1
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Zlamalova E, Rodger C, Greco F, Cheers SR, Kleniuk J, Nadadhur AG, Kadlecova Z, Reid E. Atlastin-1 regulates endosomal tubulation and lysosomal proteolysis in human cortical neurons. Neurobiol Dis 2024; 199:106556. [PMID: 38851544 PMCID: PMC11300884 DOI: 10.1016/j.nbd.2024.106556] [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: 04/05/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024] Open
Abstract
Mutation of the ATL1 gene is one of the most common causes of hereditary spastic paraplegia (HSP), a group of genetic neurodegenerative conditions characterised by distal axonal degeneration of the corticospinal tract axons. Atlastin-1, the protein encoded by ATL1, is one of three mammalian atlastins, which are homologous dynamin-like GTPases that control endoplasmic reticulum (ER) morphology by fusing tubules to form the three-way junctions that characterise ER networks. However, it is not clear whether atlastin-1 is required for correct ER morphology in human neurons and if so what the functional consequences of lack of atlastin-1 are. Using CRISPR-inhibition we generated human cortical neurons lacking atlastin-1. We demonstrate that ER morphology was altered in these neurons, with a reduced number of three-way junctions. Neurons lacking atlastin-1 had longer endosomal tubules, suggestive of defective tubule fission. This was accompanied by reduced lysosomal proteolytic capacity. As well as demonstrating that atlastin-1 is required for correct ER morphology in human neurons, our results indicate that lack of a classical ER-shaping protein such as atlastin-1 may cause altered endosomal tubulation and lysosomal proteolytic dysfunction. Furthermore, they strengthen the idea that defective lysosome function contributes to the pathogenesis of a broad group of HSPs, including those where the primary localisation of the protein involved is not at the endolysosomal system.
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Affiliation(s)
- Eliska Zlamalova
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Catherine Rodger
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Francesca Greco
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Samuel R Cheers
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Julia Kleniuk
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Aishwarya G Nadadhur
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Zuzana Kadlecova
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Evan Reid
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK.
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2
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Wan C, Puscher H, Ouyang Y, Wu J, Tian Y, Li S, Yin Q, Shen J. An AAGAB-to-CCDC32 handover mechanism controls the assembly of the AP2 adaptor complex. Proc Natl Acad Sci U S A 2024; 121:e2409341121. [PMID: 39145939 DOI: 10.1073/pnas.2409341121] [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: 05/09/2024] [Accepted: 07/13/2024] [Indexed: 08/16/2024] Open
Abstract
Vesicular transport relies on multimeric trafficking complexes to capture cargo and drive vesicle budding and fusion. Faithful assembly of the trafficking complexes is essential to their functions but remains largely unexplored. Assembly of AP2 adaptor, a heterotetrameric protein complex regulating clathrin-mediated endocytosis, is assisted by the chaperone AAGAB. Here, we found that AAGAB initiates AP2 assembly by stabilizing its α and σ2 subunits, but the AAGAB:α:σ2 complex cannot recruit additional AP2 subunits. We identified CCDC32 as another chaperone regulating AP2 assembly. CCDC32 recognizes the AAGAB:α:σ2 complex, and its binding leads to the formation of an α:σ2:CCDC32 ternary complex. The α:σ2:CCDC32 complex serves as a template that sequentially recruits the µ2 and β2 subunits of AP2 to complete AP2 assembly, accompanied by CCDC32 release. The AP2-regulating function of CCDC32 is disrupted by a disease-causing mutation. These findings demonstrate that AP2 is assembled by a handover mechanism switching from AAGAB-based initiation complexes to CCDC32-based template complexes. A similar mechanism may govern the assembly of other trafficking complexes exhibiting the same configuration as AP2.
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Affiliation(s)
- Chun Wan
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Harrison Puscher
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Yan Ouyang
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Jingyi Wu
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Yuan Tian
- Department of Biological Sciences and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
| | - Suzhao Li
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Qian Yin
- Department of Biological Sciences and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
| | - Jingshi Shen
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
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3
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Robinson MS, Antrobus R, Sanger A, Davies AK, Gershlick DC. The role of the AP-1 adaptor complex in outgoing and incoming membrane traffic. J Cell Biol 2024; 223:e202310071. [PMID: 38578286 PMCID: PMC10996651 DOI: 10.1083/jcb.202310071] [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: 10/27/2023] [Revised: 02/17/2024] [Accepted: 03/12/2024] [Indexed: 04/06/2024] Open
Abstract
The AP-1 adaptor complex is found in all eukaryotes, but it has been implicated in different pathways in different organisms. To look directly at AP-1 function, we generated stably transduced HeLa cells coexpressing tagged AP-1 and various tagged membrane proteins. Live cell imaging showed that AP-1 is recruited onto tubular carriers trafficking from the Golgi apparatus to the plasma membrane, as well as onto transferrin-containing early/recycling endosomes. Analysis of single AP-1 vesicles showed that they are a heterogeneous population, which starts to sequester cargo 30 min after exit from the ER. Vesicle capture showed that AP-1 vesicles contain transmembrane proteins found at the TGN and early/recycling endosomes, as well as lysosomal hydrolases, but very little of the anterograde adaptor GGA2. Together, our results support a model in which AP-1 retrieves proteins from post-Golgi compartments back to the TGN, analogous to COPI's role in the early secretory pathway. We propose that this is the function of AP-1 in all eukaryotes.
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Affiliation(s)
- Margaret S. Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Anneri Sanger
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Alexandra K. Davies
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - David C. Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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4
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Wang R, Cong Y, Qian D, Yan C, Gong D. Structural basis for double-stranded RNA recognition by SID1. Nucleic Acids Res 2024; 52:6718-6727. [PMID: 38742627 PMCID: PMC11194109 DOI: 10.1093/nar/gkae395] [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: 01/27/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
The nucleic acid transport properties of the systemic RNAi-defective (SID) 1 family make them attractive targets for developing RNA-based therapeutics and drugs. However, the molecular basis for double-stranded (ds) RNA recognition by SID1 family remains elusive. Here, we report the cryo-EM structures of Caenorhabditis elegans (c) SID1 alone and in complex with dsRNA, both at a resolution of 2.2 Å. The dimeric cSID1 interacts with two dsRNA molecules simultaneously. The dsRNA is located at the interface between β-strand rich domain (BRD)1 and BRD2 and nearly parallel to the membrane plane. In addition to extensive ionic interactions between basic residues and phosphate backbone, several hydrogen bonds are formed between 2'-hydroxyl group of dsRNA and the contact residues. Additionally, the electrostatic potential surface shows three basic regions are fitted perfectly into three major grooves of dsRNA. These structural characteristics enable cSID1 to bind dsRNA in a sequence-independent manner and to distinguish between DNA and RNA. The cSID1 exhibits no conformational changes upon binding dsRNA, with the exception of a few binding surfaces. Structural mapping of dozens of loss-of-function mutations allows potential interpretation of their diverse functional mechanisms. Our study marks an important step toward mechanistic understanding of the SID1 family-mediated dsRNA uptake.
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Affiliation(s)
- Runhao Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Ye Cong
- School of Life Sciences, Tsinghua University, Beijing, 100084, China. Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China
| | - Dandan Qian
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Chuangye Yan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China. Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China
| | - Deshun Gong
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
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5
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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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6
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Adamowski M, Randuch M, Matijević I, Narasimhan M, Friml J. SH3Ps recruit auxilin-like vesicle uncoating factors for clathrin-mediated endocytosis. Cell Rep 2024; 43:114195. [PMID: 38717900 DOI: 10.1016/j.celrep.2024.114195] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/09/2024] [Accepted: 04/19/2024] [Indexed: 06/01/2024] Open
Abstract
Clathrin-mediated endocytosis (CME) is an essential process of cargo uptake operating in all eukaryotes. In animals and yeast, BAR-SH3 domain proteins, endophilins and amphiphysins, function at the conclusion of CME to recruit factors for vesicle scission and uncoating. Arabidopsis thaliana contains the BAR-SH3 domain proteins SH3P1-SH3P3, but their role is poorly understood. Here, we identify SH3Ps as functional homologs of endophilin/amphiphysin. SH3P1-SH3P3 bind to discrete foci at the plasma membrane (PM), and SH3P2 recruits late to a subset of clathrin-coated pits. The SH3P2 PM recruitment pattern is nearly identical to its interactor, a putative uncoating factor, AUXILIN-LIKE1. Notably, SH3P1-SH3P3 are required for most of AUXILIN-LIKE1 recruitment to the PM. This indicates a plant-specific modification of CME, where BAR-SH3 proteins recruit auxilin-like uncoating factors rather than the uncoating phosphatases, synaptojanins. SH3P1-SH3P3 act redundantly in overall CME with the plant-specific endocytic adaptor TPLATE complex but not due to an SH3 domain in its TASH3 subunit.
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Affiliation(s)
- Maciek Adamowski
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria; Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, 05-870 Błonie, Poland
| | - Marek Randuch
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Ivana Matijević
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Madhumitha Narasimhan
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Jiří Friml
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
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7
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Montgomery AC, Mendoza CS, Garbouchian A, Quinones GB, Bentley M. Polarized transport requires AP-1-mediated recruitment of KIF13A and KIF13B at the trans-Golgi. Mol Biol Cell 2024; 35:ar61. [PMID: 38446634 PMCID: PMC11151104 DOI: 10.1091/mbc.e23-10-0401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024] Open
Abstract
Neurons are polarized cells that require accurate membrane trafficking to maintain distinct protein complements at dendritic and axonal membranes. The Kinesin-3 family members KIF13A and KIF13B are thought to mediate dendrite-selective transport, but the mechanism by which they are recruited to polarized vesicles and the differences in the specific trafficking role of each KIF13 have not been defined. We performed live-cell imaging in cultured hippocampal neurons and found that KIF13A is a dedicated dendrite-selective kinesin. KIF13B confers two different transport modes, dendrite- and axon-selective transport. Both KIF13s are maintained at the trans-Golgi network by interactions with the heterotetrameric adaptor protein complex AP-1. Interference with KIF13 binding to AP-1 resulted in disruptions to both dendrite- and axon-selective trafficking. We propose that AP-1 is the molecular link between the sorting of polarized cargoes into vesicles and the recruitment of kinesins that confer polarized transport.
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Affiliation(s)
- Andrew C Montgomery
- Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Christina S Mendoza
- Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Alex Garbouchian
- Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Geraldine B Quinones
- Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Marvin Bentley
- Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
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8
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Wallace NS, Gadbery JE, Cohen CI, Kendall AK, Jackson LP. Tepsin binds LC3B to promote ATG9A trafficking and delivery. Mol Biol Cell 2024; 35:ar56. [PMID: 38381558 PMCID: PMC11064669 DOI: 10.1091/mbc.e23-09-0359-t] [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: 09/20/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024] Open
Abstract
Tepsin is an established accessory protein found in Adaptor Protein 4 (AP-4) coated vesicles, but the biological role of tepsin remains unknown. AP-4 vesicles originate at the trans-Golgi network (TGN) and target the delivery of ATG9A, a scramblase required for autophagosome biogenesis, to the cell periphery. Using in silico methods, we identified a putative LC3-Interacting Region (LIR) motif in tepsin. Biochemical experiments using purified recombinant proteins indicate tepsin directly binds LC3B preferentially over other members of the mammalian ATG8 family. Calorimetry and structural modeling data indicate this interaction occurs with micromolar affinity using the established LC3B LIR docking site. Loss of tepsin in cultured cells dysregulates ATG9A export from the TGN as well as ATG9A distribution at the cell periphery. Tepsin depletion in a mRFP-GFP-LC3B HeLa reporter cell line using siRNA knockdown increases autophagosome volume and number, but does not appear to affect flux through the autophagic pathway. Reintroduction of wild-type tepsin partially rescues ATG9A cargo trafficking defects. In contrast, reintroducing tepsin with a mutated LIR motif or missing N-terminus drives diffuse ATG9A subcellular distribution. Together, these data suggest roles for tepsin in cargo export from the TGN; ensuring delivery of ATG9A-positive vesicles; and in overall maintenance of autophagosome structure.
