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Breckels LM, Hutchings C, Ingole KD, Kim S, Lilley KS, Makwana MV, McCaskie KJA, Villanueva E. Advances in spatial proteomics: Mapping proteome architecture from protein complexes to subcellular localizations. Cell Chem Biol 2024; 31:1665-1687. [PMID: 39303701 DOI: 10.1016/j.chembiol.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
Abstract
Proteins are responsible for most intracellular functions, which they perform as part of higher-order molecular complexes, located within defined subcellular niches. Localization is both dynamic and context specific and mislocalization underlies a multitude of diseases. It is thus vital to be able to measure the components of higher-order protein complexes and their subcellular location dynamically in order to fully understand cell biological processes. Here, we review the current range of highly complementary approaches that determine the subcellular organization of the proteome. We discuss the scale and resolution at which these approaches are best employed and the caveats that should be taken into consideration when applying them. We also look to the future and emerging technologies that are paving the way for a more comprehensive understanding of the functional roles of protein isoforms, which is essential for unraveling the complexities of cell biology and the development of disease treatments.
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Affiliation(s)
- Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Charlotte Hutchings
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kishor D Ingole
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Suyeon Kim
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Mehul V Makwana
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kieran J A McCaskie
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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2
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Delgado de la Herran H, Vecellio Reane D, Cheng Y, Katona M, Hosp F, Greotti E, Wettmarshausen J, Patron M, Mohr H, Prudente de Mello N, Chudenkova M, Gorza M, Walia S, Feng MSF, Leimpek A, Mielenz D, Pellegata NS, Langer T, Hajnóczky G, Mann M, Murgia M, Perocchi F. Systematic mapping of mitochondrial calcium uniporter channel (MCUC)-mediated calcium signaling networks. EMBO J 2024:10.1038/s44318-024-00219-w. [PMID: 39261663 DOI: 10.1038/s44318-024-00219-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 08/08/2024] [Accepted: 08/15/2024] [Indexed: 09/13/2024] Open
Abstract
The mitochondrial calcium uniporter channel (MCUC) mediates mitochondrial calcium entry, regulating energy metabolism and cell death. Although several MCUC components have been identified, the molecular basis of mitochondrial calcium signaling networks and their remodeling upon changes in uniporter activity have not been assessed. Here, we map the MCUC interactome under resting conditions and upon chronic loss or gain of mitochondrial calcium uptake. We identify 89 high-confidence interactors that link MCUC to several mitochondrial complexes and pathways, half of which are associated with human disease. As a proof-of-concept, we validate the mitochondrial intermembrane space protein EFHD1 as a binding partner of the MCUC subunits MCU, EMRE, and MCUB. We further show a MICU1-dependent inhibitory effect of EFHD1 on calcium uptake. Next, we systematically survey compensatory mechanisms and functional consequences of mitochondrial calcium dyshomeostasis by analyzing the MCU interactome upon EMRE, MCUB, MICU1, or MICU2 knockdown. While silencing EMRE reduces MCU interconnectivity, MCUB loss-of-function leads to a wider interaction network. Our study provides a comprehensive and high-confidence resource to gain insights into players and mechanisms regulating mitochondrial calcium signaling and their relevance in human diseases.
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Affiliation(s)
- Hilda Delgado de la Herran
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Denis Vecellio Reane
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Yiming Cheng
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Máté Katona
- Department of Pathology, Anatomy, and Cell Biology, MitoCare Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Fabian Hosp
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Roche Pharma Research and Early Development, Large Molecule Research, Mass Spectrometry, Penzberg, Germany
| | - Elisa Greotti
- Neuroscience Institute, National Research Council of Italy, Padua, Italy
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Padova Neuroscience Center, University of Padova, Padua, Italy
| | - Jennifer Wettmarshausen
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Maria Patron
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Aging, Cologne, Germany
| | - Hermine Mohr
- Institute of Diabetes and Cancer, Helmholtz Center Munich, Munich, Germany
| | - Natalia Prudente de Mello
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Margarita Chudenkova
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Matteo Gorza
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Safal Walia
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Michael Sheng-Fu Feng
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Anja Leimpek
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, University of Erlangen, Nikolaus-Fiebiger-Zentrum, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Natalia S Pellegata
- Institute of Diabetes and Cancer, Helmholtz Center Munich, Munich, Germany
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Thomas Langer
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Aging, Cologne, Germany
| | - György Hajnóczky
- Department of Pathology, Anatomy, and Cell Biology, MitoCare Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Health Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Marta Murgia
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Department of Biomedical Sciences, University of Padova, Padua, Italy.
| | - Fabiana Perocchi
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany.
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany.
- Munich Cluster for Systems Neurology, Munich, Germany.
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3
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Allsup BL, Gharpure S, Bryson BD. Proximity labeling defines the phagosome lumen proteome of murine and primary human macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611277. [PMID: 39282337 PMCID: PMC11398489 DOI: 10.1101/2024.09.04.611277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Proteomic analyses of the phagosome has significantly improved our understanding of the proteins which contribute to critical phagosome functions such as apoptotic cell clearance and microbial killing. However, previous methods of isolating phagosomes for proteomic analysis have relied on cell fractionation with some intrinsic limitations. Here, we present an alternative and modular proximity-labeling based strategy for mass spectrometry proteomic analysis of the phagosome lumen, termed PhagoID. We optimize proximity labeling in the phagosome and apply PhagoID to immortalized murine macrophages as well as primary human macrophages. Analysis of proteins detected by PhagoID in murine macrophages demonstrate that PhagoID corroborates previous proteomic studies, but also nominates novel proteins with unexpected residence at the phagosome for further study. A direct comparison between the proteins detected by PhagoID between mouse and human macrophages further reveals that human macrophage phagosomes have an increased abundance of proteins involved in the oxidative burst and antigen presentation. Our study develops and benchmarks a new approach to measure the protein composition of the phagosome and validates a subset of these findings, ultimately using PhagoID to grant further insight into the core constituent proteins and species differences at the phagosome lumen.
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Affiliation(s)
- Benjamin L Allsup
- Department of Biological Engineering, MIT, Cambridge, USA
- Ragon Institute of Mass General, Harvard, and MIT, Cambridge, USA
| | - Supriya Gharpure
- Ragon Institute of Mass General, Harvard, and MIT, Cambridge, USA
| | - Bryan D Bryson
- Department of Biological Engineering, MIT, Cambridge, USA
- Ragon Institute of Mass General, Harvard, and MIT, Cambridge, USA
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4
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Cavarischia-Rega C, Sharma K, Fitzgerald JC, Macek B. Proteome dynamics in iPSC-derived human dopaminergic neurons. Mol Cell Proteomics 2024:100838. [PMID: 39251023 DOI: 10.1016/j.mcpro.2024.100838] [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: 03/28/2024] [Revised: 08/18/2024] [Accepted: 08/25/2024] [Indexed: 09/11/2024] Open
Abstract
Dopaminergic neurons participate in fundamental physiological processes and are the cell type primarily affected in Parkinson's disease. Their analysis is challenging due to the intricate nature of their function, involvement in diverse neurological processes, heterogeneity and localization in deep brain regions. Consequently, most of the research on the protein dynamics of dopaminergic neurons has been performed in animal cells ex vivo. Here we use iPSC-derived human mid-brain specific dopaminergic neurons to study general features of their proteome biology and provide datasets for protein turnover and dynamics, including a human axonal translatome. We cover the proteome to a depth of 9,409 proteins and use dynamic SILAC to measure the half-life of more than 4,300 proteins. We report uniform turnover rates of conserved cytosolic protein complexes such as the proteasome and map the variable rates of turnover of the respiratory chain complexes in these cells. We use differential dynamic SILAC labeling in combination with microfluidic devices to analyze local protein synthesis and transport between axons and soma. We report 105 potentially novel axonal markers and detect translocation of 269 proteins between axons and the soma in the time frame of our analysis (120 hours). Importantly, we provide evidence for local synthesis of 154 proteins in the axon and their retrograde transport to the soma, among them several proteins involved in RNA editing such as ADAR1 and the RNA helicase DHX30, involved in the assembly of mitochondrial ribosomes. Our study provides a workflow and resource for future applications of quantitative proteomics in iPSC-derived human neurons.
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Affiliation(s)
- Claudia Cavarischia-Rega
- Quantitative Proteomics, Department of Biology, Interfaculty Institute of Cell Biology, University of Tübingen, Germany
| | - Karan Sharma
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Germany
| | - Julia C Fitzgerald
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Germany.
| | - Boris Macek
- Quantitative Proteomics, Department of Biology, Interfaculty Institute of Cell Biology, University of Tübingen, Germany.
