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Van den Bossche F, Tevel V, Gilis F, Gaussin JF, Boonen M, Jadot M. Residence of the Nucleotide Sugar Transporter Family Members SLC35F1 and SLC35F6 in the Endosomal/Lysosomal Pathway. Int J Mol Sci 2024; 25:6718. [PMID: 38928424 PMCID: PMC11203873 DOI: 10.3390/ijms25126718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/14/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
The SLC35 (Solute Carrier 35) family members acting as nucleotide sugar transporters are typically localized in the endoplasmic reticulum or Golgi apparatus. It is, therefore, intriguing that some reports document the presence of orphan transporters SLC35F1 and SLC35F6 within the endosomal and lysosomal system. Here, we compared the subcellular distribution of these proteins and found that they are concentrated in separate compartments; i.e., recycling endosomes for SLC35F1 and lysosomes for SLC35F6. Swapping the C-terminal tail of these proteins resulted in a switch of localization, with SLC35F1 being trafficked to lysosomes while SLC35F6 remained in endosomes. This suggested the presence of specific sorting signals in these C-terminal regions. Using site-directed mutagenesis, fluorescence microscopy, and cell surface biotinylation assays, we found that the EQERLL360 signal located in the cytoplasmic tail of human SLC35F6 is involved in its lysosomal sorting (as previously shown for this conserved sequence in mouse SLC35F6), and that SLC35F1 localization in the recycling pathway depends on two YXXΦ-type signals: a Y367KQF sequence facilitates its internalization from the plasma membrane, while a Y392TSL motif prevents its transport to lysosomes, likely by promoting SLC35F1 recycling to the cell surface. Taken together, these results support that some SLC35 members may function at different levels of the endosomal and lysosomal system.
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Affiliation(s)
- François Van den Bossche
- Physiological Chemistry Laboratory, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium; (F.V.d.B.); (V.T.); (F.G.)
- Laboratory of Intracellular Trafficking Biology, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium;
| | - Virginie Tevel
- Physiological Chemistry Laboratory, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium; (F.V.d.B.); (V.T.); (F.G.)
- Laboratory of Intracellular Trafficking Biology, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium;
| | - Florentine Gilis
- Physiological Chemistry Laboratory, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium; (F.V.d.B.); (V.T.); (F.G.)
- Laboratory of Intracellular Trafficking Biology, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium;
| | - Jean-François Gaussin
- Laboratory of Intracellular Trafficking Biology, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium;
| | - Marielle Boonen
- Laboratory of Intracellular Trafficking Biology, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium;
| | - Michel Jadot
- Physiological Chemistry Laboratory, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium; (F.V.d.B.); (V.T.); (F.G.)
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2
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Gopaldass N, Chen KE, Collins B, Mayer A. Assembly and fission of tubular carriers mediating protein sorting in endosomes. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00746-8. [PMID: 38886588 DOI: 10.1038/s41580-024-00746-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2024] [Indexed: 06/20/2024]
Abstract
Endosomes are central protein-sorting stations at the crossroads of numerous membrane trafficking pathways in all eukaryotes. They have a key role in protein homeostasis and cellular signalling and are involved in the pathogenesis of numerous diseases. Endosome-associated protein assemblies or coats collect transmembrane cargo proteins and concentrate them into retrieval domains. These domains can extend into tubular carriers, which then pinch off from the endosomal membrane and deliver the cargoes to appropriate subcellular compartments. Here we discuss novel insights into the structure of a number of tubular membrane coats that mediate the recruitment of cargoes into these carriers, focusing on sorting nexin-based coats such as Retromer, Commander and ESCPE-1. We summarize current and emerging views of how selective tubular endosomal carriers form and detach from endosomes by fission, highlighting structural aspects, conceptual challenges and open questions.
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Affiliation(s)
- Navin Gopaldass
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
| | - Kai-En Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Brett Collins
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Andreas Mayer
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
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3
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Singla A, Boesch DJ, Joyce Fung HY, Ngoka C, Enriquez AS, Song R, Kramer DA, Han Y, Juneja P, Billadeau DD, Bai X, Chen Z, Turer EE, Burstein E, Chen B. Structural basis for Retriever-SNX17 assembly and endosomal sorting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584676. [PMID: 38559023 PMCID: PMC10980035 DOI: 10.1101/2024.03.12.584676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
During endosomal recycling, Sorting Nexin 17 (SNX17) facilitates the transport of numerous membrane cargo proteins by tethering them to the Retriever complex. Despite its importance, the mechanisms underlying this interaction have remained elusive. Here, we report the structure of the Retriever-SNX17 complex determined using cryogenic electron microscopy (cryo-EM). Our structure reveals that the C-terminal tail of SNX17 engages with a highly conserved interface between the VPS35L and VPS26C subunits of Retriever. Through comprehensive biochemical, cellular, and proteomic analyses, we demonstrate that disrupting this interface impairs the Retriever-SNX17 interaction, subsequently affecting the recycling of SNX17-dependent cargos and altering the composition of the plasma membrane proteome. Intriguingly, we find that the SNX17-binding pocket on Retriever can be utilized by other ligands that share a consensus acidic C-terminal tail motif. By showing how SNX17 is linked to Retriever, our findings uncover a fundamental mechanism underlying endosomal trafficking of critical cargo proteins and reveal a mechanism by which Retriever can engage with other regulatory factors.
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Affiliation(s)
- Amika Singla
- Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Daniel J. Boesch
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Ho Yee Joyce Fung
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Chigozie Ngoka
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Avery S. Enriquez
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Ran Song
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Daniel A. Kramer
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Yan Han
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Puneet Juneja
- Cryo-EM facility, Office of Biotechnology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Daniel D. Billadeau
- Division of Oncology Research, College of Medicine, Mayo Clinic, Rochester MN, 55905, USA
| | - Xiaochen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Emre E. Turer
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ezra Burstein
- Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
- On sabbatical leave at Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
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4
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Naslavsky N, Caplan S. Advances and challenges in understanding endosomal sorting and fission. FEBS J 2023; 290:4187-4195. [PMID: 36413090 PMCID: PMC10200825 DOI: 10.1111/febs.16687] [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: 09/20/2022] [Revised: 11/04/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
Endosomes play crucial roles in the cell, serving as focal and 'triage' points for internalized lipids and receptors. As such, endosomes are a critical branching point that determines whether receptors are sorted for degradation or recycling. This Viewpoint aims to highlight recent advances in endosome research, including key endosomal functions such as sorting and fission. Moreover, the Viewpoint addresses key technical and conceptual challenges in studying endosomes.
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Affiliation(s)
- Naava Naslavsky
- Department of Biochemistry & Molecular Biology and Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Steve Caplan
- Department of Biochemistry & Molecular Biology and Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
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5
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Kliche J, Garvanska DH, Simonetti L, Badgujar D, Dobritzsch D, Nilsson J, Davey NE, Ivarsson Y. Large-scale phosphomimetic screening identifies phospho-modulated motif-based protein interactions. Mol Syst Biol 2023; 19:e11164. [PMID: 37219487 PMCID: PMC10333884 DOI: 10.15252/msb.202211164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
Phosphorylation is a ubiquitous post-translation modification that regulates protein function by promoting, inhibiting or modulating protein-protein interactions. Hundreds of thousands of phosphosites have been identified but the vast majority have not been functionally characterised and it remains a challenge to decipher phosphorylation events modulating interactions. We generated a phosphomimetic proteomic peptide-phage display library to screen for phosphosites that modulate short linear motif-based interactions. The peptidome covers ~13,500 phospho-serine/threonine sites found in the intrinsically disordered regions of the human proteome. Each phosphosite is represented as wild-type and phosphomimetic variant. We screened 71 protein domains to identify 248 phosphosites that modulate motif-mediated interactions. Affinity measurements confirmed the phospho-modulation of 14 out of 18 tested interactions. We performed a detailed follow-up on a phospho-dependent interaction between clathrin and the mitotic spindle protein hepatoma-upregulated protein (HURP), demonstrating the essentiality of the phospho-dependency to the mitotic function of HURP. Structural characterisation of the clathrin-HURP complex elucidated the molecular basis for the phospho-dependency. Our work showcases the power of phosphomimetic ProP-PD to discover novel phospho-modulated interactions required for cellular function.