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Affiliation(s)
- Natalie S. Wallace
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - John E. Gadbery
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Cameron I. Cohen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
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9
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Marmorale LJ, Jin H, Reidy TG, Palomino-Alonso B, Zysnarski CJ, Jordan-Javed F, Lahiri S, Duncan MC. Fast-evolving cofactors regulate the role of HEATR5 complexes in intra-Golgi trafficking. J Cell Biol 2024; 223:e202309047. [PMID: 38240799 PMCID: PMC10798858 DOI: 10.1083/jcb.202309047] [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: 09/11/2023] [Revised: 11/22/2023] [Accepted: 12/18/2023] [Indexed: 01/22/2024] Open
Abstract
The highly conserved HEATR5 proteins are best known for their roles in membrane traffic mediated by the adaptor protein complex-1 (AP1). HEATR5 proteins rely on fast-evolving cofactors to bind to AP1. However, how HEATR5 proteins interact with these cofactors is unknown. Here, we report that the budding yeast HEATR5 protein, Laa1, functions in two biochemically distinct complexes. These complexes are defined by a pair of mutually exclusive Laa1-binding proteins, Laa2 and the previously uncharacterized Lft1/Yml037c. Despite limited sequence similarity, biochemical analysis and structure predictions indicate that Lft1 and Laa2 bind Laa1 via structurally similar mechanisms. Both Laa1 complexes function in intra-Golgi recycling. However, only the Laa2-Laa1 complex binds to AP1 and contributes to its localization. Finally, structure predictions indicate that human HEATR5 proteins bind to a pair of fast-evolving interacting partners via a mechanism similar to that observed in yeast. These results reveal mechanistic insight into how HEATR5 proteins bind their cofactors and indicate that Laa1 performs functions besides recruiting AP1.
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Affiliation(s)
- Lucas J. Marmorale
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Huan Jin
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Thomas G. Reidy
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Brandon Palomino-Alonso
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Christopher J. Zysnarski
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Fatima Jordan-Javed
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Sagar Lahiri
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Mara C. Duncan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
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10
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Hoshi N, Uemura T, Tachibana K, Abe S, Murakami-Nishimagi Y, Okano M, Noda M, Saito K, Kono K, Ohtake T, Waguri S. Endosomal protein expression of γ1-adaptin is associated with tumor growth activity and relapse-free survival in breast cancer. Breast Cancer 2024; 31:305-316. [PMID: 38265632 PMCID: PMC10902087 DOI: 10.1007/s12282-023-01539-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/20/2023] [Indexed: 01/25/2024]
Abstract
BACKGROUND γ1-Adaptin is a subunit of adaptor protein complex-1 (AP-1), which regulates intracellular transport between the trans-Golgi network (TGN) and endosomes. Since expression levels of AP-1 subunits have been reported to be associated with cell proliferation and cancer malignancy, we investigated the relationships between the immunohistochemical expression of γ1-adaptin and both clinicopathological factors and relapse-free survival (RFS) in breast cancer tissue. MATERIALS AND METHODS SK-BR-3 cell line depleted of γ1-adaptin was used for cell proliferation, migration, and invasion assay. Intracellular localization of γ1-adaptin was examined with immunohistochemistry (IHC) using an antibody against γ1-adaptin, and with double immunohistofluorescence (IHF) microscopy using markers for the TGN and endosome. γ1-Adaptin intensities in IHC samples from 199 primary breast cancer patients were quantified and assessed in relation to clinicopathological factors and RFS. RESULTS Cell growth, migration, and invasion of SK-BR-3 cells were significantly suppressed by the depletion of γ1-adaptin. Although the staining patterns in the cancer tissues varied among cases by IHC, double IHF demonstrated that γ1-adaptin was mainly localized in EEA1-positive endosomes, but not in the TGN. γ1-Adaptin intensity was significantly higher in the tumor regions than in non-tumor regions. It was also higher in patients with Ki-67 (high), ER (-), PgR (-), and HER2 (+). Among subtypes of breast cancer, γ1-adaptin intensity was higher in HER2 than in luminal A or luminal B. The results of the survival analysis indicated that high γ1-adaptin intensity was significantly associated with worse RFS, and this association was also observed in group with ER (+), PgR (+), HER2 (-), Ki-67 (high), or luminal B. In addition, the Cox proportional hazards model showed that high γ1-adaptin intensity was an independent prognostic factor. CONCLUSION These results suggest that the endosomal expression of γ1-adaptin is positively correlated with breast cancer malignancy and could be a novel prognostic marker.
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Affiliation(s)
- Nobuhiro Hoshi
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Takefumi Uemura
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Kazunoshin Tachibana
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Sadahiko Abe
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yuko Murakami-Nishimagi
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Maiko Okano
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Masaru Noda
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Katsuharu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Koji Kono
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Tohru Ohtake
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Fukushima, Japan.
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11
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Tavares LA, Rodrigues RL, Santos da Costa C, Nascimento JA, Vargas de Carvalho J, Nogueira de Carvalho A, Mardones GA, daSilva LLP. AP-1γ2 is an adaptor protein 1 variant required for endosome-to-Golgi trafficking of the mannose-6-P receptor (CI-MPR) and ATP7B copper transporter. J Biol Chem 2024; 300:105700. [PMID: 38307383 PMCID: PMC10909764 DOI: 10.1016/j.jbc.2024.105700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/04/2024] Open
Abstract
Selective retrograde transport from endosomes back to the trans-Golgi network (TGN) is important for maintaining protein homeostasis, recycling receptors, and returning molecules that were transported to the wrong compartments. Two important transmembrane proteins directed to this pathway are the Cation-Independent Mannose-6-phosphate receptor (CI-MPR) and the ATP7B copper transporter. Among CI-MPR functions is the delivery of acid hydrolases to lysosomes, while ATP7B facilitates the transport of cytosolic copper ions into organelles or the extracellular space. Precise subcellular localization of CI-MPR and ATP7B is essential for the proper functioning of these proteins. This study shows that both CI-MPR and ATP7B interact with a variant of the clathrin adaptor 1 (AP-1) complex that contains a specific isoform of the γ-adaptin subunit called γ2. Through synchronized anterograde trafficking and cell-surface uptake assays, we demonstrated that AP-1γ2 is dispensable for ATP7B and CI-MPR exit from the TGN while being critically required for ATP7B and CI-MPR retrieval from endosomes to the TGN. Moreover, AP-1γ2 depletion leads to the retention of endocytosed CI-MPR in endosomes enriched in retromer complex subunits. These data underscore the importance of AP-1γ2 as a key component in the sorting and trafficking machinery of CI-MPR and ATP7B, highlighting its essential role in the transport of proteins from endosomes.
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Affiliation(s)
- Lucas Alves Tavares
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Roger Luiz Rodrigues
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Cristina Santos da Costa
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Jonas Alburqueque Nascimento
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Julianne Vargas de Carvalho
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Andreia Nogueira de Carvalho
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Gonzalo A Mardones
- Escuela de Medicina, Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
| | - Luis L P daSilva
- Center for Virology Research and Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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12
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Saffari A, Brechmann B, Böger C, Saber WA, Jumo H, Whye D, Wood D, Wahlster L, Alecu JE, Ziegler M, Scheffold M, Winden K, Hubbs J, Buttermore ED, Barrett L, Borner GHH, Davies AK, Ebrahimi-Fakhari D, Sahin M. High-content screening identifies a small molecule that restores AP-4-dependent protein trafficking in neuronal models of AP-4-associated hereditary spastic paraplegia. Nat Commun 2024; 15:584. [PMID: 38233389 PMCID: PMC10794252 DOI: 10.1038/s41467-023-44264-1] [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: 06/07/2023] [Accepted: 12/06/2023] [Indexed: 01/19/2024] Open
Abstract
Unbiased phenotypic screens in patient-relevant disease models offer the potential to detect therapeutic targets for rare diseases. In this study, we developed a high-throughput screening assay to identify molecules that correct aberrant protein trafficking in adapter protein complex 4 (AP-4) deficiency, a rare but prototypical form of childhood-onset hereditary spastic paraplegia characterized by mislocalization of the autophagy protein ATG9A. Using high-content microscopy and an automated image analysis pipeline, we screened a diversity library of 28,864 small molecules and identified a lead compound, BCH-HSP-C01, that restored ATG9A pathology in multiple disease models, including patient-derived fibroblasts and induced pluripotent stem cell-derived neurons. We used multiparametric orthogonal strategies and integrated transcriptomic and proteomic approaches to delineate potential mechanisms of action of BCH-HSP-C01. Our results define molecular regulators of intracellular ATG9A trafficking and characterize a lead compound for the treatment of AP-4 deficiency, providing important proof-of-concept data for future studies.
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Affiliation(s)
- Afshin Saffari
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Child Neurology and Inherited Metabolic Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Barbara Brechmann
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Cedric Böger
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Wardiya Afshar Saber
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Hellen Jumo
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Dosh Whye
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Delaney Wood
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lara Wahlster
- Department of Hematology & Oncology, Boston Children's Hospital & Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Julian E Alecu
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marvin Ziegler
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marlene Scheffold
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kellen Winden
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jed Hubbs
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Elizabeth D Buttermore
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lee Barrett
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, 82152, Germany
| | - Alexandra K Davies
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, 82152, Germany
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK
| | - Darius Ebrahimi-Fakhari
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Movement Disorders Program, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Mustafa Sahin
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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13
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Weeratunga S, Gormal RS, Liu M, Eldershaw D, Livingstone EK, Malapaka A, Wallis TP, Bademosi AT, Jiang A, Healy MD, Meunier FA, Collins BM. Interrogation and validation of the interactome of neuronal Munc18-interacting Mint proteins with AlphaFold2. J Biol Chem 2024; 300:105541. [PMID: 38072052 PMCID: PMC10820826 DOI: 10.1016/j.jbc.2023.105541] [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: 09/20/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024] Open
Abstract
Munc18-interacting proteins (Mints) are multidomain adaptors that regulate neuronal membrane trafficking, signaling, and neurotransmission. Mint1 and Mint2 are highly expressed in the brain with overlapping roles in the regulation of synaptic vesicle fusion required for neurotransmitter release by interacting with the essential synaptic protein Munc18-1. Here, we have used AlphaFold2 to identify and then validate the mechanisms that underpin both the specific interactions of neuronal Mint proteins with Munc18-1 as well as their wider interactome. We found that a short acidic α-helical motif within Mint1 and Mint2 is necessary and sufficient for specific binding to Munc18-1 and binds a conserved surface on Munc18-1 domain3b. In Munc18-1/2 double knockout neurosecretory cells, mutation of the Mint-binding site reduces the ability of Munc18-1 to rescue exocytosis, and although Munc18-1 can interact with Mint and Sx1a (Syntaxin1a) proteins simultaneously in vitro, we find that they have mutually reduced affinities, suggesting an allosteric coupling between the proteins. Using AlphaFold2 to then examine the entire cellular network of putative Mint interactors provides a structural model for their assembly with a variety of known and novel regulatory and cargo proteins including ADP-ribosylation factor (ARF3/ARF4) small GTPases and the AP3 clathrin adaptor complex. Validation of Mint1 interaction with a new predicted binder TJAP1 (tight junction-associated protein 1) provides experimental support that AlphaFold2 can correctly predict interactions across such large-scale datasets. Overall, our data provide insights into the diversity of interactions mediated by the Mint family and show that Mints may help facilitate a key trigger point in SNARE (soluble N-ethylmaleimide-sensitive factor attachment receptor) complex assembly and vesicle fusion.
