1
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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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2
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Shortill SP, Frier MS, Davey M, Conibear E. N-terminal signals in the SNX-BAR paralogs Vps5 and Vin1 guide endosomal coat complex formation. Mol Biol Cell 2024; 35:ar76. [PMID: 38598303 DOI: 10.1091/mbc.e24-01-0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024] Open
Abstract
Endosomal coats incorporate membrane-binding subunits such as sorting nexin (SNX) proteins. The Saccharomyces cerevisiae SNX-BAR paralogs Vin1 and Vps5 are respective subunits of the endosomal VINE and retromer complexes whose dimerizing BAR domains are required for complex assembly and membrane association. However, a degree of promiscuity is predicted for yeast BAR-BAR pairings, and recent work has implicated the unstructured N-terminal domains of Vin1 and Vps5 in coat formation. Here, we map N-terminal signals in both SNX-BAR paralogs that contribute to the assembly and function of two distinct endosomal coats in vivo. Whereas Vin1 leverages a polybasic region and adjacent hydrophobic motif to bind Vrl1 and form VINE, the N-terminus of Vps5 interacts with the retromer subunit Vps29 at two sites, including a conserved hydrophobic pocket in Vps29 that engages other accessory proteins in humans. We also examined the sole isoform of Vps5 from the milk yeast Kluyveromyces lactis and found that ancestral yeasts may have used a nested N-terminal signal to form both VINE and retromer. Our results suggest that the specific assembly of Vps5-family SNX-BAR coats depends on inputs from unique N-terminal sequence features in addition to BAR domain coupling, expanding our understanding of endosomal coat biology.
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Affiliation(s)
- Shawn P Shortill
- Department of Medical Genetics, University of British Columbia, Vancouver, BC VH6 3N1, Canada
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Mia S Frier
- Department of Medical Genetics, University of British Columbia, Vancouver, BC VH6 3N1, Canada
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Elizabeth Conibear
- Department of Medical Genetics, University of British Columbia, Vancouver, BC VH6 3N1, Canada
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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3
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Quirion L, Robert A, Boulais J, Huang S, Bernal Astrain G, Strakhova R, Jo CH, Kherdjemil Y, Faubert D, Thibault MP, Kmita M, Baskin JM, Gingras AC, Smith MJ, Côté JF. Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways. J Cell Sci 2024; 137:jcs262140. [PMID: 38606629 PMCID: PMC11166204 DOI: 10.1242/jcs.262140] [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: 03/23/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024] Open
Abstract
The ADP-ribosylation factors (ARFs) and ARF-like (ARL) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we used proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ∼3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely, SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.
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Affiliation(s)
- Laura Quirion
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Amélie Robert
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Jonathan Boulais
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Shiying Huang
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Gabriela Bernal Astrain
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Regina Strakhova
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Chang Hwa Jo
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Yacine Kherdjemil
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Denis Faubert
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | | | - Marie Kmita
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Experimental Medicine, McGill University, Montréal, QC H3G 2M1, Canada
| | - Jeremy M. Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Matthew J. Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Jean-François Côté
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
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4
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Pha K, Mirrashidi K, Sherry J, Tran CJ, Herrera CM, McMahon E, Elwell CA, Engel JN. The Chlamydia effector IncE employs two short linear motifs to reprogram host vesicle trafficking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590830. [PMID: 38712241 PMCID: PMC11071397 DOI: 10.1101/2024.04.23.590830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Chlamydia trachomatis, a leading cause of bacteria sexually transmitted infections, creates a specialized intracellular replicative niche by translocation and insertion of a diverse array of effectors (Incs) into the inclusion membrane. Here, we characterize IncE, a multi-functional Inc that encodes two non-overlapping short linear motifs (SLiMs) within its short cytosolic C-terminus. The proximal SLiM mimics an R-SNARE motif to recruit syntaxin (STX) 7 and 12-containing vesicles to the inclusion. The distal SLiM mimics the Sorting Nexin (SNX) 5 and 6 cargo binding site to recruit SNX6-containing vesicles to the inclusion. By simultaneously binding to two distinct vesicle classes, IncE reprograms host cell trafficking to promote the formation of a class of hybrid vesicles at the inclusion that are required for C. trachomatis intracellular development. Our work suggests that Incs may have evolved SLiMs to facilitate rapid evolution in a limited protein space to disrupt host cell processes.
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5
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Overduin M, Bhat R. Recognition and remodeling of endosomal zones by sorting nexins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184305. [PMID: 38408696 DOI: 10.1016/j.bbamem.2024.184305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/05/2024] [Accepted: 02/18/2024] [Indexed: 02/28/2024]
Abstract
The proteolipid code determines how cytosolic proteins find and remodel membrane surfaces. Here, we investigate how this process works with sorting nexins Snx1 and Snx3. Both proteins form sorting machines by recognizing membrane zones enriched in phosphatidylinositol 3-phosphate (PI3P), phosphatidylserine (PS) and cholesterol. This co-localized combination forms a unique "lipid codon" or lipidon that we propose is responsible for endosomal targeting, as revealed by structures and interactions of their PX domain-based readers. We outline a membrane recognition and remodeling mechanism for Snx1 and Snx3 involving this code element alongside transmembrane pH gradients, dipole moment-guided docking and specific protein-protein interactions. This generates an initial membrane-protein assembly (memtein) that then recruits retromer and additional PX proteins to recruit cell surface receptors for sorting to the trans-Golgi network (TGN), lysosome and plasma membranes. Post-translational modification (PTM) networks appear to regulate how the sorting machines form and operate at each level. The commonalities and differences between these sorting nexins show how the proteolipid code orchestrates parallel flows of molecular information from ribosome emergence to organelle genesis, and illuminates a universally applicable model of the membrane.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
| | - Rakesh Bhat
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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6
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Quirion L, Robert A, Boulais J, Huang S, Bernal Astrain G, Strakhova R, Jo CH, Kherdjemil Y, Thibault MP, Faubert D, Kmita M, Baskin JM, Gingras AC, Smith MJ, Cote JF. Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.01.530598. [PMID: 36909472 PMCID: PMC10002736 DOI: 10.1101/2023.03.01.530598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The ADP-ribosylation factors (ARFs) and ARF-like (ARLs) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we utilized proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ~3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.
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7
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Chen Q, Sun M, Han X, Xu H, Liu Y. Structural determinants specific for retromer protein sorting nexin 5 in regulating subcellular retrograde membrane trafficking. J Biomed Res 2023; 37:492-506. [PMID: 37964759 PMCID: PMC10687533 DOI: 10.7555/jbr.37.20230112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 11/16/2023] Open
Abstract
The endosomal trafficking of signaling membrane proteins, such as receptors, transporters and channels, is mediated by the retromer-mediated sorting machinery, composed of a cargo-selective vacuolar protein sorting trimer and a membrane-deforming subunit of sorting nexin proteins. Recent studies have shown that the isoforms, sorting nexin 5 (SNX5) and SNX6, have played distinctive regulatory roles in retrograde membrane trafficking. However, the molecular insight determined functional differences within the proteins remains unclear. We reported that SNX5 and SNX6 had distinct binding affinity to the cargo protein vesicular monoamine transporter 2 (VMAT2). SNX5, but not SNX6, specifically interacted with VMAT2 through the Phox domain, which contains an alpha-helix binding motif. Using chimeric mutagenesis, we identified that several key residues within this domain were unique in SNX5, but not SNX6, and played an auxiliary role in its binding to VMAT2. Importantly, we generated a set of mutant SNX6, in which the corresponding key residues were mutated to those in SNX5. In addition to the gain in binding affinity to VMAT2, their overexpression functionally rescued the altered retrograde trafficking of VMAT2 induced by siRNA-mediated depletion of SNX5. These data strongly suggest that SNX5 and SNX6 have different functions in retrograde membrane trafficking, which is determined by the different structural elements within the Phox domain of two proteins. Our work provides a new information on the role of SNX5 and SNX6 in the molecular regulation of retrograde membrane trafficking and vesicular membrane targeting in monoamine neurotransmission and neurological diseases.
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Affiliation(s)
- Qing Chen
- Jiangsu Key Laboratory of Xenotransplantation, and Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Meiheng Sun
- Jiangsu Key Laboratory of Xenotransplantation, and Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xu Han
- Jiangsu Key Laboratory of Xenotransplantation, and Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Hongfei Xu
- Jiangsu Key Laboratory of Xenotransplantation, and Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yongjian Liu
- Jiangsu Key Laboratory of Xenotransplantation, and Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Neuroscience, University of Pittsburgh Kenneth P. Dietrich School of Arts and Sciences, Pittsburgh, PA 15260, USA
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8
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Štepihar D, Florke Gee RR, Hoyos Sanchez MC, Fon Tacer K. Cell-specific secretory granule sorting mechanisms: the role of MAGEL2 and retromer in hypothalamic regulated secretion. Front Cell Dev Biol 2023; 11:1243038. [PMID: 37799273 PMCID: PMC10548473 DOI: 10.3389/fcell.2023.1243038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/31/2023] [Indexed: 10/07/2023] Open
Abstract
Intracellular protein trafficking and sorting are extremely arduous in endocrine and neuroendocrine cells, which synthesize and secrete on-demand substantial quantities of proteins. To ensure that neuroendocrine secretion operates correctly, each step in the secretion pathways is tightly regulated and coordinated both spatially and temporally. At the trans-Golgi network (TGN), intrinsic structural features of proteins and several sorting mechanisms and distinct signals direct newly synthesized proteins into proper membrane vesicles that enter either constitutive or regulated secretion pathways. Furthermore, this anterograde transport is counterbalanced by retrograde transport, which not only maintains membrane homeostasis but also recycles various proteins that function in the sorting of secretory cargo, formation of transport intermediates, or retrieval of resident proteins of secretory organelles. The retromer complex recycles proteins from the endocytic pathway back to the plasma membrane or TGN and was recently identified as a critical player in regulated secretion in the hypothalamus. Furthermore, melanoma antigen protein L2 (MAGEL2) was discovered to act as a tissue-specific regulator of the retromer-dependent endosomal protein recycling pathway and, by doing so, ensures proper secretory granule formation and maturation. MAGEL2 is a mammalian-specific and maternally imprinted gene implicated in Prader-Willi and Schaaf-Yang neurodevelopmental syndromes. In this review, we will briefly discuss the current understanding of the regulated secretion pathway, encompassing anterograde and retrograde traffic. Although our understanding of the retrograde trafficking and sorting in regulated secretion is not yet complete, we will review recent insights into the molecular role of MAGEL2 in hypothalamic neuroendocrine secretion and how its dysregulation contributes to the symptoms of Prader-Willi and Schaaf-Yang patients. Given that the activation of many secreted proteins occurs after they enter secretory granules, modulation of the sorting efficiency in a tissue-specific manner may represent an evolutionary adaptation to environmental cues.
