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Sun Y, Chen S, Hou Y, Kang SH, Lin JM. Organelle Proximity Analysis for Enhanced Quantification of Mitochondria-Endoplasmic Reticulum Interactions in Single Cells via Super-Resolution Microscopy. Anal Chem 2024; 96:11557-11565. [PMID: 38959297 DOI: 10.1021/acs.analchem.4c02338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Mitochondria (MT) and the endoplasmic reticulum (ER) maintain lipid and calcium homeostasis through membrane contacts, particularly MT-ER contacts (MERCs), spanning distances from 10 to 50 nm. However, the variation of different distance ranges and the metabolic factors influencing this variation remain poorly understood. This study employed microfluidic chip-based super-resolution microscopy in conjunction with a Moore-Neighbor tracing-incorporated organelle proximity analysis algorithm. This approach enabled precise three-dimensional localization of single-fluorescence protein molecules within narrow and irregular membrane proximities. It achieved lateral localization precision of less than 20 nm, resulting in a minimum MERC distance of approximately 8 nm in spatial and mean distances across multiple threshold ranges. Additionally, we demonstrated that the MERC distance variation was correlated with MT size rather than ER width. The proportion of each distance range varied significantly after the stimuli. Free cholesterol showed a negative correlation with various distances, while distances of 10-30 nm were associated with glucose, glutamine, and pyruvic acid. Furthermore, the 30-40 nm range was influenced by citric acid. These results underscore the role of advanced subcellular organelle analysis in elucidating the single-molecule behavior and organelle morphology in single-cell studies.
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Affiliation(s)
- Yucheng Sun
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Shiyu Chen
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ying Hou
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Seong Ho Kang
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Jin-Ming Lin
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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2
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Liu Y, Gong XT, Wang KN, He S, Wang Y, Lin Q, Liu Z, Yu X, Liu B. Dual-targeted fluorescent probe for tracking polarity and phase transition processes during lipophagy. MATERIALS HORIZONS 2024; 11:3287-3297. [PMID: 38842407 DOI: 10.1039/d4mh00190g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Eukaryotic cells regulate various cellular processes through membrane-bound and membrane-less organelles, enabling active signal communication and material exchange. Lysosomes and lipid droplets are representative organelles, contributing to cell lipophagy when their interaction and metabolism are disrupted. Our limited understanding of the interacting behaviours and physicochemical properties of different organelles during lipophagy hinders accurate diagnosis and treatment of related diseases. In this contribution, we report a fluorescent probe, PTZ, engineered for dual-targeting of lipid droplets and lysosomes. PTZ can track liquid-liquid phase separation and respond to polarity shifts through ratiometric fluorescence emission, elucidating the lipophagy process from the perspective of organelle behavior and physicochemical properties. Leveraging on the multifunctionality of PTZ, we have successfully tracked the polarity and dynamic changes of lysosomes and lipid droplets during lipophagy. Furthermore, an unknown homogeneous transition of lipid droplets and lysosomes was discovered, which provided a new perspective for understanding lipophagy processes. And this work is expected to serve as a reference for diagnosis and treatment of lipophagy-related diseases.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
| | - Xiao-Ting Gong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, China
| | - Kang-Nan Wang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
| | - Simeng He
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Yumeng Wang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
| | - Qiaowen Lin
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
| | - Zhiqiang Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
| | - Xiaoqiang Yu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, China
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3
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Campanella M, Kannan B. Mitochondrial sites of contact with the nucleus. J Cell Biol 2024; 223:e202305010. [PMID: 38669038 PMCID: PMC11046832 DOI: 10.1083/jcb.202305010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2024] Open
Abstract
Membrane contact sites (MCS) between mitochondria and the nucleus have been recently described. Termed nucleus associated mitochondria (NAM), they prime the expression of genes required for cellular resistance to stressors, thus offering a tethering mechanism for homeostatic communication. Here, we discuss the composition of NAM and their physiological and pathological significance.
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Affiliation(s)
- Michelangelo Campanella
- William Harvey Research Institute, Queen Mary University of London, London, UK
- Institute Gustave Roussy, Villejuif, France
- Department of Biomedical Science, University of Padua, Padua, Italy
| | - Brindha Kannan
- William Harvey Research Institute, Queen Mary University of London, London, UK
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4
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Schmitz M, Ballestin JB, Liang J, Tomas F, Freist L, Voigt K, Di Ventura B, Öztürk MA. Int&in: A machine learning-based web server for active split site identification in inteins. Protein Sci 2024; 33:e4985. [PMID: 38717278 PMCID: PMC11078102 DOI: 10.1002/pro.4985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/06/2024] [Accepted: 03/24/2024] [Indexed: 05/12/2024]
Abstract
Inteins are proteins that excise themselves out of host proteins and ligate the flanking polypeptides in an auto-catalytic process called protein splicing. In nature, inteins are either contiguous or split. In the case of split inteins, the two fragments must first form a complex for the splicing to occur. Contiguous inteins have previously been artificially split in two fragments because split inteins allow for distinct applications than contiguous ones. Even naturally split inteins have been split at unnatural split sites to obtain fragments with reduced affinity for one another, which are useful to create conditional inteins or to study protein-protein interactions. So far, split sites in inteins have been heuristically identified. We developed Int&in, a web server freely available for academic research (https://intein.biologie.uni-freiburg.de) that runs a machine learning model using logistic regression to predict active and inactive split sites in inteins with high accuracy. The model was trained on a dataset of 126 split sites generated using the gp41-1, Npu DnaE and CL inteins and validated using 97 split sites extracted from the literature. Despite the limited data size, the model, which uses various protein structural features, as well as sequence conservation information, achieves an accuracy of 0.79 and 0.78 for the training and testing sets, respectively. We envision Int&in will facilitate the engineering of novel split inteins for applications in synthetic and cell biology.
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Affiliation(s)
- Mirko Schmitz
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
- 4HF Biotec GmbHFreiburgGermany
| | - Jara Ballestin Ballestin
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
- Bioprocess Innovation Unit, ViraTherapeutics GmbHRumAustria
| | - Junsheng Liang
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
| | - Franziska Tomas
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Leon Freist
- Institute of Biology III, University of FreiburgFreiburgGermany
| | - Karsten Voigt
- Institute of Biology III, University of FreiburgFreiburgGermany
| | - Barbara Di Ventura
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
| | - Mehmet Ali Öztürk
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
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5
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Li D, Cai Y, Guo J, Liu Y, Lu F, Li Q, Liu Y, Li Y. Screening signal peptidase based on split-GFP assembly technology to promote the secretion of alkaline protease AprE in Bacillus amyloliquefaciens. Int J Biol Macromol 2024; 269:132166. [PMID: 38723822 DOI: 10.1016/j.ijbiomac.2024.132166] [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: 02/04/2024] [Revised: 04/04/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024]
Abstract
Improving the ability of bacteria to secrete protein is essential for large-scale production of food enzymes. However, due to the lack of effective tracking technology for target proteins, the optimization of the secretory system is facing many problems. In this study, we utilized the split-GFP system to achieve self-assembly into mature GFP in Bacillus amyloliquefaciens and successfully tracked the alkaline protease AprE. The split-GFP system was employed to assess the signal peptidases, a crucial component in the secretory system, and signal peptidase sipA was identified as playing a role in the secretion of AprE. Deletion of sipA resulted in a higher accumulation of the precursor protein of AprE compared to other signal peptidase deletion strains. To explore the mechanism of signal peptidase on signal peptide, molecular docking and calculation of free energy were performed. The action strength of the signal peptidase is determined by its binding affinity with the tripeptides at the C-terminal of the signal peptide. The functions of signal peptides YdbK and NucB rely on sipA, and overexpression of sipA by integrating it into genome of B. amyloliquefaciens increased the activity of extracellular AprE by 19.9 %. These findings provide insights into enhancing the secretion efficiency of chassis strains.
