proteins (ERAPs) during EV secretion, using pathways reminiscent of viral replication and secretion. Here, we present highlights of the literature involving ER/ERAPs in EV biogenesis and propose mechanistic parallels with ERAPs exploited during viral infections. We propose that ERAPs play an active role in the release of EVs and viral particles, and we present views on whether viruses hijack or enhance pre-existing ERAP-dependent secretory machineries or whether they repurpose ERAPs to create new secretory pathways.
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Affiliation(s)
- Yonis Bare
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS UMR9004, Université Montpellier, Montpellier, France.
| | - Kyra Defourny
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands; VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Marine Bretou
- Université Paris Cité, Institut de Psychiatrie et Neurosciences de Paris (IPNP), INSERM U1266, Paris, France
| | - Guillaume Van Niel
- CRCI2NA, Nantes Université, INSERM UMR1307, CNRS UMR6075, Université d'Angers, Nantes, France; GHU-Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Paris, France
| | - Esther Nolte-'t Hoen
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Raphael Gaudin
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS UMR9004, Université Montpellier, Montpellier, France.
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2
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Denus M, Filaquier A, Fargues W, Néel E, Stewart SE, Colladant M, Curel T, Mezghrani A, Marin P, Claeysen S, Rubinsztein DC, Parmentier ML, Villeneuve J. A Sensitive and Versatile Cell-Based Assay Combines Luminescence and Trapping Approaches to Monitor Unconventional Protein Secretion. Traffic 2025; 26:e70009. [PMID: 40396394 DOI: 10.1111/tra.70009] [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: 12/06/2024] [Revised: 04/16/2025] [Accepted: 05/07/2025] [Indexed: 05/22/2025]
Abstract
In addition to the conventional endoplasmic reticulum (ER)-Golgi secretory pathway, alternative routes are increasingly recognized for their critical roles in exporting a growing number of secreted factors. These alternative processes, collectively referred to as unconventional protein secretion (UcPS), challenge traditional views of protein and membrane trafficking. Unlike the well-characterized molecular machinery of the conventional secretory pathway, the mechanisms underlying UcPS remain poorly understood. Various UcPS pathways may involve direct transport of cytosolic proteins across the plasma membrane or the incorporation of cargo proteins into intracellular compartments redirected for secretion. Identifying the specific chaperones, transporters and fusion machinery involved in UcPS cargo recognition, selection and transport is crucial to decipher how cargo proteins are selectively or synergistically directed through multiple secretory routes. These processes can vary depending on cell type and in response to particular stress conditions or cellular demands, underscoring the need for standardized tools and methods to study UcPS. Here, we combine the sensitivity of split NanoLuc Binary Technology with the versatility of the Retention Using Selective Hooks (RUSH) system to develop a straightforward and reliable cell-based assay for investigating both conventional and unconventional protein secretion. This system allows for the identification of intracellular compartments involved in UcPS cargo trafficking. Additionally, its sensitivity enabled us to demonstrate that disease-associated mutants or variants of Tau and superoxide dismutase-1 (SOD1) show altered secretion via UcPS. Finally, we leveraged this assay to screen for Alzheimer's disease risk factors, revealing a functional link between amyloid-beta production and Tau UcPS. This robust assay provides a powerful tool for increasing our knowledge of protein secretion mechanisms in physiological and pathological contexts.
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Affiliation(s)
- Morgane Denus
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Aurore Filaquier
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - William Fargues
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Eloïse Néel
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Sarah E Stewart
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Maëlle Colladant
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Thomas Curel
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Alexandre Mezghrani
- Centre de Biologie Structurale (CBS), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Philippe Marin
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Sylvie Claeysen
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - David C Rubinsztein
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, UK
- UK Dementia Research Institute, Cambridge, UK
| | - Marie-Laure Parmentier
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Julien Villeneuve
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
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3
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Lin L. Unconventional protein secretion: Exploring membrane proteins and beyond. Curr Opin Cell Biol 2025; 93:102469. [PMID: 39903992 DOI: 10.1016/j.ceb.2025.102469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Revised: 01/16/2025] [Accepted: 01/16/2025] [Indexed: 02/06/2025]
Abstract
Protein secretion is essential for cellular communication and function, enabling the delivery of both soluble and integral membrane proteins to the extracellular space and the cell surface. While the classical endoplasmic reticulum (ER)-Golgi pathway has been extensively studied, emerging evidence highlights the existence of unconventional protein secretion (UcPS) pathways. Among these, the mechanisms that enable membrane proteins to bypass the Golgi apparatus remain poorly understood. In this review, I discuss recent advances that shed light on the processes governing Golgi-bypassing membrane secretion. These findings reveal that UcPS of membrane proteins is evolutionarily conserved, operates under both physiological and stress conditions, and involves diverse intermediate carriers and molecular players. Looking ahead, advances in technology and the development of more sophisticated functional assays, along with in vivo models, are expected to further unravel the molecular mechanisms and biological roles of these unconventional pathways.