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5
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Hidalgo-Gutierrez A, Shintaku J, Ramon J, Barriocanal-Casado E, Pesini A, Saneto RP, Garrabou G, Milisenda JC, Matas-Garcia A, Gort L, Ugarteburu O, Gu Y, Koganti L, Wang T, Tadesse S, Meneri M, Sciacco M, Wang S, Tanji K, Horwitz MS, Dorschner MO, Mansukhani M, Comi GP, Ronchi D, Marti R, Ribes A, Tort F, Hirano M. Guanylate Kinase 1 Deficiency: A Novel and Potentially Treatable Mitochondrial DNA Depletion/Deletions Disease. Ann Neurol 2024. [PMID: 39230499 DOI: 10.1002/ana.27071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/08/2024] [Accepted: 08/15/2024] [Indexed: 09/05/2024]
Abstract
OBJECTIVE Mitochondrial DNA (mtDNA) depletion/deletions syndrome (MDDS) comprises a group of diseases caused by primary autosomal defects of mtDNA maintenance. Our objective was to study the etiology of MDDS in 4 patients who lack pathogenic variants in known genetic causes. METHODS Whole exome sequencing of the probands was performed to identify pathogenic variants. We validated the mitochondrial defect by analyzing mtDNA, mitochondrial dNTP pools, respiratory chain activities, and GUK1 activity. To confirm pathogenicity of GUK1 deficiency, we expressed 2 GUK1 isoforms in patient cells. RESULTS We identified biallelic GUK1 pathogenic variants in all 4 probands who presented with ptosis, ophthalmoparesis, and myopathic proximal limb weakness, as well as variable hepatopathy and altered T-lymphocyte profiles. Muscle biopsies from all probands showed mtDNA depletion, deletions, or both, as well as reduced activities of mitochondrial respiratory chain enzymes. GUK1 encodes guanylate kinase, originally identified as a cytosolic enzyme. Long and short isoforms of GUK1 exist. We observed that the long isoform is intramitochondrial and the short is cytosolic. In probands' fibroblasts, we noted decreased GUK1 activity causing unbalanced mitochondrial dNTP pools and mtDNA depletion in both replicating and quiescent fibroblasts indicating that GUK1 deficiency impairs de novo and salvage nucleotide pathways. Proband fibroblasts treated with deoxyguanosine and/or forodesine, a purine phosphatase inhibitor, ameliorated mtDNA depletion, indicating potential pharmacological therapies. INTERPRETATION Primary GUK1 deficiency is a new and potentially treatable cause of MDDS. The cytosolic isoform of GUK1 may contribute to the T-lymphocyte abnormality, which has not been observed in other MDDS disorders. ANN NEUROL 2024.
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Affiliation(s)
| | - Jonathan Shintaku
- Department of Neurology, Columbia University Irving Medical Center, New York, NY
| | - Javier Ramon
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Vall d'Hebron Research Institute, Autonomous University of Barcelona, Barcelona, Spain
| | | | - Alba Pesini
- Department of Neurology, Columbia University Irving Medical Center, New York, NY
| | | | - Gloria Garrabou
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Inherited Metabolic Diseases and Muscle Disorder's Lab, Cellex - IDIBAPS, Faculty of Medicine and Health Science - University of Barcelona (UB), Barcelona, Spain
| | - Jose Cesar Milisenda
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Inherited Metabolic Diseases and Muscle Disorder's Lab, Cellex - IDIBAPS, Faculty of Medicine and Health Science - University of Barcelona (UB), Barcelona, Spain
- Department of Internal Medicine, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Ana Matas-Garcia
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Inherited Metabolic Diseases and Muscle Disorder's Lab, Cellex - IDIBAPS, Faculty of Medicine and Health Science - University of Barcelona (UB), Barcelona, Spain
- Department of Internal Medicine, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Laura Gort
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clinic de Barcelona-IDIBAPS, Barcelona, Spain
| | - Olatz Ugarteburu
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clinic de Barcelona-IDIBAPS, Barcelona, Spain
| | - Yue Gu
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Lahari Koganti
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Tian Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY
| | - Saba Tadesse
- Department of Neurology, Columbia University Irving Medical Center, New York, NY
| | - Megi Meneri
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Monica Sciacco
- IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY
| | - Kurenai Tanji
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Marshall S Horwitz
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Michael O Dorschner
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Mahesh Mansukhani
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Giacomo Pietro Comi
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Dario Ronchi
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Ramon Marti
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Vall d'Hebron Research Institute, Autonomous University of Barcelona, Barcelona, Spain
| | - Antonia Ribes
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clinic de Barcelona-IDIBAPS, Barcelona, Spain
| | - Frederic Tort
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clinic de Barcelona-IDIBAPS, Barcelona, Spain
| | - Michio Hirano
- Department of Neurology, Columbia University Irving Medical Center, New York, NY
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6
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Kim J, Goldstein M, Zecchel L, Ghorayeb R, Maxwell CA, Weidberg H. ATAD1 prevents clogging of TOM and damage caused by un-imported mitochondrial proteins. Cell Rep 2024; 43:114473. [PMID: 39024102 DOI: 10.1016/j.celrep.2024.114473] [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: 10/06/2023] [Revised: 05/26/2024] [Accepted: 06/24/2024] [Indexed: 07/20/2024] Open
Abstract
Mitochondria require the constant import of nuclear-encoded proteins for proper functioning. Impaired protein import not only depletes mitochondria of essential factors but also leads to toxic accumulation of un-imported proteins outside the organelle. Here, we investigate the consequences of impaired mitochondrial protein import in human cells. We demonstrate that un-imported proteins can clog the mitochondrial translocase of the outer membrane (TOM). ATAD1, a mitochondrial ATPase, removes clogged proteins from TOM to clear the entry gate into the mitochondria. ATAD1 interacts with both TOM and stalled proteins, and its knockout results in extensive accumulation of mitochondrial precursors as well as decreased protein import. Increased ATAD1 expression contributes to improved fitness of cells with inefficient mitochondrial protein import. Overall, we demonstrate the importance of the ATAD1 quality control pathway in surveilling protein import and its contribution to cellular health.
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Affiliation(s)
- John Kim
- Life Sciences Institute, Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Madeleine Goldstein
- Life Sciences Institute, Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Lauren Zecchel
- Life Sciences Institute, Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ryan Ghorayeb
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Christopher A Maxwell
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada; Michael Cuccione Childhood Cancer Research Program, British Columbia Children's Hospital, Vancouver, BC, Canada
| | - Hilla Weidberg
- Life Sciences Institute, Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada.
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7
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Zhou Q, Cao T, Li F, Zhang M, Li X, Zhao H, Zhou Y. Mitochondria: a new intervention target for tumor invasion and metastasis. Mol Med 2024; 30:129. [PMID: 39179991 PMCID: PMC11344364 DOI: 10.1186/s10020-024-00899-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 08/14/2024] [Indexed: 08/26/2024] Open
Abstract
Mitochondria, responsible for cellular energy synthesis and signal transduction, intricately regulate diverse metabolic processes, mediating fundamental biological phenomena such as cell growth, aging, and apoptosis. Tumor invasion and metastasis, key characteristics of malignancies, significantly impact patient prognosis. Tumor cells frequently exhibit metabolic abnormalities in mitochondria, including alterations in metabolic dynamics and changes in the expression of relevant metabolic genes and associated signal transduction pathways. Recent investigations unveil further insights into mitochondrial metabolic abnormalities, revealing their active involvement in tumor cell proliferation, resistance to chemotherapy, and a crucial role in tumor cell invasion and metastasis. This paper comprehensively outlines the latest research advancements in mitochondrial structure and metabolic function. Emphasis is placed on summarizing the role of mitochondrial metabolic abnormalities in tumor invasion and metastasis, including alterations in the mitochondrial genome (mutations), activation of mitochondrial-to-nuclear signaling, and dynamics within the mitochondria, all intricately linked to the processes of tumor invasion and metastasis. In conclusion, the paper discusses unresolved scientific questions in this field, aiming to provide a theoretical foundation and novel perspectives for developing innovative strategies targeting tumor invasion and metastasis based on mitochondrial biology.
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Affiliation(s)
- Quanling Zhou
- Department of Pathophysiology, Zunyi Medical University, Zunyi Guizhou, 563000, China
- Department of Physics, Zunyi Medical University, Zunyi Guizhou, 563000, China
| | - Tingping Cao
- Department of Pathophysiology, Zunyi Medical University, Zunyi Guizhou, 563000, China
- Department of Physics, Zunyi Medical University, Zunyi Guizhou, 563000, China
| | - Fujun Li
- Department of Pathophysiology, Zunyi Medical University, Zunyi Guizhou, 563000, China
- Department of Physics, Zunyi Medical University, Zunyi Guizhou, 563000, China
| | - Ming Zhang
- Department of Physics, Zunyi Medical University, Zunyi Guizhou, 563000, China
| | - Xiaohui Li
- Department of Physics, Zunyi Medical University, Zunyi Guizhou, 563000, China
| | - Hailong Zhao
- Department of Pathophysiology, Zunyi Medical University, Zunyi Guizhou, 563000, China
| | - Ya Zhou
- Department of Pathophysiology, Zunyi Medical University, Zunyi Guizhou, 563000, China.
- Department of Physics, Zunyi Medical University, Zunyi Guizhou, 563000, China.
- Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Guizhou, 563000, China.
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8
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Rubalcava-Gracia D, Bubb K, Levander F, Burr SP, August AV, Chinnery PF, Koolmeister C, Larsson NG. LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation. Nucleic Acids Res 2024:gkae662. [PMID: 39087558 DOI: 10.1093/nar/gkae662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 07/15/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
In mammals, the leucine-rich pentatricopeptide repeat protein (LRPPRC) and the stem-loop interacting RNA-binding protein (SLIRP) form a complex in the mitochondrial matrix that is required throughout the life cycle of most mitochondrial mRNAs. Although pathogenic mutations in the LRPPRC and SLIRP genes cause devastating human mitochondrial diseases, the in vivo function of the corresponding proteins is incompletely understood. We show here that loss of SLIRP in mice causes a decrease of complex I levels whereas other OXPHOS complexes are unaffected. We generated knock-in mice to study the in vivo interdependency of SLIRP and LRPPRC by mutating specific amino acids necessary for protein complex formation. When protein complex formation is disrupted, LRPPRC is partially degraded and SLIRP disappears. Livers from Lrpprc knock-in mice had impaired mitochondrial translation except for a marked increase in the synthesis of ATP8. Furthermore, the introduction of a heteroplasmic pathogenic mtDNA mutation (m.C5024T of the tRNAAla gene) into Slirp knockout mice causes an additive effect on mitochondrial translation leading to embryonic lethality and reduced growth of mouse embryonic fibroblasts. To summarize, we report that the LRPPRC/SLIRP protein complex is critical for maintaining normal complex I levels and that it also coordinates mitochondrial translation in a tissue-specific manner.
