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Galbraith CG, English BP, Boehm U, Galbraith JA. Compartmentalized Cytoplasmic Flows Direct Protein Transport to the Cell's Leading Edge. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593794. [PMID: 38798549 PMCID: PMC11118383 DOI: 10.1101/2024.05.12.593794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Inside the cell, proteins essential for signaling, morphogenesis, and migration navigate complex pathways, typically via vesicular trafficking or microtubule-driven mechanisms 1-3 . However, the process by which soluble cytoskeletal monomers maneuver through the cytoplasm's ever-changing environment to reach their destinations without using these pathways remains unknown. 4-6 Here, we show that actin cytoskeletal treadmilling leads to the formation of a semi-permeable actin-myosin barrier, creating a specialized compartment separated from the rest of the cell body that directs proteins toward the cell edge by advection, diffusion facilitated by fluid flow. Contraction at this barrier generates a molecularly non-specific fluid flow that transports actin, actin-binding proteins, adhesion proteins, and even inert proteins forward. The local curvature of the barrier specifically targets these proteins toward protruding edges of the leading edge, sites of new filament growth, effectively coordinating protein distribution with cellular dynamics. Outside this compartment, diffusion remains the primary mode of protein transport, contrasting sharply with the directed advection within. This discovery reveals a novel protein transport mechanism that redefines the front of the cell as a pseudo-organelle, actively orchestrating protein mobilization for cellular front activities such as protrusion and adhesion. By elucidating a new model of protein dynamics at the cellular front, this work contributes a critical piece to the puzzle of how cells adapt their internal structures for targeted and rapid response to extracellular cues. The findings challenge the current understanding of intracellular transport, suggesting that cells possess highly specialized and previously unrecognized organizational strategies for managing protein distribution efficiently, providing a new framework for understanding the cellular architecture's role in rapid response and adaptation to environmental changes.
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2
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Benvenuto G, Leone S, Astoricchio E, Bormke S, Jasek S, D'Aniello E, Kittelmann M, McDonald K, Hartenstein V, Baena V, Escrivà H, Bertrand S, Schierwater B, Burkhardt P, Ruiz-Trillo I, Jékely G, Ullrich-Lüter J, Lüter C, D'Aniello S, Arnone MI, Ferraro F. Evolution of the ribbon-like organization of the Golgi apparatus in animal cells. Cell Rep 2024; 43:113791. [PMID: 38428420 DOI: 10.1016/j.celrep.2024.113791] [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: 05/11/2023] [Revised: 10/31/2023] [Accepted: 01/29/2024] [Indexed: 03/03/2024] Open
Abstract
The "ribbon," a structural arrangement in which Golgi stacks connect to each other, is considered to be restricted to vertebrate cells. Although ribbon disruption is linked to various human pathologies, its functional role in cellular processes remains unclear. In this study, we investigate the evolutionary origin of the Golgi ribbon. We observe a ribbon-like architecture in the cells of several metazoan taxa suggesting its early emergence in animal evolution predating the appearance of vertebrates. Supported by AlphaFold2 modeling, we propose that the evolution of Golgi reassembly and stacking protein (GRASP) binding by golgin tethers may have driven the joining of Golgi stacks resulting in the ribbon-like configuration. Additionally, we find that Golgi ribbon assembly is a shared developmental feature of deuterostomes, implying a role in embryogenesis. Overall, our study points to the functional significance of the Golgi ribbon beyond vertebrates and underscores the need for further investigations to unravel its elusive biological roles.
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Affiliation(s)
- Giovanna Benvenuto
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Serena Leone
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Emanuele Astoricchio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | | | - Sanja Jasek
- Living Systems Institute, University of Exeter, Exeter, UK; Heidelberg University, Centre for Organismal Studies (COS), Heidelberg, Germany
| | - Enrico D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Maike Kittelmann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Kent McDonald
- Electron Microscope Lab, University of California Berkeley, Berkeley, CA, USA
| | - Volker Hartenstein
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Valentina Baena
- Department of Cell Biology, UConn Health, Farmington, CT, USA
| | - Héctor Escrivà
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-Mer, France
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-Mer, France
| | - Bernd Schierwater
- Institute of Ecology and Evolution, Hannover University of Veterinary Medicine Foundation, Hannover, Germany
| | | | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, Barcelona, Spain; ICREA, Barcelona, Spain
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Exeter, UK; Heidelberg University, Centre for Organismal Studies (COS), Heidelberg, Germany
| | | | | | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Maria Ina Arnone
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Francesco Ferraro
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy.
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3
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Spruit CM, Sweet IR, Maliepaard JCL, Bestebroer T, Lexmond P, Qiu B, Damen MJA, Fouchier RAM, Reiding KR, Snijder J, Herfst S, Boons GJ, de Vries RP. Contemporary human H3N2 influenza A viruses require a low threshold of suitable glycan receptors for efficient infection. Glycobiology 2023; 33:784-800. [PMID: 37471650 PMCID: PMC10629718 DOI: 10.1093/glycob/cwad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/03/2023] [Accepted: 07/16/2023] [Indexed: 07/22/2023] Open
Abstract
Recent human H3N2 influenza A viruses have evolved to employ elongated glycans terminating in α2,6-linked sialic acid as their receptors. These glycans are displayed in low abundancies by (humanized) Madin-Darby Canine Kidney cells, which are commonly employed to propagate influenza A virus, resulting in low or no viral propagation. Here, we examined whether the overexpression of the glycosyltransferases β-1,3-N-acetylglucosaminyltransferase and β-1,4-galactosyltransferase 1, which are responsible for the elongation of poly-N-acetyllactosamines (LacNAcs), would result in improved A/H3N2 propagation. Stable overexpression of β-1,3-N-acetylglucosaminyltransferase and β-1,4-galactosyltransferase 1 in Madin-Darby Canine Kidney and "humanized" Madin-Darby Canine Kidney cells was achieved by lentiviral integration and subsequent antibiotic selection and confirmed by qPCR and protein mass spectrometry experiments. Flow cytometry and glycan mass spectrometry experiments using the β-1,3-N-acetylglucosaminyltransferase and/or β-1,4-galactosyltransferase 1 knock-in cells demonstrated increased binding of viral hemagglutinins and the presence of a larger number of LacNAc repeating units, especially on "humanized" Madin-Darby Canine Kidney-β-1,3-N-acetylglucosaminyltransferase cells. An increase in the number of glycan receptors did, however, not result in a greater infection efficiency of recent human H3N2 viruses. Based on these results, we propose that H3N2 influenza A viruses require a low number of suitable glycan receptors to infect cells and that an increase in the glycan receptor display above this threshold does not result in improved infection efficiency.
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Affiliation(s)
- Cindy M Spruit
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG Utrecht, The Netherlands
| | - Igor R Sweet
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG Utrecht, The Netherlands
| | - Joshua C L Maliepaard
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Theo Bestebroer
- Department of Viroscience, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Pascal Lexmond
- Department of Viroscience, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Boning Qiu
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG Utrecht, The Netherlands
| | - Mirjam J A Damen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Karli R Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Geert-Jan Boons
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG Utrecht, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
| | - Robert P de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG Utrecht, The Netherlands
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4
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Xu X, Lambert NA, Wu G. Sequence-directed concentration of G protein-coupled receptors in COPII vesicles. iScience 2023; 26:107969. [PMID: 37810244 PMCID: PMC10551652 DOI: 10.1016/j.isci.2023.107969] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/02/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest superfamily of plasma membrane signaling proteins. However, virtually nothing is known about their recruitment to COPII vesicles for forward delivery after synthesis in the endoplasmic reticulum (ER). Here, we demonstrate that some GPCRs are highly concentrated at ER exit sites (ERES) before COPII budding. Angiotensin II type 2 receptor (AT2R) and CXCR4 concentration are directed by a di-acidic motif and a 9-residue domain, respectively, and these motifs also control receptor ER-Golgi traffic. We further show that AT2R interacts with Sar1 GTPase and that distinct GPCRs have different ER-Golgi transport rates via COPII which is independent of their concentration at ERES. Collectively, these data demonstrate that GPCRs can be actively captured by COPII via specific motifs and direct interaction with COPII components that in turn affects their export dynamics, and provide important insights into COPII targeting and forward trafficking of nascent GPCRs.
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Affiliation(s)
- Xin Xu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Nevin A. Lambert
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Guangyu Wu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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5
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Gallo R, Rai AK, McIntyre ABR, Meyer K, Pelkmans L. DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites. Dev Cell 2023; 58:1880-1897.e11. [PMID: 37643612 DOI: 10.1016/j.devcel.2023.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/16/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
The dual-specificity kinase DYRK3 controls the formation and dissolution of multiple biomolecular condensates, regulating processes including stress recovery and mitotic progression. Here, we report that DYRK3 functionally interacts with proteins associated with endoplasmic reticulum (ER) exit sites (ERESs) and that inhibition of DYRK3 perturbs the organization of the ERES-Golgi interface and secretory trafficking. DYRK3-mediated regulation of ERES depends on the N-terminal intrinsically disordered region (IDR) of the peripheral membrane protein SEC16A, which co-phase separates with ERES components to form liquid-like condensates on the surface of the ER. By modulating the liquid-like properties of ERES, we show that their physical state is essential for functional cargo trafficking through the early secretory pathway. Our findings support a mechanism whereby phosphorylation by DYRK3 and its reversal by serine-threonine phosphatases regulate the material properties of ERES to create a favorable physicochemical environment for directional membrane traffic in eukaryotic cells.
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Affiliation(s)
- Raffaella Gallo
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Arpan Kumar Rai
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
| | - Alexa B R McIntyre
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Katrina Meyer
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
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6
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Cheatham AM, Sharma NR, Satpute-Krishnan P. Competition for calnexin binding regulates secretion and turnover of misfolded GPI-anchored proteins. J Cell Biol 2023; 222:e202108160. [PMID: 37702712 PMCID: PMC10499038 DOI: 10.1083/jcb.202108160] [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: 09/02/2021] [Revised: 03/19/2023] [Accepted: 08/10/2023] [Indexed: 09/14/2023] Open
Abstract
In mammalian cells, misfolded glycosylphosphatidylinositol (GPI)-anchored proteins (GPI-APs) are cleared out of the ER to the Golgi via a constitutive and a stress-inducible pathway called RESET. From the Golgi, misfolded GPI-APs transiently access the cell surface prior to rapid internalization for lysosomal degradation. What regulates the release of misfolded GPI-APs for RESET during steady-state conditions and how this release is accelerated during ER stress is unknown. Using mutants of prion protein or CD59 as model misfolded GPI-APs, we demonstrate that inducing calnexin degradation or upregulating calnexin-binding glycoprotein expression triggers the release of misfolded GPI-APs for RESET. Conversely, blocking protein synthesis dramatically inhibits the dissociation of misfolded GPI-APs from calnexin and subsequent turnover. We demonstrate an inverse correlation between newly synthesized calnexin substrates and RESET substrates that coimmunoprecipitate with calnexin. These findings implicate competition by newly synthesized substrates for association with calnexin as a key factor in regulating the release of misfolded GPI-APs from calnexin for turnover via the RESET pathway.