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Affiliation(s)
- Long Lin
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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4
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Song MS, Sim HJ, Eun SH, Jung MK, Hwang SJ, Ham MH, Kwak K, Lee HJ, Kim JY, Jang DG, Chung HC, Shin DH, Kim YJ, Noh SH, Mun JY, Lee JM, Lee MG. Tubular ER structures shaped by ER-phagy receptors engage in stress-induced Golgi bypass. Dev Cell 2025:S1534-5807(25)00031-0. [PMID: 39919755 DOI: 10.1016/j.devcel.2025.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 10/04/2024] [Accepted: 01/15/2025] [Indexed: 02/09/2025]
Abstract
Cellular stresses, particularly endoplasmic reticulum (ER) stress induced by ER-to-Golgi transport blockade, trigger Golgi-independent secretion of cytosolic and transmembrane proteins. However, the molecular mechanisms underlying this unconventional protein secretion (UPS) remain largely elusive. Here, we report that an ER tubulovesicular structure (ER tubular body [ER-TB]), shaped by the tubular ER-phagy receptors ATL3 and RTN3L, plays an important role in stress-induced UPS of transmembrane proteins such as cystic fibrosis transmembrane conductance regulator (CFTR) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Correlative light-electron microscopy analyses demonstrate the formation of ER-TB under UPS-inducing conditions in HEK293 and HeLa cells. Individual gene knockdowns of ATL3 and RTN3 inhibit ER-TB formation and the UPS of trafficking-deficient ΔF508-CFTR. Combined supplementation of ATL3 and RTN3L induces ER-TB formation and UPS. ATL3 also participates in the SARS-CoV-2-associated convoluted membrane formation and Golgi-independent trafficking of SARS-CoV-2 spike protein. These findings suggest that ER-TB serves a common function in mediating stress-induced UPS, which participates in various physiological and pathophysiological processes.
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Affiliation(s)
- Min Seok Song
- Department of Pharmacology, Woo Choo Lee Institute for Precision Drug Development, Graduate School of Medical Science Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Department of Physiology, Gyeongsang National University College of Medicine, Jinju 52727, Republic of Korea
| | - Hun Ju Sim
- Department of Pharmacology, Woo Choo Lee Institute for Precision Drug Development, Graduate School of Medical Science Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Sung Ho Eun
- Department of Pharmacology, Woo Choo Lee Institute for Precision Drug Development, Graduate School of Medical Science Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Department of Gastroenterology, National Health Insurance Service Ilsan Hospital, Goyang 10444, Republic of Korea
| | - Min Kyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41068, Republic of Korea
| | - Su Jin Hwang
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Graduate School of Medical Science Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Min Hee Ham
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Graduate School of Medical Science Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Kihyuck Kwak
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Graduate School of Medical Science Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hea Ji Lee
- Digital Omics Research Center, Korea Basic Science Institute (KBSI), Ochang, Cheongju 28119, Republic of Korea
| | - Jin Young Kim
- Digital Omics Research Center, Korea Basic Science Institute (KBSI), Ochang, Cheongju 28119, Republic of Korea; Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Dong Geon Jang
- Department of Pharmacology, Woo Choo Lee Institute for Precision Drug Development, Graduate School of Medical Science Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hee Chun Chung
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Graduate School of Medical Science Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Dong Hoon Shin
- Department of Pharmacology, Woo Choo Lee Institute for Precision Drug Development, Graduate School of Medical Science Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Ye Jin Kim
- Department of Pharmacology, Woo Choo Lee Institute for Precision Drug Development, Graduate School of Medical Science Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Shin Hye Noh
- Department of Pharmacology, Woo Choo Lee Institute for Precision Drug Development, Graduate School of Medical Science Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41068, Republic of Korea
| | - Jae Myun Lee
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Graduate School of Medical Science Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.
| | - Min Goo Lee
- Department of Pharmacology, Woo Choo Lee Institute for Precision Drug Development, Graduate School of Medical Science Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.
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5
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Néel E, Chiritoiu-Butnaru M, Fargues W, Denus M, Colladant M, Filaquier A, Stewart SE, Lehmann S, Zurzolo C, Rubinsztein DC, Marin P, Parmentier ML, Villeneuve J. The endolysosomal system in conventional and unconventional protein secretion. J Cell Biol 2024; 223:e202404152. [PMID: 39133205 PMCID: PMC11318669 DOI: 10.1083/jcb.202404152] [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: 05/02/2024] [Revised: 07/12/2024] [Accepted: 07/26/2024] [Indexed: 08/13/2024] Open
Abstract
Most secreted proteins are transported through the "conventional" endoplasmic reticulum-Golgi apparatus exocytic route for their delivery to the cell surface and release into the extracellular space. Nonetheless, formative discoveries have underscored the existence of alternative or "unconventional" secretory routes, which play a crucial role in exporting a diverse array of cytosolic proteins outside the cell in response to intrinsic demands, external cues, and environmental changes. In this context, lysosomes emerge as dynamic organelles positioned at the crossroads of multiple intracellular trafficking pathways, endowed with the capacity to fuse with the plasma membrane and recognized for their key role in both conventional and unconventional protein secretion. The recent recognition of lysosomal transport and exocytosis in the unconventional secretion of cargo proteins provides new and promising insights into our understanding of numerous physiological processes.