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Affiliation(s)
- Dengke Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yian Cai
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jiejie Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Qinggang Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Yexue Liu
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Yu Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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6
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Germani S, Van Ho AT, Cherubini A, Varone E, Chernorudskiy A, Renna GM, Fumagalli S, Gobbi M, Lucchetti J, Bolis M, Guarrera L, Craparotta I, Rastelli G, Piccoli G, de Napoli C, Nogara L, Poggio E, Brini M, Cattaneo A, Bachi A, Simmen T, Calì T, Quijano-Roy S, Boncompagni S, Blaauw B, Ferreiro A, Zito E. SEPN1-related myopathy depends on the oxidoreductase ERO1A and is druggable with the chemical chaperone TUDCA. Cell Rep Med 2024; 5:101439. [PMID: 38402623 PMCID: PMC10982971 DOI: 10.1016/j.xcrm.2024.101439] [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: 05/09/2023] [Revised: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 02/27/2024]
Abstract
Selenoprotein N (SEPN1) is a protein of the endoplasmic reticulum (ER) whose inherited defects originate SEPN1-related myopathy (SEPN1-RM). Here, we identify an interaction between SEPN1 and the ER-stress-induced oxidoreductase ERO1A. SEPN1 and ERO1A, both enriched in mitochondria-associated membranes (MAMs), are involved in the redox regulation of proteins. ERO1A depletion in SEPN1 knockout cells restores ER redox, re-equilibrates short-range MAMs, and rescues mitochondrial bioenergetics. ERO1A knockout in a mouse background of SEPN1 loss blunts ER stress and improves multiple MAM functions, including Ca2+ levels and bioenergetics, thus reversing diaphragmatic weakness. The treatment of SEPN1 knockout mice with the ER stress inhibitor tauroursodeoxycholic acid (TUDCA) mirrors the results of ERO1A loss. Importantly, muscle biopsies from patients with SEPN1-RM exhibit ERO1A overexpression, and TUDCA-treated SEPN1-RM patient-derived primary myoblasts show improvement in bioenergetics. These findings point to ERO1A as a biomarker and a viable target for intervention and to TUDCA as a pharmacological treatment for SEPN1-RM.
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Affiliation(s)
- Serena Germani
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy; Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Andrew Tri Van Ho
- Basic and Translational Myology Laboratory, Université Paris, BFA, UMR 8251, CNRS, 75013 Paris, France
| | | | - Ersilia Varone
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | | | | | | | - Marco Gobbi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Jacopo Lucchetti
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Marco Bolis
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy; Bioinformatics Core Unit, Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland
| | - Luca Guarrera
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | | | - Giorgia Rastelli
- CAST, Center for Advanced Studies and Technology & DNICS, Department of Neuroscience, Imaging and Clinical Sciences, University G. D'Annunzio of Chieti-Pescara, 66100 Chieti, Italy
| | - Giorgia Piccoli
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Cosimo de Napoli
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Leonardo Nogara
- Department of Biomedical Sciences, University of Padua, Padua, Italy; Department of Pharmaceutical Sciences, University of Padova, Padova, Italy
| | - Elena Poggio
- Department of Biology, University of Padova, Padova, Italy
| | - Marisa Brini
- Department of Pharmaceutical Sciences, University of Padova, Padova, Italy; Department of Biology, University of Padova, Padova, Italy; Study Center for Neurodegeneration (CESNE), University of Padova, Padova, Italy
| | | | - Angela Bachi
- IFOM-ETS AIRC Institute of Molecular Oncology, Milan, Italy
| | - Thomas Simmen
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Tito Calì
- Department of Biomedical Sciences, University of Padua, Padua, Italy; Study Center for Neurodegeneration (CESNE), University of Padova, Padova, Italy; Padova Neuroscience Center, University of Padova, Padova, Italy
| | - Susana Quijano-Roy
- APHP-Université Paris-Saclay, Reference Center for Neuromuscular Disorders Nord-Est-Ile de France, FILNEMUS, ERN-Euro-NMD, Creteil, France; Pediatric Neurology and ICU Department, DMU Santé Enfant Adolescent (SEA), Raymond Poincaré University Hospital, Garches, France
| | - Simona Boncompagni
- CAST, Center for Advanced Studies and Technology & DNICS, Department of Neuroscience, Imaging and Clinical Sciences, University G. D'Annunzio of Chieti-Pescara, 66100 Chieti, Italy
| | - Bert Blaauw
- Department of Biomedical Sciences, University of Padua, Padua, Italy; Venetian Institute of Molecular Medicine, Padova, Italy.
| | - Ana Ferreiro
- Basic and Translational Myology Laboratory, Université Paris, BFA, UMR 8251, CNRS, 75013 Paris, France; APHP, Reference Center for Neuromuscular Disorders Nord-Est-Ile de France, Neuromyology Department, Groupe Hospitalier Pitié-Salpêtrière, Paris, France.
| | - Ester Zito
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy; Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy.
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7
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Gercke D, Lenz F, Jose J. Split-GFP complementation at the bacterial cell surface for antibody-free labeling and quantification of heterologous protein display. Enzyme Microb Technol 2024; 174:110391. [PMID: 38176324 DOI: 10.1016/j.enzmictec.2023.110391] [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: 10/18/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
The split-GFP system is a versatile tool with numerous applications, but it has been underutilized for the labeling of heterologous surface-displayed proteins. By inserting the 16 amino acid sequence of the GFP11-tag between a protein of interest and an autotransporter protein, it is possible to present a protein at the outer membrane of gram-negative bacteria and to fluorescently label it by complementation with externally added GFP1-10. The labeled cells could be clearly discerned from cells without the protein of interest using flow cytometry and the insertion of the GFP11-tag caused no significant alteration of the catalytic activity for the tested model enzyme CsBglA. Furthermore, the amount of the protein of interest on the cells could be quantified by comparing the green fluorescence resulting from the complementation to that of standards with known concentrations. This allows a precise characterization of whole-cell biocatalysts, which is difficult with existing methods. The split-GFP complementation approach was shown to be specific, in a similar manner as commercial antibodies. It is cost-efficient, minimizes the possibility of adverse effects on protein expression or solubility, and can be performed at high throughput.
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Affiliation(s)
- David Gercke
- Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Corrensstrasse 48, 48149 Münster, Germany
| | - Florian Lenz
- Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Corrensstrasse 48, 48149 Münster, Germany
| | - Joachim Jose
- Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Corrensstrasse 48, 48149 Münster, Germany.
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8
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Hofstadter WA, Tsopurashvili E, Cristea IM. Viral regulation of organelle membrane contact sites. PLoS Biol 2024; 22:e3002529. [PMID: 38442090 PMCID: PMC10914265 DOI: 10.1371/journal.pbio.3002529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
At the core of organelle functions lies their ability and need to form dynamic organelle-organelle networks that drive intracellular communication and coordination of cellular pathways. These networks are facilitated by membrane contact sites (MCSs) that promote both intra-organelle and inter-organelle communication. Given their multiple functions, MCSs and the proteins that form them are commonly co-opted by viruses during infection to promote viral replication. This Essay discusses mechanisms acquired by diverse human viruses to regulate MCS functions in either proviral processes or host defense. It also examines techniques used for examining MCSs in the context of viral infections.