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Affiliation(s)
- Diana Rubalcava-Gracia
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Bubb
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Levander
- Department en Immunotechnology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Stephen P Burr
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit,University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Amelie V August
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit,University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Camilla Koolmeister
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nils-Göran Larsson
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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9
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Diaz-Vegas A, Cooke KC, Cutler HB, Yau B, Masson SWC, Harney D, Fuller OK, Potter M, Madsen S, Craw NR, Zhang Y, Moreno CL, Kebede MA, Neely GG, Stöckli J, Burchfield JG, James DE. Deletion of miPEP in adipocytes protects against obesity and insulin resistance by boosting muscle metabolism. Mol Metab 2024; 86:101983. [PMID: 38960128 PMCID: PMC11292358 DOI: 10.1016/j.molmet.2024.101983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
Mitochondria facilitate thousands of biochemical reactions, covering a broad spectrum of anabolic and catabolic processes. Here we demonstrate that the adipocyte mitochondrial proteome is markedly altered across multiple models of insulin resistance and reveal a consistent decrease in the level of the mitochondrial processing peptidase miPEP. OBJECTIVE To determine the role of miPEP in insulin resistance. METHODS To experimentally test this observation, we generated adipocyte-specific miPEP knockout mice to interrogate its role in the aetiology of insulin resistance. RESULTS We observed a strong phenotype characterised by enhanced insulin sensitivity and reduced adiposity, despite normal food intake and physical activity. Strikingly, these phenotypes vanished when mice were housed at thermoneutrality, suggesting that metabolic protection conferred by miPEP deletion hinges upon a thermoregulatory process. Tissue specific analysis of miPEP deficient mice revealed an increment in muscle metabolism, and upregulation of the protein FBP2 that is involved in ATP hydrolysis in the gluconeogenic pathway. CONCLUSION These findings suggest that miPEP deletion initiates a compensatory increase in skeletal muscle metabolism acting as a protective mechanism against diet-induced obesity and insulin resistance.
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Affiliation(s)
- Alexis Diaz-Vegas
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia.
| | - Kristen C Cooke
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Harry B Cutler
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Belinda Yau
- School of Medical Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Stewart W C Masson
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Dylan Harney
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Oliver K Fuller
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Meg Potter
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Søren Madsen
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Niamh R Craw
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Yiju Zhang
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Cesar L Moreno
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Melkam A Kebede
- School of Medical Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - G Gregory Neely
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Jacqueline Stöckli
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - James G Burchfield
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - David E James
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia; School of Medical Sciences, University of Sydney, Camperdown, New South Wales, Australia.
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10
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Li ZH, Zhou XL. Eukaryotic AlaX provides multiple checkpoints for quality and quantity of aminoacyl-tRNAs in translation. Nucleic Acids Res 2024; 52:7825-7842. [PMID: 38869066 PMCID: PMC11260482 DOI: 10.1093/nar/gkae486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/27/2024] [Indexed: 06/14/2024] Open
Abstract
Translational fidelity relies critically on correct aminoacyl-tRNA supply. The trans-editing factor AlaX predominantly hydrolyzes Ser-tRNAAla, functioning as a third sieve of alanyl-tRNA synthetase (AlaRS). Despite extensive studies in bacteria and archaea, the mechanism of trans-editing in mammals remains largely unknown. Here, we show that human AlaX (hAlaX), which is exclusively distributed in the cytoplasm, is an active trans-editing factor with strict Ser-specificity. In vitro, both hAlaX and yeast AlaX (ScAlaX) were capable of hydrolyzing nearly all Ser-mischarged cytoplasmic and mitochondrial tRNAs; and robustly edited cognate Ser-charged cytoplasmic and mitochondrial tRNASers. In vivo or cell-based studies revealed that loss of ScAlaX or hAlaX readily induced Ala- and Thr-to-Ser misincorporation. Overexpression of hAlaX impeded the decoding efficiency of consecutive Ser codons, implying its regulatory role in Ser codon decoding. Remarkably, yeast cells with ScAlaX deletion responded differently to translation inhibitor treatment, with a gain in geneticin resistance, but sensitivity to cycloheximide, both of which were rescued by editing-capable ScAlaX, alanyl- or threonyl-tRNA synthetase. Altogether, our results demonstrated the previously undescribed editing peculiarities of eukaryotic AlaXs, which provide multiple checkpoints to maintain the speed and fidelity of genetic decoding.
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Affiliation(s)
- Zi-Han Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Xiao-Long Zhou
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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11
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Deshmukh V, Martin JF. SETD3 is a mechanosensitive enzyme that methylates actin on His73 to regulate mitochondrial dynamics and function. J Cell Sci 2024; 137:jcs261268. [PMID: 38896010 PMCID: PMC11304411 DOI: 10.1242/jcs.261268] [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: 04/21/2023] [Accepted: 06/06/2024] [Indexed: 06/21/2024] Open
Abstract
Mitochondria, which act as sensors of metabolic homeostasis and metabolite signaling, form a dynamic intracellular network that continuously changes shape, size and localization to respond to localized cellular energy demands. Mitochondrial dynamics and function depend on interactions with the F-actin cytoskeleton that are poorly understood. Here, we show that SET domain protein 3 (SETD3), a recently described actin histidine methyltransferase, directly methylates actin at histidine-73 and enhances F-actin polymerization on mitochondria. SETD3 is a mechano-sensitive enzyme that is localized on the outer mitochondrial membrane and promotes actin polymerization around mitochondria. SETD3 loss of function leads to diminished F-actin around mitochondria and a decrease in mitochondrial branch length, branch number and mitochondrial movement. Our functional analysis revealed that SETD3 is required for oxidative phosphorylation, and mitochondrial complex I assembly and function. Our data further indicate that SETD3 regulates F-actin formation around mitochondria and is essential for maintaining mitochondrial morphology, movement and function. Finally, we discovered that SETD3 levels are regulated by extracellular matrix (ECM) stiffness and regulate mitochondrial shape in response to changes in ECM stiffness. These findings provide new insight into the mechanism for F-actin polymerization around mitochondria.
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Affiliation(s)
- Vaibhav Deshmukh
- Department of Integrative Physiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - James F. Martin
- Department of Integrative Physiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
- Cardiomyocyte Renewal Lab, Texas Heart Institute, 6770 Bertner Avenue, Houston, Texas 77030, USA
- Center for Organ Repair and Renewal, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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12
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Iwata R, Vanderhaeghen P. Metabolic mechanisms of species-specific developmental tempo. Dev Cell 2024; 59:1628-1639. [PMID: 38906137 PMCID: PMC11266843 DOI: 10.1016/j.devcel.2024.05.027] [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: 01/19/2024] [Revised: 04/27/2024] [Accepted: 05/23/2024] [Indexed: 06/23/2024]
Abstract
Development consists of a highly ordered suite of steps and transitions, like choreography. Although these sequences are often evolutionarily conserved, they can display species variations in duration and speed, thereby modifying final organ size or function. Despite their evolutionary significance, the mechanisms underlying species-specific scaling of developmental tempo have remained unclear. Here, we will review recent findings that implicate global cellular mechanisms, particularly intermediary and protein metabolism, as species-specific modifiers of developmental tempo. In various systems, from somitic cell oscillations to neuronal development, metabolic pathways display species differences. These have been linked to mitochondrial metabolism, which can influence the species-specific speed of developmental transitions. Thus, intermediary metabolic pathways regulate developmental tempo together with other global processes, including proteostasis and chromatin remodeling. By linking metabolism and the evolution of developmental trajectories, these findings provide opportunities to decipher how species-specific cellular timing can influence organism fitness.
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Affiliation(s)
- Ryohei Iwata
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KUL, 3000 Leuven, Belgium
| | - Pierre Vanderhaeghen
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KUL, 3000 Leuven, Belgium.
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13
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Zheng W, Chai P, Zhu J, Zhang K. High-resolution in situ structures of mammalian respiratory supercomplexes. Nature 2024; 631:232-239. [PMID: 38811722 PMCID: PMC11222160 DOI: 10.1038/s41586-024-07488-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes1-4. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: I1III2IV1, I1III2IV2, I2III2IV2 and I2III4IV2, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context.
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Affiliation(s)
- Wan Zheng
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jiapeng Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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14
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den Brave F, Schulte U, Fakler B, Pfanner N, Becker T. Mitochondrial complexome and import network. Trends Cell Biol 2024; 34:578-594. [PMID: 37914576 DOI: 10.1016/j.tcb.2023.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023]
Abstract
Mitochondria perform crucial functions in cellular metabolism, protein and lipid biogenesis, quality control, and signaling. The systematic analysis of protein complexes and interaction networks provided exciting insights into the structural and functional organization of mitochondria. Most mitochondrial proteins do not act as independent units, but are interconnected by stable or dynamic protein-protein interactions. Protein translocases are responsible for importing precursor proteins into mitochondria and form central elements of several protein interaction networks. These networks include molecular chaperones and quality control factors, metabolite channels and respiratory chain complexes, and membrane and organellar contact sites. Protein translocases link the distinct networks into an overarching network, the mitochondrial import network (MitimNet), to coordinate biogenesis, membrane organization and function of mitochondria.