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Affiliation(s)
- Saroja Weeratunga
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Rachel S Gormal
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Meihan Liu
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Denaye Eldershaw
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Emma K Livingstone
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Anusha Malapaka
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Tristan P Wallis
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Adekunle T Bademosi
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Anmin Jiang
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Michael D Healy
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Frederic A Meunier
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia; School of Biomedical Sciences, The University of Queensland, Queensland, Australia
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia.
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14
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Marsilia C, Batra M, Pokrovskaya ID, Wang C, Chaput D, Naumova DA, Lupashin VV, Suvorova ES. Essential role of the conserved oligomeric Golgi complex in Toxoplasma gondii. mBio 2023; 14:e0251323. [PMID: 37966241 PMCID: PMC10746232 DOI: 10.1128/mbio.02513-23] [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: 09/18/2023] [Accepted: 10/05/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE The Golgi is an essential eukaryotic organelle and a major place for protein sorting and glycosylation. Among apicomplexan parasites, Toxoplasma gondii retains the most developed Golgi structure and produces many glycosylated factors necessary for parasite survival. Despite its importance, Golgi function received little attention in the past. In the current study, we identified and characterized the conserved oligomeric Golgi complex and its novel partners critical for protein transport in T. gondii tachyzoites. Our results suggest that T. gondii broadened the role of the conserved elements and reinvented the missing components of the trafficking machinery to accommodate the specific needs of the opportunistic parasite T. gondii.
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Affiliation(s)
- Clem Marsilia
- Division of Infectious Diseases, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Mrinalini Batra
- Division of Infectious Diseases, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Irina D. Pokrovskaya
- Department of Physiology and Cell Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Changqi Wang
- College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Dale Chaput
- Proteomics Core, College of Arts and Sciences, University of South Florida, Tampa, Florida, USA
| | - Daria A. Naumova
- Division of Infectious Diseases, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Vladimir V. Lupashin
- Department of Physiology and Cell Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Elena S. Suvorova
- Division of Infectious Diseases, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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15
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Madan V, Albacete‐Albacete L, Jin L, Scaturro P, Watson JL, Muschalik N, Begum F, Boulanger J, Bauer K, Kiebler MA, Derivery E, Bullock SL. HEATR5B associates with dynein-dynactin and promotes motility of AP1-bound endosomal membranes. EMBO J 2023; 42:e114473. [PMID: 37872872 PMCID: PMC10690479 DOI: 10.15252/embj.2023114473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/25/2023] Open
Abstract
The microtubule motor dynein mediates polarised trafficking of a wide variety of organelles, vesicles and macromolecules. These functions are dependent on the dynactin complex, which helps recruit cargoes to dynein's tail and activates motor movement. How the dynein-dynactin complex orchestrates trafficking of diverse cargoes is unclear. Here, we identify HEATR5B, an interactor of the adaptor protein-1 (AP1) clathrin adaptor complex, as a novel player in dynein-dynactin function. HEATR5B was recovered in a biochemical screen for proteins whose association with the dynein tail is augmented by dynactin. We show that HEATR5B binds directly to the dynein tail and dynactin and stimulates motility of AP1-associated endosomal membranes in human cells. We also demonstrate that the Drosophila HEATR5B homologue is an essential gene that selectively promotes dynein-based transport of AP1-bound membranes to the Golgi apparatus. As HEATR5B lacks the coiled-coil architecture typical of dynein adaptors, our data point to a non-canonical process orchestrating motor function on a specific cargo. We additionally show that HEATR5B promotes association of AP1 with endosomal membranes independently of dynein. Thus, HEATR5B co-ordinates multiple events in AP1-based trafficking.
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Affiliation(s)
- Vanesa Madan
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
- Present address:
AbcamCambridgeUK
| | - Lucas Albacete‐Albacete
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Li Jin
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | | | - Joseph L Watson
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Nadine Muschalik
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Farida Begum
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Jérôme Boulanger
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Karl Bauer
- Biomedical Center, Department for Cell Biology, Medical FacultyLudwig‐Maximilians‐University of MunichMunichGermany
| | - Michael A Kiebler
- Biomedical Center, Department for Cell Biology, Medical FacultyLudwig‐Maximilians‐University of MunichMunichGermany
| | - Emmanuel Derivery
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Simon L Bullock
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
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16
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Marmorale LJ, Jin H, Reidy TG, Palomino-Alonso B, Zysnarski C, Jordan-Javed F, Lahiri S, Duncan MC. Two functionally distinct HEATR5 protein complexes are defined by fast-evolving co-factors in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554671. [PMID: 37662263 PMCID: PMC10473696 DOI: 10.1101/2023.08.24.554671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The highly conserved HEATR5 proteins are best known for their roles in membrane traffic mediated by the adaptor protein complex-1 (AP1). HEATR5 proteins rely on fast-evolving co-factors to bind to AP1. However, how HEATR5 proteins interact with these co-factors is unknown. Here, we report that the budding yeast HEATR5 protein, Laa1, functions in two biochemically distinct complexes. These complexes are defined by a pair of mutually exclusive Laa1-binding proteins, Laa2 and the previously uncharacterized Lft1/Yml037c. Despite limited sequence similarity, biochemical analysis and structure predictions indicate that Lft1 and Laa2 bind Laa1 via structurally similar mechanisms. Both Laa1 complexes function in intra-Golgi recycling. However, only the Laa2-Laa1 complex binds to AP1 and contributes to its localization. Finally, structure predictions indicate that human HEATR5 proteins bind to a pair of fast-evolving interacting partners via a mechanism similar to that observed in yeast. These results reveal mechanistic insight into how HEATR5 proteins bind their co-factors and indicate that Laa1 performs functions besides recruiting AP1.
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Affiliation(s)
- Lucas J. Marmorale
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor MI
- Present address: Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ
| | - Huan Jin
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor MI
| | - Thomas G. Reidy
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor MI
- Present address: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | | | | | - Fatima Jordan-Javed
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor MI
| | - Sagar Lahiri
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor MI
| | - Mara C Duncan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor MI
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17
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Sigrist SJ, Haucke V. Orchestrating vesicular and nonvesicular membrane dynamics by intrinsically disordered proteins. EMBO Rep 2023; 24:e57758. [PMID: 37680133 PMCID: PMC10626433 DOI: 10.15252/embr.202357758] [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: 07/05/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
Compartmentalization by membranes is a common feature of eukaryotic cells and serves to spatiotemporally confine biochemical reactions to control physiology. Membrane-bound organelles such as the endoplasmic reticulum (ER), the Golgi complex, endosomes and lysosomes, and the plasma membrane, continuously exchange material via vesicular carriers. In addition to vesicular trafficking entailing budding, fission, and fusion processes, organelles can form membrane contact sites (MCSs) that enable the nonvesicular exchange of lipids, ions, and metabolites, or the secretion of neurotransmitters via subsequent membrane fusion. Recent data suggest that biomolecule and information transfer via vesicular carriers and via MCSs share common organizational principles and are often mediated by proteins with intrinsically disordered regions (IDRs). Intrinsically disordered proteins (IDPs) can assemble via low-affinity, multivalent interactions to facilitate membrane tethering, deformation, fission, or fusion. Here, we review our current understanding of how IDPs drive the formation of multivalent protein assemblies and protein condensates to orchestrate vesicular and nonvesicular transport with a special focus on presynaptic neurotransmission. We further discuss how dysfunction of IDPs causes disease and outline perspectives for future research.
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Affiliation(s)
- Stephan J Sigrist
- Department of Biology, Chemistry, PharmacyFreie Universität BerlinBerlinGermany
| | - Volker Haucke
- Department of Biology, Chemistry, PharmacyFreie Universität BerlinBerlinGermany
- Department of Molecular Pharmacology and Cell BiologyLeibniz Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
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18
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Saffari A, Brechmann B, Boeger C, Saber WA, Jumo H, Whye D, Wood D, Wahlster L, Alecu J, Ziegler M, Scheffold M, Winden K, Hubbs J, Buttermore E, Barrett L, Borner G, Davies A, Sahin M, Ebrahimi-Fakhari D. High-Content Small Molecule Screen Identifies a Novel Compound That Restores AP-4-Dependent Protein Trafficking in Neuronal Models of AP-4-Associated Hereditary Spastic Paraplegia. RESEARCH SQUARE 2023:rs.3.rs-3036166. [PMID: 37398196 PMCID: PMC10312991 DOI: 10.21203/rs.3.rs-3036166/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Unbiased phenotypic screens in patient-relevant disease models offer the potential to detect novel therapeutic targets for rare diseases. In this study, we developed a high-throughput screening assay to identify molecules that correct aberrant protein trafficking in adaptor protein complex 4 (AP-4) deficiency, a rare but prototypical form of childhood-onset hereditary spastic paraplegia, characterized by mislocalization of the autophagy protein ATG9A. Using high-content microscopy and an automated image analysis pipeline, we screened a diversity library of 28,864 small molecules and identified a lead compound, C-01, that restored ATG9A pathology in multiple disease models, including patient-derived fibroblasts and induced pluripotent stem cell-derived neurons. We used multiparametric orthogonal strategies and integrated transcriptomic and proteomic approaches to delineate putative molecular targets of C-01 and potential mechanisms of action. Our results define molecular regulators of intracellular ATG9A trafficking and characterize a lead compound for the treatment of AP-4 deficiency, providing important proof-of-concept data for future Investigational New Drug (IND)-enabling studies.