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Affiliation(s)
- Denis Štepihar
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, United States
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX, United States
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Rebecca R. Florke Gee
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, United States
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX, United States
| | - Maria Camila Hoyos Sanchez
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, United States
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX, United States
| | - Klementina Fon Tacer
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, United States
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX, United States
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9
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Lopez-Robles C, Scaramuzza S, Astorga-Simon EN, Ishida M, Williamson CD, Baños-Mateos S, Gil-Carton D, Romero-Durana M, Vidaurrazaga A, Fernandez-Recio J, Rojas AL, Bonifacino JS, Castaño-Díez D, Hierro A. Architecture of the ESCPE-1 membrane coat. Nat Struct Mol Biol 2023; 30:958-969. [PMID: 37322239 PMCID: PMC10352136 DOI: 10.1038/s41594-023-01014-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023]
Abstract
Recycling of membrane proteins enables the reuse of receptors, ion channels and transporters. A key component of the recycling machinery is the endosomal sorting complex for promoting exit 1 (ESCPE-1), which rescues transmembrane proteins from the endolysosomal pathway for transport to the trans-Golgi network and the plasma membrane. This rescue entails the formation of recycling tubules through ESCPE-1 recruitment, cargo capture, coat assembly and membrane sculpting by mechanisms that remain largely unknown. Herein, we show that ESCPE-1 has a single-layer coat organization and suggest how synergistic interactions between ESCPE-1 protomers, phosphoinositides and cargo molecules result in a global arrangement of amphipathic helices to drive tubule formation. Our results thus define a key process of tubule-based endosomal sorting.
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Affiliation(s)
| | | | | | - Morié Ishida
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Chad D Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | | | - David Gil-Carton
- CIC bioGUNE, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- BREM Basque Resource for Electron Microscopy, Leioa, Spain
| | - Miguel Romero-Durana
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | | | - Juan Fernandez-Recio
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | | | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Daniel Castaño-Díez
- BioEM Lab, Biozentrum, University of Basel, Basel, Switzerland.
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain.
| | - Aitor Hierro
- CIC bioGUNE, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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10
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Simonetti B, Daly JL, Cullen PJ. Out of the ESCPE room: Emerging roles of endosomal SNX-BARs in receptor transport and host-pathogen interaction. Traffic 2023; 24:234-250. [PMID: 37089068 PMCID: PMC10768393 DOI: 10.1111/tra.12885] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/22/2023] [Accepted: 03/28/2023] [Indexed: 04/25/2023]
Abstract
Several functions of the human cell, such as sensing nutrients, cell movement and interaction with the surrounding environment, depend on a myriad of transmembrane proteins and their associated proteins and lipids (collectively termed "cargoes"). To successfully perform their tasks, cargo must be sorted and delivered to the right place, at the right time, and in the right amount. To achieve this, eukaryotic cells have evolved a highly organized sorting platform, the endosomal network. Here, a variety of specialized multiprotein complexes sort cargo into itineraries leading to either their degradation or their recycling to various organelles for further rounds of reuse. A key sorting complex is the Endosomal SNX-BAR Sorting Complex for Promoting Exit (ESCPE-1) that promotes the recycling of an array of cargos to the plasma membrane and/or the trans-Golgi network. ESCPE-1 recognizes a hydrophobic-based sorting motif in numerous cargoes and orchestrates their packaging into tubular carriers that pinch off from the endosome and travel to the target organelle. A wide range of pathogens mimic this sorting motif to hijack ESCPE-1 transport to promote their invasion and survival within infected cells. In other instances, ESCPE-1 exerts restrictive functions against pathogens by limiting their replication and infection. In this review, we discuss ESCPE-1 assembly and functions, with a particular focus on recent advances in the understanding of its role in membrane trafficking, cellular homeostasis and host-pathogen interaction.
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Affiliation(s)
- Boris Simonetti
- Charles River Laboratories, Discovery House, Quays Office ParkConference Avenue, PortisheadBristolUK
| | - James L. Daly
- Department of Infectious DiseasesSchool of Immunology and Microbial Sciences, Guy's Hospital, King's College LondonLondonUK
| | - Peter J. Cullen
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences BuildingUniversity of BristolBristolUK
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11
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Tornero-Écija A, Zapata-Del-Baño A, Antón-Esteban L, Vincent O, Escalante R. The association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5. Life Sci Alliance 2023; 6:e202201852. [PMID: 36977596 PMCID: PMC10053439 DOI: 10.26508/lsa.202201852] [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: 11/25/2022] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Human VPS13 proteins are implicated in severe neurological diseases. These proteins play an important role in lipid transport at membrane contact sites between different organelles. Identification of adaptors that regulate the subcellular localization of these proteins at specific membrane contact sites is essential to understand their function and role in disease. We have identified the sorting nexin SNX5 as an interactor of VPS13A that mediates its association with endosomal subdomains. As for the yeast sorting nexin and Vps13 endosomal adaptor Ypt35, this association involves the VPS13 adaptor-binding (VAB) domain in VPS13A and a PxP motif in SNX5. Notably, this interaction is impaired by mutation of a conserved asparagine residue in the VAB domain, which is also required for Vps13-adaptor binding in yeast and is pathogenic in VPS13D. VPS13A fragments containing the VAB domain co-localize with SNX5, whereas the more C-terminal part of VPS13A directs its localization to the mitochondria. Overall, our results suggest that a fraction of VPS13A localizes to junctions between the endoplasmic reticulum, mitochondria, and SNX5-containing endosomes.
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Affiliation(s)
- Alba Tornero-Écija
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | | | - Laura Antón-Esteban
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | - Olivier Vincent
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | - Ricardo Escalante
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
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12
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Zanin N, Viaris de Lesegno C, Podkalicka J, Meyer T, Gonzalez Troncoso P, Bun P, Danglot L, Chmiest D, Urbé S, Piehler J, Blouin CM, Lamaze C. STAM and Hrs interact sequentially with IFN-α Receptor to control spatiotemporal JAK-STAT endosomal activation. Nat Cell Biol 2023; 25:425-438. [PMID: 36797476 DOI: 10.1038/s41556-022-01085-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 12/21/2022] [Indexed: 02/18/2023]
Abstract
Activation of the JAK-STAT pathway by type I interferons (IFNs) requires clathrin-dependent endocytosis of the IFN-α and -β receptor (IFNAR), indicating a role for endosomal sorting in this process. The molecular machinery that brings the selective activation of IFN-α/β-induced JAK-STAT signalling on endosomes remains unknown. Here we show that the constitutive association of STAM with IFNAR1 and TYK2 kinase at the plasma membrane prevents TYK2 activation by type I IFNs. IFN-α-stimulated IFNAR endocytosis delivers the STAM-IFNAR complex to early endosomes where it interacts with Hrs, thereby relieving TYK2 inhibition by STAM and triggering signalling of IFNAR at the endosome. In contrast, when stimulated by IFN-β, IFNAR signalling occurs independently of Hrs as IFNAR is sorted to a distinct endosomal subdomain. Our results identify the molecular machinery that controls the spatiotemporal activation of IFNAR by IFN-α and establish the central role of endosomal sorting in the differential regulation of JAK-STAT signalling by IFN-α and IFN-β.
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Affiliation(s)
- Natacha Zanin
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), Paris, France.,Namur Research Institute for Life Sciences (NARILIS), URBC, University of Namur, Namur, Belgium
| | - Christine Viaris de Lesegno
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Joanna Podkalicka
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), Paris, France.,Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, Paris, France.,Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Thomas Meyer
- Department of Biology and Center for Cellular Nanoanalytics, University of Osnabruck, Osnabruck, Germany
| | - Pamela Gonzalez Troncoso
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Philippe Bun
- Membrane Traffic in Healthy and Diseased Brain, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Université de Paris, Paris, France.,NeurImag Imaging Facility, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Université de Paris, Paris, France
| | - Lydia Danglot
- Membrane Traffic in Healthy and Diseased Brain, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Université de Paris, Paris, France.,NeurImag Imaging Facility, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Université de Paris, Paris, France
| | - Daniela Chmiest
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), Paris, France.,Department of Biochemistry, CIIL Biomedical Research Center, University of Lausanne, Epalinges, Switzerland
| | - Sylvie Urbé
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics, University of Osnabruck, Osnabruck, Germany
| | - Cédric M Blouin
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France. .,Centre National de la Recherche Scientifique (CNRS), Paris, France.
| | - Christophe Lamaze
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France. .,Centre National de la Recherche Scientifique (CNRS), Paris, France.
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13
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Gopaldass N, De Leo MG, Courtellemont T, Mercier V, Bissig C, Roux A, Mayer A. Retromer oligomerization drives SNX-BAR coat assembly and membrane constriction. EMBO J 2023; 42:e112287. [PMID: 36644906 PMCID: PMC9841331 DOI: 10.15252/embj.2022112287] [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: 08/04/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 01/17/2023] Open
Abstract
Proteins exit from endosomes through tubular carriers coated by retromer, a complex that impacts cellular signaling, lysosomal biogenesis and numerous diseases. The coat must overcome membrane tension to form tubules. We explored the dynamics and driving force of this process by reconstituting coat formation with yeast retromer and the BAR-domain sorting nexins Vps5 and Vps17 on oriented synthetic lipid tubules. This coat oligomerizes bidirectionally, forming a static tubular structure that does not exchange subunits. High concentrations of sorting nexins alone constrict membrane tubes to an invariant radius of 19 nm. At lower concentrations, oligomers of retromer must bind and interconnect the sorting nexins to drive constriction. Constricting less curved membranes into tubes, which requires more energy, coincides with an increased surface density of retromer on the sorting nexin layer. Retromer-mediated crosslinking of sorting nexins at variable densities may thus tune the energy that the coat can generate to deform the membrane. In line with this, genetic ablation of retromer oligomerization impairs endosomal protein exit in yeast and human cells.