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Affiliation(s)
- Amber M. Cheatham
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Nishi Raj Sharma
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Prasanna Satpute-Krishnan
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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7
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Nakagawa N, Iwasato T. Golgi polarity shift instructs dendritic refinement in the neonatal cortex by mediating NMDA receptor signaling. Cell Rep 2023; 42:112843. [PMID: 37516101 DOI: 10.1016/j.celrep.2023.112843] [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: 03/07/2023] [Revised: 05/15/2023] [Accepted: 07/05/2023] [Indexed: 07/31/2023] Open
Abstract
Dendritic refinement is a critical component of activity-dependent neuronal circuit maturation, through which individual neurons establish specific connectivity with their target axons. Here, we demonstrate that the developmental shift of Golgi polarity is a key process in dendritic refinement. During neonatal development, the Golgi apparatus in layer 4 spiny stellate (SS) neurons in the mouse barrel cortex lose their original apical positioning and acquire laterally polarized distributions. This lateral Golgi polarity, which is oriented toward the barrel center, peaks on postnatal days 5-7 (P5-P7) and disappears by P15, which aligns with the developmental time course of SS neuron dendritic refinement. Genetic ablation of N-methyl-D-aspartate (NMDA) receptors, key players in dendritic refinement, disturbs the lateral Golgi polarity. Golgi polarity manipulation disrupts the asymmetric dendritic projection pattern and the primary-whisker-specific response of SS neurons. Our results elucidate activity-dependent Golgi dynamics and their critical role in developmental neuronal circuit refinement.
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Affiliation(s)
- Naoki Nakagawa
- Laboratory of Mammalian Neural Circuits, National Institute of Genetics (NIG), Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.
| | - Takuji Iwasato
- Laboratory of Mammalian Neural Circuits, National Institute of Genetics (NIG), Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.
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8
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Durrieu L, Bush A, Grande A, Johansson R, Janzén D, Katz A, Cedersund G, Colman-Lerner A. Characterization of cell-to-cell variation in nuclear transport rates and identification of its sources. iScience 2022; 26:105906. [PMID: 36686393 PMCID: PMC9852351 DOI: 10.1016/j.isci.2022.105906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/10/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022] Open
Abstract
Nuclear transport is an essential part of eukaryotic cell function. Here, we present scFRAP, a model-assisted fluorescent recovery after photobleaching (FRAP)- based method to determine nuclear import and export rates independently in individual live cells. To overcome the inherent noise of single-cell measurements, we performed sequential FRAPs on the same cell. We found large cell-to-cell variation in transport rates within isogenic yeast populations. For passive transport, the variability in NPC number might explain most of the variability. Using this approach, we studied mother-daughter cell asymmetry in the active nuclear shuttling of the transcription factor Ace2, which is specifically concentrated in daughter cell nuclei in early G1. Rather than reduced export in the daughter cell, as previously hypothesized, we found that this asymmetry is mainly due to an increased import in daughters. These results shed light on cell-to-cell variation in cellular dynamics and its sources.
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Affiliation(s)
- Lucía Durrieu
- Department of Physiology, Molecular and Cellular Biology, School of Exact and Natural Sciences, University of Buenos Aires (UBA), C1428EGA, Argentina,Institute of Physiology, Molecular Biology and Neurosciences, National Council of Scientific and Technical Research (IFIBYNE-UBA-CONICET), C1428EGA, Argentina
| | - Alan Bush
- Department of Physiology, Molecular and Cellular Biology, School of Exact and Natural Sciences, University of Buenos Aires (UBA), C1428EGA, Argentina,Institute of Physiology, Molecular Biology and Neurosciences, National Council of Scientific and Technical Research (IFIBYNE-UBA-CONICET), C1428EGA, Argentina,Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - Alicia Grande
- Department of Physiology, Molecular and Cellular Biology, School of Exact and Natural Sciences, University of Buenos Aires (UBA), C1428EGA, Argentina,Institute of Physiology, Molecular Biology and Neurosciences, National Council of Scientific and Technical Research (IFIBYNE-UBA-CONICET), C1428EGA, Argentina
| | - Rikard Johansson
- Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - David Janzén
- Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - Andrea Katz
- Department of Physiology, Molecular and Cellular Biology, School of Exact and Natural Sciences, University of Buenos Aires (UBA), C1428EGA, Argentina
| | - Gunnar Cedersund
- Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - Alejandro Colman-Lerner
- Department of Physiology, Molecular and Cellular Biology, School of Exact and Natural Sciences, University of Buenos Aires (UBA), C1428EGA, Argentina,Institute of Physiology, Molecular Biology and Neurosciences, National Council of Scientific and Technical Research (IFIBYNE-UBA-CONICET), C1428EGA, Argentina,Corresponding author
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9
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Arab M, Nayak SC, Vitali T, Lowe M. Immunofluorescence Microscopy of the Mammalian Golgi Apparatus. Methods Mol Biol 2022; 2557:101-111. [PMID: 36512212 DOI: 10.1007/978-1-0716-2639-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Immunofluorescence is a technique that uses antibodies and fluorophores to label structures inside cells. The cells are normally fixed and permeabilized, and then structures are labelled using primary antibodies directly conjugated to fluorophores, or, more commonly, first with an antibody against an antigen of interest followed by a secondary antibody conjugated to a fluorophore that binds to the primary antibody. Fluorescence can be visualized using widefield, confocal, or super-resolution microscopy. Here we focus on labelling of the Golgi apparatus and show that different fixation and permeabilization conditions can significantly affect labelling of Golgi proteins and describe how to optimize fluorescent detection of Golgi proteins.
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Affiliation(s)
- Maryam Arab
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sanjeev Chavan Nayak
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Teresa Vitali
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Martin Lowe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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10
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Fasano G, Muto V, Radio FC, Venditti M, Mosaddeghzadeh N, Coppola S, Paradisi G, Zara E, Bazgir F, Ziegler A, Chillemi G, Bertuccini L, Tinari A, Vetro A, Pantaleoni F, Pizzi S, Conti LA, Petrini S, Bruselles A, Prandi IG, Mancini C, Chandramouli B, Barth M, Bris C, Milani D, Selicorni A, Macchiaiolo M, Gonfiantini MV, Bartuli A, Mariani R, Curry CJ, Guerrini R, Slavotinek A, Iascone M, Dallapiccola B, Ahmadian MR, Lauri A, Tartaglia M. Dominant ARF3 variants disrupt Golgi integrity and cause a neurodevelopmental disorder recapitulated in zebrafish. Nat Commun 2022; 13:6841. [PMID: 36369169 PMCID: PMC9652361 DOI: 10.1038/s41467-022-34354-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
Vesicle biogenesis, trafficking and signaling via Endoplasmic reticulum-Golgi network support essential developmental processes and their disruption lead to neurodevelopmental disorders and neurodegeneration. We report that de novo missense variants in ARF3, encoding a small GTPase regulating Golgi dynamics, cause a developmental disease in humans impairing nervous system and skeletal formation. Microcephaly-associated ARF3 variants affect residues within the guanine nucleotide binding pocket and variably perturb protein stability and GTP/GDP binding. Functional analysis demonstrates variably disruptive consequences of ARF3 variants on Golgi morphology, vesicles assembly and trafficking. Disease modeling in zebrafish validates further the dominant behavior of the mutants and their differential impact on brain and body plan formation, recapitulating the variable disease expression. In-depth in vivo analyses traces back impaired neural precursors' proliferation and planar cell polarity-dependent cell movements as the earliest detectable effects. Our findings document a key role of ARF3 in Golgi function and demonstrate its pleiotropic impact on development.
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Affiliation(s)
- Giulia Fasano
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Valentina Muto
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Francesca Clementina Radio
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Martina Venditti
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Niloufar Mosaddeghzadeh
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Simona Coppola
- grid.416651.10000 0000 9120 6856National Center for Rare Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Graziamaria Paradisi
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy ,grid.12597.380000 0001 2298 9743Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Erika Zara
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy ,grid.7841.aDepartment of Biology and Biotechnology “Charles Darwin”, Università “Sapienza”, Rome, 00185 Italy
| | - Farhad Bazgir
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alban Ziegler
- grid.7252.20000 0001 2248 3363UFR Santé de l’Université d’Angers, INSERM U1083, CNRS UMR6015, MITOVASC, SFR ICAT, F-49000 Angers, France ,grid.411147.60000 0004 0472 0283Département de Génétique, CHU d’Angers, 49000 Angers, France
| | - Giovanni Chillemi
- grid.12597.380000 0001 2298 9743Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy ,grid.5326.20000 0001 1940 4177Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Centro Nazionale delle Ricerche, 70126 Bari, Italy
| | - Lucia Bertuccini
- grid.416651.10000 0000 9120 6856Servizio grandi strumentazioni e core facilities, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Antonella Tinari
- grid.416651.10000 0000 9120 6856Centro di riferimento per la medicina di genere, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Annalisa Vetro
- grid.8404.80000 0004 1757 2304Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50139 Florence, Italy
| | - Francesca Pantaleoni
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Simone Pizzi
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Libenzio Adrian Conti
- grid.414603.4Confocal Microscopy Core Facility, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Stefania Petrini
- grid.414603.4Confocal Microscopy Core Facility, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Alessandro Bruselles
- grid.416651.10000 0000 9120 6856Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Ingrid Guarnetti Prandi
- grid.12597.380000 0001 2298 9743Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Cecilia Mancini
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Balasubramanian Chandramouli
- grid.431603.30000 0004 1757 1950Super Computing Applications and Innovation, CINECA, 40033 Casalecchio di Reno, Italy
| | - Magalie Barth
- grid.411147.60000 0004 0472 0283Département de Génétique, CHU d’Angers, 49000 Angers, France
| | - Céline Bris
- grid.7252.20000 0001 2248 3363UFR Santé de l’Université d’Angers, INSERM U1083, CNRS UMR6015, MITOVASC, SFR ICAT, F-49000 Angers, France ,grid.411147.60000 0004 0472 0283Département de Génétique, CHU d’Angers, 49000 Angers, France
| | - Donatella Milani
- grid.414818.00000 0004 1757 8749Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Angelo Selicorni
- grid.512106.1Mariani Center for Fragile Children Pediatric Unit, Azienda Socio Sanitaria Territoriale Lariana, 22100 Como, Italy
| | - Marina Macchiaiolo
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Michaela V. Gonfiantini
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Andrea Bartuli
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Riccardo Mariani
- grid.414603.4Department of Laboratories Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Cynthia J. Curry
- grid.266102.10000 0001 2297 6811Genetic Medicine, Dept of Pediatrics, University of California San Francisco, Ca, Fresno, Ca, San Francisco, CA 94143 USA
| | - Renzo Guerrini
- grid.8404.80000 0004 1757 2304Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50139 Florence, Italy
| | - Anne Slavotinek
- grid.266102.10000 0001 2297 6811Genetic Medicine, Dept of Pediatrics, University of California San Francisco, Ca, Fresno, Ca, San Francisco, CA 94143 USA
| | - Maria Iascone
- grid.460094.f0000 0004 1757 8431Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Bruno Dallapiccola
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Mohammad Reza Ahmadian
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Antonella Lauri
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marco Tartaglia
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
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11
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Li RS, Wen C, Huang CZ, Li N. Functional molecules and nano-materials for the Golgi apparatus-targeted imaging and therapy. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Colanzi A, Parashuraman S, Reis CA, Ungar D. Editorial: Does the golgi complex enable oncogenesis? Front Cell Dev Biol 2022; 10:1000946. [PMID: 36111334 PMCID: PMC9468973 DOI: 10.3389/fcell.2022.1000946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Antonino Colanzi
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), Naples, Italy
- *Correspondence: Antonino Colanzi, ; Setharaman Parashuraman, ; Celso A. Reis, ; Daniel Ungar,
| | - Setharaman Parashuraman
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), Naples, Italy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, India
- *Correspondence: Antonino Colanzi, ; Setharaman Parashuraman, ; Celso A. Reis, ; Daniel Ungar,
| | - Celso A. Reis
- Institute for Research and Innovation in Health—i3S, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Institute of Biomedical Sciences of Abel Salazar, University of Porto, Porto, Portugal
- *Correspondence: Antonino Colanzi, ; Setharaman Parashuraman, ; Celso A. Reis, ; Daniel Ungar,
| | - Daniel Ungar
- Department of Biology, University of York, York, United Kingdom
- *Correspondence: Antonino Colanzi, ; Setharaman Parashuraman, ; Celso A. Reis, ; Daniel Ungar,
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13
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Parutto P, Heck J, Lu M, Kaminski C, Avezov E, Heine M, Holcman D. High-throughput super-resolution single-particle trajectory analysis reconstructs organelle dynamics and membrane reorganization. CELL REPORTS METHODS 2022; 2:100277. [PMID: 36046627 PMCID: PMC9421586 DOI: 10.1016/j.crmeth.2022.100277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/11/2022] [Accepted: 07/25/2022] [Indexed: 11/03/2022]
Abstract
Super-resolution imaging can generate thousands of single-particle trajectories. These data can potentially reconstruct subcellular organization and dynamics, as well as measure disease-linked changes. However, computational methods that can derive quantitative information from such massive datasets are currently lacking. We present data analysis and algorithms that are broadly applicable to reveal local binding and trafficking interactions and organization of dynamic subcellular sites. We applied this analysis to the endoplasmic reticulum and neuronal membrane. The method is based on spatiotemporal segmentation that explores data at multiple levels and detects the architecture and boundaries of high-density regions in areas measuring hundreds of nanometers. By connecting dense regions, we reconstructed the network topology of the endoplasmic reticulum (ER), as well as molecular flow redistribution and the local space explored by trajectories. The presented methods are available as an ImageJ plugin that can be applied to large datasets of overlapping trajectories offering a standard of single-particle trajectory (SPT) metrics.