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Affiliation(s)
- Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Bernd Fakler
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany.
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15
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Liu Y, Liu H, Zhang F, Xu H. The initiation of mitochondrial DNA replication. Biochem Soc Trans 2024; 52:1243-1251. [PMID: 38884788 PMCID: PMC11346463 DOI: 10.1042/bst20230952] [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: 03/11/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]
Abstract
Mitochondrial DNA replication is initiated by the transcription of mitochondrial RNA polymerase (mtRNAP), as mitochondria lack a dedicated primase. However, the mechanism determining the switch between continuous transcription and premature termination to generate RNA primers for mitochondrial DNA (mtDNA) replication remains unclear. The pentatricopeptide repeat domain of mtRNAP exhibits exoribonuclease activity, which is required for the initiation of mtDNA replication in Drosophila. In this review, we explain how this exonuclease activity contributes to primer synthesis in strand-coupled mtDNA replication, and discuss how its regulation might co-ordinate mtDNA replication and transcription in both Drosophila and mammals.
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Affiliation(s)
- Yi Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Haibin Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Fan Zhang
- National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, U.S.A
| | - Hong Xu
- National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, U.S.A
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16
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Tan S, Dengler AS, Darawsheh RZ, Kory N. The iAAA-mitochondrial protease YME1L1 regulates the degradation of the short-lived mitochondrial transporter SLC25A38. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593764. [PMID: 38979268 PMCID: PMC11230184 DOI: 10.1101/2024.05.12.593764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Mitochondrial transporters facilitate the exchange of diverse metabolic intermediates across the inner mitochondrial membrane, ensuring an adequate supply of substrates and cofactors to support redox and biosynthetic reactions within the mitochondrial matrix. However, the regulatory mechanisms governing the abundance of these transporters, crucial for maintaining metabolic compartmentalization and mitochondrial functions, remain poorly defined. Through analysis of protein half-life data and mRNA-protein correlations, we identified SLC25A38, a mitochondrial glycine transporter, as a short- lived protein with a half-life of 4 hours under steady-state conditions. Pharmacological inhibition and genetic depletion of various cellular proteolytic systems revealed that SLC25A38 is rapidly degraded by the iAAA-mitochondrial protease YME1L1. Depolarization of the mitochondrial membrane potential induced by the mitochondrial uncoupler carbonyl cyanide m-chlorophenylhydrozone prevented the degradation of SLC25A38. This dual regulation of SLC25A38 abundance by YME1L1 and mitochondrial membrane potential suggests a link between SLC25A38 turnover, the integrity of the inner mitochondrial membrane, and electron transport chain function. These findings open avenues for investigating whether mitochondrial glycine import coordinates with mitochondrial bioenergetics.
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17
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Moisoi N. Mitochondrial proteases modulate mitochondrial stress signalling and cellular homeostasis in health and disease. Biochimie 2024:S0300-9084(24)00141-X. [PMID: 38906365 DOI: 10.1016/j.biochi.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/16/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
Maintenance of mitochondrial homeostasis requires a plethora of coordinated quality control and adaptations' mechanisms in which mitochondrial proteases play a key role. Their activation or loss of function reverberate beyond local mitochondrial biochemical and metabolic remodelling into coordinated cellular pathways and stress responses that feedback onto the mitochondrial functionality and adaptability. Mitochondrial proteolysis modulates molecular and organellar quality control, metabolic adaptations, lipid homeostasis and regulates transcriptional stress responses. Defective mitochondrial proteolysis results in disease conditions most notably, mitochondrial diseases, neurodegeneration and cancer. Here, it will be discussed how mitochondrial proteases and mitochondria stress signalling impact cellular homeostasis and determine the cellular decision to survive or die, how these processes may impact disease etiopathology, and how modulation of proteolysis may offer novel therapeutic strategies.
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Affiliation(s)
- Nicoleta Moisoi
- Leicester School of Pharmacy, Leicester Institute for Pharmaceutical Health and Social Care Innovations, Faculty of Health and Life Sciences, De Montfort University, The Gateway, Hawthorn Building 1.03, LE1 9BH, Leicester, UK.
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18
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Zarges C, Riemer J. Oxidative protein folding in the intermembrane space of human mitochondria. FEBS Open Bio 2024. [PMID: 38867508 DOI: 10.1002/2211-5463.13839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/03/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
The mitochondrial intermembrane space hosts a machinery for oxidative protein folding, the mitochondrial disulfide relay. This machinery imports a large number of soluble proteins into the compartment, where they are retained through oxidative folding. Additionally, the disulfide relay enhances the stability of many proteins by forming disulfide bonds. In this review, we describe the mitochondrial disulfide relay in human cells, its components, and their coordinated collaboration in mechanistic detail. We also discuss the human pathologies associated with defects in this machinery and its protein substrates, providing a comprehensive overview of its biological importance and implications for health.
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Affiliation(s)
| | - Jan Riemer
- Institute for Biochemistry, University of Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
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19
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Crameri JJ, Palmer CS, Stait T, Jackson TD, Lynch M, Sinclair A, Frajman LE, Compton AG, Coman D, Thorburn DR, Frazier AE, Stojanovski D. Reduced Protein Import via TIM23 SORT Drives Disease Pathology in TIMM50-Associated Mitochondrial Disease. Mol Cell Biol 2024; 44:226-244. [PMID: 38828998 PMCID: PMC11204040 DOI: 10.1080/10985549.2024.2353652] [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: 01/22/2024] [Accepted: 05/07/2024] [Indexed: 06/05/2024] Open
Abstract
TIMM50 is a core subunit of the TIM23 complex, the mitochondrial inner membrane translocase responsible for the import of pre-sequence-containing precursors into the mitochondrial matrix and inner membrane. Here we describe a mitochondrial disease patient who is homozygous for a novel variant in TIMM50 and establish the first proteomic map of mitochondrial disease associated with TIMM50 dysfunction. We demonstrate that TIMM50 pathogenic variants reduce the levels and activity of endogenous TIM23 complex, which significantly impacts the mitochondrial proteome, resulting in a combined oxidative phosphorylation (OXPHOS) defect and changes to mitochondrial ultrastructure. Using proteomic data sets from TIMM50 patient fibroblasts and a TIMM50 HEK293 cell model of disease, we reveal that laterally released substrates imported via the TIM23SORT complex pathway are most sensitive to loss of TIMM50. Proteins involved in OXPHOS and mitochondrial ultrastructure are enriched in the TIM23SORT substrate pool, providing a biochemical mechanism for the specific defects in TIMM50-associated mitochondrial disease patients. These results highlight the power of using proteomics to elucidate molecular mechanisms of disease and uncovering novel features of fundamental biology, with the implication that human TIMM50 may have a more pronounced role in lateral insertion than previously understood.
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Affiliation(s)
- Jordan J. Crameri
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria, Australia
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Catherine S. Palmer
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria, Australia
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Tegan Stait
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Thomas D. Jackson
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria, Australia
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Matthew Lynch
- Neurosciences Department, Queensland Children’s Hospital, South Brisbane, Queensland, Australia
- Department of Metabolic Medicine, Queensland Children’s Hospital, South Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, St Lucia, Queensland, Australia
| | - Adriane Sinclair
- Neurosciences Department, Queensland Children’s Hospital, South Brisbane, Queensland, Australia
| | - Leah E. Frajman
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Alison G. Compton
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - David Coman
- Department of Metabolic Medicine, Queensland Children’s Hospital, South Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, St Lucia, Queensland, Australia
| | - David R. Thorburn
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Ann E. Frazier
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria, Australia
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
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20
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Borgert L, Becker T, den Brave F. Conserved quality control mechanisms of mitochondrial protein import. J Inherit Metab Dis 2024. [PMID: 38790152 DOI: 10.1002/jimd.12756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024]
Abstract
Mitochondria carry out essential functions for the cell, including energy production, various biosynthesis pathways, formation of co-factors and cellular signalling in apoptosis and inflammation. The functionality of mitochondria requires the import of about 900-1300 proteins from the cytosol in baker's yeast Saccharomyces cerevisiae and human cells, respectively. The vast majority of these proteins pass the outer membrane in a largely unfolded state through the translocase of the outer mitochondrial membrane (TOM) complex. Subsequently, specific protein translocases sort the precursor proteins into the outer and inner membranes, the intermembrane space and matrix. Premature folding of mitochondrial precursor proteins, defects in the mitochondrial protein translocases or a reduction of the membrane potential across the inner mitochondrial membrane can cause stalling of precursors at the protein import apparatus. Consequently, the translocon is clogged and non-imported precursor proteins accumulate in the cell, which in turn leads to proteotoxic stress and eventually cell death. To prevent such stress situations, quality control mechanisms remove non-imported precursor proteins from the TOM channel. The highly conserved ubiquitin-proteasome system of the cytosol plays a critical role in this process. Thus, the surveillance of protein import via the TOM complex involves the coordinated activity of mitochondria-localized and cytosolic proteins to prevent proteotoxic stress in the cell.