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Affiliation(s)
- Johanna Kliche
- Department of Chemistry, BMCUppsala UniversityUppsalaSweden
| | - Dimitriya Hristoforova Garvanska
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | | | - Dilip Badgujar
- Department of Chemistry, BMCUppsala UniversityUppsalaSweden
| | | | - Jakob Nilsson
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Norman E Davey
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Ylva Ivarsson
- Department of Chemistry, BMCUppsala UniversityUppsalaSweden
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6
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Rivero-Ríos P, Tsukahara T, Uygun T, Chen A, Chavis GD, Giridharan SSP, Iwase S, Sutton MA, Weisman LS. Recruitment of the SNX17-Retriever recycling pathway regulates synaptic function and plasticity. J Cell Biol 2023; 222:e202207025. [PMID: 37141105 PMCID: PMC10165670 DOI: 10.1083/jcb.202207025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 03/10/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Trafficking of cell-surface proteins from endosomes to the plasma membrane is a key mechanism to regulate synaptic function. In non-neuronal cells, proteins recycle to the plasma membrane either via the SNX27-Retromer-WASH pathway or via the recently discovered SNX17-Retriever-CCC-WASH pathway. While SNX27 is responsible for the recycling of key neuronal receptors, the roles of SNX17 in neurons are less understood. Here, using cultured hippocampal neurons, we demonstrate that the SNX17 pathway regulates synaptic function and plasticity. Disruption of this pathway results in a loss of excitatory synapses and prevents structural plasticity during chemical long-term potentiation (cLTP). cLTP drives SNX17 recruitment to synapses, where its roles are in part mediated by regulating the surface expression of β1-integrin. SNX17 recruitment relies on NMDAR activation, CaMKII signaling, and requires binding to the Retriever and PI(3)P. Together, these findings provide molecular insights into the regulation of SNX17 at synapses and define key roles for SNX17 in synaptic maintenance and in regulating enduring forms of synaptic plasticity.
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Affiliation(s)
- Pilar Rivero-Ríos
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Takao Tsukahara
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tunahan Uygun
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Alex Chen
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Garrett D. Chavis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
- Molecular and Integrative Physiology Graduate Program, University, Ann Arbor, MI, USA
| | - Sai Srinivas Panapakkam Giridharan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Michael A. Sutton
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Molecular and Integrative Physiology Graduate Program, University, Ann Arbor, MI, USA
| | - Lois S. Weisman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
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7
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Carosi JM, Denton D, Kumar S, Sargeant TJ. Receptor Recycling by Retromer. Mol Cell Biol 2023; 43:317-334. [PMID: 37350516 PMCID: PMC10348044 DOI: 10.1080/10985549.2023.2222053] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/01/2023] [Indexed: 06/24/2023] Open
Abstract
The highly conserved retromer complex controls the fate of hundreds of receptors that pass through the endolysosomal system and is a central regulatory node for diverse metabolic programs. More than 20 years ago, retromer was discovered as an essential regulator of endosome-to-Golgi transport in yeast; since then, significant progress has been made to characterize how metazoan retromer components assemble to enable its engagement with endosomal membranes, where it sorts cargo receptors from endosomes to the trans-Golgi network or plasma membrane through recognition of sorting motifs in their cytoplasmic tails. In this review, we examine retromer regulation by exploring its assembled structure with an emphasis on how a range of adaptor proteins shape the process of receptor trafficking. Specifically, we focus on how retromer is recruited to endosomes, selects cargoes, and generates tubulovesicular carriers that deliver cargoes to target membranes. We also examine how cells adapt to distinct metabolic states by coordinating retromer expression and function. We contrast similarities and differences between retromer and its related complexes: retriever and commander/CCC, as well as their interplay in receptor trafficking. We elucidate how loss of retromer regulation is central to the pathology of various neurogenerative and metabolic diseases, as well as microbial infections, and highlight both opportunities and cautions for therapeutics that target retromer. Finally, with a focus on understanding the mechanisms that govern retromer regulation, we outline new directions for the field moving forward.
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Affiliation(s)
- Julian M. Carosi
- Lysosomal Health in Ageing, Lifelong Health, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Centre for Cancer Biology, University of South Australia (UniSA), Adelaide, South Australia, Australia
- School of Biological Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, South Australia, Australia
| | - Donna Denton
- Centre for Cancer Biology, University of South Australia (UniSA), Adelaide, South Australia, Australia
| | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia (UniSA), Adelaide, South Australia, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Timothy J. Sargeant
- Lysosomal Health in Ageing, Lifelong Health, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
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8
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Jha SG, Larson ER. Diversity of retromer-mediated vesicular trafficking pathways in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1184047. [PMID: 37409293 PMCID: PMC10319002 DOI: 10.3389/fpls.2023.1184047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/31/2023] [Indexed: 07/07/2023]
Abstract
The plant endomembrane system is organized and regulated by large gene families that encode proteins responsible for the spatiotemporal delivery and retrieval of cargo throughout the cell and to and from the plasma membrane. Many of these regulatory molecules form functional complexes like the SNAREs, exocyst, and retromer, which are required for the delivery, recycling, and degradation pathways of cellular components. The functions of these complexes are well conserved in eukaryotes, but the extreme expansion of the protein subunit families in plants suggests that plant cells require more regulatory specialization when compared with other eukaryotes. The retromer is associated with retrograde sorting and trafficking of protein cargo back towards the TGN and vacuole in plants, while in animals, there is new evidence that the VPS26C ortholog is associated with recycling or 'retrieving' proteins back to the PM from the endosomes. The human VPS26C was shown to rescue vps26c mutant phenotypes in Arabidopsis thaliana, suggesting that the retriever function could be conserved in plants. This switch from retromer to retriever function may be associated with core complexes that include the VPS26C subunit in plants, similar to what has been suggested in other eukaryotic systems. We review what is known about retromer function in light of recent findings on functional diversity and specialization of the retromer complex in plants.
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Affiliation(s)
- Suryatapa Ghosh Jha
- William Myron Keck Science Department - Biology, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, United States
| | - Emily R. Larson
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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9
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Jäverfelt S, Hellsén G, Kaji I, Goldenring JR, Pelaseyed T. The MYO1B and MYO5B motor proteins and the SNX27 sorting nexin regulate membrane mucin MUC17 trafficking in enterocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.530313. [PMID: 36945389 PMCID: PMC10028800 DOI: 10.1101/2023.03.06.530313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
A dense glycocalyx, composed of the megaDalton-sized membrane mucin MUC17, coats the microvilli in the apical brush border of transporting intestinal epithelial cells, called enterocytes. The establishment of the MUC17-based glycocalyx in the mouse small intestine occurs at the critical suckling-weaning transition. The enterocytic glycocalyx extends 1 µm into the intestinal lumen and prevents the gut bacteria from directly attaching to the enterocytes. To date, the mechanism behind apical targeting of MUC17 to the brush border remains unknown. Here, we show that the actin-based motor proteins MYO1B and MYO5B, and the sorting nexin SNX27 regulate the intracellular trafficking of MUC17 in enterocytes. We demonstrate that MUC17 turnover at the brush border is slow and controlled by MYO1B and SNX27. Furthermore, we report that MYO1B regulates MUC17 protein levels in enterocytes, whereas MYO5B specifically governs MUC17 levels at the brush border. Together, our results extend our understanding of the intracellular trafficking of membrane mucins and provide mechanistic insights into how defective trafficking pathways render enterocytes sensitive to bacterial invasion.
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10
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Zambo B, Morlet B, Negroni L, Trave G, Gogl G. Native holdup (nHU) to measure binding affinities from cell extracts. SCIENCE ADVANCES 2022; 8:eade3828. [PMID: 36542723 PMCID: PMC9770967 DOI: 10.1126/sciadv.ade3828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Characterizing macromolecular interactions is essential for understanding cellular processes, yet most methods currently used to detect protein interactions from cells are qualitative. Here, we introduce the native holdup (nHU) approach to estimate equilibrium binding constants of protein interactions directly from cell extracts. Compared to other pull-down-based assays, nHU requires less sample preparation and can be coupled to any analytical methods as readouts, such as Western blotting or mass spectrometry. We use nHU to explore interactions of SNX27, a cargo adaptor of the retromer complex and find good agreement between in vitro affinities and those measured directly from cell extracts using nHU. We discuss the strengths and limitations of nHU and provide simple protocols that can be implemented in most laboratories.
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Affiliation(s)
- Boglarka Zambo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
| | - Gilles Trave
- Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
- Corresponding author. (G.T.); (G.G.)
| | - Gergo Gogl
- Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
- Corresponding author. (G.T.); (G.G.)