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Affiliation(s)
| | | | | | | | | | - Dosh Whye
- Boston Children's Hospital, Harvard Medical School
| | - Delaney Wood
- Boston Children's Hospital, Harvard Medical School
| | | | - Julian Alecu
- Boston Children's Hospital, Harvard Medical School
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19
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Maciejowski WJ, Gile GH, Jerlström-Hultqvist J, Dacks JB. Ancient and pervasive expansion of adaptin-related vesicle coat machinery across Parabasalia. Int J Parasitol 2023; 53:233-245. [PMID: 36898426 DOI: 10.1016/j.ijpara.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 03/11/2023]
Abstract
The eukaryotic phylum Parabasalia is composed primarily of anaerobic, endobiotic organisms such as the veterinary parasite Tritrichomonas foetus and the human parasite Trichomonas vaginalis, the latter causing the most prevalent, non-viral, sexually transmitted disease world-wide. Although a parasitic lifestyle is generally associated with a reduction in cell biology, T. vaginalis provides a striking counter-example. The 2007 T. vaginalis genome paper reported a massive and selective expansion of encoded proteins involved in vesicle trafficking, particularly those implicated in the late secretory and endocytic systems. Chief amongst these were the hetero-tetrameric adaptor proteins or 'adaptins', with T. vaginalis encoding ∼3.5 times more such proteins than do humans. The provenance of such a complement, and how it relates to the transition from a free-living or endobiotic state to parasitism, remains unclear. In this study, we performed a comprehensive bioinformatic and molecular evolutionary investigation of the heterotetrameric cargo adaptor-derived coats, comparing the molecular complement and evolution of these proteins between T. vaginalis, T. foetus and the available diversity of endobiotic parabasalids. Notably, with the recent discovery of Anaeramoeba spp. as the free-living sister lineage to all parabasalids, we were able to delve back to time points earlier in the lineage's history than ever before. We found that, although T. vaginalis still encodes the most HTAC subunits amongst parabasalids, the duplications giving rise to the complement took place more deeply and at various stages across the lineage. While some duplications appear to have convergently shaped the parasitic lineages, the largest jump is in the transition from free-living to endobiotic lifestyle with both gains and losses shaping the encoded complement. This work details the evolution of a cellular system across an important lineage of parasites and provides insight into the evolutionary dynamics of an example of expansion of protein machinery, counter to the more common trends observed in many parasitic systems.
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Affiliation(s)
- William J Maciejowski
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Canada; Women and Children's Health Research Institute, University of Alberta, Edmonton, Canada
| | - Gillian H Gile
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, Arizona, USA
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, BMC, Box 586, Uppsala Universitet, SE-751 24 Uppsala, Sweden. https://twitter.com/jon_hultqvist
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Canada; Women and Children's Health Research Institute, University of Alberta, Edmonton, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
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20
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Wang P, Siao W, Zhao X, Arora D, Wang R, Eeckhout D, Van Leene J, Kumar R, Houbaert A, De Winne N, Mylle E, Vandorpe M, Korver RA, Testerink C, Gevaert K, Vanneste S, De Jaeger G, Van Damme D, Russinova E. Adaptor protein complex interaction map in Arabidopsis identifies P34 as a common stability regulator. NATURE PLANTS 2023; 9:355-371. [PMID: 36635451 PMCID: PMC7615410 DOI: 10.1038/s41477-022-01328-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Adaptor protein (AP) complexes are evolutionarily conserved vesicle transport regulators that recruit coat proteins, membrane cargoes and coated vesicle accessory proteins. As in plants endocytic and post-Golgi trafficking intersect at the trans-Golgi network, unique mechanisms for sorting cargoes of overlapping vesicular routes are anticipated. The plant AP complexes are part of the sorting machinery, but despite some functional information, their cargoes, accessory proteins and regulation remain largely unknown. Here, by means of various proteomics approaches, we generated the overall interactome of the five AP and the TPLATE complexes in Arabidopsis thaliana. The interactome converged on a number of hub proteins, including the thus far unknown adaptin binding-like protein, designated P34. P34 interacted with the clathrin-associated AP complexes, controlled their stability and, subsequently, influenced clathrin-mediated endocytosis and various post-Golgi trafficking routes. Altogether, the AP interactome network offers substantial resources for further discoveries of unknown endomembrane trafficking regulators in plant cells.
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Affiliation(s)
- Peng Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Wei Siao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Xiuyang Zhao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Deepanksha Arora
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Ren Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Rahul Kumar
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Anaxi Houbaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Michael Vandorpe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Ruud A Korver
- Plant Physiology and Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Christa Testerink
- Plant Physiology and Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
- Laboratory of Plant Physiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
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21
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Thattai M. Molecular and cellular constraints on vesicle traffic evolution. Curr Opin Cell Biol 2023; 80:102151. [PMID: 36610080 DOI: 10.1016/j.ceb.2022.102151] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/30/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023]
Abstract
In eukaryotic cells, the budding and fusion of intracellular transport vesicles is carefully orchestrated in space and time. Locally, a vesicle's source compartment, its cargo, and its destination compartment are controlled by dynamic multi-protein specificity modules. Globally, vesicle constituents must be recycled to ensure homeostasis of compartment compositions. The emergence of a novel vesicle pathway therefore requires new specificity modules as well as new recycling routes. Here, we review recent research on local (molecular) constraints on gene module duplication and global (cellular) constraints on intracellular recycling. By studying the evolution of vesicle traffic, we may discover general principles of how complex traits arise via multiple intermediate steps.
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Affiliation(s)
- Mukund Thattai
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, TIFR, Bangalore, India.
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22
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Wu C, Chen H, Yuan M, Zhang M, Abubakar YS, Chen X, Zhong H, Zheng W, Zheng H, Zhou J. FgAP1 σ Is Critical for Vegetative Growth, Conidiation, Virulence, and DON Biosynthesis in Fusarium graminearum. J Fungi (Basel) 2023; 9:jof9020145. [PMID: 36836259 PMCID: PMC9962196 DOI: 10.3390/jof9020145] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
The AP1 complex is a highly conserved clathrin adaptor that plays important roles in regulating cargo protein sorting and intracellular vesicle trafficking in eukaryotes. However, the functions of the AP1 complex in the plant pathogenic fungi including the devastating wheat pathogen Fusarium graminearum are still unclear. In this study, we investigated the biological functions of FgAP1σ, a subunit of the AP1 complex in F. graminearum. Disruption of FgAP1σ causes seriously impaired fungal vegetative growth, conidiogenesis, sexual development, pathogenesis, and deoxynivalenol (DON) production. The ΔFgap1σ mutants were found to be less sensitive to KCl- and sorbitol-induced osmotic stresses but more sensitive to SDS-induced stress than the wild-type PH-1. Although the growth inhibition rate of the ΔFgap1σ mutants was not significantly changed under calcofluor white (CFW) and Congo red (CR) stresses, the protoplasts released from ΔFgap1σ hyphae were decreased compared with the wild-type PH-1, suggesting that FgAP1σ is necessary for cell wall integrity and osmotic stresses in F. graminearum. Subcellular localization assays showed that FgAP1σ was predominantly localized to endosomes and the Golgi apparatus. In addition, FgAP1β-GFP, FgAP1γ-GFP, and FgAP1μ-GFP also localize to the Golgi apparatus. FgAP1β interacts with FgAP1σ, FgAP1γ, and FgAP1μ, while FgAP1σ regulates the expression of FgAP1β, FgAP1γ, and FgAP1μ in F. graminearum. Furthermore, the loss of FgAP1σ blocks the transportation of the v-SNARE protein FgSnc1 from the Golgi to the plasma membrane and delays the internalization of FM4-64 dye into the vacuole. Taken together, our results demonstrate that FgAP1σ plays vital roles in vegetative growth, conidiogenesis, sexual reproduction, DON production, pathogenicity, cell wall integrity, osmotic stress, exocytosis, and endocytosis in F. graminearum. These findings unveil the functions of the AP1 complex in filamentous fungi, most notably in F. graminearum, and lay solid foundations for effective prevention and control of Fusarium head blight (FHB).
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Affiliation(s)
- Congxian Wu
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Public Technology Service Center, Fujian Medical University, Fuzhou 350122, China
| | - Huilin Chen
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingyue Yuan
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meiru Zhang
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yakubu Saddeeq Abubakar
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria 810107, Nigeria
| | - Xin Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haoming Zhong
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huawei Zheng
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China
- Correspondence: (H.Z.); (J.Z.)
| | - Jie Zhou
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (H.Z.); (J.Z.)
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23
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Abstract
The global prevalences of obesity and type 2 diabetes mellitus have reached epidemic status, presenting a heavy burden on society. It is therefore essential to find novel mechanisms and targets that could be utilized in potential treatment strategies and, as such, intracellular membrane trafficking has re-emerged as a regulatory tool for controlling metabolic homeostasis. Membrane trafficking is an essential physiological process that is responsible for the sorting and distribution of signalling receptors, membrane transporters and hormones or other ligands between different intracellular compartments and the plasma membrane. Dysregulation of intracellular transport is associated with many human diseases, including cancer, neurodegeneration, immune deficiencies and metabolic diseases, such as type 2 diabetes mellitus and its associated complications. This Review focuses on the latest advances on the role of endosomal membrane trafficking in metabolic physiology and pathology in vivo, highlighting the importance of this research field in targeting metabolic diseases.
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Affiliation(s)
- Jerome Gilleron
- Université Côte d'Azur, Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1065 C3M, Team Cellular and Molecular Pathophysiology of Obesity, Nice, France.
| | - Anja Zeigerer
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
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24
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Moretto E, Miozzo F, Longatti A, Bonnet C, Coussen F, Jaudon F, Cingolani LA, Passafaro M. The tetraspanin TSPAN5 regulates AMPAR exocytosis by interacting with the AP4 complex. eLife 2023; 12:76425. [PMID: 36795458 PMCID: PMC9934860 DOI: 10.7554/elife.76425] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/25/2023] [Indexed: 02/17/2023] Open
Abstract
Intracellular trafficking of AMPA receptors is a tightly regulated process which involves several adaptor proteins, and is crucial for the activity of excitatory synapses both in basal conditions and during synaptic plasticity. We found that, in rat hippocampal neurons, an intracellular pool of the tetraspanin TSPAN5 promotes exocytosis of AMPA receptors without affecting their internalisation. TSPAN5 mediates this function by interacting with the adaptor protein complex AP4 and Stargazin and possibly using recycling endosomes as a delivery route. This work highlights TSPAN5 as a new adaptor regulating AMPA receptor trafficking.