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Affiliation(s)
- Lion Borgert
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Thomas Becker
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Fabian den Brave
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
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21
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Suomalainen A, Nunnari J. Mitochondria at the crossroads of health and disease. Cell 2024; 187:2601-2627. [PMID: 38788685 DOI: 10.1016/j.cell.2024.04.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Mitochondria reside at the crossroads of catabolic and anabolic metabolism-the essence of life. How their structure and function are dynamically tuned in response to tissue-specific needs for energy, growth repair, and renewal is being increasingly understood. Mitochondria respond to intrinsic and extrinsic stresses and can alter cell and organismal function by inducing metabolic signaling within cells and to distal cells and tissues. Here, we review how the centrality of mitochondrial functions manifests in health and a broad spectrum of diseases and aging.
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Affiliation(s)
- Anu Suomalainen
- University of Helsinki, Stem Cells and Metabolism Program, Faculty of Medicine, Helsinki, Finland; HiLife, University of Helsinki, Helsinki, Finland; HUS Diagnostics, Helsinki University Hospital, Helsinki, Finland.
| | - Jodi Nunnari
- Altos Labs, Bay Area Institute, Redwood Shores, CA, USA.
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22
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McShane E, Churchman LS. Central dogma rates in human mitochondria. Hum Mol Genet 2024; 33:R34-R41. [PMID: 38779776 PMCID: PMC11112385 DOI: 10.1093/hmg/ddae036] [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: 12/28/2023] [Revised: 12/28/2023] [Accepted: 02/29/2024] [Indexed: 05/25/2024] Open
Abstract
In human cells, the nuclear and mitochondrial genomes engage in a complex interplay to produce dual-encoded oxidative phosphorylation (OXPHOS) complexes. The coordination of these dynamic gene expression processes is essential for producing matched amounts of OXPHOS protein subunits. This review focuses on our current understanding of the mitochondrial central dogma rates, highlighting the striking differences in gene expression rates between mitochondrial and nuclear genes. We synthesize a coherent model of mitochondrial gene expression kinetics, highlighting the emerging principles and emphasizing where more precise measurements would be beneficial. Such an understanding is pivotal for grasping the unique aspects of mitochondrial function and its role in cellular energetics, and it has profound implications for aging, metabolic disorders, and neurodegenerative diseases.
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Affiliation(s)
- Erik McShane
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, United States
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, United States
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23
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Hughes LA, Rackham O, Filipovska A. Illuminating mitochondrial translation through mouse models. Hum Mol Genet 2024; 33:R61-R79. [PMID: 38779771 PMCID: PMC11112386 DOI: 10.1093/hmg/ddae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria are hubs of metabolic activity with a major role in ATP conversion by oxidative phosphorylation (OXPHOS). The mammalian mitochondrial genome encodes 11 mRNAs encoding 13 OXPHOS proteins along with 2 rRNAs and 22 tRNAs, that facilitate their translation on mitoribosomes. Maintaining the internal production of core OXPHOS subunits requires modulation of the mitochondrial capacity to match the cellular requirements and correct insertion of particularly hydrophobic proteins into the inner mitochondrial membrane. The mitochondrial translation system is essential for energy production and defects result in severe, phenotypically diverse diseases, including mitochondrial diseases that typically affect postmitotic tissues with high metabolic demands. Understanding the complex mechanisms that underlie the pathologies of diseases involving impaired mitochondrial translation is key to tailoring specific treatments and effectively targeting the affected organs. Disease mutations have provided a fundamental, yet limited, understanding of mitochondrial protein synthesis, since effective modification of the mitochondrial genome has proven challenging. However, advances in next generation sequencing, cryoelectron microscopy, and multi-omic technologies have revealed unexpected and unusual features of the mitochondrial protein synthesis machinery in the last decade. Genome editing tools have generated unique models that have accelerated our mechanistic understanding of mitochondrial translation and its physiological importance. Here we review the most recent mouse models of disease pathogenesis caused by defects in mitochondrial protein synthesis and discuss their value for preclinical research and therapeutic development.
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Affiliation(s)
- Laetitia A Hughes
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
| | - Oliver Rackham
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
- Curtin Medical School, Curtin University, Kent Street, Bentley, WA 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Kent Street, Bentley, WA 6102, Australia
| | - Aleksandra Filipovska
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 19 Innovation Walk, Clayton, Clayton, VIC 3168, Australia
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24
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Krakowczyk M, Lenkiewicz AM, Sitarz T, Malinska D, Borrero M, Mussulini BHM, Linke V, Szczepankiewicz AA, Biazik JM, Wydrych A, Nieznanska H, Serwa RA, Chacinska A, Bragoszewski P. OMA1 protease eliminates arrested protein import intermediates upon mitochondrial depolarization. J Cell Biol 2024; 223:e202306051. [PMID: 38530280 PMCID: PMC10964989 DOI: 10.1083/jcb.202306051] [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: 06/16/2023] [Revised: 12/28/2023] [Accepted: 02/16/2024] [Indexed: 03/27/2024] Open
Abstract
Most mitochondrial proteins originate from the cytosol and require transport into the organelle. Such precursor proteins must be unfolded to pass through translocation channels in mitochondrial membranes. Misfolding of transported proteins can result in their arrest and translocation failure. Arrested proteins block further import, disturbing mitochondrial functions and cellular proteostasis. Cellular responses to translocation failure have been defined in yeast. We developed the cell line-based translocase clogging model to discover molecular mechanisms that resolve failed import events in humans. The mechanism we uncover differs significantly from these described in fungi, where ATPase-driven extraction of blocked protein is directly coupled with proteasomal processing. We found human cells to rely primarily on mitochondrial factors to clear translocation channel blockage. The mitochondrial membrane depolarization triggered proteolytic cleavage of the stalled protein, which involved mitochondrial protease OMA1. The cleavage allowed releasing the protein fragment that blocked the translocase. The released fragment was further cleared in the cytosol by VCP/p97 and the proteasome.
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Affiliation(s)
- Magda Krakowczyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Anna M. Lenkiewicz
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Sitarz
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Dominika Malinska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Mayra Borrero
- IMol Polish Academy of Sciences, Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Ben Hur Marins Mussulini
- IMol Polish Academy of Sciences, Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Vanessa Linke
- IMol Polish Academy of Sciences, Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | | | - Joanna M. Biazik
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- University of New South Wales, Sydney, Australia
| | - Agata Wydrych
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Hanna Nieznanska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Remigiusz A. Serwa
- IMol Polish Academy of Sciences, Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Chacinska
- IMol Polish Academy of Sciences, Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Piotr Bragoszewski
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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25
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Reisman EG, Hawley JA, Hoffman NJ. Exercise-Regulated Mitochondrial and Nuclear Signalling Networks in Skeletal Muscle. Sports Med 2024; 54:1097-1119. [PMID: 38528308 PMCID: PMC11127882 DOI: 10.1007/s40279-024-02007-2] [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] [Accepted: 02/18/2024] [Indexed: 03/27/2024]
Abstract
Exercise perturbs energy homeostasis in skeletal muscle and engages integrated cellular signalling networks to help meet the contraction-induced increases in skeletal muscle energy and oxygen demand. Investigating exercise-associated perturbations in skeletal muscle signalling networks has uncovered novel mechanisms by which exercise stimulates skeletal muscle mitochondrial biogenesis and promotes whole-body health and fitness. While acute exercise regulates a complex network of protein post-translational modifications (e.g. phosphorylation) in skeletal muscle, previous investigations of exercise signalling in human and rodent skeletal muscle have primarily focused on a select group of exercise-regulated protein kinases [i.e. 5' adenosine monophosphate-activated protein kinase (AMPK), protein kinase A (PKA), Ca2+/calmodulin-dependent protein kinase (CaMK) and mitogen-activated protein kinase (MAPK)] and only a small subset of their respective protein substrates. Recently, global mass spectrometry-based phosphoproteomic approaches have helped unravel the extensive complexity and interconnection of exercise signalling pathways and kinases beyond this select group and phosphorylation and/or translocation of exercise-regulated mitochondrial and nuclear protein substrates. This review provides an overview of recent advances in our understanding of the molecular events associated with acute endurance exercise-regulated signalling pathways and kinases in skeletal muscle with a focus on phosphorylation. We critically appraise recent evidence highlighting the involvement of mitochondrial and nuclear protein phosphorylation and/or translocation in skeletal muscle adaptive responses to an acute bout of endurance exercise that ultimately stimulate mitochondrial biogenesis and contribute to exercise's wider health and fitness benefits.
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Affiliation(s)
- Elizabeth G Reisman
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Level 5, 215 Spring Street, Melbourne, VIC, 3000, Australia
| | - John A Hawley
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Level 5, 215 Spring Street, Melbourne, VIC, 3000, Australia
| | - Nolan J Hoffman
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Level 5, 215 Spring Street, Melbourne, VIC, 3000, Australia.