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Affiliation(s)
- Navin Gopaldass
- Department of ImmunobiologyUniversity of LausanneEpalingesSwitzerland
| | | | | | - Vincent Mercier
- Department of BiochemistryUniversity of GenevaGenevaSwitzerland
| | - Christin Bissig
- Department of ImmunobiologyUniversity of LausanneEpalingesSwitzerland
| | - Aurélien Roux
- Department of BiochemistryUniversity of GenevaGenevaSwitzerland
- Swiss National Centre for Competence in Research Program Chemical BiologyGenevaSwitzerland
| | - Andreas Mayer
- Department of ImmunobiologyUniversity of LausanneEpalingesSwitzerland
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14
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Da Graça J, Morel E. Canonical and Non-Canonical Roles of SNX1 and SNX2 in Endosomal Membrane Dynamics. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231217867. [PMID: 38033809 PMCID: PMC10683387 DOI: 10.1177/25152564231217867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023]
Abstract
Sorting nexins (SNXs) are a family of membrane-binding proteins known to play a critical role in regulating endocytic pathway sorting and endosomal membrane trafficking. Among them, SNX1 and SNX2 are members of the SNX-BAR subfamily and possess a membrane-curvature domain and a phosphoinositide-binding domain, which enables their stabilization at the phosphatidylinositol-3-phosphate (PI3P)-positive surface of endosomes. While their binding to PI3P-positive platforms facilitates interaction with endosomal partners and stabilization at the endosomal membrane, their SNX-BAR region is pivotal for generating membrane tubulation from endosomal compartments. In this context, their primary identified biological roles-and their partnership-are tightly associated with the retromer and endosomal SNX-BAR sorting complex for promoting exit 1 complex trafficking, facilitating the transport of cargoes from early endosomes to the secretory pathway. However, recent literature indicates that these proteins also possess biological functions in other aspects of endosomal features and sorting processes. Notably, SNX2 has been found to regulate endosome-endoplasmic reticulum (ER) contact sites through its interaction with VAP proteins at the ER membrane. Furthermore, data from our laboratory show that SNX1 and SNX2 are involved in the tubulation of early endosomes toward ER sites associated with autophagy initiation during starvation. These findings shed light on a novel role of SNXs in inter-organelle tethering and communication. In this concise review, we will explore the non-retromer functions of SNX1 and SNX2, specifically focusing on their involvement in endosomal membrane dynamics during stress sensing and autophagy-associated processes.
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Affiliation(s)
- Juliane Da Graça
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Paris, France
| | - Etienne Morel
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Paris, France
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15
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Buser DP, Spang A. Protein sorting from endosomes to the TGN. Front Cell Dev Biol 2023; 11:1140605. [PMID: 36895788 PMCID: PMC9988951 DOI: 10.3389/fcell.2023.1140605] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/09/2023] [Indexed: 02/23/2023] Open
Abstract
Retrograde transport from endosomes to the trans-Golgi network is essential for recycling of protein and lipid cargoes to counterbalance anterograde membrane traffic. Protein cargo subjected to retrograde traffic include lysosomal acid-hydrolase receptors, SNARE proteins, processing enzymes, nutrient transporters, a variety of other transmembrane proteins, and some extracellular non-host proteins such as viral, plant, and bacterial toxins. Efficient delivery of these protein cargo molecules depends on sorting machineries selectively recognizing and concentrating them for their directed retrograde transport from endosomal compartments. In this review, we outline the different retrograde transport pathways governed by various sorting machineries involved in endosome-to-TGN transport. In addition, we discuss how this transport route can be analyzed experimentally.
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Affiliation(s)
| | - Anne Spang
- Biozentrum, University of Basel, Basel, Switzerland
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16
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Royero P, Quatraccioni A, Früngel R, Silva MH, Bast A, Ulas T, Beyer M, Opitz T, Schultze JL, Graham ME, Oberlaender M, Becker A, Schoch S, Beck H. Circuit-selective cell-autonomous regulation of inhibition in pyramidal neurons by Ste20-like kinase. Cell Rep 2022; 41:111757. [PMID: 36476865 PMCID: PMC9756112 DOI: 10.1016/j.celrep.2022.111757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 10/18/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Maintaining an appropriate balance between excitation and inhibition is critical for neuronal information processing. Cortical neurons can cell-autonomously adjust the inhibition they receive to individual levels of excitatory input, but the underlying mechanisms are unclear. We describe that Ste20-like kinase (SLK) mediates cell-autonomous regulation of excitation-inhibition balance in the thalamocortical feedforward circuit, but not in the feedback circuit. This effect is due to regulation of inhibition originating from parvalbumin-expressing interneurons, while inhibition via somatostatin-expressing interneurons is unaffected. Computational modeling shows that this mechanism promotes stable excitatory-inhibitory ratios across pyramidal cells and ensures robust and sparse coding. Patch-clamp RNA sequencing yields genes differentially regulated by SLK knockdown, as well as genes associated with excitation-inhibition balance participating in transsynaptic communication and cytoskeletal dynamics. These data identify a mechanism for cell-autonomous regulation of a specific inhibitory circuit that is critical to ensure that a majority of cortical pyramidal cells participate in information coding.
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Affiliation(s)
- Pedro Royero
- Institute of Experimental Epileptology and Cognition Research, University of Bonn, University of Bonn Medical Center, Venusberg-Campus 1, 53105 Bonn, Germany,International Max Planck Research School for Brain and Behavior, Bonn, Germany
| | - Anne Quatraccioni
- Department of Neuropathology, University Hospital Bonn, Section for Translational Epilepsy Research, 53127 Bonn, Germany,International Max Planck Research School for Brain and Behavior, Bonn, Germany
| | - Rieke Früngel
- In Silico Brain Sciences Group, Max-Planck Institute for Neurobiology of Behavior – Caesar, Bonn, Germany,International Max Planck Research School for Brain and Behavior, Bonn, Germany
| | - Mariella Hurtado Silva
- Synapse Proteomics, Children’s Medical Research Institute, The University of Sydney, Sydney, NSW, Australia
| | - Arco Bast
- In Silico Brain Sciences Group, Max-Planck Institute for Neurobiology of Behavior – Caesar, Bonn, Germany,International Max Planck Research School for Brain and Behavior, Bonn, Germany
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany,Genomics & Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Marc Beyer
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany,Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V., Bonn, Germany
| | - Thoralf Opitz
- Institute of Experimental Epileptology and Cognition Research, University of Bonn, University of Bonn Medical Center, Venusberg-Campus 1, 53105 Bonn, Germany
| | - Joachim L. Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany,Genomics & Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Mark E. Graham
- Institute of Experimental Epileptology and Cognition Research, University of Bonn, University of Bonn Medical Center, Venusberg-Campus 1, 53105 Bonn, Germany
| | - Marcel Oberlaender
- In Silico Brain Sciences Group, Max-Planck Institute for Neurobiology of Behavior – Caesar, Bonn, Germany
| | - Albert Becker
- Department of Neuropathology, University Hospital Bonn, Section for Translational Epilepsy Research, 53127 Bonn, Germany
| | - Susanne Schoch
- Department of Neuropathology, University Hospital Bonn, Section for Translational Epilepsy Research, 53127 Bonn, Germany
| | - Heinz Beck
- Institute of Experimental Epileptology and Cognition Research, University of Bonn, University of Bonn Medical Center, Venusberg-Campus 1, 53105 Bonn, Germany,Deutsches Zentrum für Neurodegenerative Erkrankungen e.V., Bonn, Germany,Corresponding author
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17
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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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18
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Liu N, Liu K, Yang C. WDR91 specifies the endosomal retrieval subdomain for retromer-dependent recycling. J Cell Biol 2022; 221:213515. [PMID: 36190447 PMCID: PMC9531996 DOI: 10.1083/jcb.202203013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 08/04/2022] [Accepted: 09/19/2022] [Indexed: 12/13/2022] Open
Abstract
Retromer-dependent endosomal recycling of membrane receptors requires Rab7, sorting nexin (SNX)-retromer, and factors that regulate endosomal actin organization. It is not fully understood how these factors cooperate to form endosomal subdomains for cargo retrieval and recycling. Here, we report that WDR91, a Rab7 effector, is the key factor that specifies the endosomal retrieval subdomain. Loss of WDR91 causes defective recycling of both intracellular and cell surface receptors. WDR91 interacts with SNXs through their PX domain, and with VPS35, thus promoting their interaction with Rab7. WDR91 also interacts with the WASH subunit FAM21. In WDR91-deficient cells, Rab7, SNX-retromer, and FAM21 fail to localize to endosomal subdomains, and endosomal actin organization is impaired. Re-expression of WDR91 enables Rab7, SNX-retromer, and FAM21 to concentrate at WDR91-specific endosomal subdomains, where retromer-mediated membrane tubulation and release occur. Thus, WDR91 coordinates Rab7 with SNX-retromer and WASH to establish the endosomal retrieval subdomains required for retromer-mediated endosomal recycling.
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Affiliation(s)
- Nan Liu
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Kai Liu
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Chonglin Yang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China,Correspondence to Chonglin Yang:
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19
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Dhawan K, Naslavsky N, Caplan S. Coronin2A links actin-based endosomal processes to the EHD1 fission machinery. Mol Biol Cell 2022; 33:ar107. [PMID: 35921168 DOI: 10.1091/mbc.e21-12-0624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Fission of transport vesicles from endosomes is a crucial step in the recycling of lipids and receptors to the plasma membrane, but this process remains poorly understood. Although key components of the fission machinery, including the actin cytoskeleton and the ATPase Eps15 homology domain protein 1 (EHD1), have been implicated in endosomal fission, how this process is coordinately regulated is not known. We have identified the actin regulatory protein Coronin2A (CORO2A) as a novel EHD1 interaction partner. CORO2A localizes to stress fibers and actin microfilaments but also can be observed in partial overlap with EHD1 on endosomal structures. siRNA knockdown of CORO2A led to enlarged lamellae-like actin-rich protrusions, consistent with a role of other Coronin family proteins in attenuating actin-branching. Moreover, CORO2A depletion also caused a marked decrease in the internalization of clathrin-dependent cargo but had little impact on the uptake of clathrin-independent cargo, highlighting key differences in the role of branched actin for different modes of endocytosis. However, CORO2A was required for recycling of clathrin-independent cargo, and its depletion led to enlarged endosomes, supporting a role for CORO2A in the fission of endosomal vesicles. Our data support a novel role for CORO2A in coordinating endosomal fission and recycling with EHD1. [Media: see text].