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Affiliation(s)
- Edoardo Moretto
- Institute of Neuroscience, CNRVedano al LambroItaly,NeuroMI Milan Center for Neuroscience, University of Milano-BicoccaMilanItaly
| | | | | | - Caroline Bonnet
- University of Bordeaux, Interdisciplinary Institute for NeuroscienceBordeauxFrance
| | - Francoise Coussen
- University of Bordeaux, Interdisciplinary Institute for NeuroscienceBordeauxFrance
| | - Fanny Jaudon
- Department of Life Sciences, University of TriesteTriesteItaly,IRCCS Ospedale Policlinico San MartinoGenoaItaly
| | - Lorenzo A Cingolani
- Department of Life Sciences, University of TriesteTriesteItaly,Center for Synaptic Neuroscience and Technology (NSYN), Istituto Italiano di Tecnologia (IIT)GenoaItaly
| | - Maria Passafaro
- Institute of Neuroscience, CNRVedano al LambroItaly,NeuroMI Milan Center for Neuroscience, University of Milano-BicoccaMilanItaly
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25
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Pembridge OG, Wallace NS, Clements TP, Jackson LP. AP-4 loss in CRISPR-edited zebrafish affects early embryo development. Adv Biol Regul 2023; 87:100945. [PMID: 36642642 PMCID: PMC9992121 DOI: 10.1016/j.jbior.2022.100945] [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: 11/11/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Mutations in the heterotetrametric adaptor protein 4 (AP-4; ε/β4/μ4/σ4 subunits) membrane trafficking coat complex lead to complex neurological disorders characterized by spastic paraplegia, microcephaly, and intellectual disabilities. Understanding molecular mechanisms underlying these disorders continues to emerge with recent identification of an essential autophagy protein, ATG9A, as an AP-4 cargo. Significant progress has been made uncovering AP-4 function in cell culture and patient-derived cell lines, and ATG9A trafficking by AP-4 is considered a potential target for gene therapy approaches. In contrast, understanding how AP-4 trafficking affects development and function at the organismal level has long been hindered by loss of conserved AP-4 genes in key model systems (S. cerevisiae, C. elegans, D. melanogaster). However, zebrafish (Danio rerio) have retained AP-4 and can serve as an important model system for studying both the nervous system and overall development. We undertook gene editing in zebrafish using a CRISPR-ExoCas9 knockout system to determine how loss of single AP-4, or its accessory protein tepsin, genes affect embryo development 24 h post-fertilization (hpf). Single gene-edited embryos display abnormal head morphology and neural necrosis. We further conducted the first exploration of how AP-4 single gene knockouts in zebrafish embryos affect expression levels and patterns of two autophagy genes, atg9a and map1lc3b. This work suggests zebrafish may be further adapted and developed as a tool to uncover AP-4 function in membrane trafficking and autophagy in the context of a model organism.
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Affiliation(s)
- Olivia G Pembridge
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Natalie S Wallace
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Thomas P Clements
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Lauren P Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
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26
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Buser DP, Spang A. Protein sorting from endosomes to the TGN. Front Cell Dev Biol 2023; 11:1140605. [PMID: 36895788 PMCID: PMC9988951 DOI: 10.3389/fcell.2023.1140605] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/09/2023] [Indexed: 02/23/2023] Open
Abstract
Retrograde transport from endosomes to the trans-Golgi network is essential for recycling of protein and lipid cargoes to counterbalance anterograde membrane traffic. Protein cargo subjected to retrograde traffic include lysosomal acid-hydrolase receptors, SNARE proteins, processing enzymes, nutrient transporters, a variety of other transmembrane proteins, and some extracellular non-host proteins such as viral, plant, and bacterial toxins. Efficient delivery of these protein cargo molecules depends on sorting machineries selectively recognizing and concentrating them for their directed retrograde transport from endosomal compartments. In this review, we outline the different retrograde transport pathways governed by various sorting machineries involved in endosome-to-TGN transport. In addition, we discuss how this transport route can be analyzed experimentally.
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Affiliation(s)
| | - Anne Spang
- Biozentrum, University of Basel, Basel, Switzerland
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27
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Kümmel D, Herrmann E, Langemeyer L, Ungermann C. Molecular insights into endolysosomal microcompartment formation and maintenance. Biol Chem 2022; 404:441-454. [PMID: 36503831 DOI: 10.1515/hsz-2022-0294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022]
Abstract
Abstract
The endolysosomal system of eukaryotic cells has a key role in the homeostasis of the plasma membrane, in signaling and nutrient uptake, and is abused by viruses and pathogens for entry. Endocytosis of plasma membrane proteins results in vesicles, which fuse with the early endosome. If destined for lysosomal degradation, these proteins are packaged into intraluminal vesicles, converting an early endosome to a late endosome, which finally fuses with the lysosome. Each of these organelles has a unique membrane surface composition, which can form segmented membrane microcompartments by membrane contact sites or fission proteins. Furthermore, these organelles are in continuous exchange due to fission and fusion events. The underlying machinery, which maintains organelle identity along the pathway, is regulated by signaling processes. Here, we will focus on the Rab5 and Rab7 GTPases of early and late endosomes. As molecular switches, Rabs depend on activating guanine nucleotide exchange factors (GEFs). Over the last years, we characterized the Rab7 GEF, the Mon1-Ccz1 (MC1) complex, and key Rab7 effectors, the HOPS complex and retromer. Structural and functional analyses of these complexes lead to a molecular understanding of their function in the context of organelle biogenesis.
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Affiliation(s)
- Daniel Kümmel
- Institute of Biochemistry, University of Münster , Corrensstraße 36 , D-48149 Münster , Germany
| | - Eric Herrmann
- Institute of Biochemistry, University of Münster , Corrensstraße 36 , D-48149 Münster , Germany
| | - Lars Langemeyer
- Department of Biology/Chemistry, Biochemistry section , Osnabrück University , Barbarastraße 13 , D-49076 Osnabrück , Germany
- Center of Cellular Nanoanalytics (CellNanOs) , Osnabrück University , Barbarastraße 11 , D-49076 Osnabrück , Germany
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry section , Osnabrück University , Barbarastraße 13 , D-49076 Osnabrück , Germany
- Center of Cellular Nanoanalytics (CellNanOs) , Osnabrück University , Barbarastraße 11 , D-49076 Osnabrück , Germany
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28
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Park SY, Muschalik N, Chadwick J, Munro S. In vivo characterization of Drosophila golgins reveals redundancy and plasticity of vesicle capture at the Golgi apparatus. Curr Biol 2022; 32:4549-4564.e6. [PMID: 36103876 PMCID: PMC9849145 DOI: 10.1016/j.cub.2022.08.054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 06/29/2022] [Accepted: 08/18/2022] [Indexed: 01/26/2023]
Abstract
The Golgi is the central sorting station in the secretory pathway and thus the destination of transport vesicles arriving from the endoplasmic reticulum and endosomes and from within the Golgi itself. Cell viability, therefore, requires that the Golgi accurately receives multiple classes of vesicle. One set of proteins proposed to direct vesicle arrival at the Golgi are the golgins, long coiled-coil proteins localized to specific parts of the Golgi stack. In mammalian cells, three of the golgins, TMF, golgin-84, and GMAP-210, can capture intra-Golgi transport vesicles when placed in an ectopic location. However, the individual golgins are not required for cell viability, and mouse knockout mutants only have defects in specific tissues. To further illuminate this system, we examine the Drosophila orthologs of these three intra-Golgi golgins. We show that ectopic forms can capture intra-Golgi transport vesicles, but strikingly, the cargo present in the vesicles captured by each golgin varies between tissues. Loss-of-function mutants show that the golgins are individually dispensable, although the loss of TMF recapitulates the male fertility defects observed in mice. However, the deletion of multiple golgins results in defects in glycosylation and loss of viability. Examining the vesicles captured by a particular golgin when another golgin is missing reveals that the vesicle content in one tissue changes to resemble that of a different tissue. This reveals a plasticity in Golgi organization between tissues, providing an explanation for why the Golgi is sufficiently robust to tolerate the loss of many of the individual components of its membrane traffic machinery.
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Affiliation(s)
- Sung Yun Park
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Nadine Muschalik
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jessica Chadwick
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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29
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Kha QH, Tran TO, Nguyen TTD, Nguyen VN, Than K, Le NQK. An interpretable deep learning model for classifying adaptor protein complexes from sequence information. Methods 2022; 207:90-96. [PMID: 36174933 DOI: 10.1016/j.ymeth.2022.09.007] [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: 05/08/2022] [Revised: 08/19/2022] [Accepted: 09/22/2022] [Indexed: 11/15/2022] Open
Abstract
Adaptor proteins (APs) are a family of proteins that aids in intracellular membrane trafficking, and their impairments or defects are closely related to various disorders. Traditional methods to identify and classify APs require time and complex techniques, which were then advanced by machine learning and computational approaches to facilitate the APs recognition task. However, most studies focused on recognizing separate ones in the APs family or the APs in general with non-APs, lacking one comprehensive strategy to distinguish the complexes of AP subtypes. Herein, we proposed a novel method to implement one novel task as discriminating the AP complexes in the APs family, utilizing an interpretable deep neural network architecture on sequence-based encoding features. This work also introduced a benchmark data set of AP complexes originating from the UniProt and GeneOntology databases. To assess the robustness of our proposed method, we compared our performance to various machine learning algorithms and feature extraction strategies. Furthermore, the interpretation of the model's prediction performance was implemented using t-distributed stochastic neighbor embedding (t-SNE), uniform manifold approximation and projection (UMAP), and SHapley Additive exPlanations (SHAP) analysis to show the distribution of AP complexes on optimal features. The promising performance of our architecture can assist scientists not only in AP complexes distinction but also in general protein sequences. Moreover, we have also made our work publicly on GitHub https://github.com/khanhlee/adaptor-dnn.
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Affiliation(s)
- Quang-Hien Kha
- International Master/Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Thi-Oanh Tran
- International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Trinh-Trung-Duong Nguyen
- Personalised Medicine Cluster, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Van-Nui Nguyen
- University of Information and Communication Technology, Thai Nguyen University, Thai Nguyen, Viet Nam
| | - Khoat Than
- School of Information and Communication Technology, Hanoi University of Science and Technology, Viet Nam
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 106, Taiwan; Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei 106, Taiwan; Translational Imaging Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan.
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30
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Li F, Wu Z, Gao Y, Bowling FZ, Franklin JM, Hu C, Suhandynata RT, Frohman MA, Airola MV, Zhou H, Guan K. Defining the proximal interaction networks of Arf GTPases reveals a mechanism for the regulation of PLD1 and PI4KB. EMBO J 2022; 41:e110698. [PMID: 35844135 PMCID: PMC9433938 DOI: 10.15252/embj.2022110698] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/25/2022] [Accepted: 06/03/2022] [Indexed: 12/16/2022] Open
Abstract
The Arf GTPase family is involved in a wide range of cellular regulation including membrane trafficking and organelle-structure assembly. Here, we have generated a proximity interaction network for the Arf family using the miniTurboID approach combined with TMT-based quantitative mass spectrometry. Our interactome confirmed known interactions and identified many novel interactors that provide leads for defining Arf pathway cell biological functions. We explored the unexpected finding that phospholipase D1 (PLD1) preferentially interacts with two closely related but poorly studied Arf family GTPases, ARL11 and ARL14, showing that PLD1 is activated by ARL11/14 and may recruit these GTPases to membrane vesicles, and that PLD1 and ARL11 collaborate to promote macrophage phagocytosis. Moreover, ARL5A and ARL5B were found to interact with and recruit phosphatidylinositol 4-kinase beta (PI4KB) at trans-Golgi, thus promoting PI4KB's function in PI4P synthesis and protein secretion.