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26
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McShane E, Couvillion M, Ietswaart R, Prakash G, Smalec BM, Soto I, Baxter-Koenigs AR, Choquet K, Churchman LS. A kinetic dichotomy between mitochondrial and nuclear gene expression processes. Mol Cell 2024; 84:1541-1555.e11. [PMID: 38503286 PMCID: PMC11236289 DOI: 10.1016/j.molcel.2024.02.028] [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: 09/05/2023] [Revised: 12/12/2023] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
Oxidative phosphorylation (OXPHOS) complexes, encoded by both mitochondrial and nuclear DNA, are essential producers of cellular ATP, but how nuclear and mitochondrial gene expression steps are coordinated to achieve balanced OXPHOS subunit biogenesis remains unresolved. Here, we present a parallel quantitative analysis of the human nuclear and mitochondrial messenger RNA (mt-mRNA) life cycles, including transcript production, processing, ribosome association, and degradation. The kinetic rates of nearly every stage of gene expression differed starkly across compartments. Compared with nuclear mRNAs, mt-mRNAs were produced 1,100-fold more, degraded 7-fold faster, and accumulated to 160-fold higher levels. Quantitative modeling and depletion of mitochondrial factors LRPPRC and FASTKD5 identified critical points of mitochondrial regulatory control, revealing that the mitonuclear expression disparities intrinsically arise from the highly polycistronic nature of human mitochondrial pre-mRNA. We propose that resolving these differences requires a 100-fold slower mitochondrial translation rate, illuminating the mitoribosome as a nexus of mitonuclear co-regulation.
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Affiliation(s)
- Erik McShane
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Mary Couvillion
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Ietswaart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gyan Prakash
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan M Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Iliana Soto
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Autum R Baxter-Koenigs
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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27
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Zhu Y, Akkaya KC, Ruta J, Yokoyama N, Wang C, Ruwolt M, Lima DB, Lehmann M, Liu F. Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies. Nat Commun 2024; 15:3290. [PMID: 38632225 PMCID: PMC11024108 DOI: 10.1038/s41467-024-47569-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
The functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes. Here, we develop a cross-link assisted spatial proteomics (CLASP) strategy that addresses these shortcomings. Using human mitochondria as a model system, we show that CLASP can elucidate spatial proteomes of all mitochondrial sub-compartments and provide topological insight into the mitochondrial membrane proteome. Biochemical and imaging-based follow-up studies confirm that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. We also validate the CLASP concept in synaptic vesicles, demonstrating its applicability to different sub-cellular compartments. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, and establishes a method for concomitant profiling of sub-organelle and membrane proteomes.
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Affiliation(s)
- Ying Zhu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Kerem Can Akkaya
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Julia Ruta
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Nanako Yokoyama
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Cong Wang
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Max Ruwolt
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Diogo Borges Lima
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Martin Lehmann
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Fan Liu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117, Berlin, Germany.
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28
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Zheng W, Chai P, Zhu J, Zhang K. High-resolution In-situ Structures of Mammalian Mitochondrial Respiratory Supercomplexes in Reaction within Native Mitochondria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587796. [PMID: 38617346 PMCID: PMC11014577 DOI: 10.1101/2024.04.02.587796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Mitochondria play a pivotal role in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane via a series of respiratory complexes. Despite extensive in-vitro structural studies, revealing the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of the loss of the native environment during purification. Here, we directly image porcine mitochondria using an in-situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states, achieving up to 1.8-Å local resolution. We identify four major supercomplex organizations: I1III2IV1, I1III2IV2, I2III2IV2, and I2III4IV2, which can potentially expand into higher-order arrays on the inner membranes. The formation of these diverse supercomplexes is largely contributed by 'protein-lipids-protein' interactions, which in turn dramatically impact the local geometry of the surrounding membranes. Our in-situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. By comparing supercomplex structures from mitochondria treated under distinct conditions, we elucidate how conformational changes and ligand binding states interplay between complexes I and III in response to environmental redox alterations. Our approach, by preserving the native membrane environment, enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, spanning from atomic-level details to the broader subcellular context.
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Affiliation(s)
- Wan Zheng
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA
| | - Jiapeng Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA
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29
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Binotti B, Ninov M, Cepeda AP, Ganzella M, Matti U, Riedel D, Urlaub H, Sambandan S, Jahn R. ATG9 resides on a unique population of small vesicles in presynaptic nerve terminals. Autophagy 2024; 20:883-901. [PMID: 37881948 PMCID: PMC11062364 DOI: 10.1080/15548627.2023.2274204] [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: 02/01/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023] Open
Abstract
In neurons, autophagosome biogenesis occurs mainly in distal axons, followed by maturation during retrograde transport. Autophagosomal growth depends on the supply of membrane lipids which requires small vesicles containing ATG9, a lipid scramblase essential for macroautophagy/autophagy. Here, we show that ATG9-containing vesicles are enriched in synapses and resemble synaptic vesicles in size and density. The proteome of ATG9-containing vesicles immuno-isolated from nerve terminals showed conspicuously low levels of trafficking proteins except of the AP2-complex and some enzymes involved in endosomal phosphatidylinositol metabolism. Super resolution microscopy of nerve terminals and isolated vesicles revealed that ATG9-containing vesicles represent a distinct vesicle population with limited overlap not only with synaptic vesicles but also other membranes of the secretory pathway, uncovering a surprising heterogeneity in their membrane composition. Our results are compatible with the view that ATG9-containing vesicles function as lipid shuttles that scavenge membrane lipids from various intracellular membranes to support autophagosome biogenesis.Abbreviations: AP: adaptor related protein complex: ATG2: autophagy related 2; ATG9: autophagy related 9; DNA PAINT: DNA-based point accumulation for imaging in nanoscale topography; DyMIN STED: dynamic minimum stimulated emission depletion; EL: endosome and lysosome; ER: endoplasmic reticulum; GA: Golgi apparatus; iBAQ: intensity based absolute quantification; LAMP: lysosomal-associated membrane protein; M6PR: mannose-6-phosphate receptor, cation dependent; Minflux: minimal photon fluxes; Mito: mitochondria; MS: mass spectrometry; PAS: phagophore assembly site; PM: plasma membrane; Px: peroxisome; RAB26: RAB26, member RAS oncogene family; RAB3A: RAB3A, member RAS oncogene family; RAB5A: RAB5A, member RAS oncogene family; SNARE: soluble N-ethylmaleimide-sensitive-factor attachment receptor; SVs: synaptic vesicles; SYP: synaptophysin; TGN: trans-Golgi network; TRAPP: transport protein particle; VTI1: vesicle transport through interaction with t-SNAREs.
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Affiliation(s)
- Beyenech Binotti
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Momchil Ninov
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Germany
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Andreia P. Cepeda
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Marcelo Ganzella
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Ulf Matti
- Abberior Instruments GmbH, Göttingen, Germany
| | - Dietmar Riedel
- Facility for Transmission Electron Microscopy, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Germany
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging : from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
| | - Sivakumar Sambandan
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Synaptic Metal Ion Dynamics and Signalin, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Reinhard Jahn
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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30
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Liu Z, Guo F, Zhu Y, Qin S, Hou Y, Guo H, Lin F, Chen PR, Fan X. Bioorthogonal photocatalytic proximity labeling in primary living samples. Nat Commun 2024; 15:2712. [PMID: 38548729 PMCID: PMC10978841 DOI: 10.1038/s41467-024-46985-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
In situ profiling of subcellular proteomics in primary living systems, such as native tissues or clinic samples, is crucial for understanding life processes and diseases, yet challenging due to methodological obstacles. Here we report CAT-S, a bioorthogonal photocatalytic chemistry-enabled proximity labeling method, that expands proximity labeling to a wide range of primary living samples for in situ profiling of mitochondrial proteomes. Powered by our thioQM labeling warhead development and targeted bioorthogonal photocatalytic chemistry, CAT-S enables the labeling of mitochondrial proteins in living cells with high efficiency and specificity. We apply CAT-S to diverse cell cultures, dissociated mouse tissues as well as primary T cells from human blood, portraying the native-state mitochondrial proteomic characteristics, and unveiled hidden mitochondrial proteins (PTPN1, SLC35A4 uORF, and TRABD). Furthermore, CAT-S allows quantification of proteomic perturbations on dysfunctional tissues, exampled by diabetic mouse kidneys, revealing the alterations of lipid metabolism that may drive disease progression. Given the advantages of non-genetic operation, generality, and spatiotemporal resolution, CAT-S may open exciting avenues for subcellular proteomic investigations of primary samples that are otherwise inaccessible.
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Affiliation(s)
- Ziqi Liu
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Fuhu Guo
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yufan Zhu
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Shengnan Qin
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yuchen Hou
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Haotian Guo
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Feng Lin
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
| | - Xinyuan Fan
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
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31
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Horten P, Song K, Garlich J, Hardt R, Colina-Tenorio L, Horvath SE, Schulte U, Fakler B, van der Laan M, Becker T, Stuart RA, Pfanner N, Rampelt H. Identification of MIMAS, a multifunctional mega-assembly integrating metabolic and respiratory biogenesis factors of mitochondria. Cell Rep 2024; 43:113772. [PMID: 38393949 PMCID: PMC11010658 DOI: 10.1016/j.celrep.2024.113772] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/03/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The mitochondrial inner membrane plays central roles in bioenergetics and metabolism and contains several established membrane protein complexes. Here, we report the identification of a mega-complex of the inner membrane, termed mitochondrial multifunctional assembly (MIMAS). Its large size of 3 MDa explains why MIMAS has escaped detection in the analysis of mitochondria so far. MIMAS combines proteins of diverse functions from respiratory chain assembly to metabolite transport, dehydrogenases, and lipid biosynthesis but not the large established supercomplexes of the respiratory chain, ATP synthase, or prohibitin scaffold. MIMAS integrity depends on the non-bilayer phospholipid phosphatidylethanolamine, in contrast to respiratory supercomplexes whose stability depends on cardiolipin. Our findings suggest that MIMAS forms a protein-lipid mega-assembly in the mitochondrial inner membrane that integrates respiratory biogenesis and metabolic processes in a multifunctional platform.