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Affiliation(s)
- Kanika Dhawan
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha NE 68198
| | - Naava Naslavsky
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha NE 68198
| | - Steve Caplan
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha NE 68198.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha NE 68198
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20
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Kendall AK, Chandra M, Xie B, Wan W, Jackson LP. Improved mammalian retromer cryo-EM structures reveal a new assembly interface. J Biol Chem 2022; 298:102523. [PMID: 36174678 PMCID: PMC9636581 DOI: 10.1016/j.jbc.2022.102523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 08/30/2022] [Accepted: 09/03/2022] [Indexed: 12/05/2022] Open
Abstract
Retromer (VPS26/VPS35/VPS29 subunits) assembles with multiple sorting nexin proteins on membranes to mediate endosomal recycling of transmembrane protein cargoes. Retromer has been implicated in other cellular processes, including mitochondrial homeostasis, nutrient sensing, autophagy, and fission events. Mechanisms for mammalian retromer assembly remain undefined, and retromer engages multiple sorting nexin proteins to sort cargoes to different destinations. Published structures demonstrate mammalian retromer forms oligomers in vitro, but several structures were poorly resolved. We report here improved retromer oligomer structures using single-particle cryo-EM by combining data collected from tilted specimens with multiple advancements in data processing, including using a 3D starting model for enhanced automated particle picking in RELION. We used a retromer mutant (3KE retromer) that breaks VPS35-mediated interfaces to determine a structure of a new assembly interface formed by the VPS26A and VPS35 N-termini. The interface reveals how an N-terminal VPS26A arrestin saddle can link retromer chains by engaging a neighboring VPS35 N- terminus, on the opposite side from the well-characterized C-VPS26/N-VPS35 interaction observed within heterotrimers. The new interaction interface exhibits substantial buried surface area (∼7000 Å2) and further suggests that metazoan retromer may serve as an adaptable scaffold.
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Affiliation(s)
- Amy K Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Mintu Chandra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Boyang Xie
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - William Wan
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, 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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21
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Kumar G, Srivastava A. Membrane Remodeling Due to a Mixture of Multiple Types of Curvature Proteins. J Chem Theory Comput 2022; 18:5659-5671. [PMID: 35981766 DOI: 10.1021/acs.jctc.2c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an extension of the Monte Carlo based mesoscopic membrane model, where the membrane is represented as a dynamically triangulated surface and the proteins are modeled as anisotropic inclusions formulated as in-plane nematic field variables adhering to the deformable elastic sheet. In the extended model, we have augmented the Hamiltonian to study membrane deformation due to a mixture of multiple types of curvature generating proteins. This feature opens the door for understanding how multiple kinds of curvature-generating proteins may be working in a coordinated manner to induce desired membrane morphologies. For example, among other things, we study membrane deformations and tubulation due to a mixture of positive and negative curvature proteins as mimics of various proteins from BAR domain family. We also study the effect of membrane anisotropy that manifests as differential binding affinity and organization of curvature proteins, leading to insights into the tightly regulated cargo sorting and transport processes. Our simulation results show different morphology of deformed vesicles that depend on membrane tension, the curvatures and number of the participating proteins as well as on protein-protein and membrane-protein interactions.
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Affiliation(s)
- Gaurav Kumar
- Molecular Biophysics Unit (MBU), Indian Institute of Science (IISc)-Bangalore, C. V. Raman Road, Bangalore, KA 560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit (MBU), Indian Institute of Science (IISc)-Bangalore, C. V. Raman Road, Bangalore, KA 560012, India
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22
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FERARI and cargo adaptors coordinate cargo flow through sorting endosomes. Nat Commun 2022; 13:4620. [PMID: 35941155 PMCID: PMC9359993 DOI: 10.1038/s41467-022-32377-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/27/2022] [Indexed: 11/08/2022] Open
Abstract
Cellular organization, compartmentalization and cell-to-cell communication are crucially dependent on endosomal pathways. Sorting endosomes provide a transit point for various trafficking pathways and decide the fate of proteins: recycling, secretion or degradation. FERARI (Factors for Endosome Recycling and Rab Interactions) play a key role in shaping these compartments and coordinate Rab GTPase function with membrane fusion and fission of vesicles through a kiss-and-run mechanism. Here, we show that FERARI also mediate kiss-and-run of Rab5-positive vesicles with sorting endosomes. During these encounters, cargo flows from Rab5-positive vesicles into sorting endosomes and from there in Rab11-positive vesicles. Cargo flow from sorting endosomes into Rab11 structures relies on the cargo adaptor SNX6, while cargo retention in the Rab11 compartment is dependent on AP1. The available cargo amount appears to regulate the duration of kisses. We propose that FERARI, together with cargo adaptors, coordinate the vectorial flow of cargo through sorting endosomes.
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23
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Li DY, Wen JH, Liang S, Tang JX. The Essential Role of Sorting Nexin 5 in Virus-Induced Autophagy. Front Immunol 2022; 13:947384. [PMID: 35898490 PMCID: PMC9309476 DOI: 10.3389/fimmu.2022.947384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022] Open
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24
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ESCPE-1 mediates retrograde endosomal sorting of the SARS-CoV-2 host factor Neuropilin-1. Proc Natl Acad Sci U S A 2022; 119:e2201980119. [PMID: 35696571 PMCID: PMC9231623 DOI: 10.1073/pnas.2201980119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Endosomal sorting maintains cellular homeostasis by recycling transmembrane proteins and associated proteins and lipids (termed "cargoes") from the endosomal network to multiple subcellular destinations, including retrograde traffic to the trans-Golgi network (TGN). Viral and bacterial pathogens subvert retrograde trafficking machinery to facilitate infectivity. Here, we develop a proteomic screen to identify retrograde cargo proteins of the endosomal SNX-BAR sorting complex promoting exit 1 (ESCPE-1). Using this methodology, we identify Neuropilin-1 (NRP1), a recently characterized host factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as a cargo directly bound and trafficked by ESCPE-1. ESCPE-1 mediates retrograde trafficking of engineered nanoparticles functionalized with the NRP1-interacting peptide of the SARS-CoV-2 spike (S) protein. CRISPR-Cas9 deletion of ESCPE-1 subunits reduces SARS-CoV-2 infection levels in cell culture. ESCPE-1 sorting of NRP1 may therefore play a role in the intracellular membrane trafficking of NRP1-interacting viruses such as SARS-CoV-2.
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25
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Shortill SP, Frier MS, Conibear E. You can go your own way: SNX-BAR coat complexes direct traffic at late endosomes. Curr Opin Cell Biol 2022; 76:102087. [DOI: 10.1016/j.ceb.2022.102087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/23/2022] [Accepted: 04/01/2022] [Indexed: 12/20/2022]
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26
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Abstract
Complex mechanisms govern the sorting of membrane (cargo) proteins at endosomes to ensure that protein localization to the post-Golgi endomembrane system is accurately maintained. Endosomal retrieval complexes mediate sorting by recognizing specific motifs and signals in the cytoplasmic domains of cargo proteins transiting through endosomes. In this review, the recent progress in understanding the molecular mechanisms of how the retromer complex, in conjunction with sorting nexin (SNX) proteins, operates in cargo recognition and sorting is discussed. New data revealing the importance of different SNX proteins and detailing how post-translational modifications can modulate cargo sorting to respond to changes in the environment are highlighted along with the key role that endosomal protein sorting plays in SARS-CoV-2 infection.
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Affiliation(s)
- Xin Yong
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lejiao Mao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Matthew N J Seaman
- Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, CB2 0XY, UK
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
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Xie S, Dierlam C, Smith E, Duran R, Williams A, Davis A, Mathew D, Naslavsky N, Iyer J, Caplan S. The retromer complex regulates C. elegans development and mammalian ciliogenesis. J Cell Sci 2022; 135:jcs259396. [PMID: 35510502 PMCID: PMC9189432 DOI: 10.1242/jcs.259396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 04/11/2022] [Indexed: 11/20/2022] Open
Abstract
The mammalian retromer consists of subunits VPS26 (either VPS26A or VPS26B), VPS29 and VPS35, and a loosely associated sorting nexin (SNX) heterodimer or a variety of other SNX proteins. Despite involvement in yeast and mammalian cell trafficking, the role of retromer in development is poorly understood, and its impact on primary ciliogenesis remains unknown. Using CRISPR/Cas9 editing, we demonstrate that vps-26-knockout worms have reduced brood sizes, impaired vulval development and decreased body length, all of which have been linked to ciliogenesis defects. Although preliminary studies did not identify worm ciliary defects, and impaired development limited additional ciliogenesis studies, we turned to mammalian cells to investigate the role of retromer in ciliogenesis. VPS35 localized to the primary cilium of mammalian cells, and depletion of VPS26, VPS35, VPS29, SNX1, SNX2, SNX5 or SNX27 led to decreased ciliogenesis. Retromer also coimmunoprecipitated with the centriolar protein, CP110 (also known as CCP110), and was required for its removal from the mother centriole. Herein, we characterize new roles for retromer in C. elegans development and in the regulation of ciliogenesis in mammalian cells, suggesting a novel role for retromer in CP110 removal from the mother centriole.
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Affiliation(s)
- Shuwei Xie
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Carter Dierlam
- Department of Chemistry and Biochemistry, University of Tulsa, Tulsa, OK 74104, USA
| | - Ellie Smith
- Department of Chemistry and Biochemistry, University of Tulsa, Tulsa, OK 74104, USA
| | - Ramon Duran
- Department of Chemistry and Biochemistry, University of Tulsa, Tulsa, OK 74104, USA
| | - Allana Williams
- Department of Chemistry and Biochemistry, University of Tulsa, Tulsa, OK 74104, USA
| | - Angelina Davis
- School of Science and Mathematics, Tulsa Community College, Tulsa, OK 74115, USA
| | - Danita Mathew
- Department of Chemistry and Biochemistry, University of Tulsa, Tulsa, OK 74104, USA
| | - Naava Naslavsky
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jyoti Iyer
- Department of Chemistry and Biochemistry, University of Tulsa, Tulsa, OK 74104, USA
| | - Steve Caplan
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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28
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Mechanisms regulating the sorting of soluble lysosomal proteins. Biosci Rep 2022; 42:231123. [PMID: 35394021 PMCID: PMC9109462 DOI: 10.1042/bsr20211856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Lysosomes are key regulators of many fundamental cellular processes such as metabolism, autophagy, immune response, cell signalling and plasma membrane repair. These highly dynamic organelles are composed of various membrane and soluble proteins, which are essential for their proper functioning. The soluble proteins include numerous proteases, glycosidases and other hydrolases, along with activators, required for catabolism. The correct sorting of soluble lysosomal proteins is crucial to ensure the proper functioning of lysosomes and is achieved through the coordinated effort of many sorting receptors, resident ER and Golgi proteins, and several cytosolic components. Mutations in a number of proteins involved in sorting soluble proteins to lysosomes result in human disease. These can range from rare diseases such as lysosome storage disorders, to more prevalent ones, such as Alzheimer’s disease, Parkinson’s disease and others, including rare neurodegenerative diseases that affect children. In this review, we discuss the mechanisms that regulate the sorting of soluble proteins to lysosomes and highlight the effects of mutations in this pathway that cause human disease. More precisely, we will review the route taken by soluble lysosomal proteins from their translation into the ER, their maturation along the Golgi apparatus, and sorting at the trans-Golgi network. We will also highlight the effects of mutations in this pathway that cause human disease.