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Affiliation(s)
- Eloïse Néel
- Institute of Functional Genomics, University of Montpellier, CNRS, INSERM , Montpellier, France
| | | | - William Fargues
- Institute of Functional Genomics, University of Montpellier, CNRS, INSERM , Montpellier, France
| | - Morgane Denus
- Institute of Functional Genomics, University of Montpellier, CNRS, INSERM , Montpellier, France
| | - Maëlle Colladant
- Institute of Functional Genomics, University of Montpellier, CNRS, INSERM , Montpellier, France
| | - Aurore Filaquier
- Institute of Functional Genomics, University of Montpellier, CNRS, INSERM , Montpellier, France
| | - Sarah E Stewart
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Sylvain Lehmann
- Laboratoire de Biochimie-Protéomique Clinique-Plateforme de Protéomique Clinique, Université de Montpellier, Institute for Regenerative Medicine and Biotherapy Centre Hospitalier Universitaire de Montpellier, Institute for Neurosciences of Montpellier INSERM , Montpellier, France
| | - Chiara Zurzolo
- Unité de Trafic Membranaire et Pathogenèse, Institut Pasteur, UMR3691 CNRS , Paris, France
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute , Cambridge, UK
| | - Philippe Marin
- Institute of Functional Genomics, University of Montpellier, CNRS, INSERM , Montpellier, France
| | - Marie-Laure Parmentier
- Institute of Functional Genomics, University of Montpellier, CNRS, INSERM , Montpellier, France
| | - Julien Villeneuve
- Institute of Functional Genomics, University of Montpellier, CNRS, INSERM , Montpellier, France
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6
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Huber RJ, Kim WD. Trafficking of adhesion and aggregation-modulating proteins during the early stages of Dictyostelium development. Cell Signal 2024; 121:111292. [PMID: 38986731 DOI: 10.1016/j.cellsig.2024.111292] [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: 07/03/2024] [Accepted: 07/06/2024] [Indexed: 07/12/2024]
Abstract
The social amoeba Dictyostelium discoideum has been studied for close to a century to better understand conserved cellular and developmental processes. The life cycle of this model eukaryote is composed of a unicellular growth phase and a multicellular developmental phase that is induced by starvation. When starved, individual cells undergo chemotactic aggregation to form multicellular mounds that develop into slugs. Terminal differentiation of cells within slugs forms fruiting bodies, each composed of a stalk that supports a mass of viable spores that germinate and restart the life cycle when nutrients become available. Calcium-dependent cell adhesion protein A (CadA) and countin (CtnA) are two proteins that regulate adhesion and aggregation, respectively, during the early stages of D. discoideum development. While the functions of these proteins have been well-studied, the mechanisms regulating their trafficking are not fully understood. In this study, we reveal pathways and cellular components that regulate the intracellular and extracellular amounts of CadA and CtnA during aggregation. During growth and starvation, CtnA localizes to cytoplasmic vesicles and punctae. We show that CtnA is glycosylated and this post-translational modification is required for its secretion. Upon autophagy induction, a signal peptide for secretion facilitates the release of CtnA from cells via a pathway involving the μ subunit of the AP3 complex (Apm3) and the WASP and SCAR homolog, WshA. Additionally, CtnA secretion is negatively regulated by the D. discoideum orthologs of the human non-selective cation channel mucolipin-1 (Mcln) and sorting receptor sortilin (Sort1). As for CadA, it localizes to the cell periphery in growth-phase and starved cells. The intracellular and extracellular amounts of CadA are modulated by autophagy genes (atg1, atg9), Apm3, WshA, and Mcln. We integrate these data with previously published findings to generate a comprehensive model summarizing the trafficking of CadA and CtnA in D. discoideum. Overall, this study enhances our understanding of protein trafficking during D. discoideum aggregation, and more broadly, provides insight into the multiple pathways that regulate protein trafficking and secretion in all eukaryotes.
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Affiliation(s)
- Robert J Huber
- Department of Biology, Trent University, Peterborough, Ontario, Canada.
| | - William D Kim
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
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7
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Chang C, Tang X, Schönthal AH, Chen M, Woodley DT, Wang Y, Liang C, Li W. Discovery of Cell Number-Interstitial Fluid Volume (CIF) Ratio Reveals Secretory Autophagy Pathway to Supply eHsp90α for Wound Healing. Cells 2024; 13:1280. [PMID: 39120311 PMCID: PMC11312289 DOI: 10.3390/cells13151280] [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: 06/11/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Cell secretion repairs tissue damage and restores homeostasis throughout adult life. The extracellular heat shock protein-90alpha (eHsp90α) has been reported as an exosome cargo and a potential driver of wound healing. However, neither the mechanism of secretion nor the genetic evidence for eHsp90α in wound healing has been substantiated. Herein, we show that tissue injury causes massive deposition of eHsp90α in tissues and secretion of eHsp90α by cells. Sequential centrifugations of conditioned medium from relevant cell lines revealed the relative distributions of eHsp90α in microvesicle, exosome and trypsin-sensitive supernatant fractions to be approximately <2%, <4% and >95%, respectively. Establishing the cell-number-to-interstitial-fluid-volume (CIF) ratio for the microenvironment of human tissues as 1 × 109 cells: 1 mL interstitial fluid enabled us to predict the corresponding tissue concentrations of eHsp90α in these fractions as 3.74 μg/mL, 5.61 μg/mL and 178 μg/mL. Remarkably, the 178 μg/mL eHsp90α matches the previously reported 100-300 μg/mL of recombinant eHsp90α whose topical application promotes maximum wound healing in animal models. More importantly, we demonstrate that two parallel secretory autophagy-regulating gene families, the autophagy-regulating (AR) genes and the Golgi reassembly-stacking protein (GRASP) genes work together to mediate the secretion of the physiological concentration of eHsp90α to promote wound healing. Thus, utilization of the CIF ratio-based extrapolation method may enable investigators to rapidly predict biomarker targets from cell-conditioned-medium data.