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Affiliation(s)
- William A. Hofstadter
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Elene Tsopurashvili
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
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9
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Giamogante F, Barazzuol L, Maiorca F, Poggio E, Esposito A, Masato A, Napolitano G, Vagnoni A, Calì T, Brini M. A SPLICS reporter reveals [Formula: see text]-synuclein regulation of lysosome-mitochondria contacts which affects TFEB nuclear translocation. Nat Commun 2024; 15:1516. [PMID: 38374070 PMCID: PMC10876553 DOI: 10.1038/s41467-024-46007-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
Mitochondrial and lysosomal activities are crucial to maintain cellular homeostasis: optimal coordination is achieved at their membrane contact sites where distinct protein machineries regulate organelle network dynamics, ions and metabolites exchange. Here we describe a genetically encoded SPLICS reporter for short- and long- juxtapositions between mitochondria and lysosomes. We report the existence of narrow and wide lysosome-mitochondria contacts differently modulated by mitophagy, autophagy and genetic manipulation of tethering factors. The overexpression of α-synuclein (α-syn) reduces the apposition of mitochondria/lysosomes membranes and affects their privileged Ca2+ transfer, impinging on TFEB nuclear translocation. We observe enhanced TFEB nuclear translocation in α-syn-overexpressing cells. We propose that α-syn, by interfering with mitochondria/lysosomes tethering impacts on local Ca2+ regulated pathways, among which TFEB mediated signaling, and in turn mitochondrial and lysosomal function. Defects in mitochondria and lysosome represent a common hallmark of neurodegenerative diseases: targeting their communication could open therapeutic avenues.
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Affiliation(s)
- Flavia Giamogante
- Department of Biomedical Sciences (DSB), University of Padova, Padova, Italy
| | - Lucia Barazzuol
- Department of Biomedical Sciences (DSB), University of Padova, Padova, Italy
| | | | - Elena Poggio
- Department of Biology (DIBIO), University of Padova, Padova, Italy
| | - Alessandra Esposito
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Anna Masato
- Department of Biology (DIBIO), University of Padova, Padova, Italy
- UK-Dementia Research Institute at UCL, University College London, London, UK
| | - Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Alessio Vagnoni
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Tito Calì
- Department of Biomedical Sciences (DSB), University of Padova, Padova, Italy.
- Padova Neuroscience Center (PNC), University of Padova, Padova, Italy.
- Study Center for Neurodegeneration (CESNE), University of Padova, Padova, Italy.
| | - Marisa Brini
- Department of Biology (DIBIO), University of Padova, Padova, Italy.
- Study Center for Neurodegeneration (CESNE), University of Padova, Padova, Italy.
- Department of Pharmaceutical and Pharmacological Sciences (DSF), University of Padova, Padova, Italy.
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10
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Elwakiel A, Mathew A, Isermann B. The role of endoplasmic reticulum-mitochondria-associated membranes in diabetic kidney disease. Cardiovasc Res 2024; 119:2875-2883. [PMID: 38367274 DOI: 10.1093/cvr/cvad190] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 02/19/2024] Open
Abstract
Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease worldwide. The pathomechanisms of DKD are multifactorial, yet haemodynamic and metabolic changes in the early stages of the disease appear to predispose towards irreversible functional loss and histopathological changes. Recent studies highlight the importance of endoplasmic reticulum-mitochondria-associated membranes (ER-MAMs), structures conveying important cellular homeostatic and metabolic effects, in the pathology of DKD. Disruption of ER-MAM integrity in diabetic kidneys is associated with DKD progression, but the regulation of ER-MAMs and their pathogenic contribution remain largely unknown. Exploring the cell-specific components and dynamic changes of ER-MAMs in diabetic kidneys may lead to the identification of new approaches to detect and stratify diabetic patients with DKD. In addition, these insights may lead to novel therapeutic approaches to target and/or reverse disease progression. In this review, we discuss the association of ER-MAMs with key pathomechanisms driving DKD such as insulin resistance, dyslipidaemia, ER stress, and inflammasome activation and the importance of further exploration of ER-MAMs as diagnostic and therapeutic targets in DKD.
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Affiliation(s)
- Ahmed Elwakiel
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Paul-List-Straße 13/15, 04103 Leipzig, Germany
| | - Akash Mathew
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Paul-List-Straße 13/15, 04103 Leipzig, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Paul-List-Straße 13/15, 04103 Leipzig, Germany
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11
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Cui M, Yamano K, Yamamoto K, Yamamoto-Imoto H, Minami S, Yamamoto T, Matsui S, Kaminishi T, Shima T, Ogura M, Tsuchiya M, Nishino K, Layden BT, Kato H, Ogawa H, Oki S, Okada Y, Isaka Y, Kosako H, Matsuda N, Yoshimori T, Nakamura S. HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence. Proc Natl Acad Sci U S A 2024; 121:e2306454120. [PMID: 38170752 PMCID: PMC10786298 DOI: 10.1073/pnas.2306454120] [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: 04/23/2023] [Accepted: 11/15/2023] [Indexed: 01/05/2024] Open
Abstract
Mitochondrial and lysosomal functions are intimately linked and are critical for cellular homeostasis, as evidenced by the fact that cellular senescence, aging, and multiple prominent diseases are associated with concomitant dysfunction of both organelles. However, it is not well understood how the two important organelles are regulated. Transcription factor EB (TFEB) is the master regulator of lysosomal function and is also implicated in regulating mitochondrial function; however, the mechanism underlying the maintenance of both organelles remains to be fully elucidated. Here, by comprehensive transcriptome analysis and subsequent chromatin immunoprecipitation-qPCR, we identified hexokinase domain containing 1 (HKDC1), which is known to function in the glycolysis pathway as a direct TFEB target. Moreover, HKDC1 was upregulated in both mitochondrial and lysosomal stress in a TFEB-dependent manner, and its function was critical for the maintenance of both organelles under stress conditions. Mechanistically, the TFEB-HKDC1 axis was essential for PINK1 (PTEN-induced kinase 1)/Parkin-dependent mitophagy via its initial step, PINK1 stabilization. In addition, the functions of HKDC1 and voltage-dependent anion channels, with which HKDC1 interacts, were essential for the clearance of damaged lysosomes and maintaining mitochondria-lysosome contact. Interestingly, HKDC1 regulated mitophagy and lysosomal repair independently of its prospective function in glycolysis. Furthermore, loss function of HKDC1 accelerated DNA damage-induced cellular senescence with the accumulation of hyperfused mitochondria and damaged lysosomes. Our results show that HKDC1, a factor downstream of TFEB, maintains both mitochondrial and lysosomal homeostasis, which is critical to prevent cellular senescence.