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Affiliation(s)
- Pierre Parutto
- Group of Data Modeling and Computational Biology, IBENS, Ecole Normale Supérieure, 75005 Paris, France
| | - Jennifer Heck
- Research Group Functional Neurobiology at the Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Meng Lu
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Clemens Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Edward Avezov
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, UK
| | - Martin Heine
- Research Group Functional Neurobiology at the Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - David Holcman
- Group of Data Modeling and Computational Biology, IBENS, Ecole Normale Supérieure, 75005 Paris, France
- DAMPT, University of Cambridge, DAMPT and Churchill College, Cambridge CB30DS, UK
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14
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Sarkar P, Chattopadhyay A. Statin-induced Increase in Actin Polymerization Modulates GPCR Dynamics and Compartmentalization. Biophys J 2022:S0006-3495(22)00708-1. [DOI: 10.1016/j.bpj.2022.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/16/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022] Open
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15
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Ayala I, Colanzi A. Structural Organization and Function of the Golgi Ribbon During Cell Division. Front Cell Dev Biol 2022; 10:925228. [PMID: 35813197 PMCID: PMC9263219 DOI: 10.3389/fcell.2022.925228] [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: 04/21/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022] Open
Abstract
The Golgi complex has a central role in the secretory traffic. In vertebrate cells it is generally organized in polarized stacks of cisternae that are laterally connected by membranous tubules, forming a structure known as Golgi ribbon. The steady state ribbon arrangement results from a dynamic equilibrium between formation and cleavage of the membrane tubules connecting the stacks. This balance is of great physiological relevance as the unlinking of the ribbon during G2 is required for mitotic entry. A block of this process induces a potent G2 arrest of the cell cycle, indicating that a mitotic “Golgi checkpoint” controls the correct pre-mitotic segregation of the Golgi ribbon. Then, after mitosis onset, the Golgi stacks undergo an extensive disassembly, which is necessary for proper spindle formation. Notably, several Golgi-associated proteins acquire new roles in spindle formation and mitotic progression during mitosis. Here we summarize the current knowledge about the basic principle of the Golgi architecture and its functional relationship with cell division to highlight crucial aspects that need to be addressed to help us understand the physiological significance of the ribbon and the pathological implications of alterations of this organization.
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16
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Page KM, McCormack JJ, Lopes-da-Silva M, Patella F, Harrison-Lavoie K, Burden JJ, Quah YYB, Scaglioni D, Ferraro F, Cutler DF. Structure modeling hints at a granular organization of the Golgi ribbon. BMC Biol 2022; 20:111. [PMID: 35549945 PMCID: PMC9102599 DOI: 10.1186/s12915-022-01305-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 04/21/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND In vertebrate cells, the Golgi functional subunits, mini-stacks, are linked into a tri-dimensional network. How this "ribbon" architecture relates to Golgi functions remains unclear. Are all connections between mini-stacks equal? Is the local structure of the ribbon of functional importance? These are difficult questions to address, without a quantifiable readout of the output of ribbon-embedded mini-stacks. Endothelial cells produce secretory granules, the Weibel-Palade bodies (WPB), whose von Willebrand Factor (VWF) cargo is central to hemostasis. The Golgi apparatus controls WPB size at both mini-stack and ribbon levels. Mini-stack dimensions delimit the size of VWF "boluses" whilst the ribbon architecture allows their linear co-packaging, thereby generating WPBs of different lengths. This Golgi/WPB size relationship suits mathematical analysis. RESULTS WPB lengths were quantized as multiples of the bolus size and mathematical modeling simulated the effects of different Golgi ribbon organizations on WPB size, to be compared with the ground truth of experimental data. An initial simple model, with the Golgi as a single long ribbon composed of linearly interlinked mini-stacks, was refined to a collection of mini-ribbons and then to a mixture of mini-stack dimers plus long ribbon segments. Complementing these models with cell culture experiments led to novel findings. Firstly, one-bolus sized WPBs are secreted faster than larger secretory granules. Secondly, microtubule depolymerization unlinks the Golgi into equal proportions of mini-stack monomers and dimers. Kinetics of binding/unbinding of mini-stack monomers underpinning the presence of stable dimers was then simulated. Assuming that stable mini-stack dimers and monomers persist within the ribbon resulted in a final model that predicts a "breathing" arrangement of the Golgi, where monomer and dimer mini-stacks within longer structures undergo continuous linking/unlinking, consistent with experimentally observed WPB size distributions. CONCLUSIONS Hypothetical Golgi organizations were validated against a quantifiable secretory output. The best-fitting Golgi model, accounting for stable mini-stack dimers, is consistent with a highly dynamic ribbon structure, capable of rapid rearrangement. Our modeling exercise therefore predicts that at the fine-grained level the Golgi ribbon is more complex than generally thought. Future experiments will confirm whether such a ribbon organization is endothelial-specific or a general feature of vertebrate cells.
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Affiliation(s)
- Karen M. Page
- grid.83440.3b0000000121901201Department of Mathematics, University College London, Gower Street, London, WC1E 6BT UK
| | - Jessica J. McCormack
- grid.83440.3b0000000121901201MRC Laboratory for Molecular cell Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Mafalda Lopes-da-Silva
- grid.83440.3b0000000121901201MRC Laboratory for Molecular cell Biology, University College London, Gower Street, London, WC1E 6BT UK ,grid.10772.330000000121511713Current address: iNOVA4Health, CEDOC-Chronic Diseases Research Center, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal
| | - Francesca Patella
- grid.83440.3b0000000121901201MRC Laboratory for Molecular cell Biology, University College London, Gower Street, London, WC1E 6BT UK ,Current address: Kinomica, Alderley Park, Alderley Edge, Macclesfield, SK10 4TG UK
| | - Kimberly Harrison-Lavoie
- grid.83440.3b0000000121901201MRC Laboratory for Molecular cell Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Jemima J. Burden
- grid.83440.3b0000000121901201MRC Laboratory for Molecular cell Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Ying-Yi Bernadette Quah
- grid.83440.3b0000000121901201MRC Laboratory for Molecular cell Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Dominic Scaglioni
- grid.83440.3b0000000121901201MRC Laboratory for Molecular cell Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Francesco Ferraro
- Department of Biology and Evolution of Marine Organisms, BEOM, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Daniel F. Cutler
- grid.83440.3b0000000121901201MRC Laboratory for Molecular cell Biology, University College London, Gower Street, London, WC1E 6BT UK
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17
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Seiler DK, Hay JC. Genetically encoded fluorescent tools: Shining a little light on ER-to-Golgi transport. Free Radic Biol Med 2022; 183:14-24. [PMID: 35272000 PMCID: PMC9097910 DOI: 10.1016/j.freeradbiomed.2022.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 12/11/2022]
Abstract
Since the first fluorescent proteins (FPs) were identified and isolated over fifty years ago, FPs have become commonplace yet indispensable tools for studying the constitutive secretory pathway in live cells. At the same time, genetically encoded chemical tags have provided a new use for much older fluorescent dyes. Innovation has also produced several specialized methods to allow synchronous release of cargo proteins from the endoplasmic reticulum (ER), enabling precise characterization of sequential trafficking steps in the secretory pathway. Without the constant innovation of the researchers who design these tools to control, image, and quantitate protein secretion, major discoveries about ER-to-Golgi transport and later stages of the constitutive secretory pathway would not have been possible. We review many of the tools and tricks, some 25 years old and others brand new, that have been successfully implemented to study ER-to-Golgi transport in intact and living cells.
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Affiliation(s)
- Danette Kowal Seiler
- Division of Biological Sciences, Center for Structural & Functional Neuroscience, University of Montana, Missoula, MT, 59812, USA
| | - Jesse C Hay
- Division of Biological Sciences, Center for Structural & Functional Neuroscience, University of Montana, Missoula, MT, 59812, USA.
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18
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Kakanj P, Bhide S, Moussian B, Leptin M. Autophagy-mediated plasma membrane removal promotes the formation of epithelial syncytia. EMBO J 2022; 41:e109992. [PMID: 35262206 PMCID: PMC9194749 DOI: 10.15252/embj.2021109992] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 01/18/2023] Open
Abstract
Epithelial wound healing in Drosophila involves the formation of multinucleate cells surrounding the wound. We show that autophagy, a cellular degradation process often deployed in stress responses, is required for the formation of a multinucleated syncytium during wound healing, and that autophagosomes that appear near the wound edge acquire plasma membrane markers. In addition, uncontrolled autophagy in the unwounded epidermis leads to the degradation of endo‐membranes and the lateral plasma membrane, while apical and basal membranes and epithelial barrier function remain intact. Proper functioning of TORC1 is needed to prevent destruction of the larval epidermis by autophagy, in a process that depends on phagophore initiation and expansion but does not require autophagosomes fusion with lysosomes. Autophagy induction can also affect other sub‐cellular membranes, as shown by its suppression of experimentally induced laminopathy‐like nuclear defects. Our findings reveal a function for TORC1‐mediated regulation of autophagy in maintaining membrane integrity and homeostasis in the epidermis and during wound healing.