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11
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Smylla TK, Wagner K, Huber A. The Role of Reversible Phosphorylation of Drosophila Rhodopsin. Int J Mol Sci 2022; 23:ijms232314674. [PMID: 36499010 PMCID: PMC9740569 DOI: 10.3390/ijms232314674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Vertebrate and fly rhodopsins are prototypical GPCRs that have served for a long time as model systems for understanding GPCR signaling. Although all rhodopsins seem to become phosphorylated at their C-terminal region following activation by light, the role of this phosphorylation is not uniform. Two major functions of rhodopsin phosphorylation have been described: (1) inactivation of the activated rhodopsin either directly or by facilitating binding of arrestins in order to shut down the visual signaling cascade and thus eventually enabling a high-temporal resolution of the visual system. (2) Facilitating endocytosis of activated receptors via arrestin binding that in turn recruits clathrin to the membrane for clathrin-mediated endocytosis. In vertebrate rhodopsins the shutdown of the signaling cascade may be the main function of rhodopsin phosphorylation, as phosphorylation alone already quenches transducin activation and, in addition, strongly enhances arrestin binding. In the Drosophila visual system rhodopsin phosphorylation is not needed for receptor inactivation. Its role here may rather lie in the recruitment of arrestin 1 and subsequent endocytosis of the activated receptor. In this review, we summarize investigations of fly rhodopsin phosphorylation spanning four decades and contextualize them with regard to the most recent insights from vertebrate phosphorylation barcode theory.
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12
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Prasad V, Bartenschlager R. A snapshot of protein trafficking in SARS-CoV-2 infection. Biol Cell 2022; 115:e2200073. [PMID: 36314261 PMCID: PMC9874443 DOI: 10.1111/boc.202200073] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/27/2022] [Accepted: 10/13/2022] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 is a human pathogenic virus responsible for the COVID-19 (coronavirus disease 2019) pandemic. The infection cycle of SARS-CoV-2 involves several related steps, including virus entry, gene expression, RNA replication, assembly of infectious virions and their egress. For all of these steps, the virus relies on and exploits host cell factors, cellular organelles, and processes such as endocytosis, nuclear transport, protein secretion, metabolite transport at membrane contact sites (MSC) and exocytotic pathways. To do this, SARS-CoV-2 has evolved multifunctional viral proteins that hijack cellular factors and modulate their function by unique strategies. In this Review, we highlight cellular trafficking factors, processes, and organelles of relevance to the SARS-CoV-2 infection cycle and how viral proteins make use of and perturb cellular transport during the viral infection cycle.
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Affiliation(s)
- Vibhu Prasad
- Department of Infectious DiseasesMolecular VirologyHeidelberg UniversityHeidelbergGermany
| | - Ralf Bartenschlager
- Department of Infectious DiseasesMolecular VirologyHeidelberg UniversityHeidelbergGermany,Division Virus‐Associated CarcinogenesisGerman Cancer Research CenterHeidelbergGermany,German Center for Infection ResearchHeidelberg Partner SiteHeidelbergGermany
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13
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Host Cell Signatures of the Envelopment Site within Beta-Herpes Virions. Int J Mol Sci 2022; 23:ijms23179994. [PMID: 36077391 PMCID: PMC9456339 DOI: 10.3390/ijms23179994] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022] Open
Abstract
Beta-herpesvirus infection completely reorganizes the membrane system of the cell. This system is maintained by the spatiotemporal arrangement of more than 3000 cellular proteins that continuously adapt the configuration of membrane organelles according to cellular needs. Beta-herpesvirus infection establishes a new configuration known as the assembly compartment (AC). The AC membranes are loaded with virus-encoded proteins during the long replication cycle and used for the final envelopment of the newly formed capsids to form infectious virions. The identity of the envelopment membranes is still largely unknown. Electron microscopy and immunofluorescence studies suggest that the envelopment occurs as a membrane wrapping around the capsids, similar to the growth of phagophores, in the area of the AC with the membrane identities of early/recycling endosomes and the trans-Golgi network. During wrapping, host cell proteins that define the identity and shape of these membranes are captured along with the capsids and incorporated into the virions as host cell signatures. In this report, we reviewed the existing information on host cell signatures in human cytomegalovirus (HCMV) virions. We analyzed the published proteomes of the HCMV virion preparations that identified a large number of host cell proteins. Virion purification methods are not yet advanced enough to separate all of the components of the rich extracellular material, including the large amounts of non-vesicular extracellular particles (NVEPs). Therefore, we used the proteomic data from large and small extracellular vesicles (lEVs and sEVs) and NVEPs to filter out the host cell proteins identified in the viral proteomes. Using these filters, we were able to narrow down the analysis of the host cell signatures within the virions and determine that envelopment likely occurs at the membranes derived from the tubular recycling endosomes. Many of these signatures were also found at the autophagosomes, suggesting that the CMV-infected cell forms membrane organelles with phagophore growth properties using early endosomal host cell machinery that coordinates endosomal recycling.
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14
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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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15
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G-Protein Phosphorylation: Aspects of Binding Specificity and Function in the Plant Kingdom. Int J Mol Sci 2022; 23:ijms23126544. [PMID: 35742988 PMCID: PMC9224535 DOI: 10.3390/ijms23126544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022] Open
Abstract
Plant survival depends on adaptive mechanisms that constantly rely on signal recognition and transduction. The predominant class of signal discriminators is receptor kinases, with a vast member composition in plants. The transduction of signals occurs in part by a simple repertoire of heterotrimeric G proteins, with a core composed of α-, β-, and γ-subunits, together with a 7-transmembrane Regulator G Signaling (RGS) protein. With a small repertoire of G proteins in plants, phosphorylation by receptor kinases is critical in regulating the active state of the G-protein complex. This review describes the in vivo detected phosphosites in plant G proteins and conservation scores, and their in vitro corresponding kinases. Furthermore, recently described outcomes, including novel arrestin-like internalization of RGS and a non-canonical phosphorylation switching mechanism that drives G-protein plasticity, are discussed.
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16
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Chen D, Zhao YG, Zhang H. Endomembrane remodeling in SARS-CoV-2 infection. CELL INSIGHT 2022; 1:100031. [PMID: 37193051 PMCID: PMC9112566 DOI: 10.1016/j.cellin.2022.100031] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/18/2022]
Abstract
During severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the viral proteins intimately interact with host factors to remodel the endomembrane system at various steps of the viral lifecycle. The entry of SARS-CoV-2 can be mediated by endocytosis-mediated internalization. Virus-containing endosomes then fuse with lysosomes, in which the viral S protein is cleaved to trigger membrane fusion. Double-membrane vesicles generated from the ER serve as platforms for viral replication and transcription. Virions are assembled at the ER-Golgi intermediate compartment and released through the secretory pathway and/or lysosome-mediated exocytosis. In this review, we will focus on how SARS-CoV-2 viral proteins collaborate with host factors to remodel the endomembrane system for viral entry, replication, assembly and egress. We will also describe how viral proteins hijack the host cell surveillance system-the autophagic degradation pathway-to evade destruction and benefit virus production. Finally, potential antiviral therapies targeting the host cell endomembrane system will be discussed.
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Affiliation(s)
- Di Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan G. Zhao
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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17
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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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18
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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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19
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Yoshida S, Hasegawa T. Beware of Misdelivery: Multifaceted Role of Retromer Transport in Neurodegenerative Diseases. Front Aging Neurosci 2022; 14:897688. [PMID: 35601613 PMCID: PMC9120357 DOI: 10.3389/fnagi.2022.897688] [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: 03/16/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Retromer is a highly integrated multimeric protein complex that mediates retrograde cargo sorting from endosomal compartments. In concert with its accessory proteins, the retromer drives packaged cargoes to tubular and vesicular structures, thereby transferring them to the trans-Golgi network or to the plasma membrane. In addition to the endosomal trafficking, the retromer machinery participates in mitochondrial dynamics and autophagic processes and thus contributes to cellular homeostasis. The retromer components and their associated molecules are expressed in different types of cells including neurons and glial cells, and accumulating evidence from genetic and biochemical studies suggests that retromer dysfunction is profoundly involved in the pathogenesis of neurodegenerative diseases including Alzheimer’s Disease and Parkinson’s disease. Moreover, targeting retromer components could alleviate the neurodegenerative process, suggesting that the retromer complex may serve as a promising therapeutic target. In this review, we will provide the latest insight into the regulatory mechanisms of retromer and discuss how its dysfunction influences the pathological process leading to neurodegeneration.