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Affiliation(s)
- Mengying Cui
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Koji Yamano
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo156-8506, Japan
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo113-8510, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Hitomi Yamamoto-Imoto
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Satoshi Minami
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
- Department of Nephrology, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Takeshi Yamamoto
- Department of Nephrology, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Sho Matsui
- Department of Nephrology, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Tatsuya Kaminishi
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka565-0871, Japan
| | - Takayuki Shima
- Department of Biochemistry, Nara Medical University, Kashihara, Nara634-8521, Japan
| | - Monami Ogura
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Megumi Tsuchiya
- Laboratory of Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima770-8503, Japan
| | - Brian T. Layden
- Division of Endocrinology, Diabetes, and Metabolism, University of Illinois Chicago, Chicago, IL60612
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL60612
| | - Hisakazu Kato
- Department of Medical Biochemistry, Graduate School of Medicine/Frontier Bioscience, Osaka University, Suita, Osaka565-0871, Japan
| | - Hidesato Ogawa
- Laboratory of Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Shinya Oki
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto606-8501, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka565-0871, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center, World Premier International Research Center (WPI-IFReC), Osaka University, Suita, Osaka565-0871, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima770-8503, Japan
| | - Noriyuki Matsuda
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo156-8506, Japan
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo113-8510, Japan
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka565-0871, Japan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Shuhei Nakamura
- Department of Biochemistry, Nara Medical University, Kashihara, Nara634-8521, Japan
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12
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Cardoen B, Vandevoorde KR, Gao G, Ortiz-Silva M, Alan P, Liu W, Tiliakou E, Vogl AW, Hamarneh G, Nabi IR. Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria-ER contacts. J Cell Biol 2024; 223:e202206109. [PMID: 37948126 PMCID: PMC10638097 DOI: 10.1083/jcb.202206109] [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: 06/23/2022] [Revised: 09/20/2022] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
Identification and morphological analysis of mitochondria-ER contacts (MERCs) by fluorescent microscopy is limited by subpixel resolution interorganelle distances. Here, the membrane contact site (MCS) detection algorithm, MCS-DETECT, reconstructs subpixel resolution MERCs from 3D super-resolution image volumes. MCS-DETECT shows that elongated ribosome-studded riboMERCs, present in HT-1080 but not COS-7 cells, are morphologically distinct from smaller smooth contacts and larger contacts induced by mitochondria-ER linker expression in COS-7 cells. RiboMERC formation is associated with increased mitochondrial potential, reduced in Gp78 knockout HT-1080 cells and induced by Gp78 ubiquitin ligase activity in COS-7 and HeLa cells. Knockdown of riboMERC tether RRBP1 eliminates riboMERCs in both wild-type and Gp78 knockout HT-1080 cells. By MCS-DETECT, Gp78-dependent riboMERCs present complex tubular shapes that intercalate between and contact multiple mitochondria. MCS-DETECT of 3D whole-cell super-resolution image volumes, therefore, identifies novel dual control of tubular riboMERCs, whose formation is dependent on RRBP1 and size modulated by Gp78 E3 ubiquitin ligase activity.
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Affiliation(s)
- Ben Cardoen
- School of Computing Science, Simon Fraser University, Burnaby, Canada
| | - Kurt R. Vandevoorde
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Guang Gao
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Milene Ortiz-Silva
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Parsa Alan
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - William Liu
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Ellie Tiliakou
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - A. Wayne Vogl
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Ghassan Hamarneh
- School of Computing Science, Simon Fraser University, Burnaby, Canada
| | - Ivan R. Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
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13
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Chevet E, De Matteis MA, Eskelinen EL, Farhan H. Dynamic tandem proximity-based proteomics-Protein trafficking at the proteome-scale. Traffic 2023; 24:546-548. [PMID: 37581229 DOI: 10.1111/tra.12914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/25/2023] [Indexed: 08/16/2023]
Abstract
TransitID is a new methodology based on proximity labeling allowing for the study of protein trafficking a the proteome scale.
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Affiliation(s)
- Eric Chevet
- INSERM U1242, University of Rennes, Rennes, France
- Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II-Medical School, Naples, Italy
| | | | - Hesso Farhan
- Institute of Pathophysiology, Medical University of Innsbruck, Innsbruck, Austria
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14
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Lemos FO, de Ridder I, Bootman MD, Bultynck G, Parys JB. The Complex Effects of PKM2 and PKM2:IP 3R Disruption on Intracellular Ca 2+ Handling and Cellular Functions. Cells 2023; 12:2527. [PMID: 37947604 PMCID: PMC10647343 DOI: 10.3390/cells12212527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/12/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Pyruvate kinase M (PKM) 2 was described to interact with the inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) and suppress its activity. To further investigate the physiological importance of the PKM2:IP3R interaction, we developed and characterized HeLa PKM2 knockout (KO) cells. In the HeLa PKM2 KO cells, the release of Ca2+ to the cytosol appears to be more sensitive to low agonist concentrations than in HeLa wild-type (WT) cells. However, upon an identical IP3-induced Ca2+ release, Ca2+ uptake in the mitochondria is decreased in HeLa PKM2 KO cells, which may be explained by the smaller number of contact sites between the ER and the mitochondria. Furthermore, in HeLa PKM2 KO cells, mitochondria are more numerous, though they are smaller and less branched and have a hyperpolarized membrane potential. TAT-D5SD, a cell-permeable peptide representing a sequence derived from IP3R1 that can disrupt the PKM2:IP3R interaction, induces Ca2+ release into the cytosol and Ca2+ uptake into mitochondria in both HeLa WT and PKM2 KO cells. Moreover, TAT-D5SD induced apoptosis in HeLa WT and PKM2 KO cells but not in HeLa cells completely devoid of IP3Rs. These results indicate that PKM2 separately regulates cytosolic and mitochondrial Ca2+ handling and that the cytotoxic effect of TAT-D5SD depends on IP3R activity but not on PKM2. However, the tyrosine kinase Lck, which also interacts with the D5SD sequence, is expressed neither in HeLa WT nor PKM2 KO cells, and we can also exclude a role for PKM1, which is upregulated in HeLa PKM2 KO cells, indicating that the TAT-D5SD peptide has a more complex mode of action than anticipated.
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Affiliation(s)
- Fernanda O. Lemos
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Herestraat 49, Campus Gasthuisberg O&NI—B802, 3000 Leuven, Belgium; (I.d.R.); (G.B.)
| | - Ian de Ridder
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Herestraat 49, Campus Gasthuisberg O&NI—B802, 3000 Leuven, Belgium; (I.d.R.); (G.B.)
| | - Martin D. Bootman
- School of Life, Health and Chemical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, UK;
| | - Geert Bultynck
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Herestraat 49, Campus Gasthuisberg O&NI—B802, 3000 Leuven, Belgium; (I.d.R.); (G.B.)
| | - Jan B. Parys
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Herestraat 49, Campus Gasthuisberg O&NI—B802, 3000 Leuven, Belgium; (I.d.R.); (G.B.)
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15
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Zhang H, Bernaleau L, Delacrétaz M, Hasanovic E, Drobek A, Eibel H, Rebsamen M. SLC15A4 controls endolysosomal TLR7-9 responses by recruiting the innate immune adaptor TASL. Cell Rep 2023; 42:112916. [PMID: 37527038 DOI: 10.1016/j.celrep.2023.112916] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023] Open
Abstract
Endolysosomal Toll-like receptors (TLRs) play crucial roles in immune responses to pathogens, while aberrant activation of these pathways is associated with autoimmune diseases, including systemic lupus erythematosus (SLE). The endolysosomal solute carrier family 15 member 4 (SLC15A4) is required for TLR7/8/9-induced responses and disease development in SLE models. SLC15A4 has been proposed to affect TLR7-9 activation through its transport activity, as well as by assembling an IRF5-activating complex with TASL, but the relative contribution of these functions remains unclear. Here, we show that the essential role of SLC15A4 is to recruit TASL to endolysosomes, while its transport activity is dispensable when TASL is tethered to this compartment. Endolysosomal-localized TASL rescues TLR7-9-induced IRF5 activation as well as interferon β and cytokine production in SLC15A4-deficient cells. SLC15A4 acts as signaling scaffold, and this function is essential to control TLR7-9-mediated inflammatory responses. These findings support targeting the SLC15A4-TASL complex as a potential therapeutic strategy for SLE and related diseases.