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Affiliation(s)
- Parisa Kakanj
- Institute for Genetics, University of Cologne, Cologne, Germany.,Director's Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Sourabh Bhide
- Director's Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD degree between EMBL and Heidelberg University, Heidelberg, Germany
| | | | - Maria Leptin
- Institute for Genetics, University of Cologne, Cologne, Germany.,Director's Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
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19
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Devireddy S, Ferguson SM. Efficient progranulin exit from the ER requires its interaction with prosaposin, a Surf4 cargo. J Cell Biol 2022; 221:212919. [PMID: 34919127 PMCID: PMC8689666 DOI: 10.1083/jcb.202104044] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/11/2021] [Accepted: 11/15/2021] [Indexed: 11/22/2022] Open
Abstract
Progranulin is a lysosomal protein whose haploinsufficiency causes frontotemporal dementia, while homozygous loss of progranulin causes neuronal ceroid lipofuscinosis, a lysosomal storage disease. The sensitivity of cells to progranulin deficiency raises important questions about how cells coordinate intracellular trafficking of progranulin to ensure its efficient delivery to lysosomes. In this study, we discover that progranulin interactions with prosaposin, another lysosomal protein, first occur within the lumen of the endoplasmic reticulum (ER) and are required for the efficient ER exit of progranulin. Mechanistically, we identify an interaction between prosaposin and Surf4, a receptor that promotes loading of lumenal cargos into COPII-coated vesicles, and establish that Surf4 is critical for the efficient export of progranulin and prosaposin from the ER. Collectively, this work demonstrates that a network of interactions occurring early in the secretory pathway promote the ER exit and subsequent lysosomal delivery of newly translated progranulin and prosaposin.
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Affiliation(s)
- Swathi Devireddy
- Departments of Cell Biology and Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT
| | - Shawn M Ferguson
- Departments of Cell Biology and Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT
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20
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Yamazaki Y, Eura Y, Kokame K. V-ATPase V0a1 promotes Weibel-Palade body biogenesis through the regulation of membrane fission. eLife 2021; 10:71526. [PMID: 34904569 PMCID: PMC8718113 DOI: 10.7554/elife.71526] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/13/2021] [Indexed: 01/09/2023] Open
Abstract
Membrane fission, the division of a membrane-bound structure into two discrete compartments, is essential for diverse cellular events, such as endocytosis and vesicle/granule biogenesis; however, the process remains unclear. The hemostatic protein von Willebrand factor is produced in vascular endothelial cells and packaged into specialized secretory granules, Weibel–Palade bodies (WPBs) at the trans-Golgi network (TGN). Here, we reported that V0a1, a V-ATPase component, is required for the membrane fission of WPBs. We identified two V0a isoforms in distinct populations of WPBs in cultured endothelial cells, V0a1 and V0a2, on mature and nascent WPBs, respectively. Although WPB buds were formed, WPBs could not separate from the TGN in the absence of V0a1. Screening using dominant–negative forms of known membrane fission regulators revealed protein kinase D (PKD) as an essential factor in biogenesis of WPBs. Further, we showed that the induction of wild-type PKDs in V0a1-depleted cells does not support the segregation of WPBs from the TGN; suggesting a primary role of V0a1 in the membrane fission of WPBs. The identification of V0a1 as a new membrane fission regulator should facilitate the understanding of molecular events that enable membrane fission.
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Affiliation(s)
- Yasuo Yamazaki
- Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Yuka Eura
- Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Koichi Kokame
- Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center, Osaka, Japan
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21
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De Niz M, Caldelari R, Kaiser G, Zuber B, Heo WD, Heussler VT, Agop-Nersesian C. Hijacking of the host cell Golgi by Plasmodium berghei liver stage parasites. J Cell Sci 2021; 134:jcs252213. [PMID: 34013963 PMCID: PMC8186485 DOI: 10.1242/jcs.252213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 04/12/2021] [Indexed: 12/28/2022] Open
Abstract
The intracellular lifestyle represents a challenge for the rapidly proliferating liver stage Plasmodium parasite. In order to scavenge host resources, Plasmodium has evolved the ability to target and manipulate host cell organelles. Using dynamic fluorescence-based imaging, we here show an interplay between the pre-erythrocytic stages of Plasmodium berghei and the host cell Golgi during liver stage development. Liver stage schizonts fragment the host cell Golgi into miniaturized stacks, which increases surface interactions with the parasitophorous vacuolar membrane of the parasite. Expression of specific dominant-negative Arf1 and Rab GTPases, which interfere with the host cell Golgi-linked vesicular machinery, results in developmental delay and diminished survival of liver stage parasites. Moreover, functional Rab11a is critical for the ability of the parasites to induce Golgi fragmentation. Altogether, we demonstrate that the structural integrity of the host cell Golgi and Golgi-associated vesicular traffic is important for optimal pre-erythrocytic development of P. berghei. The parasite hijacks the Golgi structure of the hepatocyte to optimize its own intracellular development. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Mariana De Niz
- Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland
| | - Reto Caldelari
- Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland
| | - Gesine Kaiser
- Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland
| | - Benoit Zuber
- Institute for Anatomy, University of Bern, CH-3012 Bern, Switzerland
| | - Won Do Heo
- Dept. of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Volker T. Heussler
- Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland
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22
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Weigel AV, Chang CL, Shtengel G, Xu CS, Hoffman DP, Freeman M, Iyer N, Aaron J, Khuon S, Bogovic J, Qiu W, Hess HF, Lippincott-Schwartz J. ER-to-Golgi protein delivery through an interwoven, tubular network extending from ER. Cell 2021; 184:2412-2429.e16. [PMID: 33852913 DOI: 10.1016/j.cell.2021.03.035] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 12/23/2020] [Accepted: 03/16/2021] [Indexed: 12/15/2022]
Abstract
Cellular versatility depends on accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by approximately 30% of all proteins), the physical nature of the vessel conducting the first portage (endoplasmic reticulum [ER] to Golgi apparatus) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to the ER by a thin neck. COPII localizes to this neck region and dynamically regulates cargo entry from the ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.
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Affiliation(s)
- Aubrey V Weigel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Chi-Lun Chang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Gleb Shtengel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | | | - Melanie Freeman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Advanced Bioimaging Center, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nirmala Iyer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jesse Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Satya Khuon
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - John Bogovic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Wei Qiu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
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23
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Han D, Goudeau B, Manojlovic D, Jiang D, Fang D, Sojic N. Electrochemiluminescence Loss in Photobleaching. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Dongni Han
- University of Bordeaux Bordeaux INP ISM, UMR CNRS 5255 33607 Pessac France
- School of Pharmacy and Key Laboratory of Targeted Intervention of Cardiovascular Disease Collaborative Innovation Center for Cardiovascular Disease Translational Medicine Nanjing Medical University Nanjing Jiangsu 211126 China
| | - Bertrand Goudeau
- University of Bordeaux Bordeaux INP ISM, UMR CNRS 5255 33607 Pessac France
| | - Dragan Manojlovic
- Department of Chemistry South Ural State University Chelyabinsk 454080 Russian Federation
| | - Dechen Jiang
- State Key Laboratory of Analytical Chemistry for Life and School of Chemistry and Chemical Engineering Nanjing University Nanjing Jiangsu 210093 China
| | - Danjun Fang
- School of Pharmacy and Key Laboratory of Targeted Intervention of Cardiovascular Disease Collaborative Innovation Center for Cardiovascular Disease Translational Medicine Nanjing Medical University Nanjing Jiangsu 211126 China
| | - Neso Sojic
- University of Bordeaux Bordeaux INP ISM, UMR CNRS 5255 33607 Pessac France
- Department of Chemistry South Ural State University Chelyabinsk 454080 Russian Federation
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24
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Han D, Goudeau B, Manojlovic D, Jiang D, Fang D, Sojic N. Electrochemiluminescence Loss in Photobleaching. Angew Chem Int Ed Engl 2021; 60:7686-7690. [PMID: 33410245 DOI: 10.1002/anie.202015030] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/04/2020] [Indexed: 12/11/2022]
Abstract
The effects of photobleaching on electrochemiluminescence (ECL) was investigated for the first time. The plasma membrane of Chinese Hamster Ovary (CHO) cells was labeled with a [Ru(bpy)3 ]2+ derivative. Selected regions of the fixed cells were photobleached using the confocal mode with sequential stepwise illumination or cumulatively and they were imaged by both ECL and photoluminescence (PL). ECL was generated with a model sacrificial coreactant, tri-n-propylamine. ECL microscopy of the photobleached regions shows lower ECL emission. We demonstrate a linear correlation between the ECL decrease and the PL loss due to the photobleaching of the labels immobilized on the CHO membranes. The presented strategy provides valuable information on the fundamentals of the ECL excited state and opens new opportunities for exploring cellular membranes by combining ECL microscopy with photobleaching techniques such as fluorescence recovery after photobleaching (FRAP) or fluorescence loss in photobleaching (FLIP) methods.
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Affiliation(s)
- Dongni Han
- University of Bordeaux, Bordeaux INP, ISM, UMR CNRS 5255, 33607, Pessac, France.,School of Pharmacy and Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211126, China
| | - Bertrand Goudeau
- University of Bordeaux, Bordeaux INP, ISM, UMR CNRS 5255, 33607, Pessac, France
| | - Dragan Manojlovic
- Department of Chemistry, South Ural State University, Chelyabinsk, 454080, Russian Federation
| | - Dechen Jiang
- State Key Laboratory of Analytical Chemistry for Life and School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Danjun Fang
- School of Pharmacy and Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211126, China
| | - Neso Sojic
- University of Bordeaux, Bordeaux INP, ISM, UMR CNRS 5255, 33607, Pessac, France.,Department of Chemistry, South Ural State University, Chelyabinsk, 454080, Russian Federation
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25
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Fujii S, Kurokawa K, Tago T, Inaba R, Takiguchi A, Nakano A, Satoh T, Satoh AK. Sec71 separates Golgi stacks in Drosophila S2 cells. J Cell Sci 2020; 133:jcs245571. [PMID: 33262309 PMCID: PMC10668125 DOI: 10.1242/jcs.245571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/18/2020] [Indexed: 01/19/2023] Open
Abstract
Golgi stacks are the basic structural units of the Golgi. Golgi stacks are separated from each other and scattered in the cytoplasm of Drosophila cells. Here, we report that the ARF-GEF inhibitor Brefeldin A (BFA) induces the formation of BFA bodies, which are aggregates of Golgi stacks, trans-Golgi networks and recycling endosomes. Recycling endosomes are located in the centers of BFA bodies, while Golgi stacks surround them on their trans sides. Live imaging of S2 cells revealed that Golgi stacks repeatedly merged and separated on their trans sides, and BFA caused successive merger by inhibiting separation, forming BFA bodies. S2 cells carrying genome-edited BFA-resistant mutant Sec71M717L did not form BFA bodies at high concentrations of BFA; S2 cells carrying genome-edited BFA-hypersensitive mutant Sec71F713Y produced BFA bodies at low concentrations of BFA. These results indicate that Sec71 is the sole BFA target for BFA body formation and controls Golgi stack separation. Finally, we showed that impairment of Sec71 in fly photoreceptors induces BFA body formation, with accumulation of both apical and basolateral cargoes, resulting in inhibition of polarized transport.