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Affiliation(s)
- Fu‐Long Li
- Department of Pharmacology and Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
| | - Zhengming Wu
- Department of Pharmacology and Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
| | - Yong‐Qi Gao
- Department of Cellular and Molecular MedicineUniversity of California San DiegoLa JollaCAUSA
| | - Forrest Z Bowling
- Department of Biochemistry and Cell BiologyStony Brook UniversityStony BrookNYUSA
| | - J Matthew Franklin
- Department of Pharmacology and Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
| | - Chongze Hu
- Department of Nanoengineering, Program of Materials Science and EngineeringUniversity of California San DiegoLa JollaCAUSA
| | - Raymond T Suhandynata
- Department of Cellular and Molecular MedicineUniversity of California San DiegoLa JollaCAUSA
| | - Michael A Frohman
- Department of Pharmacological SciencesStony Brook UniversityStony BrookNYUSA
| | - Michael V Airola
- Department of Biochemistry and Cell BiologyStony Brook UniversityStony BrookNYUSA
| | - Huilin Zhou
- Department of Cellular and Molecular MedicineUniversity of California San DiegoLa JollaCAUSA
| | - Kun‐Liang Guan
- Department of Pharmacology and Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
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31
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Griffiths G, Gruenberg J, Marsh M, Wohlmann J, Jones AT, Parton RG. Nanoparticle entry into cells; the cell biology weak link. Adv Drug Deliv Rev 2022; 188:114403. [PMID: 35777667 DOI: 10.1016/j.addr.2022.114403] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 12/22/2022]
Abstract
Nanoparticles (NP) are attractive options for the therapeutic delivery of active pharmaceutical drugs, proteins and nucleic acids into cells, tissues and organs. Research into the development and application of NP most often starts with a diverse group of scientists, including chemists, bioengineers and material and pharmaceutical scientists, who design, fabricate and characterize NP in vitro (Stage 1). The next step (Stage 2) generally investigates cell toxicity as well as the processes by which NP bind, are internalized and deliver their cargo to appropriate model tissue culture cells. Subsequently, in Stage 3, selected NP are tested in animal systems, mostly mouse. Whereas the chemistry-based development and analysis in Stage 1 is increasingly sophisticated, the investigations in Stage 2 are not what could be regarded as 'state-of-the-art' for the cell biology field and the quality of research into NP interactions with cells is often sub-standard. In this review we describe our current understanding of the mechanisms by which particles gain entry into mammalian cells via endocytosis. We summarize the most important areas for concern, highlight some of the most common mis-conceptions, and identify areas where NP scientists could engage with trained cell biologists. Our survey of the different mechanisms of uptake into cells makes us suspect that claims for roles for caveolae, as well as macropinocytosis, in NP uptake into cells have been exaggerated, whereas phagocytosis has been under-appreciated.
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Affiliation(s)
- Gareth Griffiths
- Department Biosciences, University of Oslo, Blindernveien 31, PO Box 1041, 0316 Oslo, Norway.
| | - Jean Gruenberg
- Department of Biochemistry, University of Geneva, 30 quai E. Ansermet, 1211-Geneva-4, Switzerland
| | - Mark Marsh
- Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Jens Wohlmann
- Department Biosciences, University of Oslo, Blindernveien 31, PO Box 1041, 0316 Oslo, Norway
| | - Arwyn T Jones
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, Cardiff, Wales CF103NB, UK
| | - Robert G Parton
- Institute for Molecular Bioscience and Centre for Microscopy and Microanalysis, The University of Queensland, Qld 4072, Australia
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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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Mattera R, De Pace R, Bonifacino JS. The adaptor protein chaperone AAGAB stabilizes AP-4 complex subunits. Mol Biol Cell 2022; 33:ar109. [PMID: 35976721 DOI: 10.1091/mbc.e22-05-0177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Adaptor protein 4 (AP-4) is a heterotetrameric complex composed of ε, β4, μ4 and σ4 subunits that mediates export of a subset of transmembrane cargos, including autophagy protein 9A (ATG9A), from the trans-Golgi network (TGN). AP-4 has received particular attention in recent years because mutations in any of its subunits cause a complicated form of hereditary spastic paraplegia (HSP or SPG) referred to as "AP-4-deficiency syndrome." The identification of proteins that interact with AP-4 has shed light on the mechanisms of AP-4-dependent cargo sorting and distribution within the cell. However, the mechanisms by which the AP-4 complex itself is assembled have remained unknown. Herein, we report that the alpha- and gamma-adaptin-binding protein (AAGAB, also known as p34) binds to and stabilizes the AP-4 ε-and σ4 subunits, thus promoting complex assembly. The importance of this binding is underscored by the observation that AAGAB-knockout cells exhibit reduced levels of AP-4 subunits and accumulation of ATG9A at the TGN like those in cells, mice, or patients with mutations in AP-4-subunit genes. These findings demonstrate that AP-4 assembly is not spontaneous but AAGAB-assisted, thus contributing to the understanding of an adaptor protein complex that is critically involved in development of the central nervous system.
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Affiliation(s)
- Rafael Mattera
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Raffaella De Pace
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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34
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Januário YC, Eden J, de Oliveira LS, De Pace R, Tavares LA, da Silva-Januário ME, Apolloni VB, Wilby EL, Altmeyer R, Burgos PV, Corrêa SAL, Gershlick DC, daSilva LLP. Clathrin adaptor AP-1-mediated Golgi export of amyloid precursor protein is crucial for the production of neurotoxic amyloid fragments. J Biol Chem 2022; 298:102172. [PMID: 35753347 PMCID: PMC9352552 DOI: 10.1016/j.jbc.2022.102172] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/28/2022] Open
Abstract
One of the hallmarks of Alzheimer's disease is the accumulation of toxic amyloid-β (Aβ) peptides in extracellular plaques. The direct precursor of Aβ is the carboxyl-terminal fragment β (or C99) of the amyloid precursor protein (APP). C99 is detected at elevated levels in Alzheimer's disease brains, and its intracellular accumulation has been linked to early neurotoxicity independently of Aβ. Despite this, the causes of increased C99 levels are poorly understood. Here, we demonstrate that APP interacts with the clathrin vesicle adaptor AP-1 (adaptor protein 1), and we map the interaction sites on both proteins. Using quantitative kinetic trafficking assays, established cell lines and primary neurons, we also show that this interaction is required for the transport of APP from the trans-Golgi network to endosomes. In addition, disrupting AP-1-mediated transport of APP alters APP processing and degradation, ultimately leading to increased C99 production and Aβ release. Our results indicate that AP-1 regulates the subcellular distribution of APP, altering its processing into neurotoxic fragments.
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Affiliation(s)
- Yunan C Januário
- Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil; Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Jessica Eden
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Luan S de Oliveira
- Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil; Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil; School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK
| | - Raffaella De Pace
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Lucas A Tavares
- Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil; Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Mara E da Silva-Januário
- Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil; Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Vinícius B Apolloni
- Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil; Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Elise L Wilby
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Randolf Altmeyer
- Statslab, Department of Pure Mathematics and Mathematical Statistics, University of Cambridgee, Cambridge, UK
| | - Patricia V Burgos
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile; Center for Aging and Regeneration (CARE), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sonia A L Corrêa
- School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK; Department of Life Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
| | - David C Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
| | - Luis L P daSilva
- Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil; Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
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35
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Duncan MC. New directions for the clathrin adaptor AP-1 in cell biology and human disease. Curr Opin Cell Biol 2022; 76:102079. [DOI: 10.1016/j.ceb.2022.102079] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/03/2022]
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36
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Tu M, Saputo S. From Beginning to End: Expanding the SERINC3 Interactome Through an in silico Analysis. Bioinform Biol Insights 2022; 16:11779322221092944. [PMID: 35494555 PMCID: PMC9052817 DOI: 10.1177/11779322221092944] [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: 08/20/2021] [Accepted: 03/07/2022] [Indexed: 11/15/2022] Open
Abstract
The serine incorporator (SERINC) family of proteins are a family of multipass transmembrane proteins associated with biosynthesis of serine-containing phospholipids and sphingolipids. Humans have 5 paralogs, SERINC1-5, which have been linked to disease including variable expression in tumor lines and possessing activity as restriction factors against HIV-1. Despite recent studies, the cellular function of SERINC proteins have yet to be fully elucidated. The goal of this study as to investigate the role of SERINC3 by expanding upon its interactome. We used a variety of bioinformatic tools to identify cellular factors that interact with SERINC3 and assessed how sequence variation might alter these interactions. Analysis of the promoter region indicates that SERINC3 is putatively regulated by transcription factors involved in tissue-specific development. Analysis of the unique 3′-untranslated region of one variant of HsSERINC3 revealed that this region serves as a conserved site of regulation by both RNA binding proteins and miRNA. In addition, SERINC3 is putatively regulated at the protein level by several posttranslational modifications. Our results show that extra-membrane portions of SERINC3 are subject to variation in the coding sequence as well as areas of relatively low conservation. Overall, our data suggest that regions of low homology as well as presence of variations in the nucleotide and protein sequences of HsSERINC3 suggest that these variations may lead to aberrant function and alternative regulatory mechanisms in homologs. The functional consequences of these sequence and structural variations need to be explored systematically to fully appreciate the role of SERINC3 in both health and disease.
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Affiliation(s)
- Mckenzie Tu
- Department of Chemistry and Biochemistry, SUNY Brockport, Brockport, NY, USA
| | - Sarah Saputo
- Department of Chemistry and Biochemistry, SUNY Brockport, Brockport, NY, USA
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37
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Mechanisms regulating the sorting of soluble lysosomal proteins. Biosci Rep 2022; 42:231123. [PMID: 35394021 PMCID: PMC9109462 DOI: 10.1042/bsr20211856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Lysosomes are key regulators of many fundamental cellular processes such as metabolism, autophagy, immune response, cell signalling and plasma membrane repair. These highly dynamic organelles are composed of various membrane and soluble proteins, which are essential for their proper functioning. The soluble proteins include numerous proteases, glycosidases and other hydrolases, along with activators, required for catabolism. The correct sorting of soluble lysosomal proteins is crucial to ensure the proper functioning of lysosomes and is achieved through the coordinated effort of many sorting receptors, resident ER and Golgi proteins, and several cytosolic components. Mutations in a number of proteins involved in sorting soluble proteins to lysosomes result in human disease. These can range from rare diseases such as lysosome storage disorders, to more prevalent ones, such as Alzheimer’s disease, Parkinson’s disease and others, including rare neurodegenerative diseases that affect children. In this review, we discuss the mechanisms that regulate the sorting of soluble proteins to lysosomes and highlight the effects of mutations in this pathway that cause human disease. More precisely, we will review the route taken by soluble lysosomal proteins from their translation into the ER, their maturation along the Golgi apparatus, and sorting at the trans-Golgi network. We will also highlight the effects of mutations in this pathway that cause human disease.
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38
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Buser DP, Bader G, Spiess M. Retrograde transport of CDMPR depends on several machineries as analyzed by sulfatable nanobodies. Life Sci Alliance 2022; 5:5/7/e202101269. [PMID: 35314489 PMCID: PMC8961009 DOI: 10.26508/lsa.202101269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 11/24/2022] Open
Abstract
Nanobody toolkit enables the quantitative analysis of endosome-to-TGN transport of the mannose-6-phosphate receptor in cells depleted of retrograde transport machineries Retrograde protein transport from the cell surface and endosomes to the TGN is essential for membrane homeostasis in general and for the recycling of mannose-6-phosphate receptors (MPRs) for sorting of lysosomal hydrolases in particular. We used a nanobody-based sulfation tool to more directly determine transport kinetics from the plasma membrane to the TGN for the cation-dependent MPR (CDMPR) with and without rapid or gradual inactivation of candidate machinery proteins. Although knockdown of retromer (Vps26), epsinR, or Rab9a reduced CDMPR arrival to the TGN, no effect was observed upon silencing of TIP47. Strikingly, when retrograde transport was analyzed by rapamycin-induced rapid depletion (knocksideways) or long-term depletion by knockdown of the clathrin adaptor AP-1 or of the GGA machinery, distinct phenotypes in sulfation kinetics were observed, suggesting a potential role of GGA adaptors in retrograde and anterograde transport. Our study illustrates the usefulness of derivatized, sulfation-competent nanobodies, reveals novel insights into CDMPR trafficking biology, and further outlines that the selection of machinery inactivation is critical for phenotype analysis.