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Affiliation(s)
- Haobo Zhang
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland
| | - Léa Bernaleau
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland
| | - Maeva Delacrétaz
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland
| | - Ed Hasanovic
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland
| | - Ales Drobek
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland
| | - Hermann Eibel
- Department of Rheumatology and Clinical Immunology, Medical Center and Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency, Medical Center and Faculty of Medicine, University of Freiburg, Breisacherstr. 115, 79106 Freiburg, Germany
| | - Manuele Rebsamen
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland.
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16
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Zhou M, Kong B, Zhang X, Xiao K, Lu J, Li W, Li M, Li Z, Ji W, Hou J, Xu T. A proximity labeling strategy enables proteomic analysis of inter-organelle membrane contacts. iScience 2023; 26:107159. [PMID: 37485370 PMCID: PMC10362359 DOI: 10.1016/j.isci.2023.107159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/03/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023] Open
Abstract
Inter-organelle membrane contacts are highly dynamic and act as central hubs for many biological processes, but the protein compositions remain largely unknown due to the lack of efficient tools. Here, we developed BiFCPL to analyze the contact proteome in living cells by a bimolecular fluorescence complementation (BiFC)-based proximity labeling (PL) strategy. BiFCPL was applied to study mitochondria-endoplasmic reticulum contacts (MERCs) and mitochondria-lipid droplet (LD) contacts. We identified 403 highly confident MERC proteins, including many transiently resident proteins and potential tethers. Moreover, we demonstrated that mitochondria-LD contacts are sensitive to nutrient status. A comparative proteomic analysis revealed that 60 proteins are up- or downregulated at contact sites under metabolic challenge. We verified that SQLE, an enzyme for cholesterol synthesis, accumulates at mitochondria-LD contact sites probably to utilize local ATP for cholesterol synthesis. This work provides an efficient method to identify key proteins at inter-organelle membrane contacts in living cells.
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Affiliation(s)
- Maoge Zhou
- Guangzhou Laboratory, Guangzhou, Guangdong 510005, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bingjie Kong
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiang Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ke Xiao
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Lu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Weixing Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Li
- Guangzhou Laboratory, Guangzhou, Guangdong 510005, China
| | - Zonghong Li
- Guangzhou Laboratory, Guangzhou, Guangdong 510005, China
| | - Wei Ji
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junjie Hou
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Xu
- Guangzhou Laboratory, Guangzhou, Guangdong 510005, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Biomedical Engineering, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
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17
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Poggio E, Vallese F, Hartel AJW, Morgenstern TJ, Kanner SA, Rauh O, Giamogante F, Barazzuol L, Shepard KL, Colecraft HM, Clarke OB, Brini M, Calì T. Perturbation of the host cell Ca 2+ homeostasis and ER-mitochondria contact sites by the SARS-CoV-2 structural proteins E and M. Cell Death Dis 2023; 14:297. [PMID: 37120609 PMCID: PMC10148623 DOI: 10.1038/s41419-023-05817-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/01/2023]
Abstract
Coronavirus disease (COVID-19) is a contagious respiratory disease caused by the SARS-CoV-2 virus. The clinical phenotypes are variable, ranging from spontaneous recovery to serious illness and death. On March 2020, a global COVID-19 pandemic was declared by the World Health Organization (WHO). As of February 2023, almost 670 million cases and 6,8 million deaths have been confirmed worldwide. Coronaviruses, including SARS-CoV-2, contain a single-stranded RNA genome enclosed in a viral capsid consisting of four structural proteins: the nucleocapsid (N) protein, in the ribonucleoprotein core, the spike (S) protein, the envelope (E) protein, and the membrane (M) protein, embedded in the surface envelope. In particular, the E protein is a poorly characterized viroporin with high identity amongst all the β-coronaviruses (SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43) and a low mutation rate. Here, we focused our attention on the study of SARS-CoV-2 E and M proteins, and we found a general perturbation of the host cell calcium (Ca2+) homeostasis and a selective rearrangement of the interorganelle contact sites. In vitro and in vivo biochemical analyses revealed that the binding of specific nanobodies to soluble regions of SARS-CoV-2 E protein reversed the observed phenotypes, suggesting that the E protein might be an important therapeutic candidate not only for vaccine development, but also for the clinical management of COVID designing drug regimens that, so far, are very limited.
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Affiliation(s)
- Elena Poggio
- Department of Biology, University of Padova, Padova, Italy
| | - Francesca Vallese
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Andreas J W Hartel
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Travis J Morgenstern
- Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY, USA
| | - Scott A Kanner
- Doctoral Program in Neurobiology and Behavior, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Oliver Rauh
- Membrane Biophysics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Flavia Giamogante
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Lucia Barazzuol
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Henry M Colecraft
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY, USA
- Doctoral Program in Neurobiology and Behavior, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Oliver Biggs Clarke
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Marisa Brini
- Department of Biology, University of Padova, Padova, Italy
- Study Center for Neurodegeneration (CESNE), University of Padova, Padova, Italy
| | - Tito Calì
- Department of Biomedical Sciences, University of Padova, Padova, Italy.
- Study Center for Neurodegeneration (CESNE), University of Padova, Padova, Italy.
- Padova Neuroscience Center (PNC), University of Padova, Padova, Italy.
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18
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Bassot A, Chen J, Takahashi-Yamashiro K, Yap MC, Gibhardt CS, Le GNT, Hario S, Nasu Y, Moore J, Gutiérrez T, Mina L, Mast H, Moses A, Bhat R, Ballanyi K, Lemieux H, Sitia R, Zito E, Bogeski I, Campbell RE, Simmen T. The endoplasmic reticulum kinase PERK interacts with the oxidoreductase ERO1 to metabolically adapt mitochondria. Cell Rep 2023; 42:111899. [PMID: 36586409 DOI: 10.1016/j.celrep.2022.111899] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 10/04/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022] Open
Abstract
Endoplasmic reticulum (ER) homeostasis requires molecular regulators that tailor mitochondrial bioenergetics to the needs of protein folding. For instance, calnexin maintains mitochondria metabolism and mitochondria-ER contacts (MERCs) through reactive oxygen species (ROS) from NADPH oxidase 4 (NOX4). However, induction of ER stress requires a quick molecular rewiring of mitochondria to adapt to new energy needs. This machinery is not characterized. We now show that the oxidoreductase ERO1⍺ covalently interacts with protein kinase RNA-like ER kinase (PERK) upon treatment with tunicamycin. The PERK-ERO1⍺ interaction requires the C-terminal active site of ERO1⍺ and cysteine 216 of PERK. Moreover, we show that the PERK-ERO1⍺ complex promotes oxidization of MERC proteins and controls mitochondrial dynamics. Using proteinaceous probes, we determined that these functions improve ER-mitochondria Ca2+ flux to maintain bioenergetics in both organelles, while limiting oxidative stress. Therefore, the PERK-ERO1⍺ complex is a key molecular machinery that allows quick metabolic adaptation to ER stress.