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Affiliation(s)
- Shun Yoshida
- Division of Neurology, Department of Neuroscience and Sensory Organs, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurology, National Hospital Organization Yonezawa Hospital, Yonezawa, Japan
| | - Takafumi Hasegawa
- Division of Neurology, Department of Neuroscience and Sensory Organs, Tohoku University Graduate School of Medicine, Sendai, Japan
- *Correspondence: Takafumi Hasegawa,
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20
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Lu Y, He P, Zhang Y, Ren Y, Zhang L. The emerging roles of retromer and sorting nexins in the life cycle of viruses. Virol Sin 2022; 37:321-330. [PMID: 35513271 PMCID: PMC9057928 DOI: 10.1016/j.virs.2022.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Retromer and sorting nexins (SNXs) transport cargoes from endosomes to the trans-Golgi network or plasma membrane. Recent studies have unveiled the emerging roles for retromer and SNXs in the life cycle of viruses, including members of Coronaviridae, Flaviviridae and Retroviridae. Key components of retromer/SNXs, such as Vps35, Vps26, SNX5 and SNX27, can affect multiple steps of the viral life cycle, including facilitating the entry of viruses into cells, participating in viral replication, and promoting the assembly of virions. Here we present a comprehensive updated review on the interplay between retromer/SNXs and virus, which will shed mechanistic insights into controlling virus infection. Retromer/SNXs could regulate viral infection directly or indirectly. Retromer/SNXs plays an important role for SARS-CoV-2 infection. HPV entry is mediated by retromer/SNXs. Retromer is required for HCV replication. Retromer affects the late step of HIV replication.
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21
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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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22
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Jo T, Nho K, Bice P, Saykin AJ. Deep learning-based identification of genetic variants: application to Alzheimer's disease classification. Brief Bioinform 2022; 23:bbac022. [PMID: 35183061 PMCID: PMC8921609 DOI: 10.1093/bib/bbac022] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 01/29/2023] Open
Abstract
Deep learning is a promising tool that uses nonlinear transformations to extract features from high-dimensional data. Deep learning is challenging in genome-wide association studies (GWAS) with high-dimensional genomic data. Here we propose a novel three-step approach (SWAT-CNN) for identification of genetic variants using deep learning to identify phenotype-related single nucleotide polymorphisms (SNPs) that can be applied to develop accurate disease classification models. In the first step, we divided the whole genome into nonoverlapping fragments of an optimal size and then ran convolutional neural network (CNN) on each fragment to select phenotype-associated fragments. In the second step, using a Sliding Window Association Test (SWAT), we ran CNN on the selected fragments to calculate phenotype influence scores (PIS) and identify phenotype-associated SNPs based on PIS. In the third step, we ran CNN on all identified SNPs to develop a classification model. We tested our approach using GWAS data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) including (N = 981; cognitively normal older adults (CN) = 650 and AD = 331). Our approach identified the well-known APOE region as the most significant genetic locus for AD. Our classification model achieved an area under the curve (AUC) of 0.82, which was compatible with traditional machine learning approaches, random forest and XGBoost. SWAT-CNN, a novel deep learning-based genome-wide approach, identified AD-associated SNPs and a classification model for AD and may hold promise for a range of biomedical applications.
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Affiliation(s)
- Taeho Jo
- Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Network Science Institute, Bloomington, IN, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Network Science Institute, Bloomington, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Paula Bice
- Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Network Science Institute, Bloomington, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
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23
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González-Mancha N, Rodríguez-Rodríguez C, Alcover A, Merida I. Sorting Nexin 27 Enables MTOC and Secretory Machinery Translocation to the Immune Synapse. Front Immunol 2022; 12:814570. [PMID: 35095913 PMCID: PMC8790036 DOI: 10.3389/fimmu.2021.814570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
Sorting nexin 27 (SNX27) association to the retromer complex mediates intracellular trafficking of cargoes containing PSD95/Dlg1/ZO-1 (PDZ)-binding C-terminal sequences from endosomes to the cell surface, preventing their lysosomal degradation. Antigen recognition by T lymphocyte leads to the formation of a highly organized structure named the immune synapse (IS), which ensures cell-cell communication and sustained T cell activation. At the neuronal synapse, SNX27 recycles PDZ-binding receptors and its defective expression is associated with synaptic dysfunction and cognitive impairment. In T lymphocytes, SNX27 was found localized at recycling endosomal compartments that polarized to the IS, suggesting a function in polarized traffic to this structure. Proteomic analysis of PDZ-SNX27 interactors during IS formation identify proteins with known functions in cytoskeletal reorganization and lipid regulation, such as diacylglycerol (DAG) kinase (DGK) ζ, as well as components of the retromer and WASH complex. In this study, we investigated the consequences of SNX27 deficiency in cytoskeletal reorganization during IS formation. Our analyses demonstrate that SNX27 controls the polarization towards the cell-cell interface of the PDZ-interacting cargoes DGKζ and the retromer subunit vacuolar protein sorting protein 26, among others. SNX27 silencing abolishes the formation of a DAG gradient at the IS and prevents re-localization of the dynactin complex component dynactin-1/p150Glued, two events that correlate with impaired microtubule organizing center translocation (MTOC). SNX27 silenced cells show marked alteration in cytoskeleton organization including a failure in the organization of the microtubule network and defects in actin clearance at the IS. Reduced SNX27 expression was also found to hinder the arrangement of signaling microclusters at the IS, as well as the polarization of the secretory machinery towards the antigen presenting cells. Our results broaden the knowledge of SNX27 function in T lymphocytes by showing a function in modulating IS organization through regulated trafficking of cargoes.
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Affiliation(s)
- Natalia González-Mancha
- Department of Immunology and Oncology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Cristina Rodríguez-Rodríguez
- Department of Immunology and Oncology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Andrés Alcover
- Institut Pasteur, Université de Paris, Unité Biologie Cellulaire des Lymphocytes, INSERM U1224, Ligue Nationale Contre le Cancer, Équipe Labellisée Ligue-2018, Paris, France
| | - Isabel Merida
- Department of Immunology and Oncology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
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24
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Gock N, Follett J, Rintoul GL, Beischlag TV, Lee FJ. Endosomal recycling and dopamine neurotransmission: Exploring the links between the retromer and Parkinson's disease. Synapse 2022; 76:e22224. [DOI: 10.1002/syn.22224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/17/2021] [Accepted: 01/23/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Nathan Gock
- Faculty of Health Sciences Simon Fraser University 8888 University Dr Burnaby BC V5A 1S6 Canada
- Centre for Cell Biology, Development, and Disease Simon Fraser University 8888 University Dr Burnaby BC V5A 1S6 Canada
| | - Jordan Follett
- Laboratory of Neurogenetics and Neuroscience Department of Neurology University of Florida 1149 Newell Dr Gainesville FL 32610‐0236 United States
| | - Gordon L Rintoul
- Department of Biological Sciences Simon Fraser University 8888 University Dr Burnaby BC V5A 1S6 Canada
- Centre for Cell Biology, Development, and Disease Simon Fraser University 8888 University Dr Burnaby BC V5A 1S6 Canada
| | - Timothy V Beischlag
- Faculty of Health Sciences Simon Fraser University 8888 University Dr Burnaby BC V5A 1S6 Canada
- Centre for Cell Biology, Development, and Disease Simon Fraser University 8888 University Dr Burnaby BC V5A 1S6 Canada
| | - Frank J.S. Lee
- Faculty of Health Sciences Simon Fraser University 8888 University Dr Burnaby BC V5A 1S6 Canada
- Centre for Cell Biology, Development, and Disease Simon Fraser University 8888 University Dr Burnaby BC V5A 1S6 Canada
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25
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Yang B, Jia Y, Meng Y, Xue Y, Liu K, Li Y, Liu S, Li X, Cui K, Shang L, Cheng T, Zhang Z, Hou Y, Yang X, Yan H, Duan L, Tong Z, Wu C, Liu Z, Gao S, Zhuo S, Huang W, Gao GF, Qi J, Shang G. SNX27 suppresses SARS-CoV-2 infection by inhibiting viral lysosome/late endosome entry. Proc Natl Acad Sci U S A 2022; 119:e2117576119. [PMID: 35022217 PMCID: PMC8794821 DOI: 10.1073/pnas.2117576119] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/08/2021] [Indexed: 12/28/2022] Open
Abstract
After binding to its cell surface receptor angiotensin converting enzyme 2 (ACE2), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the host cell through directly fusing with plasma membrane (cell surface pathway) or undergoing endocytosis traveling to lysosome/late endosome for membrane fusion (endocytic pathway). However, the endocytic entry regulation by host cell remains elusive. Recent studies show ACE2 possesses a type I PDZ binding motif (PBM) through which it could interact with a PDZ domain-containing protein such as sorting nexin 27 (SNX27). In this study, we determined the ACE2-PBM/SNX27-PDZ complex structure, and, through a series of functional analyses, we found SNX27 plays an important role in regulating the homeostasis of ACE2 receptor. More importantly, we demonstrated SNX27, together with retromer complex (the core component of the endosomal protein sorting machinery), prevents ACE2/virus complex from entering lysosome/late endosome, resulting in decreased viral entry in cells where the endocytic pathway dominates. The ACE2/virus retrieval mediated by SNX27-retromer could be considered as a countermeasure against invasion of ACE2 receptor-using SARS coronaviruses.