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Affiliation(s)
- Patrick Horten
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Kuo Song
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Joshua Garlich
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Robert Hardt
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Lilia Colina-Tenorio
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Susanne E Horvath
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Bernd Fakler
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Martin van der Laan
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling, PZMS, Faculty of Medicine, Saarland University, 66421 Homburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Rosemary A Stuart
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Heike Rampelt
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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Tokatlidis K. MIMAS is a new giant multifunctional player in the mitochondrial megacomplex playground. Cell Rep 2024; 43:113874. [PMID: 38386551 DOI: 10.1016/j.celrep.2024.113874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Mitochondria are rich in multi-protein assemblies that are usually dedicated to one function. In this issue of Cell Reports, Horten et al.1 describe a 3-megadalton megacomplex in the mitochondrial inner membrane, which serves multiple functions integrating mitochondria biogenesis and metabolism.
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Affiliation(s)
- Kostas Tokatlidis
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK.
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33
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Garrelfs SF, Chornyi S, Te Brinke H, Ruiter J, Groothoff J, Wanders RJA. Glyoxylate reductase: Definitive identification in human liver mitochondria, its importance for the compartment-specific detoxification of glyoxylate. J Inherit Metab Dis 2024; 47:280-288. [PMID: 38200664 DOI: 10.1002/jimd.12711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 11/13/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
Glyoxylate is a key metabolite generated from various precursor substrates in different subcellular compartments including mitochondria, peroxisomes, and the cytosol. The fact that glyoxylate is a good substrate for the ubiquitously expressed enzyme lactate dehydrogenase (LDH) requires the presence of efficient glyoxylate detoxification systems to avoid the formation of oxalate. Furthermore, this detoxification needs to be compartment-specific since LDH is actively present in multiple subcellular compartments including peroxisomes, mitochondria, and the cytosol. Whereas the identity of these protection systems has been established for both peroxisomes and the cytosol as concluded from the deficiency of alanine glyoxylate aminotransferase (AGT) in primary hyperoxaluria type 1 (PH1) and glyoxylate reductase (GR) in PH2, the glyoxylate protection system in mitochondria has remained less well defined. In this manuscript, we show that the enzyme glyoxylate reductase has a bimodal distribution in human embryonic kidney (HEK293), hepatocellular carcinoma (HepG2), and cervical carcinoma (HeLa) cells and more importantly, in human liver, and is actively present in both the mitochondrial and cytosolic compartments. We conclude that the metabolism of glyoxylate in humans requires the complicated interaction between different subcellular compartments within the cell and discuss the implications for the different primary hyperoxalurias.
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Affiliation(s)
- Sander F Garrelfs
- Departments of Pediatrics, Emma Children's Hospital, Section Pediatric Nephrology & Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
| | - Serhii Chornyi
- Departments of Pediatrics, Emma Children's Hospital, Section Pediatric Nephrology & Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
| | - Heleen Te Brinke
- Departments of Pediatrics, Emma Children's Hospital, Section Pediatric Nephrology & Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
| | - Jos Ruiter
- Departments of Pediatrics, Emma Children's Hospital, Section Pediatric Nephrology & Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
| | - Jaap Groothoff
- Departments of Pediatrics, Emma Children's Hospital, Section Pediatric Nephrology & Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
| | - Ronald J A Wanders
- Departments of Pediatrics, Emma Children's Hospital, Section Pediatric Nephrology & Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
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34
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Anania S, Farnir M, Peiffer R, Boumahd Y, Thiry M, Agirman F, Maloujahmoum N, Bellahcène A, Peulen O. Identification of myoferlin as a mitochondria-associated membranes component required for calcium signaling in PDAC cell lines. Cell Commun Signal 2024; 22:133. [PMID: 38368370 PMCID: PMC10874564 DOI: 10.1186/s12964-024-01514-z] [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: 12/19/2023] [Accepted: 02/01/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma is an aggressive cancer type with one of the lowest survival rates due to late diagnosis and the absence of effective treatments. A better understanding of PDAC biology will help researchers to discover the Achilles' heel of cancer cells. In that regard, our research team investigated the function of an emerging oncoprotein known as myoferlin. Myoferlin is overexpressed in PDAC and its silencing/targeting has been shown to affect cancer cell proliferation, migration, mitochondrial dynamics and metabolism. Nevertheless, our comprehension of myoferlin functions in cells remains limited. In this study, we aimed to understand the molecular mechanism linking myoferlin silencing to mitochondrial dynamics. METHODS Experiments were performed on two pancreas cancer cell lines, Panc-1 and MiaPaCa-2. Myoferlin localization on mitochondria was evaluated by immunofluorescence, proximity ligation assay, and cell fractionation. The presence of myoferlin in mitochondria-associated membranes was assessed by cell fractionation and its function in mitochondrial calcium transfer was evaluated using calcium flow experiments, proximity ligation assays, co-immunoprecipitation, and timelapse fluorescence microscopy in living cells. RESULTS Myoferlin localization on mitochondria was investigated. Our results suggest that myoferlin is unlikely to be located on mitochondria. Instead, we identified myoferlin as a new component of mitochondria-associated membranes. Its silencing significantly reduces the mitochondrial calcium level upon stimulation, probably through myoferlin interaction with the inositol 1,4,5-triphosphate receptors 3. CONCLUSIONS For the first time, myoferlin was specifically demonstrated to be located in mitochondria-associated membranes where it participates to calcium flow. We hypothesized that this function explains our previous results on mitochondrial dynamics. This study improves our comprehension of myoferlin localization and function in cancer biology.
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Affiliation(s)
- Sandy Anania
- Metastasis Research Laboratory, GIGA-Cancer, Pathology Institute B23, Université de Liège, Liège, B-4000, Belgium
| | - Martin Farnir
- STAR Institute, Université de Liège, Allée du 6 Août 19, Liège, B-4000, Belgium
| | - Raphaël Peiffer
- Metastasis Research Laboratory, GIGA-Cancer, Pathology Institute B23, Université de Liège, Liège, B-4000, Belgium
| | - Yasmine Boumahd
- Metastasis Research Laboratory, GIGA-Cancer, Pathology Institute B23, Université de Liège, Liège, B-4000, Belgium
| | - Marc Thiry
- Cellular and Tissular Biology, GIGA-Neurosciences, Cell Biology L3, Université de Liège, Liège, B-4000, Belgium
| | - Ferman Agirman
- Metastasis Research Laboratory, GIGA-Cancer, Pathology Institute B23, Université de Liège, Liège, B-4000, Belgium
| | - Naima Maloujahmoum
- Metastasis Research Laboratory, GIGA-Cancer, Pathology Institute B23, Université de Liège, Liège, B-4000, Belgium
| | - Akeila Bellahcène
- Metastasis Research Laboratory, GIGA-Cancer, Pathology Institute B23, Université de Liège, Liège, B-4000, Belgium
| | - Olivier Peulen
- Metastasis Research Laboratory, GIGA-Cancer, Pathology Institute B23, Université de Liège, Liège, B-4000, Belgium.
- Center for Interdisciplinary Research on Medicines (CIRM), Mitochondria Adaptation in Cancer Group, Pathology Institute B23, Université de Liège, Liège, B-4000, Belgium.
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35
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Shi X, DeCiucis M, Grabinska KA, Kanyo J, Liu A, Lam TT, Shen H. Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis. Mol Cell 2024; 84:802-810.e6. [PMID: 38157846 PMCID: PMC10922821 DOI: 10.1016/j.molcel.2023.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/02/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
Organelle transporters define metabolic compartmentalization, and how this metabolite transport process can be modulated is poorly explored. Here, we discovered that human SLC25A39, a mitochondrial transporter critical for mitochondrial glutathione uptake, is a short-lived protein under dual regulation at the protein level. Co-immunoprecipitation mass spectrometry and CRISPR knockout (KO) in mammalian cells identified that mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1. SLC25A39 senses mitochondrial iron-sulfur cluster using four matrix cysteine residues and inhibits its degradation. SLC25A39 protein regulation is robust in developing and mature neurons. This dual transporter regulation, by protein quality control and metabolic sensing, allows modulating mitochondrial glutathione level in response to iron homeostasis, opening avenues for exploring regulation of metabolic compartmentalization. Neuronal SLC25A39 regulation connects mitochondrial protein quality control, glutathione, and iron homeostasis, which were previously unrelated biochemical features in neurodegeneration.
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Affiliation(s)
- Xiaojian Shi
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA; Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Marisa DeCiucis
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA; Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Kariona A Grabinska
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA; Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Jean Kanyo
- Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT, USA
| | - Adam Liu
- Amity High School, Woodbridge, CT, USA
| | - Tukiet T Lam
- Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Hongying Shen
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA; Systems Biology Institute, Yale West Campus, West Haven, CT, USA.