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Affiliation(s)
- Arthur Bassot
- Department of Cell Biology, Faculty of Medicine and Dentistry, Edmonton, AB T6G 2G2, Canada
| | - Junsheng Chen
- Department of Cell Biology, Faculty of Medicine and Dentistry, Edmonton, AB T6G 2G2, Canada
| | | | - Megan C Yap
- Department of Cell Biology, Faculty of Medicine and Dentistry, Edmonton, AB T6G 2G2, Canada
| | - Christine Silvia Gibhardt
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Giang N T Le
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Saaya Hario
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yusuke Nasu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jack Moore
- Alberta Proteomics and Mass Spectrometry Facility, University of Alberta, 4096 Katz Research Building, Edmonton AB T6G2E1, Canada
| | - Tomas Gutiérrez
- Department of Cell Biology, Faculty of Medicine and Dentistry, Edmonton, AB T6G 2G2, Canada
| | - Lucas Mina
- Department of Cell Biology, Faculty of Medicine and Dentistry, Edmonton, AB T6G 2G2, Canada
| | - Heather Mast
- Faculty Saint-Jean, Department of Medicine, Faculty of Medicine and Dentistry, Edmonton, AB T6G2H7, Canada
| | - Audric Moses
- Department of Pediatrics, Edmonton, AB T6G2H7, Canada
| | - Rakesh Bhat
- Precision Biolaboratories, St. Albert, AB T8N 5A7, Canada
| | - Klaus Ballanyi
- Department of Physiology, University of Alberta, Edmonton, AB T6G2H7, Canada
| | - Hélène Lemieux
- Faculty Saint-Jean, Department of Medicine, Faculty of Medicine and Dentistry, Edmonton, AB T6G2H7, Canada
| | - Roberto Sitia
- Division of Genetics and Cell Biology, Università Vita-Salute IRCCS Ospedale San Raffaele, 20132 Milano, Italy
| | - Ester Zito
- Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milano, Italy; Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino PU, Italy
| | - Ivan Bogeski
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Thomas Simmen
- Department of Cell Biology, Faculty of Medicine and Dentistry, Edmonton, AB T6G 2G2, Canada.
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19
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Unraveling Presenilin 2 Functions in a Knockout Zebrafish Line to Shed Light into Alzheimer's Disease Pathogenesis. Cells 2023; 12:cells12030376. [PMID: 36766721 PMCID: PMC9913325 DOI: 10.3390/cells12030376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
Mutations in presenilin 2 (PS2) have been causally linked to the development of inherited Alzheimer's disease (AD). Besides its role as part of the γ-secretase complex, mammalian PS2 is also involved, as an individual protein, in a growing number of cell processes, which result altered in AD. To gain more insight into PS2 (dys)functions, we have generated a presenilin2 (psen2) knockout zebrafish line. We found that the absence of the protein does not markedly influence Notch signaling at early developmental stages, suggesting a Psen2 dispensable role in the γ-secretase-mediated Notch processing. Instead, loss of Psen2 induces an exaggerated locomotor response to stimulation in fish larvae, a reduced number of ER-mitochondria contacts in zebrafish neurons, and an increased basal autophagy. Moreover, the protein is involved in mitochondrial axonal transport, since its acute downregulation reduces in vivo organelle flux in zebrafish sensory neurons. Importantly, the expression of a human AD-linked mutant of the protein increases this vital process. Overall, our results confirm zebrafish as a good model organism for investigating PS2 functions in vivo, representing an alternative tool for the characterization of new AD-linked defective cell pathways and the testing of possible correcting drugs.
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20
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Integrated multimodality microscope for accurate and efficient target-guided cryo-lamellae preparation. Nat Methods 2023; 20:268-275. [PMID: 36646896 PMCID: PMC9911353 DOI: 10.1038/s41592-022-01749-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 12/06/2022] [Indexed: 01/18/2023]
Abstract
Cryo-electron tomography (cryo-ET) is a revolutionary technique for resolving the structure of subcellular organelles and macromolecular complexes in their cellular context. However, the application of the cryo-ET is hampered by the sample preparation step. Performing cryo-focused ion beam milling at an arbitrary position on the sample is inefficient, and the target of interest is not guaranteed to be preserved when thinning the cell from several micrometers to less than 300 nm thick. Here, we report a cryogenic correlated light, ion and electron microscopy (cryo-CLIEM) technique that is capable of preparing cryo-lamellae under the guidance of three-dimensional confocal imaging. Moreover, we demonstrate a workflow to preselect and preserve nanoscale target regions inside the finished cryo-lamellae. By successfully preparing cryo-lamellae that contain a single centriole or contact sites between subcellular organelles, we show that this approach is generally applicable, and shall help in innovating more applications of cryo-ET.
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21
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Physiological roles of organelles at the pre-synapse in neurons. Int J Biochem Cell Biol 2023; 154:106345. [PMID: 36521722 DOI: 10.1016/j.biocel.2022.106345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/03/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022]
Abstract
Mitochondria, endoplasmic reticulum and lysosomes are involved in different pathways that can regulate pre-synaptic function. In particular, they could modulate ATP availability in response to rapid changes, could control synaptic protein levels and adjust Ca2+ signalling, which could all impact on neuronal activity. Organelles functions in these processes need to be considered alone when describing the impact of pre-synaptic organelles on neurotransmission. However, the interplay among organelles, which occurs either via signalling pathways or through physical membranous contacts, has to be considered. In this brief review, the physiological role of organelles localized at the pre-synapse in neuronal function is discussed.
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22
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Kamoshita M, Schrader M. Proximity-Ligation Assay to Detect Peroxisome-Organelle Interaction. Methods Mol Biol 2023; 2643:135-148. [PMID: 36952183 DOI: 10.1007/978-1-0716-3048-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Peroxisomes are essential organelles in mammals, which contribute to cellular lipid metabolism and redox homeostasis. They do not function as isolated entities but cooperate and interact with other subcellular organelles, in particular the endoplasmic reticulum, mitochondria, and lipid droplets. Those interactions are often mediated by membrane contact sites. Tether proteins at those sites bring the organelles in close proximity to facilitate metabolite and lipid transfer as well as organelle communication. There is great interest in the investigation of the physiological functions of peroxisome-organelle contacts and how they are regulated. Here, we present an antibody- and fluorescence-based proximity ligation approach used successfully in our laboratory for the detection and quantification of peroxisome-organelle interactions in cultured mammalian cells.
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Affiliation(s)
- Maki Kamoshita
- Faculty of Health and Life Sciences, Biosciences, University of Exeter, Exeter, Devon, UK
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Michael Schrader
- Faculty of Health and Life Sciences, Biosciences, University of Exeter, Exeter, Devon, UK.