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Affiliation(s)
- Bo Yang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
- Shanxi Provincial Key Laboratory for Major Infectious Disease Response, Taiyuan 030012, China
| | - Yuanyuan Jia
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Yumin Meng
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Xue
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Kefang Liu
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Li
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shichao Liu
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Xiaoxiong Li
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Kaige Cui
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Lina Shang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Tianyou Cheng
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Zhichao Zhang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Yingxiang Hou
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China
| | - Xiaozhu Yang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Hong Yan
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Liqiang Duan
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Zhou Tong
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Changxin Wu
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China
| | - Zhida Liu
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Shan Gao
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Shu Zhuo
- Signet Therapeutics Inc, Shenzhen 518000, China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control, Beijing 102629, China
| | - George Fu Gao
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China;
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Guijun Shang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China;
- Shanxi Provincial Key Laboratory for Major Infectious Disease Response, Taiyuan 030012, China
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26
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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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27
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Chen KE, Guo Q, Hill TA, Cui Y, Kendall AK, Yang Z, Hall RJ, Healy MD, Sacharz J, Norwood SJ, Fonseka S, Xie B, Reid RC, Leneva N, Parton RG, Ghai R, Stroud DA, Fairlie DP, Suga H, Jackson LP, Teasdale RD, Passioura T, Collins BM. De novo macrocyclic peptides for inhibiting, stabilizing, and probing the function of the retromer endosomal trafficking complex. SCIENCE ADVANCES 2021; 7:eabg4007. [PMID: 34851660 PMCID: PMC8635440 DOI: 10.1126/sciadv.abg4007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/14/2021] [Indexed: 05/27/2023]
Abstract
The retromer complex (Vps35-Vps26-Vps29) is essential for endosomal membrane trafficking and signaling. Mutation of the retromer subunit Vps35 causes late-onset Parkinson’s disease, while viral and bacterial pathogens can hijack the complex during cellular infection. To modulate and probe its function, we have created a novel series of macrocyclic peptides that bind retromer with high affinity and specificity. Crystal structures show that most of the cyclic peptides bind to Vps29 via a Pro-Leu–containing sequence, structurally mimicking known interactors such as TBC1D5 and blocking their interaction with retromer in vitro and in cells. By contrast, macrocyclic peptide RT-L4 binds retromer at the Vps35-Vps26 interface and is a more effective molecular chaperone than reported small molecules, suggesting a new therapeutic avenue for targeting retromer. Last, tagged peptides can be used to probe the cellular localization of retromer and its functional interactions in cells, providing novel tools for studying retromer function.
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Affiliation(s)
- Kai-En Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Qian Guo
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Timothy A. Hill
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Yi Cui
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Zhe Yang
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Ryan J. Hall
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Michael D. Healy
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Joanna Sacharz
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Suzanne J. Norwood
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Sachini Fonseka
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Boyang Xie
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Robert C. Reid
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Natalya Leneva
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Robert G. Parton
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Queensland, Australia
| | - Rajesh Ghai
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - David A. Stroud
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Victoria 3052, Australia
| | - David P. Fairlie
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Rohan D. Teasdale
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
- Sydney Analytical, School of Life and Environmental Sciences and School of Chemistry, The University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
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28
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Zhao L, Zhong K, Zhao J, Yong X, Tong A, Jia D. SARS-CoV-2 spike protein harnesses SNX27-mediated endocytic recycling pathway. MedComm (Beijing) 2021; 2:798-809. [PMID: 34909756 PMCID: PMC8661858 DOI: 10.1002/mco2.92] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 02/05/2023] Open
Abstract
SARS-CoV-2 is an enveloped positive-sense RNA virus that depends on host factors for all stages of its life. Membrane receptor ACE2 is a well-established factor for SARS-CoV-2 docking. In addition to ACE2, whole-genome genetic screens have identified additional proteins, such as endosomal trafficking regulators SNX27 and retromer, as key host factors required for SARS-CoV-2 infection. However, it is poorly understood how SARS-CoV-2 utilize host endocytic transport pathways to produce productive infection. Here, we report that SNX27 interacts with the SARS-CoV-2 spike (S) protein to facilitate S protein surface expression. Interestingly, S protein binds to the PDZ domain of SNX27, although it does not contain a PDZ-binding motif (PDZbm). Either abrogation of the SNX27 PDZ domain or S protein "MTSC" motif, which is critical for SNX27 binding, decreases surface expression of S protein and viral production. Collectively, our study highlights a novel approach utilized by SARS-CoV-2 to facilitate virion trafficking to establish virus infection.
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Affiliation(s)
- Lin Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and ChildrenDepartment of PaediatricsState Key Laboratory of Biotherapy and Collaborative Innovation Center of BiotherapyWest China Second University HospitalSichuan UniversityChengduChina
| | - Kunhong Zhong
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalWest China Medical SchoolSichuan UniversityChengduChina
| | - Jia Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and ChildrenDepartment of PaediatricsState Key Laboratory of Biotherapy and Collaborative Innovation Center of BiotherapyWest China Second University HospitalSichuan UniversityChengduChina
| | - Xin Yong
- Key Laboratory of Birth Defects and Related Diseases of Women and ChildrenDepartment of PaediatricsState Key Laboratory of Biotherapy and Collaborative Innovation Center of BiotherapyWest China Second University HospitalSichuan UniversityChengduChina
| | - Aiping Tong
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalWest China Medical SchoolSichuan UniversityChengduChina
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and ChildrenDepartment of PaediatricsState Key Laboratory of Biotherapy and Collaborative Innovation Center of BiotherapyWest China Second University HospitalSichuan UniversityChengduChina
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29
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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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30
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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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31
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Sequences in the cytoplasmic tail of SARS-CoV-2 Spike facilitate expression at the cell surface and syncytia formation. Nat Commun 2021; 12:5333. [PMID: 34504087 PMCID: PMC8429659 DOI: 10.1038/s41467-021-25589-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023] Open
Abstract
The Spike (S) protein of SARS-CoV-2 binds ACE2 to direct fusion with host cells. S comprises a large external domain, a transmembrane domain, and a short cytoplasmic tail. Understanding the intracellular trafficking of S is relevant to SARS-CoV-2 infection, and to vaccines expressing full-length S from mRNA or adenovirus vectors. Here we report a proteomic screen for cellular factors that interact with the cytoplasmic tail of S. We confirm interactions with the COPI and COPII vesicle coats, ERM family actin regulators, and the WIPI3 autophagy component. The COPII binding site promotes exit from the endoplasmic reticulum, and although binding to COPI should retain S in the early Golgi where viral budding occurs, there is a suboptimal histidine residue in the recognition motif. As a result, S leaks to the surface where it accumulates and can direct the formation of multinucleate syncytia. Thus, the trafficking signals in the tail of S indicate that syncytia play a role in the SARS-CoV-2 lifecycle.
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32
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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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33
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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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34
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Yong XLH, Zhang L, Yang L, Chen X, Tan JZA, Yu X, Chandra M, Livingstone E, Widagdo J, Vieira MM, Roche KW, Lynch JW, Keramidas A, Collins BM, Anggono V. Regulation of NMDA receptor trafficking and gating by activity-dependent CaMKIIα phosphorylation of the GluN2A subunit. Cell Rep 2021; 36:109338. [PMID: 34233182 PMCID: PMC8313361 DOI: 10.1016/j.celrep.2021.109338] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/19/2021] [Accepted: 06/11/2021] [Indexed: 01/23/2023] Open
Abstract
NMDA receptor (NMDAR)-dependent Ca2+ influx underpins multiple forms of synaptic plasticity. Most synaptic NMDAR currents in the adult forebrain are mediated by GluN2A-containing receptors, which are rapidly inserted into synapses during long-term potentiation (LTP); however, the underlying molecular mechanisms remain poorly understood. In this study, we show that GluN2A is phosphorylated at Ser-1459 by Ca2+/calmodulin-dependent kinase IIα (CaMKIIα) in response to glycine stimulation that mimics LTP in primary neurons. Phosphorylation of Ser-1459 promotes GluN2A interaction with the sorting nexin 27 (SNX27)-retromer complex, thereby enhancing the endosomal recycling of NMDARs. Loss of SNX27 or CaMKIIα function blocks the glycine-induced increase in GluN2A-NMDARs on the neuronal membrane. Interestingly, mutations of Ser-1459, including the rare S1459G human epilepsy variant, prolong the decay times of NMDAR-mediated synaptic currents in heterosynapses by increasing the duration of channel opening. These findings not only identify a critical role of Ser-1459 phosphorylation in regulating the function of NMDARs, but they also explain how the S1459G variant dysregulates NMDAR function.