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29
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Simonetti B, Guo Q, Giménez-Andrés M, Chen KE, Moody ERR, Evans AJ, Chandra M, Danson CM, Williams TA, Collins BM, Cullen PJ. SNX27-Retromer directly binds ESCPE-1 to transfer cargo proteins during endosomal recycling. PLoS Biol 2022; 20:e3001601. [PMID: 35417450 PMCID: PMC9038204 DOI: 10.1371/journal.pbio.3001601] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/25/2022] [Accepted: 03/11/2022] [Indexed: 12/14/2022] Open
Abstract
Coat complexes coordinate cargo recognition through cargo adaptors with biogenesis of transport carriers during integral membrane protein trafficking. Here, we combine biochemical, structural, and cellular analyses to establish the mechanistic basis through which SNX27-Retromer, a major endosomal cargo adaptor, couples to the membrane remodeling endosomal SNX-BAR sorting complex for promoting exit 1 (ESCPE-1). In showing that the SNX27 FERM (4.1/ezrin/radixin/moesin) domain directly binds acidic-Asp-Leu-Phe (aDLF) motifs in the SNX1/SNX2 subunits of ESCPE-1, we propose a handover model where SNX27-Retromer captured cargo proteins are transferred into ESCPE-1 transport carriers to promote endosome-to-plasma membrane recycling. By revealing that assembly of the SNX27:Retromer:ESCPE-1 coat evolved in a stepwise manner during early metazoan evolution, likely reflecting the increasing complexity of endosome-to-plasma membrane recycling from the ancestral opisthokont to modern animals, we provide further evidence of the functional diversification of yeast pentameric Retromer in the recycling of hundreds of integral membrane proteins in metazoans.
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Affiliation(s)
- Boris Simonetti
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Qian Guo
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Manuel Giménez-Andrés
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Kai-En Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Edmund R. R. Moody
- School of Biological Sciences, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Ashley J. Evans
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Mintu Chandra
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Chris M. Danson
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Tom A. Williams
- School of Biological Sciences, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Peter J. Cullen
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
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30
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Zhou C, Wu Z, Du W, Que H, Wang Y, Ouyang Q, Jian F, Yuan W, Zhao Y, Tian R, Li Y, Chen Y, Gao S, Wong CCL, Rong Y. Recycling of autophagosomal components from autolysosomes by the recycler complex. Nat Cell Biol 2022; 24:497-512. [PMID: 35332264 DOI: 10.1038/s41556-022-00861-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 02/04/2022] [Indexed: 11/09/2022]
Abstract
Autolysosomes contain components from autophagosomes and lysosomes. The contents inside the autolysosomal lumen are degraded during autophagy, while the fate of autophagosomal components on the autolysosomal membrane remains unknown. Here we report that the autophagosomal membrane components are not degraded, but recycled from autolysosomes through a process coined in this study as autophagosomal components recycling (ACR). We further identified a multiprotein complex composed of SNX4, SNX5 and SNX17 essential for ACR, which we termed 'recycler'. In this, SNX4 and SNX5 form a heterodimer that recognizes autophagosomal membrane proteins and is required for generating membrane curvature on autolysosomes, both via their BAR domains, to mediate the cargo sorting process. SNX17 interacts with both the dynein-dynactin complex and the SNX4-SNX5 dimer to facilitate the retrieval of autophagosomal membrane components. Our discovery of ACR and identification of the recycler reveal an important retrieval and recycling pathway on autolysosomes.
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Affiliation(s)
- Chuchu Zhou
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhe Wu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wanqing Du
- The State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Huilin Que
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yufen Wang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qinqin Ouyang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fenglei Jian
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weigang Yuan
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Zhao
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Tian
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Li
- The State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yang Chen
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, China.,School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China
| | - Shuaixin Gao
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, China.,School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China
| | - Catherine C L Wong
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, China.,School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China
| | - Yueguang Rong
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. .,Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, China.
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31
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Buser DP, Bader G, Spiess M. Retrograde transport of CDMPR depends on several machineries as analyzed by sulfatable nanobodies. Life Sci Alliance 2022; 5:5/7/e202101269. [PMID: 35314489 PMCID: PMC8961009 DOI: 10.26508/lsa.202101269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 11/24/2022] Open
Abstract
Nanobody toolkit enables the quantitative analysis of endosome-to-TGN transport of the mannose-6-phosphate receptor in cells depleted of retrograde transport machineries Retrograde protein transport from the cell surface and endosomes to the TGN is essential for membrane homeostasis in general and for the recycling of mannose-6-phosphate receptors (MPRs) for sorting of lysosomal hydrolases in particular. We used a nanobody-based sulfation tool to more directly determine transport kinetics from the plasma membrane to the TGN for the cation-dependent MPR (CDMPR) with and without rapid or gradual inactivation of candidate machinery proteins. Although knockdown of retromer (Vps26), epsinR, or Rab9a reduced CDMPR arrival to the TGN, no effect was observed upon silencing of TIP47. Strikingly, when retrograde transport was analyzed by rapamycin-induced rapid depletion (knocksideways) or long-term depletion by knockdown of the clathrin adaptor AP-1 or of the GGA machinery, distinct phenotypes in sulfation kinetics were observed, suggesting a potential role of GGA adaptors in retrograde and anterograde transport. Our study illustrates the usefulness of derivatized, sulfation-competent nanobodies, reveals novel insights into CDMPR trafficking biology, and further outlines that the selection of machinery inactivation is critical for phenotype analysis.
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Affiliation(s)
| | - Gaétan Bader
- Biozentrum, University of Basel, Basel, Switzerland
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32
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Zhou Q, Li J, Ge C, Chen J, Tian W, Tian H. SNX5 suppresses clear cell renal cell carcinoma progression by inducing CD44 internalization and epithelial-to-mesenchymal transition. Mol Ther Oncolytics 2022; 24:87-100. [PMID: 35024436 PMCID: PMC8717386 DOI: 10.1016/j.omto.2021.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/04/2021] [Indexed: 01/06/2023] Open
Abstract
Aberrant expression of SNX5 can contribute to tumorigenesis, invasion, and metastasis of several human cancers. However, the clinicopathological and biological significance of SNX5 in clear cell renal cell carcinoma (ccRCC) remain unclear. In this study, we found that SNX5 expression was downregulated and negatively correlated with tumor size, American Joint Committee on Cancer stage, tumor thrombus of inferior vena cava, and poor prognosis in human ccRCC. Ectopic expression of SNX5 inhibited ccRCC cell proliferation and metastasis, whereas knockdown of SNX5 increased these activities both in vitro and in vivo. Mechanistically, overexpression of SNX5 blocked internalization and intracellular trafficking of CD44 in ccRCC cells. Knockdown of SNX5 was associated with epithelial-to-mesenchymal transition (EMT) in ccRCC cells. Overexpression of SNX5 inhibited TGF-β-induced migration, invasion, and EMT in ccRCC cells. KLF9 directly bound to the SNX5 promoter and increased SNX5 transcription. Moreover, we found that the combination of SNX5 and CD44 or E-cadherin or KLF9 was a more powerful predictor of poor prognosis than either parameter alone. Collectively, our data reveal a mechanism that KLF9-mediated SNX5 expression was associated with poor prognosis via trafficking of CD44 and promoting EMT in ccRCC. SNX5 may be a potential prognostic biomarker and therapeutic target for patients with ccRCC.
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Affiliation(s)
- Qingqing Zhou
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiajun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Ge
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinsi Chen
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Tian
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hua Tian
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Abstract
Phosphoinositides are signalling lipids derived from phosphatidylinositol, a ubiquitous phospholipid in the cytoplasmic leaflet of eukaryotic membranes. Initially discovered for their roles in cell signalling, phosphoinositides are now widely recognized as key integrators of membrane dynamics that broadly impact on all aspects of cell physiology and on disease. The past decade has witnessed a vast expansion of our knowledge of phosphoinositide biology. On the endocytic and exocytic routes, phosphoinositides direct the inward and outward flow of membrane as vesicular traffic is coupled to the conversion of phosphoinositides. Moreover, recent findings on the roles of phosphoinositides in autophagy and the endolysosomal system challenge our view of lysosome biology. The non-vesicular exchange of lipids, ions and metabolites at membrane contact sites in between organelles has also been found to depend on phosphoinositides. Here we review our current understanding of how phosphoinositides shape and direct membrane dynamics to impact on cell physiology, and provide an overview of emerging concepts in phosphoinositide regulation.
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34
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Chandra M, Collins BM, Jackson LP. Biochemical basis for an interaction between SNX27 and the flexible SNX1 N-terminus. Adv Biol Regul 2022; 83:100842. [PMID: 34866035 PMCID: PMC8858909 DOI: 10.1016/j.jbior.2021.100842] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 01/03/2023]
Abstract
Metazoans require the sorting nexin (SNX) protein, SNX27, to recycle hundreds of important transmembrane protein receptors from endosomes to the plasma membrane. Cargo recycling by SNX27 requires its interaction with retromer, a heterotrimer known to assemble on membranes with multiple sorting nexins, including SNX-BAR proteins and SNX3. SNX27 has also been functionally linked to SNX-BARs, but the molecular basis of this interaction has been unknown. We identify a direct biochemical interaction between the conserved and flexible SNX1/SNX2 N-terminus and full-length SNX27 using purified proteins in pulldown experiments. Sequence alignments indicate both SNX1 and SNX2 contain two short and conserved stretches of acidic residues bearing a DxF motif in their flexible N-terminal regions. Biochemical pulldown and mapping experiments reveal forty residues in the N-terminus of either SNX1 or SNX2 can mediate binding to SNX27. SNX27 truncation analysis demonstrates the SNX27 FERM domain binds the SNX1 N-terminus. Calorimetry experiments quantified binding between the SNX1 N-terminus and SNX27 in the low micromolar affinity range (KD ∼10 μM) and suggest the second DxF motif may play a more prominent role in binding. Mutation of either DxF sequence in SNX1 abrogates measurable binding to SNX27 in the calorimeter. Modelling from both predicted and experimentally determined structures suggests the SNX27 FERM domain could accommodate both DxF motifs simultaneously. Together, these data suggest SNX27 is directly linked to specific SNX-BAR proteins through binding acidic motifs in the SNX1 or SNX2 N-terminus.