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Affiliation(s)
- Cheng Chang
- Department of Dermatology and the USC-Norris Comprehensive Cancer Centre, Los Angeles, CA 90089, USA; (C.C.); (X.T.); (M.C.); (D.T.W.)
| | - Xin Tang
- Department of Dermatology and the USC-Norris Comprehensive Cancer Centre, Los Angeles, CA 90089, USA; (C.C.); (X.T.); (M.C.); (D.T.W.)
| | - Axel H. Schönthal
- Department of Molecular Microbiology & Immunology, University of Southern California Keck Medical Centre, Los Angeles, CA 90033, USA;
| | - Mei Chen
- Department of Dermatology and the USC-Norris Comprehensive Cancer Centre, Los Angeles, CA 90089, USA; (C.C.); (X.T.); (M.C.); (D.T.W.)
| | - David T. Woodley
- Department of Dermatology and the USC-Norris Comprehensive Cancer Centre, Los Angeles, CA 90089, USA; (C.C.); (X.T.); (M.C.); (D.T.W.)
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, MI 48109, USA;
| | - Chengyu Liang
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA;
| | - Wei Li
- Department of Dermatology and the USC-Norris Comprehensive Cancer Centre, Los Angeles, CA 90089, USA; (C.C.); (X.T.); (M.C.); (D.T.W.)
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8
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Mendes LFS, Gimenes CO, da Silva MDO, Rout SK, Riek R, Costa‐Filho AJ. The potential role of liquid-liquid phase separation in the cellular fate of the compartments for unconventional protein secretion. Protein Sci 2024; 33:e5085. [PMID: 38923199 PMCID: PMC11201811 DOI: 10.1002/pro.5085] [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: 02/27/2024] [Revised: 04/30/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Eukaryotic cells have developed intricate mechanisms for biomolecule transport, particularly in stressful conditions. This interdisciplinary study delves into unconventional protein secretion (UPS) pathways activated during starvation, facilitating the export of proteins bypassing most of the components of the classical secretory machinery. Specifically, we focus on the underexplored mechanisms of the GRASP's role in UPS, particularly in biogenesis and cargo recruitment for the vesicular-like compartment for UPS. Our results show that liquid-liquid phase separation (LLPS) plays a key role in the coacervation of Grh1, the GRASP yeast homologue, under starvation-like conditions. This association seems a precursor to the Compartment for Unconventional Protein Secretion (CUPS) biogenesis. Grh1's self-association is regulated by electrostatic, hydrophobic, and hydrogen-bonding interactions. Importantly, our study demonstrates that phase-separated states of Grh1 can recruit UPS cargo under starvation-like situations. Additionally, we explore how the coacervate liquid-to-solid transition could impact cells' ability to return to normal post-stress states. Our findings offer insights into intracellular protein dynamics and cell adaptive responses to stress.
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Affiliation(s)
- Luis Felipe S. Mendes
- Group of Biophysics and Structural Biology "Sergio Mascarenhas". São Carlos Institute of PhysicsUniversity of São PauloSão CarlosSão PauloBrazil
- Department of Physics, Ribeirão Preto School of Philosophy, Science, and LiteratureUniversity of São PauloRibeirão PretoSão PauloBrazil
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH HönggerbergZürichSwitzerland
| | - Carolina O. Gimenes
- Department of Physics, Ribeirão Preto School of Philosophy, Science, and LiteratureUniversity of São PauloRibeirão PretoSão PauloBrazil
| | - Marília D. O. da Silva
- Group of Biophysics and Structural Biology "Sergio Mascarenhas". São Carlos Institute of PhysicsUniversity of São PauloSão CarlosSão PauloBrazil
| | - Saroj K. Rout
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH HönggerbergZürichSwitzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH HönggerbergZürichSwitzerland
| | - Antonio J. Costa‐Filho
- Department of Physics, Ribeirão Preto School of Philosophy, Science, and LiteratureUniversity of São PauloRibeirão PretoSão PauloBrazil
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9
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DeKryger W, Chroneos ZC. Emerging concepts of myosin 18A isoform mechanobiology in organismal and immune system physiology, development, and function. FASEB J 2024; 38:e23649. [PMID: 38776246 DOI: 10.1096/fj.202400350r] [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: 02/13/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024]
Abstract
Alternative and combinatorial splicing of myosin 18A (MYO18A) gene transcripts results in expression of MYO18A protein isoforms and isoform variants with different membrane and subcellular localizations, and functional properties. MYO18A proteins are members of the myosin superfamily consisting of a myosin-like motor domain, an IQ motif, and a coiled-coil domain. MYO18A isoforms, however, lack the ability to hydrolyze ATP and do not perform ATP-dependent motor activity. MYO18A isoforms are distinguished by different amino- and carboxy-terminal extensions and domains. The domain organization and functions of MYO18Aα, MYO18Aβ, and MYO18Aγ have been studied experimentally. MYO18Aα and MYO18Aβ have a common carboxy-terminal extension but differ by the presence or absence of an amino-terminal KE repeat and PDZ domain, respectively. The amino- and carboxy-terminal extensions of MYO18Aγ contain unique proline and serine-rich domains. Computationally predicted MYO18Aε and MYO18Aδ isoforms contain the carboxy-terminal serine-rich extension but differ by the presence or absence of the amino-terminal KE/PDZ extension. Additional isoform variants within each category arise by alternative utilization or inclusion/exclusion of small exons. MYO18Aα variants are expressed in somatic cells and mature immune cells, whereas MYO18Aβ variants occur mainly in myeloid and natural killer cells. MYO18Aγ expression is selective to cardiac and skeletal muscle. In the present review perspective, we discuss current and emerging concepts of the functional specialization of MYO18A proteins in membrane and cytoskeletal dynamics, cellular communication and signaling, endocytic and exocytic organelle movement, viral infection, and as the SP-R210 receptor for surfactant protein A.