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Affiliation(s)
- Xuan Ling Hilary Yong
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lingrui Zhang
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Liming Yang
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Xiumin Chen
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jing Zhi Anson Tan
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Xiaojun Yu
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mintu Chandra
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Emma Livingstone
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jocelyn Widagdo
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Marta M Vieira
- Receptor Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine W Roche
- Receptor Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph W Lynch
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Angelo Keramidas
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Victor Anggono
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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35
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Capitani N, Baldari CT. F-Actin Dynamics in the Regulation of Endosomal Recycling and Immune Synapse Assembly. Front Cell Dev Biol 2021; 9:670882. [PMID: 34249926 PMCID: PMC8265274 DOI: 10.3389/fcell.2021.670882] [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: 02/22/2021] [Accepted: 05/24/2021] [Indexed: 12/24/2022] Open
Abstract
Membrane proteins endocytosed at the cell surface as vesicular cargoes are sorted at early endosomes for delivery to lysosomes for degradation or alternatively recycled to different cellular destinations. Cargo recycling is orchestrated by multimolecular complexes that include the retromer, retriever, and the WASH complex, which promote the polymerization of new actin filaments at early endosomes. These endosomal actin pools play a key role at different steps of the recycling process, from cargo segregation to specific endosomal subdomains to the generation and mobility of tubulo-vesicular transport carriers. Local F-actin pools also participate in the complex redistribution of endomembranes and organelles that leads to the acquisition of cell polarity. Here, we will present an overview of the contribution of endosomal F-actin to T-cell polarization during assembly of the immune synapse, a specialized membrane domain that T cells form at the contact with cognate antigen-presenting cells.
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Affiliation(s)
- Nagaja Capitani
- Department of Life Sciences, University of Siena, Siena, Italy
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36
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Lu J, Xu S, Huo Y, Sun D, Hu Y, Wang J, Zhang X, Wang P, Li Z, Liang M, Wu Z, Liu P. Sorting nexin 3 induces heart failure via promoting retromer-dependent nuclear trafficking of STAT3. Cell Death Differ 2021; 28:2871-2887. [PMID: 33947971 DOI: 10.1038/s41418-021-00789-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/08/2021] [Accepted: 04/15/2021] [Indexed: 12/18/2022] Open
Abstract
Sorting nexins (SNXs), the retromer-associated cargo binding proteins, have emerged as critical regulators of the trafficking of proteins involved in the pathogenesis of diverse diseases. However, studies of SNXs in the development of cardiovascular diseases, especially cardiac hypertrophy and heart failure, are lacking. Here, we ask whether SNX3, the simplest structured isoform in the SNXs family, may act as a key inducer of myocardial injury. An increased level of SNX3 was observed in failing hearts from human patients and mice. Cardiac-specific Snx3 knockout (Snx3-cKO) mice and Snx3 transgenic (Snx3-cTg) mice were generated to evaluate the role of Snx3 in myocardial hypertrophy, fibrosis, and heart function by morphology, echocardiography, histological staining, and hypertrophic biomarkers. We report that Snx3-cKO in mice significantly protected against isoproterenol (ISO)-induced cardiac hypertrophy at 12 weeks. Conversely, Snx3-cTg mice were more susceptible to ISO-induced cardiac hypertrophy at 12 weeks and showed aggravated cardiac injury even heart failure at 24 weeks. Immunoprecipitation-based mass spectrometry, immunofluorescent staining, co-immunoprecipitation, localized surface plasmon resonance, and proximity ligation assay were performed to examine the direct interaction of SNX3-retromer with signal transducer and activator of transcription 3 (STAT3). We discovered that STAT3 was a new interacting partner of SNX3-retromer, and SNX3-retromer served as an essential platform for assembling gp130/JAK2/STAT3 complexes and subsequent phosphorylation of STAT3 by direct combination at EE. SNX3-retromer and STAT3 complexes were transiently imported into the nucleus after hypertrophic stimuli. The pharmacological inhibition or knockdown of STAT3 reversed SNX3 overexpression-induced myocardial injury. STAT3 overexpression blunts the beneficial function of SNX3 knockdown on hypertrophic cardiomyocytes. We show that SNX3-retromer promoted importin α3-mediated STAT3 nuclear trafficking and ultimately leading to cardiac injury. Taken together, our study reveals that SNX3 plays a key role in cardiac function and implicates SNX3 as a potential therapeutic target for cardiac hypertrophy and heart failure.
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Affiliation(s)
- Jing Lu
- School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-sen University, Guangzhou, P. R. China
| | - Suowen Xu
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Department of Endocrinology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, P. R. China
| | - Yuqing Huo
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Vascular Biology Center, Augusta University, Augusta, GA, USA
| | - Duanping Sun
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Yuehuai Hu
- School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-sen University, Guangzhou, P. R. China
| | - Junjian Wang
- School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-sen University, Guangzhou, P. R. China
| | - Xiaolei Zhang
- School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-sen University, Guangzhou, P. R. China
| | - Panxia Wang
- School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-sen University, Guangzhou, P. R. China
| | - Zhuoming Li
- School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-sen University, Guangzhou, P. R. China
| | - Mengya Liang
- Department of Cardiac Surgery, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Zhongkai Wu
- Department of Cardiac Surgery, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China.
| | - Peiqing Liu
- School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-sen University, Guangzhou, P. R. China.
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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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38
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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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39
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Abstract
Endosome-to-cell surface recycling is mediated by retromer and Snx27. In this issue, Mao et al. (2021. J. Cell Biol.https://doi.org/10.1083/jcb.202010048) detail how endosomal protein sorting responds to external stimuli and reveal that phosphorylation of Snx27 regulates its cargo-binding function resulting in reduced endosome-to-cell surface recycling.
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Affiliation(s)
- Matthew N J Seaman
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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40
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Leneva N, Kovtun O, Morado DR, Briggs JAG, Owen DJ. Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly. SCIENCE ADVANCES 2021; 7:7/13/eabf8598. [PMID: 33762348 PMCID: PMC7990337 DOI: 10.1126/sciadv.abf8598] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/05/2021] [Indexed: 05/12/2023]
Abstract
Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core (VPS26/VPS29/VPS35) is present on cargo-transporting, tubular carriers along with a range of sorting nexins. Here, we elucidate the structural basis of membrane tubulation and coupled cargo recognition by metazoan and fungal retromer coats assembled with the non-Bin1/Amphiphysin/Rvs (BAR) sorting nexin SNX3 using cryo-electron tomography. The retromer core retains its arched, scaffolding structure but changes its mode of membrane recruitment when assembled with different SNX adaptors, allowing cargo recognition at subunit interfaces. Thus, membrane bending and cargo incorporation can be modulated to allow retromer to traffic cargoes along different cellular transport routes.
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Affiliation(s)
- Natalya Leneva
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Oleksiy Kovtun
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
| | - Dustin R Morado
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - John A G Briggs
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
| | - David J Owen
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
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41
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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: 25] [Impact Index Per Article: 8.3] [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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42
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Seaman MNJ. The Retromer Complex: From Genesis to Revelations. Trends Biochem Sci 2021; 46:608-620. [PMID: 33526371 DOI: 10.1016/j.tibs.2020.12.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022]
Abstract
The retromer complex has a well-established role in endosomal protein sorting, being necessary for maintaining the dynamic localisation of hundreds of membrane proteins that traverse the endocytic system. Retromer function and dysfunction is linked with neurodegenerative diseases, including Alzheimer's and Parkinson's disease, and many pathogens, both viral and bacterial, exploit or interfere in retromer function for their own ends. In this review, the history of retromer is distilled into a concentrated form that spans the identification of retromer to recent discoveries that have shed new light on how retromer functions in endosomal protein sorting and why retromer is increasingly being viewed as a potential therapeutic target in neurodegenerative disease.