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Affiliation(s)
- Syara Fujii
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Kazuo Kurokawa
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tatsuya Tago
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Ryota Inaba
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Arata Takiguchi
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Akihiko Nakano
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takunori Satoh
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Akiko K Satoh
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
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26
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Lippincott-Schwartz J. The evolution of a cell biologist. Mol Biol Cell 2020; 31:2763-2767. [PMID: 33253077 PMCID: PMC7851866 DOI: 10.1091/mbc.e20-09-0603] [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] [Indexed: 11/11/2022] Open
Abstract
I am honored and humbled to receive the E. B. Wilson Medal and happy to share some reflections on my journey as a cell biologist. It took me a while to realize that my interest in biology would center on how cells are spatially and dynamically organized. From an initial fascination with cellular structures I came to appreciate that cells exhibit dynamism across all scales-from their molecules, to molecular complexes, to organelles. Uncovering the principles of this dynamism, including new ways to observe and quantify it, has been the guiding star of my work.
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27
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Michels L, Gorelova V, Harnvanichvech Y, Borst JW, Albada B, Weijers D, Sprakel J. Complete microviscosity maps of living plant cells and tissues with a toolbox of targeting mechanoprobes. Proc Natl Acad Sci U S A 2020; 117:18110-18118. [PMID: 32669427 PMCID: PMC7395454 DOI: 10.1073/pnas.1921374117] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mechanical patterns control a variety of biological processes in plants. The microviscosity of cellular structures effects the diffusion rate of molecules and organelles, thereby affecting processes such as metabolism and signaling. Spatial variations in local viscosity are also generated during fundamental events in the cell life cycle. While crucial to a complete understanding of plant mechanobiology, resolving subcellular microviscosity patterns in plants has remained an unsolved challenge. We present an imaging microviscosimetry toolbox of molecular rotors that yield complete microviscosity maps of cells and tissues, specifically targeting the cytosol, vacuole, plasma membrane, and wall of plant cells. These boron-dipyrromethene (BODIPY)-based molecular rotors are rigidochromic by means of coupling the rate of an intramolecular rotation, which depends on the mechanics of their direct surroundings, with their fluorescence lifetime. This enables the optical mapping of fluidity and porosity patterns in targeted cellular compartments. We show how apparent viscosity relates to cell function in the root, how the growth of cellular protrusions induces local tension, and how the cell wall is adapted to perform actuation surrounding leaf pores. These results pave the way to the noninvasive micromechanical mapping of complex tissues.
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Affiliation(s)
- Lucile Michels
- Physical Chemistry and Soft Matter, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Vera Gorelova
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Yosapol Harnvanichvech
- Physical Chemistry and Soft Matter, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Jan Willem Borst
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands;
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University & Research, 6708 WE Wageningen, The Netherlands;
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28
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Salvador Moreno N, Liu J, Haas KM, Parker LL, Chakraborty C, Kron SJ, Hodges K, Miller LD, Langefeld C, Robinson PJ, Lelièvre SA, Vidi PA. The nuclear structural protein NuMA is a negative regulator of 53BP1 in DNA double-strand break repair. Nucleic Acids Res 2019; 47:2703-2715. [PMID: 30812030 PMCID: PMC6451129 DOI: 10.1093/nar/gkz138] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/09/2019] [Accepted: 02/18/2019] [Indexed: 01/13/2023] Open
Abstract
P53-binding protein 1 (53BP1) mediates DNA repair pathway choice and promotes checkpoint activation. Chromatin marks induced by DNA double-strand breaks and recognized by 53BP1 enable focal accumulation of this multifunctional repair factor at damaged chromatin. Here, we unveil an additional level of regulation of 53BP1 outside repair foci. 53BP1 movements are constrained throughout the nucleoplasm and increase in response to DNA damage. 53BP1 interacts with the structural protein NuMA, which controls 53BP1 diffusion. This interaction, and colocalization between the two proteins in vitro and in breast tissues, is reduced after DNA damage. In cell lines and breast carcinoma NuMA prevents 53BP1 accumulation at DNA breaks, and high NuMA expression predicts better patient outcomes. Manipulating NuMA expression alters PARP inhibitor sensitivity of BRCA1-null cells, end-joining activity, and immunoglobulin class switching that rely on 53BP1. We propose a mechanism involving the sequestration of 53BP1 by NuMA in the absence of DNA damage. Such a mechanism may have evolved to disable repair functions and may be a decisive factor for tumor responses to genotoxic treatments.
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Affiliation(s)
- Naike Salvador Moreno
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Jing Liu
- Department of Physics, Indiana university-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Karen M Haas
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Laurie L Parker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Chaitali Chakraborty
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Stephen J Kron
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Kurt Hodges
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH 45219, USA
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.,Comprehensive Cancer Center of Wake Forest University
| | - Carl Langefeld
- Comprehensive Cancer Center of Wake Forest University.,Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Paul J Robinson
- Department of Basic Medical Sciences and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Sophie A Lelièvre
- Department of Basic Medical Sciences and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Pierre-Alexandre Vidi
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.,Comprehensive Cancer Center of Wake Forest University
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29
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Yu Y, Li M, Yu Y. Tracking Single Molecules in Biomembranes: Is Seeing Always Believing? ACS NANO 2019; 13:10860-10868. [PMID: 31589406 PMCID: PMC7179047 DOI: 10.1021/acsnano.9b07445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The spatial organization of molecules in cell membranes and their dynamic interactions play a central role in regulating cell functions. Single-particle tracking (SPT), a technique in which single molecules are imaged and tracked in real time, has led to breakthrough discoveries regarding these spatiotemporal complexities of cell membranes. There are, however, emerging concerns about factors that might produce misleading interpretations of SPT results. Here, we briefly review the application of SPT to understanding the nanoscale heterogeneities of plasma membranes, with a focus on the unique challenges, pitfalls, and limitations that confront the use of nanoparticles as imaging probes for tracking the dynamics of single molecules in cell membranes.
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30
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IL-2 receptors preassemble and signal in the ER/Golgi causing resistance to antiproliferative anti-IL-2Rα therapies. Proc Natl Acad Sci U S A 2019; 116:21120-21130. [PMID: 31570576 DOI: 10.1073/pnas.1901382116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Interleukin-2 (IL-2) and IL-15 play pivotal roles in T cell activation, apoptosis, and survival, and are implicated in leukemias and autoimmune diseases. Their heterotrimeric receptors share their β- and γc-chains, but have distinct α-chains. Anti-IL-2Rα (daclizumab) therapy targeting cell surface-expressed receptor subunits to inhibit T cell proliferation has only brought limited success in adult T cell leukemia/lymphoma (ATL) and in multiple sclerosis. We asked whether IL-2R subunits could already preassemble and signal efficiently in the endoplasmic reticulum (ER) and the Golgi. A combination of daclizumab and anti-IL-2 efficiently blocked IL-2-induced proliferation of IL-2-dependent wild-type (WT) ATL cells but not cells transfected with IL-2, suggesting that in IL-2-producing cells signaling may already take place before receptors reach the cell surface. In the Golgi fraction isolated from IL-2-producing ATL cells, we detected by Western blot phosphorylated Jak1, Jak3, and a phosphotyrosine signal attributed to the γc-chain, which occurred at much lower levels in the Golgi of WT ATL cells. We expressed EGFP- and mCherry-tagged receptor chains in HeLa cells to study their assembly along the secretory pathway. Confocal microscopy, Förster resonance energy transfer, and imaging fluorescence cross-correlation spectroscopy analysis revealed partial colocalization and molecular association of IL-2 (and IL-15) receptor chains in the ER/Golgi, which became more complete in the plasma membrane, further confirming our hypothesis. Our results define a paradigm of intracellular autocrine signaling and may explain resistance to antagonistic antibody therapies targeting receptors at the cell surface.
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31
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Jaiswal A, Hoerth CH, Zúñiga Pereira AM, Lorenz H. Improved spatial resolution by induced live cell and organelle swelling in hypotonic solutions. Sci Rep 2019; 9:12911. [PMID: 31501484 PMCID: PMC6733880 DOI: 10.1038/s41598-019-49408-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/23/2019] [Indexed: 12/21/2022] Open
Abstract
Induced morphology changes of cells and organelles are by far the easiest way to determine precise protein sub-locations and organelle quantities in light microscopy. By using hypotonic solutions to swell mammalian cell organelles we demonstrate that precise membrane, lumen or matrix protein locations within the endoplasmic reticulum, Golgi and mitochondria can reliably be established. We also show the benefit of this approach for organelle quantifications, especially for clumped or intertwined organelles like peroxisomes and mitochondria. Since cell and organelle swelling is reversible, it can be applied to live cells for successive high-resolution analyses. Our approach outperforms many existing imaging modalities with respect to resolution, ease-of-use and cost-effectiveness without excluding any co-utilization with existing optical (super)resolution techniques.
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Affiliation(s)
- Astha Jaiswal
- Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany
| | - Christian H Hoerth
- Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany
| | - Ana M Zúñiga Pereira
- Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany.,Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Holger Lorenz
- Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany.
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32
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Kwok ML, Chan KM. Functional characterization of copper transporters zCtr1, zAtox1, zAtp7a and zAtp7b in zebrafish liver cell line ZFL. Metallomics 2019; 11:1532-1546. [PMID: 31469368 DOI: 10.1039/c9mt00159j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Copper (Cu) is an essential element for all organisms, serving as an enzyme cofactor to maintain cellular activity and vitality. However, Cu homeostasis must be maintained at the physiological and cellular levels as Cu ions can be highly toxic. In mammals, ATP7A is expressed in most tissues, but relatively lower expression is found in the liver, and is responsible for the intestinal uptake of Cu, while ATP7B is highly expressed in the liver, kidneys and placenta, and is responsible for removal of Cu in the liver. CTR1 and ATOX1 are responsible for cellular Cu uptake and intracellular Cu transport, respectively. Here, using a zebrafish liver cell line (ZFL), we studied the cellular functions of four zebrafish Cu transporters. In zebrafish, zAtp7a is expressed mainly in the liver and zAtp7b is expressed mainly in the intestines, different from that of humans which have a high ATP7b level in the liver and high ATP7a level in the intestines. We here found that zctr1 or zatox1 overexpression increased Cu accumulation in ZFL cells. Moreover, zctr1 overexpression made ZFL cells more sensitive to Cu and Zn exposure, and overexpression of zatox1 or zatp7b increased Cu uptake and Cu tolerance in ZFL cells. Overexpression of zatp7a made ZFL cells more sensitive to Zn. Taken together, our findings suggest that zatp7b is responsible for Cu export despite its expression level being much lower than zatp7a in ZFL cells.
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Affiliation(s)
- Man Long Kwok
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, N.T., Hong Kong.
| | - King Ming Chan
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, N.T., Hong Kong.
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33
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Saraste J, Prydz K. A New Look at the Functional Organization of the Golgi Ribbon. Front Cell Dev Biol 2019; 7:171. [PMID: 31497600 PMCID: PMC6713163 DOI: 10.3389/fcell.2019.00171] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022] Open
Abstract
A characteristic feature of vertebrate cells is a Golgi ribbon consisting of multiple cisternal stacks connected into a single-copy organelle next to the centrosome. Despite numerous studies, the mechanisms that link the stacks together and the functional significance of ribbon formation remain poorly understood. Nevertheless, these questions are of considerable interest, since there is increasing evidence that Golgi fragmentation – the unlinking of the stacks in the ribbon – is intimately connected not only to normal physiological processes, such as cell division and migration, but also to pathological states, including neurodegeneration and cancer. Challenging a commonly held view that ribbon architecture involves the formation of homotypic tubular bridges between the Golgi stacks, we present an alternative model, based on direct interaction between the biosynthetic (pre-Golgi) and endocytic (post-Golgi) membrane networks and their connection with the centrosome. We propose that the central domains of these permanent pre- and post-Golgi networks function together in the biogenesis and maintenance of the more transient Golgi stacks, and thereby establish “linker compartments” that dynamically join the stacks together. This model provides insight into the reversible fragmentation of the Golgi ribbon that takes place in dividing and migrating cells and its regulation along a cell surface – Golgi – centrosome axis. Moreover, it helps to understand transport pathways that either traverse or bypass the Golgi stacks and the positioning of the Golgi apparatus in differentiated neuronal, epithelial, and muscle cells.