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Affiliation(s)
- Mintu Chandra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA,Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - 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,Corresponding author:
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35
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Placidi G, Campa CC. Deliver on Time or Pay the Fine: Scheduling in Membrane Trafficking. Int J Mol Sci 2021; 22:11773. [PMID: 34769203 PMCID: PMC8583995 DOI: 10.3390/ijms222111773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
Membrane trafficking is all about time. Automation in such a biological process is crucial to ensure management and delivery of cellular cargoes with spatiotemporal precision. Shared molecular regulators and differential engagement of trafficking components improve robustness of molecular sorting. Sequential recruitment of low affinity protein complexes ensures directionality of the process and, concomitantly, serves as a kinetic proofreading mechanism to discriminate cargoes from the whole endocytosed material. This strategy helps cells to minimize losses and operating errors in membrane trafficking, thereby matching the appealed deadline. Here, we summarize the molecular pathways of molecular sorting, focusing on their timing and efficacy. We also highlight experimental procedures and genetic approaches to robustly probe these pathways, in order to guide mechanistic studies at the interface between biochemistry and quantitative biology.
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Affiliation(s)
- Giampaolo Placidi
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy;
- Candiolo Cancer Institute, FPO-IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy
| | - Carlo C. Campa
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy;
- Candiolo Cancer Institute, FPO-IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy
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36
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Retromer dependent changes in cellular homeostasis and Parkinson's disease. Essays Biochem 2021; 65:987-998. [PMID: 34528672 PMCID: PMC8709886 DOI: 10.1042/ebc20210023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 12/18/2022]
Abstract
To date, mechanistic treatments targeting the initial cause of Parkinson's disease (PD) are limited due to the underlying biological cause(s) been unclear. Endosomes and their associated cellular homeostasis processes have emerged to have a significant role in the pathophysiology associated with PD. Several variants within retromer complex have been identified and characterised within familial PD patients. The retromer complex represents a key sorting platform within the endosomal system that regulates cargo sorting that maintains cellular homeostasis. In this review, we summarise the current understandings of how PD-associated retromer variants disrupt cellular trafficking and how the retromer complex can interact with other PD-associated genes to contribute to the disease progression.
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37
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Ghosh C, Xing Y, Li S, Hoyle RG, Sun M, Li J, Sun Y. Sorting nexin 6 interacts with Cullin3 and regulates programmed death ligand 1 expression. FEBS Lett 2021; 595:2558-2569. [PMID: 34510437 DOI: 10.1002/1873-3468.14191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/20/2021] [Accepted: 08/31/2021] [Indexed: 11/06/2022]
Abstract
Programmed death ligand 1 (PD-L1) is critical for the ability of cancer cells to evade attacks by the host immune system. However, the molecular mechanisms controlling PD-L1 expression have not been fully understood. Here, we demonstrate that sorting nexin 6 (SNX6) is a novel regulator of PD-L1 expression. Knockdown of SNX6 in cancer cells significantly decreases PD-L1 protein levels. In contrast, loss of SNX6 does not reduce PD-L1 mRNA levels. Instead, SNX6 interacts with Cullin3, an E3 ubiquitin ligase responsible for PD-L1 ubiquitination and subsequent degradation. By binding with Cullin3, SNX6 decreases the interaction between the adaptor protein speckle-type POZ protein and Cullin3, which in turn downregulates Cullin3-mediated PD-L1 ubiquitination. This research reveals a novel molecular nexus in modulating PD-L1.
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Affiliation(s)
- Chinmoy Ghosh
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Yanli Xing
- Department of Otolaryngology, Shanghai Pudong New Area Gongli Hospital, Shanghai, China
| | - Suhua Li
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Rosalie G Hoyle
- Department of Medicinal Chemistry, Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Ming Sun
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Jiong Li
- Department of Medicinal Chemistry, Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA.,Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Yue Sun
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA, USA.,Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
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38
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SNX27-FERM-SNX1 complex structure rationalizes divergent trafficking pathways by SNX17 and SNX27. Proc Natl Acad Sci U S A 2021; 118:2105510118. [PMID: 34462354 DOI: 10.1073/pnas.2105510118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The molecular events that determine the recycling versus degradation fates of internalized membrane proteins remain poorly understood. Two of the three members of the SNX-FERM family, SNX17 and SNX31, utilize their FERM domain to mediate endocytic trafficking of cargo proteins harboring the NPxY/NxxY motif. In contrast, SNX27 does not recycle NPxY/NxxY-containing cargo but instead recycles cargo containing PDZ-binding motifs via its PDZ domain. The underlying mechanism governing this divergence in FERM domain binding is poorly understood. Here, we report that the FERM domain of SNX27 is functionally distinct from SNX17 and interacts with a novel DLF motif localized within the N terminus of SNX1/2 instead of the NPxY/NxxY motif in cargo proteins. The SNX27-FERM-SNX1 complex structure reveals that the DLF motif of SNX1 binds to a hydrophobic cave surrounded by positively charged residues on the surface of SNX27. The interaction between SNX27 and SNX1/2 is critical for efficient SNX27 recruitment to endosomes and endocytic recycling of multiple cargoes. Finally, we show that the interaction between SNX27 and SNX1/2 is critical for brain development in zebrafish. Altogether, our study solves a long-standing puzzle in the field and suggests that SNX27 and SNX17 mediate endocytic recycling through fundamentally distinct mechanisms.
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39
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Unveiling the cryo-EM structure of retromer. Biochem Soc Trans 2021; 48:2261-2272. [PMID: 33125482 DOI: 10.1042/bst20200552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 12/29/2022]
Abstract
Retromer (VPS26/VPS35/VPS29) is a highly conserved eukaryotic protein complex that localizes to endosomes to sort transmembrane protein cargoes into vesicles and elongated tubules. Retromer mediates retrieval pathways from endosomes to the trans-Golgi network in all eukaryotes and further facilitates recycling pathways to the plasma membrane in metazoans. In cells, retromer engages multiple partners to orchestrate the formation of tubulovesicular structures, including sorting nexin (SNX) proteins, cargo adaptors, GTPases, regulators, and actin remodeling proteins. Retromer-mediated pathways are especially important for sorting cargoes required for neuronal maintenance, which links retromer loss or mutations to multiple human brain diseases and disorders. Structural and biochemical studies have long contributed to the understanding of retromer biology, but recent advances in cryo-electron microscopy and cryo-electron tomography have further uncovered exciting new snapshots of reconstituted retromer structures. These new structures reveal retromer assembles into an arch-shaped scaffold and suggest the scaffold may be flexible and adaptable in cells. Interactions with cargo adaptors, particularly SNXs, likely orient the scaffold with respect to phosphatidylinositol-3-phosphate (PtdIns3P)-enriched membranes. Pharmacological small molecule chaperones have further been shown to stabilize retromer in cultured cell and mouse models, but mechanisms by which these molecules bind remain unknown. This review will emphasize recent structural and biophysical advances in understanding retromer structure as the field moves towards a molecular view of retromer assembly and regulation on membranes.
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Connecting the dots: combined control of endocytic recycling and degradation. Biochem Soc Trans 2021; 48:2377-2386. [PMID: 33300959 PMCID: PMC7752043 DOI: 10.1042/bst20180255] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/29/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023]
Abstract
Endocytosis is an essential process where proteins and lipids are internalised from the plasma membrane in membrane-bound carriers, such as clathrin-coated vesicles. Once internalised into the cell these vesicles fuse with the endocytic network where their contents are sorted towards degradation in the lysosome or recycling to their origin. Initially, it was thought that cargo recycling is a passive process, but in recent years the identification and characterisation of specialised recycling complexes has established a hitherto unthought-of level of complexity that actively opposes degradation. This review will summarise recent developments regarding the composition and regulation of the recycling machineries and their relationship with the degradative pathways of the endosome.
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Tian Y, Kang Q, Shi X, Wang Y, Zhang N, Ye H, Xu Q, Xu T, Zhang R. SNX-3 mediates retromer-independent tubular endosomal recycling by opposing EEA-1-facilitated trafficking. PLoS Genet 2021; 17:e1009607. [PMID: 34081703 PMCID: PMC8219167 DOI: 10.1371/journal.pgen.1009607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/22/2021] [Accepted: 05/17/2021] [Indexed: 11/27/2022] Open
Abstract
Early endosomes are the sorting hub on the endocytic pathway, wherein sorting nexins (SNXs) play important roles for formation of the distinct membranous microdomains with different sorting functions. Tubular endosomes mediate the recycling of clathrin-independent endocytic (CIE) cargoes back toward the plasma membrane. However, the molecular mechanism underlying the tubule formation is still poorly understood. Here we screened the effect on the ARF-6-associated CIE recycling endosomal tubules for all the SNX members in Caenorhabditis elegans (C. elegans). We identified SNX-3 as an essential factor for generation of the recycling tubules. The loss of SNX-3 abolishes the interconnected tubules in the intestine of C. elegans. Consequently, the surface and total protein levels of the recycling CIE protein hTAC are strongly decreased. Unexpectedly, depletion of the retromer components VPS-26/-29/-35 has no similar effect, implying that the retromer trimer is dispensable in this process. We determined that hTAC is captured by the ESCRT complex and transported into the lysosome for rapid degradation in snx-3 mutants. Interestingly, EEA-1 is increasingly recruited on early endosomes and localized to the hTAC-containing structures in snx-3 mutant intestines. We also showed that SNX3 and EEA1 compete with each other for binding to phosphatidylinositol-3-phosphate enriching early endosomes in Hela cells. Our data demonstrate for the first time that PX domain-only C. elegans SNX-3 organizes the tubular endosomes for efficient recycling and retrieves the CIE cargo away from the maturing sorting endosomes by competing with EEA-1 for binding to the early endosomes. However, our results call into question how SNX-3 couples the cargo capture and membrane remodeling in the absence of the retromer trimer complex. Trafficking of internalized materials through the endolysosomal system is essential for the maintenance of homeostasis and signaling regulation in all eukaryotic cells. Early endosomes are the sorting hub on the endocytic pathway. After internalization, the plasma membrane lipid, proteins, and invading pathogens are delivered to early endosomes for further degradation in lysosomes or for retrieval to the plasma membrane or the trans-Golgi network for reuse. However, when, where and by what mechanism various cargo proteins are sorted from each other and into the different pathways largely remain to be explored. Here, we identified SNX-3, a PX-domain only sorting nexin family member, as a novel regulator for the tubular endosomes underlying recycling of a subset of CIE cargoes. Compared with EEA-1, the superior recruitment of SNX-3 at the CIE-derived subpopulation of endosomes is critical for preventing these endosomes from converging to the classical sorting endosomes and subsequently into the multivesicular endosomal pathway. We speculate that through a spatio-temporal interplay with the retromer, SNX-3 is involved in different recycling transport carriers. Our finding of SNX-3’s role in modulating the formation of tubular endosomes provides insight into the sorting and trafficking of CIE pathways.