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Affiliation(s)
- Matthew N J Seaman
- University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK.
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43
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Cui Y, Yang Z, Flores-Rodriguez N, Follett J, Ariotti N, Wall AA, Parton RG, Teasdale RD. Formation of retromer transport carriers is disrupted by the Parkinson disease-linked Vps35 D620N variant. Traffic 2021; 22:123-136. [PMID: 33347683 DOI: 10.1111/tra.12779] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 12/26/2022]
Abstract
Retromer core complex is an endosomal scaffold that plays a critical role in orchestrating protein trafficking within the endosomal system. Here we characterized the effect of the Parkinson's disease-linked Vps35 D620N in the endo-lysosomal system using Vps35 D620N rescue cell models. Vps35 D620N fully rescues the lysosomal and autophagy defects caused by retromer knock-out. Analogous to Vps35 knock out cells, the endosome-to-trans-Golgi network transport of cation-independent mannose 6-phosphate receptor (CI-M6PR) is impaired in Vps35 D620N rescue cells because of a reduced capacity to form endosome transport carriers. Cells expressing the Vps35 D620N variant have altered endosomal morphology, resulting in smaller, rounder structures with less tubule-like branches. At the molecular level retromer incorporating Vps35 D620N variant has a decreased binding to retromer associated proteins wiskott-aldrich syndrome protein and SCAR homologue (WASH) and SNX3 which are known to associate with retromer to form the endosome transport carriers. Hence, the partial defects on retrograde protein trafficking carriers in the presence of Vps35 D620N represents an altered cellular state able to cause Parkinson's disease.
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Affiliation(s)
- Yi Cui
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Zhe Yang
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Neftali Flores-Rodriguez
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Jordan Follett
- Institute for Molecular Biosciences and Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Ariotti
- Institute for Molecular Biosciences and Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Adam A Wall
- Institute for Molecular Biosciences and Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Robert G Parton
- Institute for Molecular Biosciences and Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Rohan D Teasdale
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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44
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Kliche J, Kuss H, Ali M, Ivarsson Y. Cytoplasmic short linear motifs in ACE2 and integrin β 3 link SARS-CoV-2 host cell receptors to mediators of endocytosis and autophagy. Sci Signal 2021; 14:14/665/eabf1117. [PMID: 33436498 PMCID: PMC7928716 DOI: 10.1126/scisignal.abf1117] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SARS-CoV-2, the virus that causes COVID-19, enters cells through endocytosis upon binding to the cell surface receptor ACE2 and potentially others, including integrins. Using bioinformatics, Mészáros et al. predicted the presence of short amino acid sequences, called short linear motifs (SLiMs), in the cytoplasmic tails of ACE2 and various integrins that may engage the endocytic and autophagic machinery. Using affinity binding assays, Kliche et al. not only confirmed that many of these predicted SLiMs interacted with target peptides in various components of the endocytosis and autophagy machinery, but also found that these interactions were regulated by the phosphorylation of SLiM-adjacent amino acids. Together, these findings have identified a potential link between autophagy and integrin signaling and could lead to new ways to prevent viral infection. The spike protein of SARS-CoV-2 binds the angiotensin-converting enzyme 2 (ACE2) on the host cell surface and subsequently enters host cells through receptor-mediated endocytosis. Additional cell receptors may be directly or indirectly involved, including integrins. The cytoplasmic tails of ACE2 and integrins contain several predicted short linear motifs (SLiMs) that may facilitate internalization of the virus as well as its subsequent propagation through processes such as autophagy. Here, we measured the binding affinity of predicted interactions between SLiMs in the cytoplasmic tails of ACE2 and integrin β3 with proteins that mediate endocytic trafficking and autophagy. We validated that a class I PDZ-binding motif mediated binding of ACE2 to the scaffolding proteins SNX27, NHERF3, and SHANK, and that a binding site for the clathrin adaptor AP2 μ2 in ACE2 overlaps with a phospho-dependent binding site for the SH2 domains of Src family tyrosine kinases. Furthermore, we validated that an LC3-interacting region (LIR) in integrin β3 bound to the ATG8 domains of the autophagy receptors MAP1LC3 and GABARAP in a manner enhanced by LIR-adjacent phosphorylation. Our results provide molecular links between cell receptors and mediators of endocytosis and autophagy that may facilitate viral entry and propagation.
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Affiliation(s)
- Johanna Kliche
- Department of Chemistry, BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Hanna Kuss
- Department of Chemistry, BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden.,WWU Münster, Institute for Evolution and Biodiversity, DE-48149 Münster, Germany
| | - Muhammad Ali
- Department of Chemistry, BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry, BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden.
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45
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McMillan KJ, Banks PJ, Hellel FLN, Carmichael RE, Clairfeuille T, Evans AJ, Heesom KJ, Lewis P, Collins BM, Bashir ZI, Henley JM, Wilkinson KA, Cullen PJ. Sorting nexin-27 regulates AMPA receptor trafficking through the synaptic adhesion protein LRFN2. eLife 2021; 10:59432. [PMID: 34251337 PMCID: PMC8296521 DOI: 10.7554/elife.59432] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/23/2021] [Indexed: 02/06/2023] Open
Abstract
The endosome-associated cargo adaptor sorting nexin-27 (SNX27) is linked to various neuropathologies through sorting of integral proteins to the synaptic surface, most notably AMPA receptors. To provide a broader view of SNX27-associated pathologies, we performed proteomics in rat primary neurons to identify SNX27-dependent cargoes, and identified proteins linked to excitotoxicity, epilepsy, intellectual disabilities, and working memory deficits. Focusing on the synaptic adhesion molecule LRFN2, we established that SNX27 binds to LRFN2 and regulates its endosomal sorting. Furthermore, LRFN2 associates with AMPA receptors and knockdown of LRFN2 results in decreased surface AMPA receptor expression, reduced synaptic activity, and attenuated hippocampal long-term potentiation. Overall, our study provides an additional mechanism by which SNX27 can control AMPA receptor-mediated synaptic transmission and plasticity indirectly through the sorting of LRFN2 and offers molecular insight into the perturbed function of SNX27 and LRFN2 in a range of neurological conditions.
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Affiliation(s)
| | - Paul J Banks
- School of Physiology, Pharmacology and Neuroscience, University of BristolBristolUnited Kingdom
| | | | | | - Thomas Clairfeuille
- Institute for Molecular Bioscience, The University of QueenslandQueenslandAustralia
| | - Ashley J Evans
- School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Kate J Heesom
- Proteomics facility, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Philip Lewis
- Proteomics facility, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of QueenslandQueenslandAustralia
| | - Zafar I Bashir
- School of Physiology, Pharmacology and Neuroscience, University of BristolBristolUnited Kingdom
| | - Jeremy M Henley
- School of Biochemistry, University of BristolBristolUnited Kingdom
| | | | - Peter J Cullen
- School of Biochemistry, University of BristolBristolUnited Kingdom
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46
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Sargent D, Moore DJ. Mechanisms of VPS35-Mediated Neurodegeneration in Parkinson's Disease. INTERNATIONAL REVIEW OF MOVEMENT DISORDERS 2021; 2:221-244. [PMID: 35497708 DOI: 10.1016/bs.irmvd.2021.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Parkinson's disease is a sporadic and common neurodegenerative movement disorder resulting from the complex interplay between genetic risk, aging and environmental exposure. Familial forms of PD account for ~10% of cases and are known to result from the inheritance of mutations in at least 15 genes. Mutations in the vacuolar protein sorting 35 ortholog (VPS35) gene cause late-onset, autosomal dominant familial PD. VPS35 is a key suunit of the pentameric retromer complex that plays a role in the retrograde sorting and recycling of transmembrane cargo proteins from endosomes to the plasma membrane and trans-Golgi network. A single heterozygous Asp620Asn (D620N) mutation in VPS35 has been identified in multiple families that segregates with PD, and a number of experimental cellular and animal models have been developed to understand its pathogenic effects. At the molecular level, the D620N mutation has been shown to impair the interaction of VPS35 with the WASH complex, that plays an accessory function in retromer-dependent sorting. In addition, the D620N mutation has been linked to the abnormal sorting of retromer cargo, including CI-M6PR, AMPA receptor subunits, MUL1, LAMP2a and ATG9A, as well as to LRRK2 hyperactivation. At the cellular level, data support an impact of D620N VPS35 on mitochondrial function, the autophagy-lysosomal pathway, Wnt signaling and neurotransmission via altered endosomal sorting. The relevance of abnormal retromer sorting and cellular pathways to PD-related neurodegenerative phenotypes induced by D620N VPS35 in rodent models is not yet clear. There is also uncertainty regarding the mechanism-of-action of the D620N mutation and whether it manifests pathogenic effects in animal models and PD through a gain-of-function and/or a partial dominant-negative mechanism. Here, we discuss the emerging molecular and cellular mechanisms underlying PD induced by familial VPS35 mutations, going from structure to cellular function to neuropathology. We further discuss studies linking reduced retromer function to other neurodegenerative diseases and potential therapeutic strategies to normalize retromer function to mitigate disease.