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Affiliation(s)
- William DeKryger
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Zissis C Chroneos
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
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10
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Denus M, Fargues W, Filaquier A, Néel É, Marin P, Parmentier ML, Villeneuve J. [Unconventional protein secretion - new perspectives in protein trafficking]. Med Sci (Paris) 2024; 40:267-274. [PMID: 38520102 DOI: 10.1051/medsci/2024013] [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] [Indexed: 03/25/2024] Open
Abstract
The characterization of the structural and functional organization of eukaryotic cells has revealed the membrane compartments and machinery required for vesicular protein transport. Most proteins essential for intercellular communication contain an N-terminal signal sequence enabling them to be incorporated into the biosynthetic or conventional secretory pathway, in which proteins are sequentially transported through the endoplasmic reticulum (ER) and the Golgi apparatus. However, major research studies have shown the existence of alternative secretory routes that are independent of the ER-Golgi and designated as unconventional secretory pathways. These pathways involve a large number of players that may divert specific compartments from their primary function in favor of secretory roles. The comprehensive description of these processes is therefore of utmost importance to unveil how proteins secreted through these alternative pathways control cell homeostasis or contribute to disease development.
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Affiliation(s)
- Morgane Denus
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
| | - William Fargues
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
| | - Aurore Filaquier
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
| | - Éloïse Néel
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
| | - Philippe Marin
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
| | - Marie-Laure Parmentier
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
| | - Julien Villeneuve
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
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11
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Li X, Liu B, Wen Y, Wang J, Guo YR, Shi A, Lin L. Coordination of RAB-8 and RAB-11 during unconventional protein secretion. J Cell Biol 2024; 223:e202306107. [PMID: 38019180 PMCID: PMC10686230 DOI: 10.1083/jcb.202306107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/17/2023] [Accepted: 11/16/2023] [Indexed: 11/30/2023] Open
Abstract
Multiple physiology-pertinent transmembrane proteins reach the cell surface via the Golgi-bypassing unconventional protein secretion (UcPS) pathway. By employing C. elegans-polarized intestine epithelia, we recently have revealed that the small GTPase RAB-8/Rab8 serves as an important player in the process. Nonetheless, its function and the relevant UcPS itinerary remain poorly understood. Here, we show that deregulated RAB-8 activity resulted in impaired apical UcPS, which increased sensitivity to infection and environmental stress. We also identified the SNARE VTI-1/Vti1a/b as a new RAB-8-interacting factor involved in the apical UcPS. Besides, RAB-11/Rab11 was capable of recruiting RABI-8/Rabin8 to reduce the guanine nucleotide exchange activity of SMGL-1/GEF toward RAB-8, indicating the necessity of a finely tuned RAB-8/RAB-11 network. Populations of RAB-8- and RAB-11-positive endosomal structures containing the apical UcPS cargo moved toward the apical side. In the absence of RAB-11 or its effectors, the cargo was retained in RAB-8- and RAB-11-positive endosomes, respectively, suggesting that these endosomes are utilized as intermediate carriers for the UcPS.
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Affiliation(s)
- Xinxin Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bowen Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yue Wen
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiabin Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yusong R. Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Anbing Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Long Lin
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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12
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Tiberti N, Manfredi M, Piubelli C, Buonfrate D. Progresses and challenges in Strongyloides spp. proteomics. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220447. [PMID: 38008115 PMCID: PMC10676815 DOI: 10.1098/rstb.2022.0447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/09/2023] [Indexed: 11/28/2023] Open
Abstract
The availability of high-quality data of helminth genomes provided over the past two decades has supported and accelerated large-scale 'omics studies and, consequently, the achievement of a more in-depth molecular characterization of a number of pathogens. This has also involved Strongyloides spp. and since their genome was made available transcriptomics has been rather frequently applied to investigate gene expression regulation across their life cycle. Strongyloides proteomics characterization has instead been somehow neglected, with only a few reports performing high-throughput or targeted analyses associated with protein identification by tandem mass spectrometry. Such investigations are however necessary in order to discern important aspects associated with human strongyloidiasis, including understanding parasite biology and the mechanisms of host-parasite interaction, but also to identify novel diagnostic and therapeutic targets. In this review article, we will give an overview of the published proteomics studies investigating strongyloidiasis at different levels, spanning from the characterization of the somatic proteome and excretory/secretory products of different parasite stages to the investigation of potentially immunogenic proteins. Moreover, in the effort to try to start filling the current gap in host-proteomics, we will also present the first serum proteomics analysis in patients suffering from human strongyloidiasis. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.