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23
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Jang W, Puchkov D, Samsó P, Liang Y, Nadler-Holly M, Sigrist SJ, Kintscher U, Liu F, Mamchaoui K, Mouly V, Haucke V. Endosomal lipid signaling reshapes the endoplasmic reticulum to control mitochondrial function. Science 2022; 378:eabq5209. [PMID: 36520888 DOI: 10.1126/science.abq5209] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cells respond to fluctuating nutrient supply by adaptive changes in organelle dynamics and in metabolism. How such changes are orchestrated on a cell-wide scale is unknown. We show that endosomal signaling lipid turnover by MTM1, a phosphatidylinositol 3-phosphate [PI(3)P] 3-phosphatase mutated in X-linked centronuclear myopathy in humans, controls mitochondrial morphology and function by reshaping the endoplasmic reticulum (ER). Starvation-induced endosomal recruitment of MTM1 impairs PI(3)P-dependent contact formation between tubular ER membranes and early endosomes, resulting in the conversion of ER tubules into sheets, the inhibition of mitochondrial fission, and sustained oxidative metabolism. Our results unravel an important role for early endosomal lipid signaling in controlling ER shape and, thereby, mitochondrial form and function to enable cells to adapt to fluctuating nutrient environments.
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Affiliation(s)
- Wonyul Jang
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Dmytro Puchkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Paula Samsó
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - YongTian Liang
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Michal Nadler-Holly
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Stephan J Sigrist
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Fan Liu
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Kamel Mamchaoui
- Centre de Recherche en Myologie, Institut de Myologie, Inserm, Sorbonne Université, 75013 Paris, France
| | - Vincent Mouly
- Centre de Recherche en Myologie, Institut de Myologie, Inserm, Sorbonne Université, 75013 Paris, France
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany.,Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany.,Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
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24
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Wu Z, Berlemann LA, Bader V, Sehr DA, Dawin E, Covallero A, Meschede J, Angersbach L, Showkat C, Michaelis JB, Münch C, Rieger B, Namgaladze D, Herrera MG, Fiesel FC, Springer W, Mendes M, Stepien J, Barkovits K, Marcus K, Sickmann A, Dittmar G, Busch KB, Riedel D, Brini M, Tatzelt J, Cali T, Winklhofer KF. LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus. EMBO J 2022; 41:e112006. [PMID: 36398858 PMCID: PMC9753471 DOI: 10.15252/embj.2022112006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
Mitochondria are increasingly recognized as cellular hubs to orchestrate signaling pathways that regulate metabolism, redox homeostasis, and cell fate decisions. Recent research revealed a role of mitochondria also in innate immune signaling; however, the mechanisms of how mitochondria affect signal transduction are poorly understood. Here, we show that the NF-κB pathway activated by TNF employs mitochondria as a platform for signal amplification and shuttling of activated NF-κB to the nucleus. TNF treatment induces the recruitment of HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), and its substrate NEMO to the outer mitochondrial membrane, where M1- and K63-linked ubiquitin chains are generated. NF-κB is locally activated and transported to the nucleus by mitochondria, leading to an increase in mitochondria-nucleus contact sites in a HOIP-dependent manner. Notably, TNF-induced stabilization of the mitochondrial kinase PINK1 furthermore contributes to signal amplification by antagonizing the M1-ubiquitin-specific deubiquitinase OTULIN. Overall, our study reveals a role for mitochondria in amplifying TNF-mediated NF-κB activation, both serving as a signaling platform, as well as a transport mode for activated NF-κB to the nuclear.
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Affiliation(s)
- Zhixiao Wu
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Lena A Berlemann
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Dominik A Sehr
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Eva Dawin
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- Leibniz‐Institut für Analytische Wissenschaften—ISAS—e.VDortmundGermany
| | | | - Jens Meschede
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Lena Angersbach
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Cathrin Showkat
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Jonas B Michaelis
- Faculty of Medicine, Institute of Biochemistry IIGoethe University FrankfurtFrankfurt am MainGermany
| | - Christian Münch
- Faculty of Medicine, Institute of Biochemistry IIGoethe University FrankfurtFrankfurt am MainGermany
| | - Bettina Rieger
- Institute for Integrative Cell Biology and Physiology, Faculty of BiologyUniversity of MünsterMünsterGermany
| | - Dmitry Namgaladze
- Institute of Biochemistry I, Faculty of MedicineGoethe‐University FrankfurtFrankfurtGermany
| | - Maria Georgina Herrera
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Fabienne C Fiesel
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Neuroscience PhD ProgramMayo Clinic Graduate School of Biomedical SciencesJacksonvilleFLUSA
| | - Wolfdieter Springer
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Neuroscience PhD ProgramMayo Clinic Graduate School of Biomedical SciencesJacksonvilleFLUSA
| | - Marta Mendes
- Proteomics of Cellular Signaling, Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
| | - Jennifer Stepien
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Katalin Barkovits
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Katrin Marcus
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Albert Sickmann
- Leibniz‐Institut für Analytische Wissenschaften—ISAS—e.VDortmundGermany
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
- Department of Life Sciences and MedicineUniversity of LuxembourgBelvauxLuxembourg
| | - Karin B Busch
- Institute for Integrative Cell Biology and Physiology, Faculty of BiologyUniversity of MünsterMünsterGermany
| | - Dietmar Riedel
- Laboratory for Electron MicroscopyMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Marisa Brini
- Department of BiologyUniversity of PaduaPaduaItaly
- Centro Studi per la Neurodegenerazione (CESNE)University of PadovaPaduaItaly
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- RESOLV Cluster of ExcellenceRuhr University BochumBochumGermany
| | - Tito Cali
- Department of Biomedical SciencesUniversity of PaduaPaduaItaly
- Centro Studi per la Neurodegenerazione (CESNE)University of PadovaPaduaItaly
- Padua Neuroscience Center (PNC)University of PaduaPaduaItaly
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- RESOLV Cluster of ExcellenceRuhr University BochumBochumGermany
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25
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Protein synthesis inhibition and loss of homeostatic functions in astrocytes from an Alzheimer's disease mouse model: a role for ER-mitochondria interaction. Cell Death Dis 2022; 13:878. [PMID: 36257957 PMCID: PMC9579125 DOI: 10.1038/s41419-022-05324-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
Abstract
Deregulation of protein synthesis and ER stress/unfolded protein response (ER stress/UPR) have been reported in astrocytes. However, the relationships between protein synthesis deregulation and ER stress/UPR, as well as their role in the altered homeostatic support of Alzheimer's disease (AD) astrocytes remain poorly understood. Previously, we reported that in astrocytic cell lines from 3xTg-AD mice (3Tg-iAstro) protein synthesis was impaired and ER-mitochondria distance was reduced. Here we show that impaired protein synthesis in 3Tg-iAstro is associated with an increase of p-eIF2α and downregulation of GADD34. Although mRNA levels of ER stress/UPR markers were increased two-three-fold, we found neither activation of PERK nor downstream induction of ATF4 protein. Strikingly, the overexpression of a synthetic ER-mitochondrial linker (EML) resulted in a reduced protein synthesis and augmented p-eIF2α without any effect on ER stress/UPR marker genes. In vivo, in hippocampi of 3xTg-AD mice, reduced protein synthesis, increased p-eIF2α and downregulated GADD34 protein were found, while no increase of p-PERK or ATF4 proteins was observed, suggesting that in AD astrocytes, both in vitro and in vivo, phosphorylation of eIF2α and impairment of protein synthesis are PERK-independent. Next, we investigated the ability of 3xTg-AD astrocytes to support metabolism and function of other cells of the central nervous system. Astrocyte-conditioned medium (ACM) from 3Tg-iAstro cells significantly reduced protein synthesis rate in primary hippocampal neurons. When added as a part of pericyte/endothelial cell (EC)/astrocyte 3D co-culture, 3Tg-iAstro, but not WT-iAstro, severely impaired formation and ramification of tubules, the effect, replicated by EML overexpression in WT-iAstro cells. Finally, a chemical chaperone 4-phenylbutyric acid (4-PBA) rescued protein synthesis, p-eIF2α levels in 3Tg-iAstro cells and tubulogenesis in pericyte/EC/3Tg-iAstro co-culture. Collectively, our results suggest that a PERK-independent, p-eIF2α-associated impairment of protein synthesis compromises astrocytic homeostatic functions, and this may be caused by the altered ER-mitochondria interaction.