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Affiliation(s)
- Jaakko Saraste
- Department of Biomedicine and Molecular Imaging Center, University of Bergen, Bergen, Norway
| | - Kristian Prydz
- Department of Biosciences, University of Oslo, Oslo, Norway
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34
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Yamase K, Tanigawa Y, Yamamoto Y, Tanaka H, Komiya T. Mouse TMCO5 is localized to the manchette microtubules involved in vesicle transfer in the elongating spermatids. PLoS One 2019; 14:e0220917. [PMID: 31393949 PMCID: PMC6687282 DOI: 10.1371/journal.pone.0220917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/25/2019] [Indexed: 12/31/2022] Open
Abstract
As a result of a high-throughput in situ hybridization screening for adult mouse testes, we found that the mRNA for Tmco5 is expressed in round and elongating spermatids. Tmco5 belongs to the Tmco (Transmembrane and coiled-coil domains) gene family and has a coiled-coil domain in the N-terminal and a transmembrane domain in the C-terminal region. A monoclonal antibody raised against recombinant TMCO5 revealed that the protein is expressed exclusively in the elongating spermatids of step 9 to 12 and is localized to the manchette, a transiently emerging construction, which predominantly consists of cytoskeleton microtubules and actin filaments. This structure serves in the transport of Golgi-derived non-acrosomal vesicles. Moreover, induced expression of TMCO5 in CHO cells resulted in the co-localization of TMCO5 with β-tubulin besides the reorganization of the Golgi apparatus. Judging from the results and considering the domain structure of TMCO5, we assume that Tmco5 may have a role in vesicle transport along the manchette.
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Affiliation(s)
- Kenya Yamase
- Department of Biological Function, Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, Japan
| | - Yoko Tanigawa
- Department of Biological Function, Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, Japan
| | - Yasufumi Yamamoto
- Department of Biological Function, Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, Japan
| | - Hiromitsu Tanaka
- Faculty of Pharmaceutical Sciences, Nagasaki International University, Sasebo, Nagasaki, Japan
| | - Tohru Komiya
- Department of Biological Function, Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, Japan
- * E-mail:
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35
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Convergent evolution in the mechanisms of ACBD3 recruitment to picornavirus replication sites. PLoS Pathog 2019; 15:e1007962. [PMID: 31381608 PMCID: PMC6695192 DOI: 10.1371/journal.ppat.1007962] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 08/15/2019] [Accepted: 07/05/2019] [Indexed: 12/17/2022] Open
Abstract
Enteroviruses, members of the family of picornaviruses, are the most common viral infectious agents in humans causing a broad spectrum of diseases ranging from mild respiratory illnesses to life-threatening infections. To efficiently replicate within the host cell, enteroviruses hijack several host factors, such as ACBD3. ACBD3 facilitates replication of various enterovirus species, however, structural determinants of ACBD3 recruitment to the viral replication sites are poorly understood. Here, we present a structural characterization of the interaction between ACBD3 and the non-structural 3A proteins of four representative enteroviruses (poliovirus, enterovirus A71, enterovirus D68, and rhinovirus B14). In addition, we describe the details of the 3A-3A interaction causing the assembly of the ACBD3-3A heterotetramers and the interaction between the ACBD3-3A complex and the lipid bilayer. Using structure-guided identification of the point mutations disrupting these interactions, we demonstrate their roles in the intracellular localization of these proteins, recruitment of downstream effectors of ACBD3, and facilitation of enterovirus replication. These structures uncovered a striking convergence in the mechanisms of how enteroviruses and kobuviruses, members of a distinct group of picornaviruses that also rely on ACBD3, recruit ACBD3 and its downstream effectors to the sites of viral replication. Enteroviruses are the most common viruses infecting humans. They cause a broad spectrum of diseases ranging from common cold to life-threatening diseases, such as poliomyelitis. To date, no effective antiviral therapy for enteroviruses has been approved yet. To ensure efficient replication, enteroviruses hijack several host factors, recruit them to the sites of virus replication, and use their physiological functions for their own purposes. Here, we characterize the complexes composed of the host protein ACBD3 and the ACBD3-binding viral proteins (called 3A) of four representative enteroviruses. Our study reveals the atomic details of these complexes and identifies the amino acid residues important for the interaction. We found out that the 3A proteins of enteroviruses bind to the same regions of ACBD3 as the 3A proteins of kobuviruses, a distinct group of viruses that also rely on ACBD3, but are oriented in the opposite directions. This observation reveals a striking case of convergent evolutionary pathways that have evolved to allow enteroviruses and kobuviruses (which are two distinct groups of the Picornaviridae family) to recruit a common host target, ACBD3, and its downstream effectors to the sites of viral replication.
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36
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Rahajeng J, Kuna RS, Makowski SL, Tran TTT, Buschman MD, Li S, Cheng N, Ng MM, Field SJ. Efficient Golgi Forward Trafficking Requires GOLPH3-Driven, PI4P-Dependent Membrane Curvature. Dev Cell 2019; 50:573-585.e5. [PMID: 31231041 PMCID: PMC7583631 DOI: 10.1016/j.devcel.2019.05.038] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 01/22/2019] [Accepted: 05/21/2019] [Indexed: 10/26/2022]
Abstract
Vesicle budding for Golgi-to-plasma membrane trafficking is a key step in secretion. Proteins that induce curvature of the Golgi membrane are predicted to be required, by analogy to vesicle budding from other membranes. Here, we demonstrate that GOLPH3, upon binding to the phosphoinositide PI4P, induces curvature of synthetic membranes in vitro and the Golgi in cells. Moreover, efficient Golgi-to-plasma membrane trafficking critically depends on the ability of GOLPH3 to curve the Golgi membrane. Interestingly, uncoupling of GOLPH3 from its binding partner MYO18A results in extensive curvature of Golgi membranes, producing dramatic tubulation of the Golgi, but does not support forward trafficking. Thus, forward trafficking from the Golgi to the plasma membrane requires the ability of GOLPH3 both to induce Golgi membrane curvature and to recruit MYO18A. These data provide fundamental insight into the mechanism of Golgi trafficking and into the function of the unique Golgi secretory oncoproteins GOLPH3 and MYO18A.
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Affiliation(s)
- Juliati Rahajeng
- Department of Medicine, Division of Endocrinology and Metabolism, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ramya S Kuna
- Department of Medicine, Division of Endocrinology and Metabolism, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stefanie L Makowski
- Department of Medicine, Division of Endocrinology and Metabolism, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thuy T T Tran
- Department of Medicine, Division of Endocrinology and Metabolism, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew D Buschman
- Department of Medicine, Division of Endocrinology and Metabolism, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sheng Li
- Department of Medicine, Division of Rheumatology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Norton Cheng
- Department of Medicine, Division of Endocrinology and Metabolism, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michelle M Ng
- Department of Medicine, Division of Endocrinology and Metabolism, University of California, San Diego, La Jolla, CA 92093, USA
| | - Seth J Field
- Department of Medicine, Division of Endocrinology and Metabolism, University of California, San Diego, La Jolla, CA 92093, USA.
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37
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The Late Endosomal Pathway Regulates the Ciliary Targeting of Tetraspanin Protein Peripherin 2. J Neurosci 2019; 39:3376-3393. [PMID: 30819798 PMCID: PMC6495125 DOI: 10.1523/jneurosci.2811-18.2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/18/2019] [Accepted: 02/10/2019] [Indexed: 12/11/2022] Open
Abstract
Peripherin 2 (PRPH2) is a tetraspanin protein concentrated in the light-sensing cilium (called the outer segment) of the vertebrate photoreceptor. The mechanism underlying the ciliary targeting of PRPH2 and the etiology of cone dystrophy caused by PRPH2 mutations remain elusive. Here we show that the late endosome (LE) is the main waystation that critically sorts newly synthesized PRPH2 to the cilium. PRPH2 is expressed in the luminal membrane of the LE. We delineate multiple C-terminal motifs of PRPH2 that distinctively regulate its LE and ciliary targeting through ubiquitination and binding to ESCRT (Endosomal Sorting Complexes Required for Transport) component Hrs. Using the newly developed TetOn-inducible system in transfected male and female mouse cones in vivo, we show that the entry of nascent PRPH2 into the cone outer segment can be blocked by either cone dystrophy-causing C-terminal mutations of PRPH2, or by short-term perturbation of the LE or recycling endosomal traffic. These findings open new avenues of research to explore the biological role of the LE in the biosynthetic pathway and the etiology of cone dystrophy caused by PRPH2 mutations and/or malfunctions of the LE.SIGNIFICANCE STATEMENT Peripherin 2 (PRPH2) is a tetraspanin protein abundantly expressed in the light-sensing cilium, the outer segment, of the vertebrate photoreceptor. The mechanism underlying the ciliary transport of PRPH2 is unclear. The present study reveals a novel ciliary targeting pathway, in which the newly synthesized PRPH2 is first targeted to the lumen of the late endosome (LE) en route to the cilia. We deciphered the protein motifs and the machinery that regulates the LE trafficking of PRPH2. Using a novel TetOn-inducible system in transfected mouse cones, we showed that the LE pathway of PRPH2 is critical for its outer segment expression. A cone dystrophy-causing mutation impairs the LE and ciliary targeting of PRPH2, implicating the relevance of LE to cone/macular degenerative diseases.
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38
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Nishimura K, Ishiwata H, Sakuragi Y, Hayashi Y, Fukuda A, Hisatake K. Live-cell imaging of subcellular structures for quantitative evaluation of pluripotent stem cells. Sci Rep 2019; 9:1777. [PMID: 30741960 PMCID: PMC6370783 DOI: 10.1038/s41598-018-37779-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 12/11/2018] [Indexed: 11/20/2022] Open
Abstract
Pluripotent stem cells (PSCs) have various degrees of pluripotency, which necessitates selection of PSCs with high pluripotency before their application to regenerative medicine. However, the quality control processes for PSCs are costly and time-consuming, and it is essential to develop inexpensive and less laborious selection methods for translation of PSCs into clinical applications. Here we developed an imaging system, termed Phase Distribution (PD) imaging system, which visualizes subcellular structures quantitatively in unstained and unlabeled cells. The PD image and its derived PD index reflected the mitochondrial content, enabling quantitative evaluation of the degrees of somatic cell reprogramming and PSC differentiation. Moreover, the PD index allowed unbiased grouping of PSC colonies into those with high or low pluripotency without the aid of invasive methods. Finally, the PD imaging system produced three-dimensional images of PSC colonies, providing further criteria to evaluate pluripotency of PSCs. Thus, the PD imaging system may be utilized for screening of live PSCs with potentially high pluripotency prior to more rigorous quality control processes.