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Affiliation(s)
- Dorian Sargent
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Darren J Moore
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503, USA
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47
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Huo Y, Gao Y, Zheng Q, Zhao D, Guo T, Zhang S, Zeng Y, Cheng Y, Gu H, Zhang L, Zhu B, Luo H, Zhang X, Zhou Y, Zhang YW, Sun H, Xu H, Wang X. Overexpression of Human SNX27 Enhances Learning and Memory Through Modulating Synaptic Plasticity in Mice. Front Cell Dev Biol 2020; 8:595357. [PMID: 33330482 PMCID: PMC7729021 DOI: 10.3389/fcell.2020.595357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 11/11/2020] [Indexed: 11/13/2022] Open
Abstract
Abnormal synaptic transmission leads to learning and memory disorders and is the main feature of neurological diseases. Sorting nexin 27 (SNX27) is an endosomal adaptor protein associated with a variety of nervous system diseases, and it is mainly responsible for the trafficking of postsynaptic membrane receptors. However, the roles of SNX27 in regulating synaptic and cognitive function are not fully understood. Here, we first generated a neuron-specific human-SNX27 transgenic mouse model (hSNX27 Tg) that exhibited enhanced excitatory synaptic transmission and long-term potentiation (LTP). In addition, we found that the hSNX27 Tg mice displayed enhanced learning and memory, lower-level anxiety-like behavior, and increased social interaction. Furthermore, we found that SNX27 overexpression upregulated the expression of glutamate receptors in the cortex and hippocampus of hSNX27 Tg mice. Together, these results indicate that SNX27 overexpression promotes synaptic function and cognition through modulating glutamate receptors.
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Affiliation(s)
- Yuanhui Huo
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Yue Gao
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Qiuyang Zheng
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Dongdong Zhao
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Tiantian Guo
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Shuo Zhang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Yuzhe Zeng
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Yiyun Cheng
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Huaping Gu
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Lishan Zhang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Bin Zhu
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Hong Luo
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Xian Zhang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Ying Zhou
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Yun-Wu Zhang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Hao Sun
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Huaxi Xu
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Xin Wang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
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King LE, Zhang HH, Gould CM, Thomas DW, Whitehead LW, Simpson KJ, Burgess AW, Faux MC. Genes regulating membrane-associated E-cadherin and proliferation in adenomatous polyposis coli mutant colon cancer cells: High content siRNA screen. PLoS One 2020; 15:e0240746. [PMID: 33057364 PMCID: PMC7561197 DOI: 10.1371/journal.pone.0240746] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/01/2020] [Indexed: 01/17/2023] Open
Abstract
Truncating mutations in the tumour suppressor gene APC occur frequently in colorectal cancers and result in the deregulation of Wnt signalling as well as changes in cell-cell adhesion. Using quantitative imaging based on the detection of membrane-associated E-cadherin, we undertook a protein coding genome-wide siRNA screen to identify genes that regulate cell surface E-cadherin in the APC-defective colorectal cancer cell line SW480. We identified a diverse set of regulators of E-cadherin that offer new insights into the regulation of cell-cell adhesion, junction formation and genes that regulate proliferation or survival of SW480 cells. Among the genes whose depletion promotes membrane-associated E-cadherin, we identified ZEB1, the microRNA200 family, and proteins such as a ubiquitin ligase UBE2E3, CDK8, sorting nexin 27 (SNX27) and the matrix metalloproteinases, MMP14 and MMP19. The screen also identified 167 proteins required for maintaining E-cadherin at cell-cell adherens junctions, including known junctional proteins, CTNND1 and CTNNA1, as well as signalling enzymes, DUSP4 and MARK2, and transcription factors, TEAD3, RUNX2 and TRAM2. A better understanding of the post-translational regulation of E-cadherin provides new opportunities for restoring cell-cell adhesion in APC-defective cells.
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Affiliation(s)
- Lauren E. King
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Hui-Hua Zhang
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Cathryn M. Gould
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Daniel W. Thomas
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Lachlan W. Whitehead
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Kaylene J. Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Antony W. Burgess
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, RMH, University of Melbourne, Parkville, VIC, Australia
- * E-mail: (MCF); (AWB)
| | - Maree C. Faux
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- * E-mail: (MCF); (AWB)
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49
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Curnock R, Cullen PJ. Mammalian copper homeostasis requires retromer-dependent recycling of the high-affinity copper transporter 1. J Cell Sci 2020; 133:133/16/jcs249201. [PMID: 32843536 PMCID: PMC7473646 DOI: 10.1242/jcs.249201] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/20/2020] [Indexed: 12/13/2022] Open
Abstract
The concentration of essential micronutrients, such as copper (used here to describe both Cu+ and Cu2+), within the cell is tightly regulated to avoid their adverse deficiency and toxicity effects. Retromer-mediated sorting and recycling of nutrient transporters within the endo-lysosomal network is an essential process in regulating nutrient balance. Cellular copper homeostasis is regulated primarily by two transporters: the copper influx transporter copper transporter 1 (CTR1; also known as SLC31A1), which controls the uptake of copper, and the copper-extruding ATPase ATP7A, a recognised retromer cargo. Here, we show that in response to fluctuating extracellular copper, retromer controls the delivery of CTR1 to the cell surface. Following copper exposure, CTR1 is endocytosed to prevent excessive copper uptake. We reveal that internalised CTR1 localises on retromer-positive endosomes and, in response to decreased extracellular copper, retromer controls the recycling of CTR1 back to the cell surface to maintain copper homeostasis. In addition to copper, CTR1 plays a central role in the trafficking of platinum. The efficacy of platinum-based cancer drugs has been correlated with CTR1 expression. Consistent with this, we demonstrate that retromer-deficient cells show reduced sensitivity to the platinum-based drug cisplatin. Summary: CTR1 (SLC31A1) is the only known mammalian importer of copper. We show that CTR1 is a retromer complex cargo protein, and that retromer is required for cellular sensitivity to extracellular copper.
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Affiliation(s)
- Rachel Curnock
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Peter J Cullen
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
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Evans AJ, Daly JL, Anuar ANK, Simonetti B, Cullen PJ. Acute inactivation of retromer and ESCPE-1 leads to time-resolved defects in endosomal cargo sorting. J Cell Sci 2020; 133:133/15/jcs246033. [PMID: 32747499 PMCID: PMC7420817 DOI: 10.1242/jcs.246033] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/05/2020] [Indexed: 01/16/2023] Open
Abstract
Human retromer, a heterotrimer of VPS26 (VPS26A or VPS26B), VPS35 and VPS29, orchestrates the endosomal retrieval of internalised cargo and promotes their cell surface recycling, a prototypical cargo being the glucose transporter GLUT1 (also known as SLC2A1). The role of retromer in the retrograde sorting of the cation-independent mannose 6-phosphate receptor (CI-MPR, also known as IGF2R) from endosomes back to the trans-Golgi network remains controversial. Here, by applying knocksideways technology, we develop a method for acute retromer inactivation. While retromer knocksideways in HeLa and H4 human neuroglioma cells resulted in time-resolved defects in cell surface sorting of GLUT1, we failed to observe a quantifiable defect in CI-MPR sorting. In contrast, knocksideways of the ESCPE-1 complex – a key regulator of retrograde CI-MPR sorting – revealed time-resolved defects in CI-MPR sorting. Together, these data are consistent with a comparatively limited role for retromer in ESCPE-1-mediated CI-MPR retrograde sorting, and establish a methodology for acute retromer and ESCPE-1 inactivation that will aid the time-resolved dissection of their functional roles in endosomal cargo sorting. Summary: Retromer, a master controller of endosomal cargo sorting, is deregulated in neurodegenerative disease. Here, we develop and apply a retromer knocksideways methodology to quantify endosomal cargo sorting upon acute perturbation.
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Affiliation(s)
- Ashley J Evans
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - James L Daly
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Anis N K Anuar
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Boris Simonetti
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Peter J Cullen
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
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