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Affiliation(s)
- Natalia Tiberti
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, 37024 Negrar di Valpolicella (Verona), Italy
| | - Marcello Manfredi
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
| | - Chiara Piubelli
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, 37024 Negrar di Valpolicella (Verona), Italy
| | - Dora Buonfrate
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, 37024 Negrar di Valpolicella (Verona), Italy
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13
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Huber RJ, Kim WD, Wilson-Smillie MLDM. Mechanisms regulating the intracellular trafficking and release of CLN5 and CTSD. Traffic 2024; 25:e12925. [PMID: 38272448 DOI: 10.1111/tra.12925] [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: 08/01/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/27/2024]
Abstract
Ceroid lipofuscinosis neuronal 5 (CLN5) and cathepsin D (CTSD) are soluble lysosomal enzymes that also localize extracellularly. In humans, homozygous mutations in CLN5 and CTSD cause CLN5 disease and CLN10 disease, respectively, which are two subtypes of neuronal ceroid lipofuscinosis (commonly known as Batten disease). The mechanisms regulating the intracellular trafficking of CLN5 and CTSD and their release from cells are not well understood. Here, we used the social amoeba Dictyostelium discoideum as a model system to examine the pathways and cellular components that regulate the intracellular trafficking and release of the D. discoideum homologs of human CLN5 (Cln5) and CTSD (CtsD). We show that both Cln5 and CtsD contain signal peptides for secretion that facilitate their release from cells. Like Cln5, extracellular CtsD is glycosylated. In addition, Cln5 release is regulated by the amount of extracellular CtsD. Autophagy induction promotes the release of Cln5, and to a lesser extent CtsD. Release of Cln5 requires the autophagy proteins Atg1, Atg5, and Atg9, as well as autophagosomal-lysosomal fusion. Atg1 and Atg5 are required for the release of CtsD. Together, these data support a model where Cln5 and CtsD are actively released from cells via their signal peptides for secretion and pathways linked to autophagy. The release of Cln5 and CtsD from cells also requires microfilaments and the D. discoideum homologs of human AP-3 complex mu subunit, the lysosomal-trafficking regulator LYST, mucopilin-1, and the Wiskott-Aldrich syndrome-associated protein WASH, which all regulate lysosomal exocytosis in this model organism. These findings suggest that lysosomal exocytosis also facilitates the release of Cln5 and CtsD from cells. In addition, we report the roles of ABC transporters, microtubules, osmotic stress, and the putative D. discoideum homologs of human sortilin and cation-independent mannose-6-phosphate receptor in regulating the intracellular/extracellular distribution of Cln5 and CtsD. In total, this study identifies the cellular mechanisms regulating the release of Cln5 and CtsD from D. discoideum cells and provides insight into how altered trafficking of CLN5 and CTSD causes disease in humans.
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Affiliation(s)
- Robert J Huber
- Department of Biology, Trent University, Peterborough, Ontario, Canada
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - William D Kim
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
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14
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Wu W, Krijgsveld J. Secretome Analysis: Reading Cellular Sign Language to Understand Intercellular Communication. Mol Cell Proteomics 2024; 23:100692. [PMID: 38081362 PMCID: PMC10793180 DOI: 10.1016/j.mcpro.2023.100692] [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: 08/07/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/06/2024] Open
Abstract
A significant portion of mammalian proteomes is secreted to the extracellular space to fulfill crucial roles in cell-to-cell communication. To best recapitulate the intricate and multi-faceted crosstalk between cells in a live organism, there is an ever-increasing need for methods to study protein secretion in model systems that include multiple cell types. In addition, posttranslational modifications further expand the complexity and versatility of cellular communication. This review aims to summarize recent strategies and model systems that employ cellular coculture, chemical biology tools, protein enrichment, and proteomic methods to characterize the composition and function of cellular secretomes. This is all geared towards gaining better understanding of organismal biology in vivo mediated by secretory signaling.
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Affiliation(s)
- Wei Wu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Department of Pharmacy, National University of Singapore, Singapore, Singapore.
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany; Medical Faculty, Heidelberg University, Heidelberg, Germany.
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15
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Parvanian S, Coelho-Rato LS, Patteson AE, Eriksson JE. Vimentin takes a hike - Emerging roles of extracellular vimentin in cancer and wound healing. Curr Opin Cell Biol 2023; 85:102246. [PMID: 37783033 PMCID: PMC11214764 DOI: 10.1016/j.ceb.2023.102246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023]
Abstract
Vimentin is a cytoskeletal protein important for many cellular processes, including proliferation, migration, invasion, stress resistance, signaling, and many more. The vimentin-deficient mouse has revealed many of these functions as it has numerous severe phenotypes, many of which are found only following a suitable challenge or stress. While these functions are usually related to vimentin as a major intracellular protein, vimentin is also emerging as an extracellular protein, exposed at the cell surface in an oligomeric form or secreted to the extracellular environment in soluble and vesicle-bound forms. Thus, this review explores the roles of the extracellular pool of vimentin (eVIM), identified in both normal and pathological states. It focuses specifically on the recent advances regarding the role of eVIM in wound healing and cancer. Finally, it discusses new technologies and future perspectives for the clinical application of eVIM.
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Affiliation(s)
- Sepideh Parvanian
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland; Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Leila S Coelho-Rato
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland
| | - Alison E Patteson
- Physics Department and BioInspired Institute, Syracuse University, Syracuse, NY, 13244, USA
| | - John E Eriksson
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland; Euro-Bioimaging ERIC, 20520 Turku, Finland.
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16
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Parvanian S, Coelho-Rato LS, Eriksson JE, Patteson AE. The molecular biophysics of extracellular vimentin and its role in pathogen-host interactions. Curr Opin Cell Biol 2023; 85:102233. [PMID: 37677998 PMCID: PMC10841047 DOI: 10.1016/j.ceb.2023.102233] [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: 05/31/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 09/09/2023]
Abstract
Vimentin, an intermediate filament protein typically located in the cytoplasm of mesenchymal cells, can also be secreted as an extracellular protein. The organization of extracellular vimentin strongly determines its functions in physiological and pathological conditions, making it a promising target for future therapeutic interventions. The extracellular form of vimentin has been found to play a role in the interaction between host cells and pathogens. In this review, we first discuss the molecular biophysics of extracellular vimentin, including its structure, secretion, and adhesion properties. We then provide a general overview of the role of extracellular vimentin in mediating pathogen-host interactions, with a focus on its interactions with viruses and bacteria. We also discuss the implications of these findings for the development of new therapeutic strategies for combating infectious diseases.