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Affiliation(s)
- Ken Nishimura
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
| | - Hiroshi Ishiwata
- Optical Technology R&D Department 2, Optical System Development Division, Olympus Corporation, 67-4 Takakura-machi, Hachioji, Tokyo, 192-0033, Japan
| | - Yuta Sakuragi
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Yohei Hayashi
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Aya Fukuda
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Koji Hisatake
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
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39
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Voss S, Li F, Rätz A, Röger M, Wu YW. Spatial Cycling of Rab GTPase, Driven by the GTPase Cycle, Controls Rab's Subcellular Distribution. Biochemistry 2019; 58:276-285. [PMID: 30605611 DOI: 10.1021/acs.biochem.8b00932] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rab GTPases (>60 members in humans) function as master regulators of intracellular membrane trafficking. Correct and specific localization of Rab proteins is required for their function. How the distinct spatial distribution of Rab GTPases in the cell is regulated remains elusive. To globally assess the subcellular localization of Rab1, we determined kinetic parameters of two pathways that control the spatial cycles of Rab1, i.e., vesicular transport and GDP dissociation inhibitor (GDI)-mediated recycling. We demonstrate that the switching between GTP and GDP binding states, which is governed by guanine nucleotide exchange factors (GEFs), GTPase-activating proteins (GAPs), GDI, and GDI displacement factor (GDF), is a major determinant of Rab1's ability to effectively cycle between cellular compartments and eventually its subcellular distribution. In silico perturbations of vesicular transport, GEFs, GAPs, GDI, and GDF using a mathematical model with simplified cellular geometries showed that these regulators play an important role in the subcellular distribution and activity of Rab1.
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Affiliation(s)
- Stephanie Voss
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Strasse 15 , 44227 Dortmund , Germany.,Max-Planck-Institute of Molecular Physiology , Otto-Hahn-Strasse 11 , 44227 Dortmund , Germany
| | - Fu Li
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Strasse 15 , 44227 Dortmund , Germany.,Max-Planck-Institute of Molecular Physiology , Otto-Hahn-Strasse 11 , 44227 Dortmund , Germany.,Department of Chemistry, Umeå Centre for Microbial Research , Umeå University , 90187 Umeå , Sweden
| | - Andreas Rätz
- TU Dortmund University , Faculty of Mathematics , Vogelpothsweg 87 , 44227 Dortmund , Germany
| | - Matthias Röger
- TU Dortmund University , Faculty of Mathematics , Vogelpothsweg 87 , 44227 Dortmund , Germany
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Strasse 15 , 44227 Dortmund , Germany.,Max-Planck-Institute of Molecular Physiology , Otto-Hahn-Strasse 11 , 44227 Dortmund , Germany.,Department of Chemistry, Umeå Centre for Microbial Research , Umeå University , 90187 Umeå , Sweden
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40
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Klein HL, Ang KKH, Arkin MR, Beckwitt EC, Chang YH, Fan J, Kwon Y, Morten MJ, Mukherjee S, Pambos OJ, El Sayyed H, Thrall ES, Vieira-da-Rocha JP, Wang Q, Wang S, Yeh HY, Biteen JS, Chi P, Heyer WD, Kapanidis AN, Loparo JJ, Strick TR, Sung P, Van Houten B, Niu H, Rothenberg E. Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes. MICROBIAL CELL 2019; 6:65-101. [PMID: 30652106 PMCID: PMC6334232 DOI: 10.15698/mic2019.01.665] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.
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Affiliation(s)
- Hannah L Klein
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Kenny K H Ang
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Emily C Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Yi-Hsuan Chang
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Jun Fan
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Michael J Morten
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Sucheta Mukherjee
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Oliver J Pambos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Hafez El Sayyed
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Elizabeth S Thrall
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - João P Vieira-da-Rocha
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Quan Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Shuang Wang
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Julie S Biteen
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.,Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Terence R Strick
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France.,Programme Equipe Labellisées, Ligue Contre le Cancer, 75013 Paris, France
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Eli Rothenberg
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
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41
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Parashuraman S, D’Angelo G. Visualizing sphingolipid biosynthesis in cells. Chem Phys Lipids 2019; 218:103-111. [DOI: 10.1016/j.chemphyslip.2018.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/11/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022]
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42
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Avci D, Malchus NS, Heidasch R, Lorenz H, Richter K, Neßling M, Lemberg MK. The intramembrane protease SPP impacts morphology of the endoplasmic reticulum by triggering degradation of morphogenic proteins. J Biol Chem 2018; 294:2786-2800. [PMID: 30578301 DOI: 10.1074/jbc.ra118.005642] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/12/2018] [Indexed: 11/06/2022] Open
Abstract
The endoplasmic reticulum (ER), as a multifunctional organelle, plays crucial roles in lipid biosynthesis and calcium homeostasis as well as the synthesis and folding of secretory and membrane proteins. Therefore, it is of high importance to maintain ER homeostasis and to adapt ER function and morphology to cellular needs. Here, we show that signal peptide peptidase (SPP) modulates the ER shape through degradation of morphogenic proteins. Elevating SPP activity induces rapid rearrangement of the ER and formation of dynamic ER clusters. Inhibition of SPP activity rescues the phenotype without the need for new protein synthesis, and this rescue depends on a pre-existing pool of proteins in the Golgi. With the help of organelle proteomics, we identified certain membrane proteins to be diminished upon SPP expression and further show that the observed morphology changes depend on SPP-mediated cleavage of ER morphogenic proteins, including the SNARE protein syntaxin-18. Thus, we suggest that SPP-mediated protein abundance control by a regulatory branch of ER-associated degradation (ERAD-R) has a role in shaping the early secretory pathway.
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Affiliation(s)
- Dönem Avci
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
| | - Nicole S Malchus
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
| | - Ronny Heidasch
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
| | - Holger Lorenz
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
| | - Karsten Richter
- German Cancer Research Center (DKFZ), Central Unit Electron Microscopy, 69120 Heidelberg, Germany
| | - Michelle Neßling
- German Cancer Research Center (DKFZ), Central Unit Electron Microscopy, 69120 Heidelberg, Germany
| | - Marius K Lemberg
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
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43
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Casar B, Badrock AP, Jiménez I, Arozarena I, Colón-Bolea P, Lorenzo-Martín LF, Barinaga-Rementería I, Barriuso J, Cappitelli V, Donoghue DJ, Bustelo XR, Hurlstone A, Crespo P. RAS at the Golgi antagonizes malignant transformation through PTPRκ-mediated inhibition of ERK activation. Nat Commun 2018; 9:3595. [PMID: 30185827 PMCID: PMC6125387 DOI: 10.1038/s41467-018-05941-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 08/02/2018] [Indexed: 11/12/2022] Open
Abstract
RAS GTPases are frequently mutated in human cancer. H- and NRAS isoforms are distributed over both plasma-membrane and endomembranes, including the Golgi complex, but how this organizational context contributes to cellular transformation is unknown. Here we show that RAS at the Golgi is selectively activated by apoptogenic stimuli and antagonizes cell survival by suppressing ERK activity through the induction of PTPRκ, which targets CRAF for dephosphorylation. Consistently, in contrast to what occurs at the plasma-membrane, RAS at the Golgi cannot induce melanoma in zebrafish. Inactivation of PTPRκ, which occurs frequently in human melanoma, often coincident with TP53 inactivation, accelerates RAS-ERK pathway-driven melanomagenesis in zebrafish. Likewise, tp53 disruption in zebrafish facilitates oncogenesis driven by RAS from the Golgi complex. Thus, RAS oncogenic potential is strictly dependent on its sublocalization, with Golgi complex-located RAS antagonizing tumor development. RAS isoforms are associated with the plasma membrane and endomembranes, but how their localization contributes to tumorigenesis is unclear. Here, the authors show that RAS signals from Golgi complex antagonize tumour formation by inducing apoptosis via ERK inhibition.
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Affiliation(s)
- Berta Casar
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, 39011, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Andrew P Badrock
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Iñaki Jiménez
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, 39011, Spain
| | - Imanol Arozarena
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, 39011, Spain.,Navarrabiomed-FMS IDISNA, Pamplona, Navarra, 31008, Spain
| | - Paula Colón-Bolea
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, 39011, Spain
| | - L Francisco Lorenzo-Martín
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, 28029, Spain.,Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Salamanca, 37007, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, Salamanca, 37007, Spain
| | - Irene Barinaga-Rementería
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Jorge Barriuso
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Vincenzo Cappitelli
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, 39011, Spain
| | - Daniel J Donoghue
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA92093, USA
| | - Xosé R Bustelo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, 28029, Spain.,Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Salamanca, 37007, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, Salamanca, 37007, Spain
| | - Adam Hurlstone
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK.
| | - Piero Crespo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, 39011, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, 28029, Spain.
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44
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Lippincott-Schwartz J, Snapp EL, Phair RD. The Development and Enhancement of FRAP as a Key Tool for Investigating Protein Dynamics. Biophys J 2018; 115:1146-1155. [PMID: 30219286 DOI: 10.1016/j.bpj.2018.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/27/2018] [Accepted: 08/06/2018] [Indexed: 01/18/2023] Open
Abstract
The saga of fluorescence recovery after photobleaching (FRAP) illustrates how disparate technical developments impact science. Starting with the classic 1976 Axelrod et al. work in Biophysical Journal, FRAP (originally fluorescence photobleaching recovery) opened the door to extraction of quantitative information from photobleaching experiments, laying the experimental and theoretical groundwork for quantifying both the mobility and the mobile fraction of a labeled population of proteins. Over the ensuing years, FRAP's reach dramatically expanded, with new developments in GFP technology and turn-key confocal microscopy, which enabled measurement of protein diffusion and binding/dissociation rates in virtually every compartment within the cell. The FRAP technique and data catalyzed an exchange of ideas between biophysicists studying membrane dynamics, cell biologists focused on intracellular dynamics, and systems biologists modeling the dynamics of cell activity. The outcome transformed the field of cellular biology, leading to a fundamental rethinking of long-held theories of cellular dynamism. Here, we review the pivotal FRAP studies that made these developments and conceptual changes possible, which gave rise to current models of complex cell dynamics.
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Affiliation(s)
| | - Erik Lee Snapp
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia.
| | - Robert D Phair
- Integrative Bioinformatics, Inc., Mountain View, California
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45
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Copeland SJ, McRae A, Guarguaglini G, Trinkle-Mulcahy L, Copeland JW. Actin-dependent regulation of cilia length by the inverted formin FHDC1. Mol Biol Cell 2018; 29:1611-1627. [PMID: 29742020 PMCID: PMC6080654 DOI: 10.1091/mbc.e18-02-0088] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A primary cilium is found on most mammalian cells, where it acts as a cellular antenna for the reception of both mechanical and chemical signals. A variety of diseases are associated with defective ciliogenesis, reflecting the ubiquity of the function of cilia and the number of proteins required for their assembly. Proper cilia length is necessary for cilia signaling and is regulated through a poorly understood balance of assembly and disassembly rates. FHDC1 is a unique member of the formin family of cytoskeletal regulatory proteins. Overexpression of FHDC1 induces F-actin accumulation and microtubule stabilization and acetylation. We find that overexpression of FHDC1 also has profound effects on ciliogenesis; in most cells FHDC1 overexpression blocks cilia assembly, but the cilia that are present are immensely elongated. FHDC1-induced cilia growth requires the FHDC1 FH2 and microtubule-binding domain and results from F-actin-dependent inhibition of cilia disassembly. FHDC1 depletion, or treatment with a pan-formin inhibitor, inhibits cilia assembly and induces cilia resorption. Endogenous FHDC1 protein localizes to cytoplasmic microtubules converging on the base of the cilia, and we identify the subdistal appendage protein Cep170 as an FHDC1 interacting protein. Our results suggest that FHDC1 plays a role in coordinating cytoskeletal dynamics during normal cilia assembly.