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26
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Giamogante F, Barazzuol L, Poggio E, Tromboni M, Brini M, Calì T. Stable Integration of Inducible SPLICS Reporters Enables Spatio-Temporal Analysis of Multiple Organelle Contact Sites upon Modulation of Cholesterol Traffic. Cells 2022; 11:cells11101643. [PMID: 35626680 PMCID: PMC9139547 DOI: 10.3390/cells11101643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/06/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022] Open
Abstract
The study of organelle contact sites has received a great impulse due to increased interest in the understanding of their involvement in many disease conditions. Split-GFP-based contact sites (SPLICS) reporters emerged as essential tools to easily detect changes in a wide range of organelle contact sites in cultured cells and in vivo, e.g., in zebrafish larvae. We report here on the generation of a new vector library of SPLICS cloned into a piggyBac system for stable and inducible expression of the reporters in a cell line of interest to overcome any potential weakness due to variable protein expression in transient transfection studies. Stable HeLa cell lines expressing SPLICS between the endoplasmic reticulum (ER) and mitochondria (MT), the ER and plasma membrane (PM), peroxisomes (PO) and ER, and PO and MT, were generated and tested for their ability to express the reporters upon treatment with doxycycline. Moreover, to take advantage of these cellular models, we decided to follow the behavior of different membrane contact sites upon modulating cholesterol traffic. Interestingly, we found that the acute pharmacological inhibition of the intracellular cholesterol transporter 1 (NPC1) differently affects membrane contact sites, highlighting the importance of different interfaces for cholesterol sensing and distribution within the cell.
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Affiliation(s)
- Flavia Giamogante
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (F.G.); (L.B.); (M.T.)
| | - Lucia Barazzuol
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (F.G.); (L.B.); (M.T.)
| | - Elena Poggio
- Department of Biology, University of Padova, 35131 Padova, Italy;
| | - Marta Tromboni
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (F.G.); (L.B.); (M.T.)
| | - Marisa Brini
- Department of Biology, University of Padova, 35131 Padova, Italy;
- Correspondence: (M.B.); (T.C.)
| | - Tito Calì
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (F.G.); (L.B.); (M.T.)
- Padova Neuroscience Center (PNC), University of Padova, 35131 Padova, Italy
- Correspondence: (M.B.); (T.C.)
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27
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Dionne U, Gingras AC. Proximity-Dependent Biotinylation Approaches to Explore the Dynamic Compartmentalized Proteome. Front Mol Biosci 2022; 9:852911. [PMID: 35309513 PMCID: PMC8930824 DOI: 10.3389/fmolb.2022.852911] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
In recent years, proximity-dependent biotinylation approaches, including BioID, APEX, and their derivatives, have been widely used to define the compositions of organelles and other structures in cultured cells and model organisms. The associations between specific proteins and given compartments are regulated by several post-translational modifications (PTMs); however, these effects have not been systematically investigated using proximity proteomics. Here, we discuss the progress made in this field and how proximity-dependent biotinylation strategies could elucidate the contributions of PTMs, such as phosphorylation, to the compartmentalization of proteins.
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Affiliation(s)
- Ugo Dionne
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Anne-Claude Gingras,
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28
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Poggio E, Brini M, Calì T. Get Closer to the World of Contact Sites: A Beginner's Guide to Proximity-Driven Fluorescent Probes. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:25152564221135748. [PMID: 37366505 PMCID: PMC10243574 DOI: 10.1177/25152564221135748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
To maintain cellular homeostasis and to coordinate the proper response to a specific stimulus, information must be integrated throughout the cell in a well-organized network, in which organelles are the crucial nodes and membrane contact sites are the main edges. Membrane contact sites are the cellular subdomains where two or more organelles come into close apposition and interact with each other. Even though many inter-organelle contacts have been identified, most of them are still not fully characterized, therefore their study is an appealing and expanding field of research. Thanks to significant technological progress, many tools are now available or are in rapid development, making it difficult to choose which one is the most suitable for answering a specific biological question. Here we distinguish two different experimental approaches for studying inter-organelle contact sites. The first one aims to morphologically characterize the sites of membrane contact and to identify the molecular players involved, relying mainly on the application of biochemical and electron microscopy (EM)-related methods. The second approach aims to understand the functional importance of a specific contact, focusing on spatio-temporal details. For this purpose, proximity-driven fluorescent probes are the experimental tools of choice, since they allow the monitoring and quantification of membrane contact sites and their dynamics in living cells under different cellular conditions or upon different stimuli. In this review, we focus on these tools with the purpose of highlighting their great versatility and how they can be applied in the study of membrane contacts. We will extensively describe all the different types of proximity-driven fluorescent tools, discussing their benefits and drawbacks, ultimately providing some suggestions to choose and apply the appropriate methods on a case-to-case basis and to obtain the best experimental outcomes.
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Affiliation(s)
- Elena Poggio
- Department of Biology (DiBio), University of
Padova, Padova, Italy
| | - Marisa Brini
- Department of Biology (DiBio), University of
Padova, Padova, Italy
- Study Center for Neurodegeneration (CESNE),
University of Padova, Padova, Italy
| | - Tito Calì
- Study Center for Neurodegeneration (CESNE),
University of Padova, Padova, Italy
- Department of Biomedical Sciences (DSB),
University of Padova, Padova, Italy
- Padova Neuroscience Center (PNC), University
of Padova, Padova, Italy
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29
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Martín-Guerrero SM, Markovinovic A, Mórotz GM, Salam S, Noble W, Miller CCJ. Targeting ER-Mitochondria Signaling as a Therapeutic Target for Frontotemporal Dementia and Related Amyotrophic Lateral Sclerosis. Front Cell Dev Biol 2022; 10:915931. [PMID: 35693938 PMCID: PMC9184680 DOI: 10.3389/fcell.2022.915931] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022] Open
Abstract
Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are two major neurodegenerative diseases. FTD is the second most common cause of dementia and ALS is the most common form of motor neuron disease. These diseases are now known to be linked. There are no cures or effective treatments for FTD or ALS and so new targets for therapeutic intervention are required but this is hampered by the large number of physiological processes that are damaged in FTD/ALS. Many of these damaged functions are now known to be regulated by signaling between the endoplasmic reticulum (ER) and mitochondria. This signaling is mediated by "tethering" proteins that serve to recruit ER to mitochondria. One tether strongly associated with FTD/ALS involves an interaction between the ER protein VAPB and the mitochondrial protein PTPIP51. Recent studies have shown that ER-mitochondria signaling is damaged in FTD/ALS and that this involves breaking of the VAPB-PTPIP51 tethers. Correcting disrupted tethering may therefore correct many other downstream damaged features of FTD/ALS. Here, we review progress on this topic with particular emphasis on targeting of the VAPB-PTPIP51 tethers as a new drug target.
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Affiliation(s)
- Sandra M Martín-Guerrero
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Andrea Markovinovic
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Gábor M Mórotz
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Shaakir Salam
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Wendy Noble
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Christopher C J Miller
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
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