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Affiliation(s)
| | - Gaétan Bader
- Biozentrum, University of Basel, Basel, Switzerland
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39
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Genetic disorders of cellular trafficking. Trends Genet 2022; 38:724-751. [DOI: 10.1016/j.tig.2022.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/11/2022] [Accepted: 02/28/2022] [Indexed: 02/06/2023]
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40
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From Drosophila to Human: Biological Function of E3 Ligase Godzilla and Its Role in Disease. Cells 2022; 11:cells11030380. [PMID: 35159190 PMCID: PMC8834447 DOI: 10.3390/cells11030380] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/29/2022] Open
Abstract
The ubiquitin–proteasome system is of fundamental importance in all fields of biology due to its impact on proteostasis and in regulating cellular processes. Ubiquitination, a type of protein post-translational modification, involves complex enzymatic machinery, such as E3 ubiquitin ligases. The E3 ligases regulate the covalent attachment of ubiquitin to a target protein and are involved in various cellular mechanisms, including the cell cycle, cell division, endoplasmic reticulum stress, and neurotransmission. Because the E3 ligases regulate so many physiological events, they are also associated with pathologic conditions, such as cancer, neurological disorders, and immune-related diseases. This review focuses specifically on the protease-associated transmembrane-containing the Really Interesting New Gene (RING) subset of E3 ligases. We describe the structure, partners, and physiological functions of the Drosophila Godzilla E3 ligase and its human homologues, RNF13, RNF167, and ZNRF4. Also, we summarize the information that has emerged during the last decade regarding the association of these E3 ligases with pathophysiological conditions, such as cancer, asthma, and rare genetic disorders. We conclude by highlighting the limitations of the current knowledge and pinpointing the unresolved questions relevant to RNF13, RNF167, and ZNRF4 ubiquitin ligases.
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41
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Graham TR. AP-3 shows off its flexibility for the cryo-EM camera. J Biol Chem 2021; 298:101491. [PMID: 34902351 PMCID: PMC8801477 DOI: 10.1016/j.jbc.2021.101491] [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] [Accepted: 12/08/2021] [Indexed: 11/29/2022] Open
Abstract
The tetrameric adaptor protein AP-3 is critical for the transport of proteins to lysosomes and lysosome-related organelles. The structures of homologous adaptors AP-1 and AP-2 have revealed a closed-to-open conformational change upon membrane recruitment and phosphoinositide binding. Recently, Schoppe et al. reported the first cryo-EM structures of AP-3 from budding yeast and described remarkably flexible solution structures that are all in the open conformation. The apparent lack of a closed conformational state, the first such description in the literature, allows AP-3 to be more reliant on cargo interaction for its initial membrane recruitment compared with AP-1.
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Affiliation(s)
- Todd R Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA.
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42
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Ford C, Parchure A, von Blume J, Burd CG. Cargo sorting at the trans-Golgi network at a glance. J Cell Sci 2021; 134:jcs259110. [PMID: 34870705 PMCID: PMC8714066 DOI: 10.1242/jcs.259110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Golgi functions principally in the biogenesis and trafficking of glycoproteins and lipids. It is compartmentalized into multiple flattened adherent membrane sacs termed cisternae, which each contain a distinct repertoire of resident proteins, principally enzymes that modify newly synthesized proteins and lipids sequentially as they traffic through the stack of Golgi cisternae. Upon reaching the final compartments of the Golgi, the trans cisterna and trans-Golgi network (TGN), processed glycoproteins and lipids are packaged into coated and non-coated transport carriers derived from the trans Golgi and TGN. The cargoes of clathrin-coated vesicles are chiefly residents of endo-lysosomal organelles, while uncoated carriers ferry cargo to the cell surface. There are outstanding questions regarding the mechanisms of protein and lipid sorting within the Golgi for export to different organelles. Nonetheless, conceptual advances have begun to define the key molecular features of cargo clients and the mechanisms underlying their sorting into distinct export pathways, which we have collated in this Cell Science at a Glance article and the accompanying poster.
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Affiliation(s)
| | | | - Julia von Blume
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Christopher G. Burd
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT 06520, USA
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43
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Uemura T, Suzuki T, Dohmae N, Waguri S. Clathrin adapters AP-1 and GGA2 support expression of epidermal growth factor receptor for cell growth. Oncogenesis 2021; 10:80. [PMID: 34799560 PMCID: PMC8604998 DOI: 10.1038/s41389-021-00367-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/20/2021] [Accepted: 10/25/2021] [Indexed: 01/03/2023] Open
Abstract
The role of Golgi/endosome-localized clathrin adapters in the maintenance of steady-state cell surface epidermal growth factor receptor (EGFR) is not well known. Here, we show that EGFR associates preferentially with both AP-1 and GGA2 in vitro. AP-1 depletion caused a reduction in the EGFR protein by promoting its lysosomal degradation. Triple immunofluorescence microscopy and proximity ligation assays demonstrated that the interaction of EGFR with AP-1 or GGA2 occurred more frequently in Rab11-positive recycling endosomes than in Rab5-positive early endosomes. Biochemical recycling assay revealed that the depletion of AP-1 or GGA2 significantly suppressed EGFR recycling to the plasma membrane regardless of the EGF stimulation. Depletion of AP-1 or GGA2 also reduced cell contents of other tyrosine kinases, MET and ErbB4, and therefore, suppressed the growth of H1975 cancer cells in culture and xenograft model. Moreover, AP-1 was expressed in endosomes at higher levels in some cancer tissues. Collectively, these results suggest that AP-1 and GGA2 function in recycling endosomes to retrieve endocytosed EGFR, thereby sustaining its cell surface expression and, consequently, cancer cell growth.
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Affiliation(s)
- Takefumi Uemura
- grid.411582.b0000 0001 1017 9540Department of Anatomy and Histology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, Fukushima 960-1295 Japan
| | - Takehiro Suzuki
- grid.509461.fBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| | - Naoshi Dohmae
- grid.509461.fBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, Fukushima, 960-1295, Japan.
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44
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Cabana VC, Bouchard AY, Sénécal AM, Ghilarducci K, Kourrich S, Cappadocia L, Lussier MP. RNF13 Dileucine Motif Variants L311S and L312P Interfere with Endosomal Localization and AP-3 Complex Association. Cells 2021; 10:cells10113063. [PMID: 34831286 PMCID: PMC8620429 DOI: 10.3390/cells10113063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/24/2022] Open
Abstract
Developmental and epileptic encephalopathies (DEE) are rare and serious neurological disorders characterized by severe epilepsy with refractory seizures and a significant developmental delay. Recently, DEE73 was linked to genetic alterations of the RNF13 gene, which convert positions 311 or 312 in the RNF13 protein from leucine to serine or proline, respectively (L311S and L312P). Using a fluorescence microscopy approach to investigate the molecular and cellular mechanisms affected by RNF13 protein variants, the current study shows that wild-type RNF13 localizes extensively with endosomes and lysosomes, while L311S and L312P do not extensively colocalize with the lysosomal marker Lamp1. Our results show that RNF13 L311S and L312P proteins affect the size of endosomal vesicles along with the temporal and spatial progression of fluorescently labeled epidermal growth factor, but not transferrin, in the endolysosomal system. Furthermore, GST-pulldown and co-immunoprecipitation show that RNF13 variants disrupt association with AP-3 complex. Knockdown of AP-3 complex subunit AP3D1 alters the lysosomal localization of wild-type RNF13 and similarly affects the size of endosomal vesicles. Importantly, our study provides a first step toward understanding the cellular and molecular mechanism altered by DEE73-associated genetic variations of RNF13.
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Affiliation(s)
- Valérie C. Cabana
- Département de Chimie, Université du Québec à Montréal, Montréal, QC H2X 2J6, Canada; (V.C.C.); (A.Y.B.); (A.M.S.); (K.G.); (L.C.)
- Centre d’Excellence en Recherche sur les Maladies Orphelines—Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada;
| | - Antoine Y. Bouchard
- Département de Chimie, Université du Québec à Montréal, Montréal, QC H2X 2J6, Canada; (V.C.C.); (A.Y.B.); (A.M.S.); (K.G.); (L.C.)
- Centre d’Excellence en Recherche sur les Maladies Orphelines—Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada;
| | - Audrey M. Sénécal
- Département de Chimie, Université du Québec à Montréal, Montréal, QC H2X 2J6, Canada; (V.C.C.); (A.Y.B.); (A.M.S.); (K.G.); (L.C.)
- Centre d’Excellence en Recherche sur les Maladies Orphelines—Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada;
| | - Kim Ghilarducci
- Département de Chimie, Université du Québec à Montréal, Montréal, QC H2X 2J6, Canada; (V.C.C.); (A.Y.B.); (A.M.S.); (K.G.); (L.C.)
- Centre d’Excellence en Recherche sur les Maladies Orphelines—Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada;
| | - Saïd Kourrich
- Centre d’Excellence en Recherche sur les Maladies Orphelines—Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada;
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC H2X 1Y4, Canada
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Laurent Cappadocia
- Département de Chimie, Université du Québec à Montréal, Montréal, QC H2X 2J6, Canada; (V.C.C.); (A.Y.B.); (A.M.S.); (K.G.); (L.C.)
- Centre d’Excellence en Recherche sur les Maladies Orphelines—Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada;
| | - Marc P. Lussier
- Département de Chimie, Université du Québec à Montréal, Montréal, QC H2X 2J6, Canada; (V.C.C.); (A.Y.B.); (A.M.S.); (K.G.); (L.C.)
- Centre d’Excellence en Recherche sur les Maladies Orphelines—Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada;
- Correspondence: ; Tel.: +1-(514)-987-3000 (ext. 5591); Fax: +1-(514)-987-4054
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The EMT activator ZEB1 accelerates endosomal trafficking to establish a polarity axis in lung adenocarcinoma cells. Nat Commun 2021; 12:6354. [PMID: 34732702 PMCID: PMC8566461 DOI: 10.1038/s41467-021-26677-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 09/20/2021] [Indexed: 12/15/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) is a transcriptionally governed process by which cancer cells establish a front-rear polarity axis that facilitates motility and invasion. Dynamic assembly of focal adhesions and other actin-based cytoskeletal structures on the leading edge of motile cells requires precise spatial and temporal control of protein trafficking. Yet, the way in which EMT-activating transcriptional programs interface with vesicular trafficking networks that effect cell polarity change remains unclear. Here, by utilizing multiple approaches to assess vesicular transport dynamics through endocytic recycling and retrograde trafficking pathways in lung adenocarcinoma cells at distinct positions on the EMT spectrum, we find that the EMT-activating transcription factor ZEB1 accelerates endocytosis and intracellular trafficking of plasma membrane-bound proteins. ZEB1 drives turnover of the MET receptor tyrosine kinase by hastening receptor endocytosis and transport to the lysosomal compartment for degradation. ZEB1 relieves a plus-end-directed microtubule-dependent kinesin motor protein (KIF13A) and a clathrin-associated adaptor protein complex subunit (AP1S2) from microRNA-dependent silencing, thereby accelerating cargo transport through the endocytic recycling and retrograde vesicular pathways, respectively. Depletion of KIF13A or AP1S2 mitigates ZEB1-dependent focal adhesion dynamics, front-rear axis polarization, and cancer cell motility. Thus, ZEB1-dependent transcriptional networks govern vesicular trafficking dynamics to effect cell polarity change. The way in which metastatic tumour cells control endocytic vesicular trafficking networks to establish a front-rear polarity axis that facilitates motility remains unclear. Here, the authors show that the EMT activator ZEB1 influences vesicular trafficking dynamics to execute cell polarity change.