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Affiliation(s)
- Sarah J Copeland
- Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Andrea McRae
- Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Giulia Guarguaglini
- Institute of Molecular Biology and Pathology, Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Laura Trinkle-Mulcahy
- Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - John W Copeland
- Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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46
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Kaberniuk AA, Morano NC, Verkhusha VV, Snapp EL. moxDendra2: an inert photoswitchable protein for oxidizing environments. Chem Commun (Camb) 2018; 53:2106-2109. [PMID: 28133646 DOI: 10.1039/c6cc09997a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Fluorescent proteins (FPs) that can be optically highlighted enable PALM super-resolution microscopy and pulse-chase experiments of cellular molecules. Most FPs evolved in cytoplasmic environments either in the original source organism or in the cytoplasm of bacteria during the course of optimization for research applications. Consequently, many FPs may fold incorrectly in the chemically distinct environments in subcellular organelles. Here, we describe the first monomeric photoswitchable (from green to bright red) FP adapted for oxidizing environments.
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Affiliation(s)
- Andrii A Kaberniuk
- Albert Einstein College of Medicine, Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Nicholas C Morano
- Albert Einstein College of Medicine, Department of Biochemistry, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Vladislav V Verkhusha
- Albert Einstein College of Medicine, Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Erik Lee Snapp
- Janelia Research Campus, HHMI, 19700 Helix Drive, Ashburn, VA 20147, USA.
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47
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Phair RD. Differential equation methods for simulation of GFP kinetics in non-steady state experiments. Mol Biol Cell 2018; 29:763-771. [PMID: 29367436 PMCID: PMC6003217 DOI: 10.1091/mbc.e17-06-0396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 11/11/2022] Open
Abstract
Genetically encoded fluorescent proteins, combined with fluorescence microscopy, are widely used in cell biology to collect kinetic data on intracellular trafficking. Methods for extraction of quantitative information from these data are based on the mathematics of diffusion and tracer kinetics. Current methods, although useful and powerful, depend on the assumption that the cellular system being studied is in a steady state, that is, the assumption that all the molecular concentrations and fluxes are constant for the duration of the experiment. Here, we derive new tracer kinetic analytical methods for non-steady state biological systems by constructing mechanistic nonlinear differential equation models of the underlying cell biological processes and linking them to a separate set of differential equations governing the kinetics of the fluorescent tracer. Linking the two sets of equations is based on a new application of the fundamental tracer principle of indistinguishability and, unlike current methods, supports correct dependence of tracer kinetics on cellular dynamics. This approach thus provides a general mathematical framework for applications of GFP fluorescence microscopy (including photobleaching [FRAP, FLIP] and photoactivation to frequently encountered experimental protocols involving physiological or pharmacological perturbations (e.g., growth factors, neurotransmitters, acute knockouts, inhibitors, hormones, cytokines, and metabolites) that initiate mechanistically informative intracellular transients. When a new steady state is achieved, these methods automatically reduce to classical steady state tracer kinetic analysis.
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Affiliation(s)
- Robert D Phair
- Integrative Bioinformatics Inc., Mountain View, CA 94041
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48
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Herrero A, Reis-Cardoso M, Jiménez-Gómez I, Doherty C, Agudo-Ibañez L, Pinto A, Calvo F, Kolch W, Crespo P, Matallanas D. Characterisation of HRas local signal transduction networks using engineered site-specific exchange factors. Small GTPases 2018; 11:371-383. [PMID: 29172991 DOI: 10.1080/21541248.2017.1406434] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ras GTPases convey signals from different types of membranes. At these locations, different Ras isoforms, interactors and regulators generate different biochemical signals and biological outputs. The study of Ras localisation-specific signal transduction networks has been hampered by our inability to specifically activate each of these Ras pools. Here, we describe a new set of site-specific tethered exchange factors, engineered by fusing the RasGRF1 CDC25 domain to sub-localisation-defining cues, whereby Ras pools at specific locations can be precisely activated. We show that the CDC25 domain has a high specificity for activating HRas but not NRas and KRas. This unexpected finding means that our constructs mainly activate endogenous HRas. Hence, their use enabled us to identify distinct pathways regulated by HRas in endomembranes and plasma membrane microdomains. Importantly, these new constructs unveil different patterns of HRas activity specified by their subcellular localisation. Overall, the targeted GEFs described herein constitute ideal tools for dissecting spatially-defined HRas biochemical and biological functions.
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Affiliation(s)
- Ana Herrero
- Systems Biology Ireland, University College Dublin , Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin , Dublin, Ireland
| | | | - Iñaki Jiménez-Gómez
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Cantabria, Santander , Spain
| | - Carolanne Doherty
- Systems Biology Ireland, University College Dublin , Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin , Dublin, Ireland
| | - Lorena Agudo-Ibañez
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Cantabria, Santander , Spain
| | - Adán Pinto
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Cantabria, Santander , Spain
| | - Fernando Calvo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Cantabria, Santander , Spain
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin , Dublin, Ireland.,Conway Institute, University College Dublin , Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin , Dublin, Ireland
| | - Piero Crespo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Cantabria, Santander , Spain.,Centro de Investigación Biomédica en Red CIBERONC, Instituto de Salud Calos III , Madrid, Spain
| | - David Matallanas
- Systems Biology Ireland, University College Dublin , Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin , Dublin, Ireland
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49
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Hirama T, Lu SM, Kay JG, Maekawa M, Kozlov MM, Grinstein S, Fairn GD. Membrane curvature induced by proximity of anionic phospholipids can initiate endocytosis. Nat Commun 2017; 8:1393. [PMID: 29123120 PMCID: PMC5680216 DOI: 10.1038/s41467-017-01554-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 09/27/2017] [Indexed: 11/09/2022] Open
Abstract
The plasma membrane is uniquely enriched in phosphatidylserine (PtdSer). This anionic phospholipid is restricted almost exclusively to the inner leaflet of the plasmalemma. Because of their high density, the headgroups of anionic lipids experience electrostatic repulsion that, being exerted asymmetrically, is predicted to favor membrane curvature. We demonstrate that cholesterol limits this repulsion and tendency to curve. Removal of cholesterol or insertion of excess PtdSer increases the charge density of the inner leaflet, generating foci of enhanced charge and curvature where endophilin and synaptojanin are recruited. From these sites emerge tubules that undergo fragmentation, resulting in marked endocytosis of PtdSer. Shielding or reduction of the surface charge or imposition of outward membrane tension minimized invagination and PtdSer endocytosis. We propose that cholesterol associates with PtdSer to form nanodomains where the headgroups of PtdSer are maintained sufficiently separated to limit spontaneous curvature while sheltering the hydrophobic sterol from the aqueous medium.
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Affiliation(s)
- Takashi Hirama
- Program in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada, M5G 1X8.,Department of Respiratory Medicine, Saitama Medical University, Moroyama, Saitama, 3500495, Japan.,Keenan Research Centre for Biomedical Science, St. Michael's Hospital, 209 Victoria Street, Toronto, ON, Canada, M5B 1T8
| | - Stella M Lu
- Program in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada, M5G 1X8.,Keenan Research Centre for Biomedical Science, St. Michael's Hospital, 209 Victoria Street, Toronto, ON, Canada, M5B 1T8.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada, M5S 1A8
| | - Jason G Kay
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, NY, 14214, USA
| | - Masashi Maekawa
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, 209 Victoria Street, Toronto, ON, Canada, M5B 1T8.,Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine; Division of Cell Growth and Tumour Regulation, Proteo-Science Center, Ehime University, Toon, Ehime, 7910295, Japan
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Room 546, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Sergio Grinstein
- Program in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada, M5G 1X8.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada, M5S 1A8.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada, M5S 1A8
| | - Gregory D Fairn
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, 209 Victoria Street, Toronto, ON, Canada, M5B 1T8. .,Department of Biochemistry, University of Toronto, Toronto, ON, Canada, M5S 1A8. .,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada, M5S 1A8. .,Department of Surgery, University of Toronto, Toronto, ON, Canada, M5T 1P5.
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50
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Kopp Y, Lang WH, Schuster TB, Martínez-Limón A, Hofbauer HF, Ernst R, Calloni G, Vabulas RM. CHIP as a membrane-shuttling proteostasis sensor. eLife 2017; 6:e29388. [PMID: 29091030 PMCID: PMC5665643 DOI: 10.7554/elife.29388] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/22/2017] [Indexed: 12/12/2022] Open
Abstract
Cells respond to protein misfolding and aggregation in the cytosol by adjusting gene transcription and a number of post-transcriptional processes. In parallel to functional reactions, cellular structure changes as well; however, the mechanisms underlying the early adaptation of cellular compartments to cytosolic protein misfolding are less clear. Here we show that the mammalian ubiquitin ligase C-terminal Hsp70-interacting protein (CHIP), if freed from chaperones during acute stress, can dock on cellular membranes thus performing a proteostasis sensor function. We reconstituted this process in vitro and found that mainly phosphatidic acid and phosphatidylinositol-4-phosphate enhance association of chaperone-free CHIP with liposomes. HSP70 and membranes compete for mutually exclusive binding to the tetratricopeptide repeat domain of CHIP. At new cellular locations, access to compartment-specific substrates would enable CHIP to participate in the reorganization of the respective organelles, as exemplified by the fragmentation of the Golgi apparatus (effector function).
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Affiliation(s)
- Yannick Kopp
- Buchmann Institute for Molecular Life SciencesGoethe University FrankfurtFrankfurt am MainGermany
- Institute of Biophysical ChemistryGoethe University FrankfurtFrankfurt am MainGermany
| | - Wei-Han Lang
- Buchmann Institute for Molecular Life SciencesGoethe University FrankfurtFrankfurt am MainGermany
- Institute of Biophysical ChemistryGoethe University FrankfurtFrankfurt am MainGermany
| | - Tobias B Schuster
- Buchmann Institute for Molecular Life SciencesGoethe University FrankfurtFrankfurt am MainGermany
- Institute of Biophysical ChemistryGoethe University FrankfurtFrankfurt am MainGermany
| | - Adrián Martínez-Limón
- Buchmann Institute for Molecular Life SciencesGoethe University FrankfurtFrankfurt am MainGermany
- Institute of Biophysical ChemistryGoethe University FrankfurtFrankfurt am MainGermany
| | - Harald F Hofbauer
- Buchmann Institute for Molecular Life SciencesGoethe University FrankfurtFrankfurt am MainGermany
- Institute of BiochemistryGoethe University FrankfurtFrankfurt am MainGermany
| | - Robert Ernst
- Buchmann Institute for Molecular Life SciencesGoethe University FrankfurtFrankfurt am MainGermany
- Institute of BiochemistryGoethe University FrankfurtFrankfurt am MainGermany
| | - Giulia Calloni
- Buchmann Institute for Molecular Life SciencesGoethe University FrankfurtFrankfurt am MainGermany
- Institute of Biophysical ChemistryGoethe University FrankfurtFrankfurt am MainGermany
| | - R Martin Vabulas
- Buchmann Institute for Molecular Life SciencesGoethe University FrankfurtFrankfurt am MainGermany
- Institute of Biophysical ChemistryGoethe University FrankfurtFrankfurt am MainGermany
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