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Affiliation(s)
- Yangli Tian
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qiaoju Kang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xuemeng Shi
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yuan Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Nali Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huan Ye
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qifeng Xu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tao Xu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (TX); (RZ)
| | - Rongying Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail: (TX); (RZ)
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Walsh RB, Dresselhaus EC, Becalska AN, Zunitch MJ, Blanchette CR, Scalera AL, Lemos T, Lee SM, Apiki J, Wang S, Isaac B, Yeh A, Koles K, Rodal AA. Opposing functions for retromer and Rab11 in extracellular vesicle traffic at presynaptic terminals. J Cell Biol 2021; 220:212178. [PMID: 34019080 PMCID: PMC8144913 DOI: 10.1083/jcb.202012034] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 03/15/2021] [Accepted: 04/29/2021] [Indexed: 12/18/2022] Open
Abstract
Neuronal extracellular vesicles (EVs) play important roles in intercellular communication and pathogenic protein propagation in neurological disease. However, it remains unclear how cargoes are selectively packaged into neuronal EVs. Here, we show that loss of the endosomal retromer complex leads to accumulation of EV cargoes including amyloid precursor protein (APP), synaptotagmin-4 (Syt4), and neuroglian (Nrg) at Drosophila motor neuron presynaptic terminals, resulting in increased release of these cargoes in EVs. By systematically exploring known retromer-dependent trafficking mechanisms, we show that EV regulation is separable from several previously identified roles of neuronal retromer. Conversely, mutations in rab11 and rab4, regulators of endosome-plasma membrane recycling, cause reduced EV cargo levels, and rab11 suppresses cargo accumulation in retromer mutants. Thus, EV traffic reflects a balance between Rab4/Rab11 recycling and retromer-dependent removal from EV precursor compartments. Our data shed light on previous studies implicating Rab11 and retromer in competing pathways in Alzheimer's disease, and suggest that misregulated EV traffic may be an underlying defect.
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Affiliation(s)
- Rylie B Walsh
- Department of Biology, Brandeis University, Waltham, MA
| | | | | | | | | | - Amy L Scalera
- Department of Biology, Brandeis University, Waltham, MA
| | - Tania Lemos
- Department of Biology, Brandeis University, Waltham, MA
| | - So Min Lee
- Department of Biology, Brandeis University, Waltham, MA
| | - Julia Apiki
- Department of Biology, Brandeis University, Waltham, MA
| | - ShiYu Wang
- Department of Biology, Brandeis University, Waltham, MA
| | - Berith Isaac
- Department of Biology, Brandeis University, Waltham, MA
| | - Anna Yeh
- Department of Biology, Brandeis University, Waltham, MA
| | - Kate Koles
- Department of Biology, Brandeis University, Waltham, MA
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Chandra M, Kendall AK, Jackson LP. Toward Understanding the Molecular Role of SNX27/Retromer in Human Health and Disease. Front Cell Dev Biol 2021; 9:642378. [PMID: 33937239 PMCID: PMC8083963 DOI: 10.3389/fcell.2021.642378] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/22/2021] [Indexed: 11/30/2022] Open
Abstract
Aberrations in membrane trafficking pathways have profound effects in cellular dynamics of cellular sorting processes and can drive severe physiological outcomes. Sorting nexin 27 (SNX27) is a metazoan-specific sorting nexin protein from the PX-FERM domain family and is required for endosomal recycling of many important transmembrane receptors. Multiple studies have shown SNX27-mediated recycling requires association with retromer, one of the best-known regulators of endosomal trafficking. SNX27/retromer downregulation is strongly linked to Down's Syndrome (DS) via glutamate receptor dysfunction and to Alzheimer's Disease (AD) through increased intracellular production of amyloid peptides from amyloid precursor protein (APP) breakdown. SNX27 is further linked to addiction via its role in potassium channel trafficking, and its over-expression is linked to tumorigenesis, cancer progression, and metastasis. Thus, the correct sorting of multiple receptors by SNX27/retromer is vital for normal cellular function to prevent human diseases. The role of SNX27 in regulating cargo recycling from endosomes to the cell surface is firmly established, but how SNX27 assembles with retromer to generate tubulovesicular carriers remains elusive. Whether SNX27/retromer may be a putative therapeutic target to prevent neurodegenerative disease is now an emerging area of study. This review will provide an update on our molecular understanding of endosomal trafficking events mediated by the SNX27/retromer complex on endosomes.
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Affiliation(s)
- Mintu Chandra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
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Fokin AI, Gautreau AM. Assembly and Activity of the WASH Molecular Machine: Distinctive Features at the Crossroads of the Actin and Microtubule Cytoskeletons. Front Cell Dev Biol 2021; 9:658865. [PMID: 33869225 PMCID: PMC8047104 DOI: 10.3389/fcell.2021.658865] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/12/2021] [Indexed: 01/10/2023] Open
Abstract
The Arp2/3 complex generates branched actin networks at different locations of the cell. The WASH and WAVE Nucleation Promoting Factors (NPFs) activate the Arp2/3 complex at the surface of endosomes or at the cell cortex, respectively. In this review, we will discuss how these two NPFs are controlled within distinct, yet related, multiprotein complexes. These complexes are not spontaneously assembled around WASH and WAVE, but require cellular assembly factors. The centrosome, which nucleates microtubules and branched actin, appears to be a privileged site for WASH complex assembly. The actin and microtubule cytoskeletons are both responsible for endosome shape and membrane remodeling. Motors, such as dynein, pull endosomes and extend membrane tubules along microtubule tracks, whereas branched actin pushes onto the endosomal membrane. It was recently uncovered that WASH assembles a super complex with dynactin, the major dynein activator, where the Capping Protein (CP) is exchanged from dynactin to the WASH complex. This CP swap initiates the first actin filament that primes the autocatalytic nucleation of branched actin at the surface of endosomes. Possible coordination between pushing and pulling forces in the remodeling of endosomal membranes is discussed.
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Affiliation(s)
- Artem I Fokin
- Laboratoire de Biologie Structurale de la Cellule, CNRS, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Alexis M Gautreau
- Laboratoire de Biologie Structurale de la Cellule, CNRS, Ecole Polytechnique, IP Paris, Palaiseau, France.,School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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Yanguas F, Valdivieso MH. Analysis of the SNARE Stx8 recycling reveals that the retromer-sorting motif has undergone evolutionary divergence. PLoS Genet 2021; 17:e1009463. [PMID: 33788833 PMCID: PMC8041195 DOI: 10.1371/journal.pgen.1009463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 04/12/2021] [Accepted: 03/03/2021] [Indexed: 11/25/2022] Open
Abstract
Fsv1/Stx8 is a Schizosaccharomyces pombe protein similar to mammalian syntaxin 8. stx8Δ cells are sensitive to salts, and the prevacuolar endosome (PVE) is altered in stx8Δ cells. These defects depend on the SNARE domain, data that confirm the conserved function of syntaxin8 and Stx8 in vesicle fusion at the PVE. Stx8 localizes at the trans-Golgi network (TGN) and the prevacuolar endosome (PVE), and its recycling depends on the retromer component Vps35, and on the sorting nexins Vps5, Vps17, and Snx3. Several experimental approaches demonstrate that Stx8 is a cargo of the Snx3-retromer. Using extensive truncation and alanine scanning mutagenesis, we identified the Stx8 sorting signal. This signal is an IEMeaM sequence that is located in an unstructured protein region, must be distant from the transmembrane (TM) helix, and where the 133I, 134E, 135M, and 138M residues are all essential for recycling. This sorting motif is different from those described for most retromer cargoes, which include aromatic residues, and resembles the sorting motif of mammalian polycystin-2 (PC2). Comparison of Stx8 and PC2 motifs leads to an IEMxx(I/M) consensus. Computer-assisted screening for this and for a loose Ψ(E/D)ΨXXΨ motif (where Ψ is a hydrophobic residue with large aliphatic chain) shows that syntaxin 8 and PC2 homologues from other organisms bear variation of this motif. The phylogeny of the Stx8 sorting motifs from the Schizosaccharomyces species shows that their divergence is similar to that of the genus, showing that they have undergone evolutionary divergence. A preliminary analysis of the motifs in syntaxin 8 and PC2 sequences from various organisms suggests that they might have also undergone evolutionary divergence, what suggests that the presence of almost-identical motifs in Stx8 and PC2 might be a case of convergent evolution. Eukaryotes possess membranous intracellular compartments, whose communication is essential for cellular homeostasis. Protein complexes that facilitate the generation, transport, and fusion of coated vesicles mediate this communication. Since alterations in these processes lead to human disease, their characterization is of biological and medical interest. Retromer is a protein complex that facilitates retrograde trafficking from the prevacuolar endosome to the Golgi, being essential for the functionality of the endolysosomal system. SNAREs are required for vesicle fusion and, after facilitating membrane merging, are supposed to return to their donor organelle for new rounds of fusion. However, little is known about this recycling. We have found that Stx8, a fungal SNARE similar to human syntaxin 8, is a retromer cargo, and have identified its retromer binding motif. Sequence screening and comparison has determined that this sorting motif is conserved mainly in fungal Stx8 sequences. Notably, this motif is similar to the retromer sorting motif that is present in a family of vertebrate ion transporters. Our initial phylogenetic analyses suggest that, although retromer and some of its cargoes are conserved, the sorting motif in the cargoes might have undergone evolutionary divergence.