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Affiliation(s)
- Sepideh Parvanian
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520, Turku, Finland; Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Leila S Coelho-Rato
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520, Turku, Finland
| | - John E Eriksson
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520, Turku, Finland; Euro-Bioimaging ERIC, 20520, Turku, Finland
| | - Alison E Patteson
- Physics Department and BioInspired Institute, Syracuse University, Syracuse, NY, 13244, USA.
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17
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Huber RJ, Gray J, Kim WD. Loss of mfsd8 alters the secretome during Dictyostelium aggregation. Eur J Cell Biol 2023; 102:151361. [PMID: 37742391 DOI: 10.1016/j.ejcb.2023.151361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/26/2023] Open
Abstract
Major facilitator superfamily domain-containing protein 8 (MFSD8) is a transmembrane protein that has been reported to function as a lysosomal chloride channel. In humans, homozygous mutations in MFSD8 cause a late-infantile form of neuronal ceroid lipofuscinosis (NCL) called CLN7 disease. In the social amoeba Dictyostelium discoideum, Mfsd8 localizes to cytoplasmic puncta and vesicles, and regulates conserved processes during the organism's life cycle. Here, we used D. discoideum to examine the effect of mfsd8-deficiency on the secretome during the early stages of multicellular development. Mass spectrometry revealed 61 proteins that were differentially released by cells after 4 and 8 h of starvation. Most proteins were present in increased amounts in mfsd8- conditioned buffer compared to WT indicating that loss of mfsd8 deregulates protein secretion and/or causes the release of proteins not normally secreted by WT cells. GO term enrichment analyses showed that many of the proteins aberrantly released by mfsd8- cells localize to compartments and regions of the cell associated with the endo-lysosomal and secretory pathways. Mass spectrometry also revealed proteins previously known to be impacted by the loss of mfsd8 (e.g., cathepsin D), as well as proteins that may underlie mfsd8-deficiency phenotypes during aggregation. Finally, we show that mfsd8-deficiency reduces intracellular proteasome 20S activity due to the abnormal release of at least one proteasomal subunit. Together, this study reveals the impact of mfsd8 loss on the secretome during D. discoideum aggregation and lays the foundation for follow up work that investigates the role of altered protein release in CLN7 disease.
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Affiliation(s)
- Robert J Huber
- Department of Biology, Trent University, Peterborough, Ontario, Canada; Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada.
| | - Joshua Gray
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - William D Kim
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
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18
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Lonsdale A, Ceballos-Laita L, Takahashi D, Uemura M, Abadía J, Davis MJ, Bacic A, Doblin MS. LSPpred Suite: Tools for Leaderless Secretory Protein Prediction in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:1428. [PMID: 37050054 PMCID: PMC10097205 DOI: 10.3390/plants12071428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Plant proteins that are secreted without a classical signal peptide leader sequence are termed leaderless secretory proteins (LSPs) and are implicated in both plant development and (a)biotic stress responses. In plant proteomics experimental workflows, identification of LSPs is hindered by the possibility of contamination from other subcellar compartments upon purification of the secretome. Applying machine learning algorithms to predict LSPs in plants is also challenging due to the rarity of experimentally validated examples for training purposes. This work attempts to address this issue by establishing criteria for identifying potential plant LSPs based on experimental observations and training random forest classifiers on the putative datasets. The resultant plant protein database LSPDB and bioinformatic prediction tools LSPpred and SPLpred are available at lsppred.lspdb.org. The LSPpred and SPLpred modules are internally validated on the training dataset, with false positives controlled at 5%, and are also able to classify the limited number of established plant LSPs (SPLpred (3/4, LSPpred 4/4). Until such time as a larger set of bona fide (independently experimentally validated) LSPs is established using imaging technologies (light/fluorescence/electron microscopy) to confirm sub-cellular location, these tools represent a bridging method for predicting and identifying plant putative LSPs for subsequent experimental validation.
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Affiliation(s)
- Andrew Lonsdale
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Laura Ceballos-Laita
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
| | - Matsuo Uemura
- Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Javier Abadía
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Melissa J. Davis
- Bioinformatics, Walter and Eliza Hall Institute for Medical Research, Melbourne, VIC 3052, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Monika S. Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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19
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Remtulla AAN, Huber RJ. The conserved cellular roles of CLN proteins: Novel insights from Dictyostelium discoideum. Eur J Cell Biol 2023; 102:151305. [PMID: 36917916 DOI: 10.1016/j.ejcb.2023.151305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/15/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
The neuronal ceroid lipofuscinoses (NCLs), collectively referred to as Batten disease, are a group of fatal neurodegenerative disorders that primarily affect children. The etiology of Batten disease is linked to mutations in 13 genes that encode distinct CLN proteins, whose functions have yet to be fully elucidated. The social amoeba Dictyostelium discoideum has been adopted as an efficient and powerful model system for studying the diverse cellular roles of CLN proteins. The genome of D. discoideum encodes several homologs of human CLN proteins, and a growing body of literature supports the conserved roles and networking of CLN proteins in D. discoideum and humans. In humans, CLN proteins have diverse cellular roles related to autophagy, signal transduction, lipid homeostasis, lysosomal ion homeostasis, and intracellular trafficking. Recent work also indicates that CLN proteins play an important role in protein secretion. Remarkably, many of these findings have found parallels in studies with D. discoideum. Accordingly, this review will highlight the translatable value of novel work with D. discoideum in the field of NCL research and propose further avenues of research using this biomedical model organism for studying the NCLs.