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46
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Soleimani Zakeri NS, Pashazadeh S, MotieGhader H. Drug Repurposing for Alzheimer's Disease Based on Protein-Protein Interaction Network. BIOMED RESEARCH INTERNATIONAL 2021; 2021:1280237. [PMID: 34692825 PMCID: PMC8531773 DOI: 10.1155/2021/1280237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/06/2021] [Accepted: 09/19/2021] [Indexed: 12/15/2022]
Abstract
Alzheimer's disease (AD) is known as a critical neurodegenerative disorder. It worsens as symptoms concerning dementia grow severe over the years. Due to the globalization of Alzheimer's disease, its prevention and treatment are vital. This study proposes a method to extract substantial gene complexes and then introduces potential drugs in Alzheimer's disease. To this end, a protein-protein interaction (PPI) network was utilized to extract five meaningful gene complexes functionally interconnected. An enrichment analysis to introduce the most important biological processes and pathways was accomplished on the obtained genes. The next step is extracting the drugs related to AD and introducing some new drugs which may be helpful for this disease. Finally, a complete network including all the genes associated with each gene complex group and genes' target drug was illustrated. For validating the proposed potential drugs, Connectivity Map (CMAP) analysis was accomplished to determine target genes that are up- or downregulated by proposed drugs. Medical studies and publications were analyzed thoroughly to introduce AD-related drugs. This analysis proves the accuracy of the proposed method in this study. Then, new drugs were introduced that can be experimentally examined as future work. Raloxifene and gentian violet are two new drugs, which have not been introduced as AD-related drugs in previous scientific and medical studies, recommended by the method of this study. Besides the primary goal, five bipartite networks representing the genes of each group and their target miRNAs were constructed to introduce target miRNAs.
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Affiliation(s)
- Negar Sadat Soleimani Zakeri
- Department of Computer Engineering, Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran
| | - Saeid Pashazadeh
- Department of Information Technology, Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran
| | - Habib MotieGhader
- Department of Computer Engineering, Gowgan Educational Center, Tabriz Branch, Islamic Azad University, Tabriz, Iran
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47
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Le L, Sirés-Campos J, Raposo G, Delevoye C, Marks MS. Melanosome Biogenesis in the Pigmentation of Mammalian Skin. Integr Comp Biol 2021; 61:1517-1545. [PMID: 34021746 PMCID: PMC8516112 DOI: 10.1093/icb/icab078] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Melanins, the main pigments of the skin and hair in mammals, are synthesized within membrane-bound organelles of melanocytes called melanosomes. Melanosome structure and function are determined by a cohort of resident transmembrane proteins, many of which are expressed only in pigment cells and localize specifically to melanosomes. Defects in the genes that encode melanosome-specific proteins or components of the machinery required for their transport in and out of melanosomes underlie various forms of ocular or oculocutaneous albinism, characterized by hypopigmentation of the hair, skin, and eyes and by visual impairment. We review major components of melanosomes, including the enzymes that catalyze steps in melanin synthesis from tyrosine precursors, solute transporters that allow these enzymes to function, and structural proteins that underlie melanosome shape and melanin deposition. We then review the molecular mechanisms by which these components are biosynthetically delivered to newly forming melanosomes-many of which are shared by other cell types that generate cell type-specific lysosome-related organelles. We also highlight unanswered questions that need to be addressed by future investigation.
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Affiliation(s)
- Linh Le
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Julia Sirés-Campos
- Institut Curie, PSL Research University, CNRS, UMR 144, Structure and Membrane Compartments, Paris, 75005, France
| | - Graça Raposo
- Institut Curie, PSL Research University, CNRS, UMR 144, Structure and Membrane Compartments, Paris, 75005, France
| | - Cédric Delevoye
- Institut Curie, PSL Research University, CNRS, UMR 144, Structure and Membrane Compartments, Paris, 75005, France
| | - Michael S Marks
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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48
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Wan C, Crisman L, Wang B, Tian Y, Wang S, Yang R, Datta I, Nomura T, Li S, Yu H, Yin Q, Shen J. AAGAB is an assembly chaperone regulating AP1 and AP2 clathrin adaptors. J Cell Sci 2021; 134:272394. [PMID: 34494650 DOI: 10.1242/jcs.258587] [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: 03/01/2021] [Accepted: 08/31/2021] [Indexed: 11/20/2022] Open
Abstract
Multimeric cargo adaptors such as AP2 play central roles in intracellular membrane trafficking. We recently discovered that the assembly of the AP2 adaptor complex, a key player in clathrin-mediated endocytosis, is a highly organized process controlled by alpha- and gamma-adaptin-binding protein (AAGAB, also known as p34). In this study, we demonstrate that besides AP2, AAGAB also regulates the assembly of AP1, a cargo adaptor involved in clathrin-mediated transport between the trans-Golgi network and the endosome. However, AAGAB is not involved in the formation of other adaptor complexes, including AP3. AAGAB promotes AP1 assembly by binding and stabilizing the γ and σ subunits of AP1, and its mutation abolishes AP1 assembly and disrupts AP1-mediated cargo trafficking. Comparative proteomic analyses indicate that AAGAB mutation massively alters surface protein homeostasis, and its loss-of-function phenotypes reflect the synergistic effects of AP1 and AP2 deficiency. Taken together, these findings establish AAGAB as an assembly chaperone for both AP1 and AP2 adaptors and pave the way for understanding the pathogenesis of AAGAB-linked diseases.
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Affiliation(s)
- Chun Wan
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Lauren Crisman
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Bing Wang
- Department of Biological Sciences and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Yuan Tian
- Department of Biological Sciences and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Shifeng Wang
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Rui Yang
- Department of Biological Sciences and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Ishara Datta
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Toshifumi Nomura
- Department of Dermatology, University of Tsukuba, Tsukuba, 305-8575, Japan
| | - Suzhao Li
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Haijia Yu
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Qian Yin
- Department of Biological Sciences and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Jingshi Shen
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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49
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Moreno-Layseca P, Jäntti NZ, Godbole R, Sommer C, Jacquemet G, Al-Akhrass H, Conway JRW, Kronqvist P, Kallionpää RE, Oliveira-Ferrer L, Cervero P, Linder S, Aepfelbacher M, Zauber H, Rae J, Parton RG, Disanza A, Scita G, Mayor S, Selbach M, Veltel S, Ivaska J. Cargo-specific recruitment in clathrin- and dynamin-independent endocytosis. Nat Cell Biol 2021; 23:1073-1084. [PMID: 34616024 DOI: 10.1038/s41556-021-00767-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 09/01/2021] [Indexed: 12/12/2022]
Abstract
Spatially controlled, cargo-specific endocytosis is essential for development, tissue homeostasis and cancer invasion. Unlike cargo-specific clathrin-mediated endocytosis, the clathrin- and dynamin-independent endocytic pathway (CLIC-GEEC, CG pathway) is considered a bulk internalization route for the fluid phase, glycosylated membrane proteins and lipids. While the core molecular players of CG-endocytosis have been recently defined, evidence of cargo-specific adaptors or selective uptake of proteins for the pathway are lacking. Here we identify the actin-binding protein Swiprosin-1 (Swip1, EFHD2) as a cargo-specific adaptor for CG-endocytosis. Swip1 couples active Rab21-associated integrins with key components of the CG-endocytic machinery-Arf1, IRSp53 and actin-and is critical for integrin endocytosis. Through this function, Swip1 supports integrin-dependent cancer-cell migration and invasion, and is a negative prognostic marker in breast cancer. Our results demonstrate a previously unknown cargo selectivity for the CG pathway and a role for specific adaptors in recruitment into this endocytic route.
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Affiliation(s)
- Paulina Moreno-Layseca
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Niklas Z Jäntti
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Rashmi Godbole
- National Centre for Biological Science (TIFR), Bangalore, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India
| | - Christian Sommer
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Hussein Al-Akhrass
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - James R W Conway
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Pauliina Kronqvist
- Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - Roosa E Kallionpää
- Auria Biobank, Turku University Hospital and University of Turku, Turku, Finland
| | | | - Pasquale Cervero
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Stefan Linder
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | | | - Henrik Zauber
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - James Rae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.,Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Queensland, Australia
| | - Andrea Disanza
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare and University of Milan, Milan, Italy
| | - Giorgio Scita
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare and University of Milan, Milan, Italy
| | - Satyajit Mayor
- National Centre for Biological Science (TIFR), Bangalore, India
| | - Matthias Selbach
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Stefan Veltel
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany. .,Hochschule Bremen, City University of Applied Sciences, Bremen, Germany.
| | - Johanna Ivaska
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland. .,Department of Life Sciences, University of Turku, Turku, Finland. .,InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
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50
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Nahalka J. Theoretical Analysis of S, M and N Structural Proteins by the Protein-RNA Recognition Code Leads to Genes/proteins that Are Relevant to the SARS-CoV-2 Life Cycle and Pathogenesis. Front Genet 2021; 12:763995. [PMID: 34659373 PMCID: PMC8511677 DOI: 10.3389/fgene.2021.763995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 12/14/2022] Open
Abstract
In this conceptual review, based on the protein-RNA recognition code, some theoretical sequences were detected in the spike (S), membrane (M) and capsid (N) proteins that may post-transcriptionally regulate the host genes/proteins in immune homeostasis, pulmonary epithelial tissue homeostasis, and lipid homeostasis. According to the review of literature, the spectrum of identified genes/proteins shows that the virus promotes IL1α/β-IL1R1 signaling (type 1 immunity) and immunity defense against helminths and venoms (type 2 immunity). In the alteration of homeostasis in the pulmonary epithelial tissue, the virus blocks the function of cilia and the molecular programs that are involved in wound healing (EMT and MET). Additionally, the protein-RNA recognition method described here identifies compatible sequences in the S1A-domain for the post-transcriptional promotion of PIKFYVE, which is one of the critical factors for SARS-CoV-2 entry to the host cell, and for the post-transcriptional repression of xylulokinase XYLB. A decrease in XYLB product (Xu5P) in plasma was proposed as one of the potential metabolomics biomarkers of COVID-19. In summary, the protein-RNA recognition code leads to protein genes relevant to the SARS-CoV-2 life cycle and pathogenesis.
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Affiliation(s)
- Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
- Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
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