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Affiliation(s)
- Francisco Yanguas
- Departamento de Microbiología y Genética, Universidad de Salamanca. Salamanca. Spain
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas (CSIC). Salamanca. Spain
| | - M.-Henar Valdivieso
- Departamento de Microbiología y Genética, Universidad de Salamanca. Salamanca. Spain
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas (CSIC). Salamanca. Spain
- * E-mail:
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Courtland JL, Bradshaw TWA, Waitt G, Soderblom EJ, Ho T, Rajab A, Vancini R, Kim IH, Soderling SH. Genetic disruption of WASHC4 drives endo-lysosomal dysfunction and cognitive-movement impairments in mice and humans. eLife 2021; 10:e61590. [PMID: 33749590 PMCID: PMC7984842 DOI: 10.7554/elife.61590] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Mutation of the Wiskott-Aldrich syndrome protein and SCAR homology (WASH) complex subunit, SWIP, is implicated in human intellectual disability, but the cellular etiology of this association is unknown. We identify the neuronal WASH complex proteome, revealing a network of endosomal proteins. To uncover how dysfunction of endosomal SWIP leads to disease, we generate a mouse model of the human WASHC4c.3056C>G mutation. Quantitative spatial proteomics analysis of SWIPP1019R mouse brain reveals that this mutation destabilizes the WASH complex and uncovers significant perturbations in both endosomal and lysosomal pathways. Cellular and histological analyses confirm that SWIPP1019R results in endo-lysosomal disruption and uncover indicators of neurodegeneration. We find that SWIPP1019R not only impacts cognition, but also causes significant progressive motor deficits in mice. A retrospective analysis of SWIPP1019R patients reveals similar movement deficits in humans. Combined, these findings support the model that WASH complex destabilization, resulting from SWIPP1019R, drives cognitive and motor impairments via endo-lysosomal dysfunction in the brain.
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Affiliation(s)
- Jamie L Courtland
- Department of Neurobiology, Duke University School of MedicineDurhamUnited States
| | - Tyler WA Bradshaw
- Department of Neurobiology, Duke University School of MedicineDurhamUnited States
| | - Greg Waitt
- Proteomics and Metabolomics Shared Resource, Duke University School of MedicineDurhamUnited States
| | - Erik J Soderblom
- Proteomics and Metabolomics Shared Resource, Duke University School of MedicineDurhamUnited States
- Department of Cell Biology, Duke University School of MedicineDurhamUnited States
| | - Tricia Ho
- Proteomics and Metabolomics Shared Resource, Duke University School of MedicineDurhamUnited States
| | - Anna Rajab
- Burjeel Hospital, VPS HealthcareMuscatOman
| | - Ricardo Vancini
- Department of Pathology, Duke University School of MedicineDurhamUnited States
| | - Il Hwan Kim
- Department of Cell Biology, Duke University School of MedicineDurhamUnited States
- Department of Anatomy and Neurobiology, University of Tennessee Heath Science CenterMemphisUnited States
| | - Scott H Soderling
- Department of Neurobiology, Duke University School of MedicineDurhamUnited States
- Department of Cell Biology, Duke University School of MedicineDurhamUnited States
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Abstract
The sorting nexin (SNX) family of proteins deform the membrane to generate transport carriers in endosomal pathways. Here, we elucidate how a prototypic member, SNX1, acts in this process. Performing cryoelectron microscopy, we find that SNX1 assembles into a protein lattice that consists of helical rows of SNX1 dimers wrapped around tubular membranes in a crosslinked fashion. We also visualize the details of this structure, which provides a molecular understanding of how various parts of SNX1 contribute to its ability to deform the membrane. Moreover, we have compared the SNX1 structure with a previously elucidated structure of an endosomal coat complex formed by retromer coupled to a SNX, which reveals how the molecular organization of the SNX in this coat complex is affected by retromer. The comparison also suggests insight into intermediary stages of assembly that results in the formation of the retromer-SNX coat complex on the membrane.
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Yong X, Mao L, Shen X, Zhang Z, Billadeau DD, Jia D. Targeting Endosomal Recycling Pathways by Bacterial and Viral Pathogens. Front Cell Dev Biol 2021; 9:648024. [PMID: 33748141 PMCID: PMC7970000 DOI: 10.3389/fcell.2021.648024] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 02/15/2021] [Indexed: 12/19/2022] Open
Abstract
Endosomes are essential cellular stations where endocytic and secretory trafficking routes converge. Proteins transiting at endosomes can be degraded via lysosome, or recycled to the plasma membrane, trans-Golgi network (TGN), or other cellular destinations. Pathways regulating endosomal recycling are tightly regulated in order to preserve organelle identity, to maintain lipid homeostasis, and to support other essential cellular functions. Recent studies have revealed that both pathogenic bacteria and viruses subvert host endosomal recycling pathways for their survival and replication. Several host factors that are frequently targeted by pathogens are being identified, including retromer, TBC1D5, SNX-BARs, and the WASH complex. In this review, we will focus on the recent advances in understanding how intracellular bacteria, human papillomavirus (HPV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hijack host endosomal recycling pathways. This exciting work not only reveals distinct mechanisms employed by pathogens to manipulate host signaling pathways, but also deepens our understanding of the molecular intricacies regulating endosomal receptor trafficking.
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Affiliation(s)
- Xin Yong
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Lejiao Mao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Xiaofei Shen
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhen Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Daniel D. Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
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Amatya B, Lee H, Asico LD, Konkalmatt P, Armando I, Felder RA, Jose PA. SNX-PXA-RGS-PXC Subfamily of SNXs in the Regulation of Receptor-Mediated Signaling and Membrane Trafficking. Int J Mol Sci 2021; 22:ijms22052319. [PMID: 33652569 PMCID: PMC7956473 DOI: 10.3390/ijms22052319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/13/2021] [Accepted: 02/22/2021] [Indexed: 12/26/2022] Open
Abstract
The SNX-PXA-RGS-PXC subfamily of sorting nexins (SNXs) belongs to the superfamily of SNX proteins. SNXs are characterized by the presence of a common phox-homology (PX) domain, along with other functional domains that play versatile roles in cellular signaling and membrane trafficking. In addition to the PX domain, the SNX-PXA-RGS-PXC subfamily, except for SNX19, contains a unique RGS (regulators of G protein signaling) domain that serves as GTPase activating proteins (GAPs), which accelerates GTP hydrolysis on the G protein α subunit, resulting in termination of G protein-coupled receptor (GPCR) signaling. Moreover, the PX domain selectively interacts with phosphatidylinositol-3-phosphate and other phosphoinositides found in endosomal membranes, while also associating with various intracellular proteins. Although SNX19 lacks an RGS domain, all members of the SNX-PXA-RGS-PXC subfamily serve as dual regulators of receptor cargo signaling and endosomal trafficking. This review discusses the known and proposed functions of the SNX-PXA-RGS-PXC subfamily and how it participates in receptor signaling (both GPCR and non-GPCR) and endosomal-based membrane trafficking. Furthermore, we discuss the difference of this subfamily of SNXs from other subfamilies, such as SNX-BAR nexins (Bin-Amphiphysin-Rvs) that are associated with retromer or other retrieval complexes for the regulation of receptor signaling and membrane trafficking. Emerging evidence has shown that the dysregulation and malfunction of this subfamily of sorting nexins lead to various pathophysiological processes and disorders, including hypertension.
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Affiliation(s)
- Bibhas Amatya
- The George Washington University, Washington, DC 20052, USA;
| | - Hewang Lee
- Department of Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC 20052, USA; (H.L.); (L.D.A.); (P.K.); (I.A.)
| | - Laureano D. Asico
- Department of Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC 20052, USA; (H.L.); (L.D.A.); (P.K.); (I.A.)
| | - Prasad Konkalmatt
- Department of Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC 20052, USA; (H.L.); (L.D.A.); (P.K.); (I.A.)
| | - Ines Armando
- Department of Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC 20052, USA; (H.L.); (L.D.A.); (P.K.); (I.A.)
| | - Robin A. Felder
- Department of Pathology, University of Virginia Health Sciences Center, Charlottesville, VA 22908, USA;
| | - Pedro A. Jose
- Department of Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC 20052, USA; (H.L.); (L.D.A.); (P.K.); (I.A.)
- Department of Pathology, University of Virginia Health Sciences Center, Charlottesville, VA 22908, USA;
- Department of Pharmacology/Physiology, The George Washington University School of Medicine & Health Sciences, Washington, DC 20052, USA
- Correspondence:
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Mao L, Liao C, Qin J, Gong Y, Zhou Y, Li S, Liu Z, Deng H, Deng W, Sun Q, Mo X, Xue Y, Billadeau DD, Dai L, Li G, Jia D. Phosphorylation of SNX27 by MAPK11/14 links cellular stress-signaling pathways with endocytic recycling. J Cell Biol 2021; 220:211812. [PMID: 33605979 PMCID: PMC7901142 DOI: 10.1083/jcb.202010048] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/28/2020] [Accepted: 01/21/2021] [Indexed: 02/08/2023] Open
Abstract
Endocytosed proteins can be delivered to lysosomes for degradation or recycled to either the trans-Golgi network or the plasma membrane. It remains poorly understood how the recycling versus degradation of cargoes is determined. Here, we show that multiple extracellular stimuli, including starvation, LPS, IL-6, and EGF treatment, can strongly inhibit endocytic recycling of multiple cargoes through the activation of MAPK11/14. The stress-induced kinases in turn directly phosphorylate SNX27, a key regulator of endocytic recycling, at serine 51 (Ser51). Phosphorylation of SNX27 at Ser51 alters the conformation of its cargo-binding pocket and decreases the interaction between SNX27 and cargo proteins, thereby inhibiting endocytic recycling. Our study indicates that endocytic recycling is highly dynamic and can crosstalk with cellular stress–signaling pathways. Suppression of endocytic recycling and enhancement of receptor lysosomal degradation serve as new mechanisms for cells to cope with stress and save energy.
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Affiliation(s)
- Lejiao Mao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Chenyi Liao
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Jiao Qin
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Yanqiu Gong
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yifei Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Shasha Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Zhe Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Huaqing Deng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Wankun Deng
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qingxiang Sun
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xianming Mo
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Xue
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Daniel D Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN
| | - Lunzhi Dai
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
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