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Affiliation(s)
- Adam A N Remtulla
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Robert J Huber
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada; Department of Biology, Trent University, Peterborough, Ontario, Canada.
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20
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Tang VT, Ginsburg D. Cargo selection in endoplasmic reticulum-to-Golgi transport and relevant diseases. J Clin Invest 2023; 133:163838. [PMID: 36594468 PMCID: PMC9797344 DOI: 10.1172/jci163838] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Most proteins destined for the extracellular space or various intracellular compartments must traverse the intracellular secretory pathway. The first step is the recruitment and transport of cargoes from the endoplasmic reticulum (ER) lumen to the Golgi apparatus by coat protein complex II (COPII), consisting of five core proteins. Additional ER transmembrane proteins that aid cargo recruitment are referred to as cargo receptors. Gene duplication events have resulted in multiple COPII paralogs present in the mammalian genome. Here, we review the functions of each COPII protein, human disorders associated with each paralog, and evidence for functional conservation between paralogs. We also provide a summary of current knowledge regarding two prototypical cargo receptors in mammals, LMAN1 and SURF4, and their roles in human health and disease.
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Affiliation(s)
- Vi T. Tang
- Department of Molecular and Integrative Physiology,,Life Sciences Institute
| | - David Ginsburg
- Life Sciences Institute,,Department of Internal Medicine,,Department of Human Genetics,,Department of Pediatrics and Communicable Diseases, and,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA
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21
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Yang L, Zhu H, Li M, Yu Q. The Tricalbin-Family Endoplasmic Reticulum-Plasma Membrane Tethering Proteins Attenuate ROS-Involved Caspofungin Sensitivity in Candida albicans. Microbiol Spectr 2022; 10:e0207922. [PMID: 36445092 PMCID: PMC9769562 DOI: 10.1128/spectrum.02079-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/07/2022] [Indexed: 12/02/2022] Open
Abstract
The endoplasmic reticulum-plasma membrane (ER-PM) contacts are one kind of important membrane contact structures in eukaryotic cells, which mediate material and message exchange between the ER and the PM. However, the specific types and functions of ER-PM tethering proteins are poorly understood in the human fungal pathogen Candida albicans. In this study, we observed that the two tricalbin-family proteins, i.e., Tcb1 and Tcb3, were colocalized with the ER-PM contacts in C. albicans. Deletion of the tricalbin-encoding genes TCB1 and TCB3 remarkably reduced ER-PM contacts, suggesting that tricalbins are ER-PM tethering proteins of C. albicans. Stress sensitivity assays showed that the TCB-deleted strains, including tcb1Δ/Δ, tcb3Δ/Δ, and tcb1Δ/Δ tcb3Δ/Δ, exhibited hypersensitivity to cell wall stress induced by caspofungin. Further investigation revealed that caspofungin induced drastic reactive oxygen species (ROS) accumulation in the mutants, which was attributed to enhanced oxidation of Ero1 in the ER lumen. Removal of intracellular ROS by the ROS scavenger vitamin C rescued the growth of the mutants under caspofungin treatment, indicating that Ero1 oxidation-related ROS accumulation was involved in caspofungin hypersensitivity of the mutants. Moreover, deletion of the TCB genes decreased secretion of extracellular aspartyl proteinases, reduced transport of the cell wall protein Hwp1 from the cytoplasm to the cell wall, and attenuated virulence of the fungal pathogen. This study sheds a light on the role of ER-PM tethering proteins in maintenance of cell wall integrity and virulence in fungal pathogens. IMPORTANCE The endoplasmic reticulum-plasma membrane contacts are important membrane contact structures in eukaryotic cells, functioning in material and message exchange between the ER and the PM. We observed that the two tricalbin-family endoplasmic reticulum-plasma membrane contact proteins are required for tolerance to caspofungin-induced cell wall stress in the pathogenic fungus Candida albicans. The tricalbin mutants exhibited hypersensitivity to cell wall stress induced by caspofungin. Further investigation revealed that Ero1 oxidation-related reactive species oxygen accumulation was involved in caspofungin hypersensitivity of the tricalbin mutants. Moreover, loss of tricalbins reduced secretion of extracellular aspartyl proteinases, decreased transport of the cell wall proteins from the cytoplasm to the cell wall, and attenuated virulence of the fungal pathogen. This study uncovers the role of ER-PM tethering proteins in sustaining protein secretion, maintenance of cell wall integrity and virulence in fungal pathogens.
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Affiliation(s)
- Li Yang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Hangqi Zhu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
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Chiritoiu-Butnaru M, Stewart SE, Zhang M, Malhotra V, Villeneuve J. Editorial: Unconventional protein secretion: From basic mechanisms to dysregulation in disease. Front Cell Dev Biol 2022; 10:1088002. [PMID: 36531948 PMCID: PMC9748678 DOI: 10.3389/fcell.2022.1088002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/21/2022] [Indexed: 01/30/2025] Open
Affiliation(s)
- Marioara Chiritoiu-Butnaru
- Department of Molecular and Cellular Biology, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Sarah E. Stewart
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University Bundoora, Melbourne, VIC, Australia
| | - Min Zhang
- Tsinghua University, School of Pharmaceutical Sciences, Beijing, China
| | - Vivek Malhotra
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Julien Villeneuve
- Institute of Functional Genomics, University of Montpellier, CNRS, INSERM, Montpellier, France
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