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36
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Ahmad RN, Zhang LT, Morita R, Tani H, Wu Y, Chujo T, Ogawa A, Harada R, Shigeta Y, Tomizawa K, Wei FY. Pathological mutations promote proteolysis of mitochondrial tRNA-specific 2-thiouridylase 1 (MTU1) via mitochondrial caseinolytic peptidase (CLPP). Nucleic Acids Res 2024; 52:1341-1358. [PMID: 38113276 PMCID: PMC10853782 DOI: 10.1093/nar/gkad1197] [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: 05/19/2022] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
MTU1 controls intramitochondrial protein synthesis by catalyzing the 2-thiouridine modification of mitochondrial transfer RNAs (mt-tRNAs). Missense mutations in the MTU1 gene are associated with life-threatening reversible infantile hepatic failure. However, the molecular pathogenesis is not well understood. Here, we investigated 17 mutations associated with this disease, and our results showed that most disease-related mutations are partial loss-of-function mutations, with three mutations being particularly severe. Mutant MTU1 is rapidly degraded by mitochondrial caseinolytic peptidase (CLPP) through a direct interaction with its chaperone protein CLPX. Notably, knockdown of CLPP significantly increased mutant MTU1 protein expression and mt-tRNA 2-thiolation, suggesting that accelerated proteolysis of mutant MTU1 plays a role in disease pathogenesis. In addition, molecular dynamics simulations demonstrated that disease-associated mutations may lead to abnormal intermolecular interactions, thereby impairing MTU1 enzyme activity. Finally, clinical data analysis underscores a significant correlation between patient prognosis and residual 2-thiolation levels, which is partially consistent with the AlphaMissense predictions. These findings provide a comprehensive understanding of MTU1-related diseases, offering prospects for modification-based diagnostics and novel therapeutic strategies centered on targeting CLPP.
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Affiliation(s)
- Raja Norazireen Raja Ahmad
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto, 860-8556, Japan
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Long-Teng Zhang
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Rikuri Morita
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Haruna Tani
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Yong Wu
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto, 860-8556, Japan
| | - Takeshi Chujo
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto, 860-8556, Japan
| | - Akiko Ogawa
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto, 860-8556, Japan
| | - Fan-Yan Wei
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
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37
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Needs HI, Glover E, Pereira GC, Witt A, Hübner W, Dodding MP, Henley JM, Collinson I. Rescue of mitochondrial import failure by intercellular organellar transfer. Nat Commun 2024; 15:988. [PMID: 38307874 PMCID: PMC10837123 DOI: 10.1038/s41467-024-45283-2] [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: 02/01/2023] [Accepted: 01/19/2024] [Indexed: 02/04/2024] Open
Abstract
Mitochondria are the powerhouses of eukaryotic cells, composed mostly of nuclear-encoded proteins imported from the cytosol. Thus, problems with the import machinery will disrupt their regenerative capacity and the cell's energy supplies - particularly troublesome for energy-demanding cells of nervous tissue and muscle. Unsurprisingly then, import breakdown is implicated in disease. Here, we explore the consequences of import failure in mammalian cells; wherein, blocking the import machinery impacts mitochondrial ultra-structure and dynamics, but, surprisingly, does not affect import. Our data are consistent with a response involving intercellular mitochondrial transport via tunnelling nanotubes to import healthy mitochondria and jettison those with blocked import sites. These observations support the existence of a widespread mechanism for the rescue of mitochondrial dysfunction.
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Affiliation(s)
- Hope I Needs
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Emily Glover
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Gonçalo C Pereira
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
- Nanna Therapeutics, Merrifield Centre, Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Alina Witt
- Fakultät für Physik, Universität Bielefeld, Bielefeld, Postfach 100131 D-33501, Germany
| | - Wolfgang Hübner
- Fakultät für Physik, Universität Bielefeld, Bielefeld, Postfach 100131 D-33501, Germany
| | - Mark P Dodding
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Jeremy M Henley
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
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38
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den Brave F, Pfanner N, Becker T. Mitochondrial entry gate as regulatory hub. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119529. [PMID: 37951505 DOI: 10.1016/j.bbamcr.2023.119529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 11/14/2023]
Abstract
Mitochondria import 1000-1300 different precursor proteins from the cytosol. The main mitochondrial entry gate is formed by the translocase of the outer membrane (TOM complex). Molecular coupling and modification of TOM subunits control and modulate protein import in response to cellular signaling. The TOM complex functions as regulatory hub to integrate mitochondrial protein biogenesis and quality control into the cellular proteostasis network.
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Affiliation(s)
- Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany.
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39
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Guerra RM, Pagliarini DJ. Reducing mitochondrial mysteries. Nat Chem Biol 2024; 20:132-133. [PMID: 37884804 PMCID: PMC11378938 DOI: 10.1038/s41589-023-01435-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Affiliation(s)
- Rachel M Guerra
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - David J Pagliarini
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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40
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Janero DR. Current strategic trends in drug discovery: the present as prologue. Expert Opin Drug Discov 2024; 19:147-159. [PMID: 37936504 DOI: 10.1080/17460441.2023.2275640] [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: 08/21/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023]
Abstract
INTRODUCTION Escalating costs and inherent uncertainties associated with drug discovery invite initiatives to improve its efficiency and de-risk campaigns for inventing better therapeutics. One such initiative involves recognizing and exploiting current approaches in therapeutics invention with molecular mechanisms of action that hold promise for designing and targeting new chemical entities as drugs. AREAS COVERED This perspective considers the current contextual framework around three drug-discovery approaches and evaluates their potential to help identify new targets/modalities in small-molecule molecular pharmacology: diversifying ligand-directed phenotypes for G protein-coupled receptor (GPCR) pharmacotherapeutic signaling; developing therapeutic-protein degraders and stabilizers for proximity-inducing pharmacology; and mining organelle biology for druggable therapeutic targets. EXPERT OPINION The contemporary drug-discovery approaches examined appear generalizable and versatile to have applications in therapeutics invention beyond those case studies discussed herein. Accordingly, they may be considered strategic trends worthy of note in advancing the field toward novel ways of addressing pharmacotherapeutically unmet medical needs.
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Affiliation(s)
- David R Janero
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, and Health Sciences Entrepreneurs, Northeastern University, Boston, MA, USA
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41
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Murphy MP, O'Neill LAJ. A break in mitochondrial endosymbiosis as a basis for inflammatory diseases. Nature 2024; 626:271-279. [PMID: 38326590 DOI: 10.1038/s41586-023-06866-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 11/14/2023] [Indexed: 02/09/2024]
Abstract
Mitochondria retain bacterial traits due to their endosymbiotic origin, but host cells do not recognize them as foreign because the organelles are sequestered. However, the regulated release of mitochondrial factors into the cytosol can trigger cell death, innate immunity and inflammation. This selective breakdown in the 2-billion-year-old endosymbiotic relationship enables mitochondria to act as intracellular signalling hubs. Mitochondrial signals include proteins, nucleic acids, phospholipids, metabolites and reactive oxygen species, which have many modes of release from mitochondria, and of decoding in the cytosol and nucleus. Because these mitochondrial signals probably contribute to the homeostatic role of inflammation, dysregulation of these processes may lead to autoimmune and inflammatory diseases. A potential reason for the increased incidence of these diseases may be changes in mitochondrial function and signalling in response to such recent phenomena as obesity, dietary changes and other environmental factors. Focusing on the mixed heritage of mitochondria therefore leads to predictions for future insights, research paths and therapeutic opportunities. Thus, whereas mitochondria can be considered 'the enemy within' the cell, evolution has used this strained relationship in intriguing ways, with increasing evidence pointing to the recent failure of endosymbiosis being critical for the pathogenesis of inflammatory diseases.
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Affiliation(s)
- Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Luke A J O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland.
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42
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Hansen FM, Kremer LS, Karayel O, Bludau I, Larsson NG, Kühl I, Mann M. Mitochondrial phosphoproteomes are functionally specialized across tissues. Life Sci Alliance 2024; 7:e202302147. [PMID: 37984987 PMCID: PMC10662294 DOI: 10.26508/lsa.202302147] [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: 05/09/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
Mitochondria are essential organelles whose dysfunction causes human pathologies that often manifest in a tissue-specific manner. Accordingly, mitochondrial fitness depends on versatile proteomes specialized to meet diverse tissue-specific requirements. Increasing evidence suggests that phosphorylation may play an important role in regulating tissue-specific mitochondrial functions and pathophysiology. Building on recent advances in mass spectrometry (MS)-based proteomics, we here quantitatively profile mitochondrial tissue proteomes along with their matching phosphoproteomes. We isolated mitochondria from mouse heart, skeletal muscle, brown adipose tissue, kidney, liver, brain, and spleen by differential centrifugation followed by separation on Percoll gradients and performed high-resolution MS analysis of the proteomes and phosphoproteomes. This in-depth map substantially quantifies known and predicted mitochondrial proteins and provides a resource of core and tissue-specific mitochondrial proteins (mitophos.de). Predicting kinase substrate associations for different mitochondrial compartments indicates tissue-specific regulation at the phosphoproteome level. Illustrating the functional value of our resource, we reproduce mitochondrial phosphorylation events on dynamin-related protein 1 responsible for its mitochondrial recruitment and fission initiation and describe phosphorylation clusters on MIGA2 linked to mitochondrial fusion.
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Affiliation(s)
- Fynn M Hansen
- https://ror.org/04py35477 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Laura S Kremer
- https://ror.org/056d84691 Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ozge Karayel
- https://ror.org/04py35477 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Isabell Bludau
- https://ror.org/04py35477 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Nils-Göran Larsson
- https://ror.org/056d84691 Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Inge Kühl
- Department of Cell Biology, Institute of Integrative Biology of the Cell, UMR9198, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Matthias Mann
- https://ror.org/04py35477 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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43
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Leitner D, Pires G, Kavanagh T, Kanshin E, Askenazi M, Ueberheide B, Devinsky O, Wisniewski T, Drummond E. Similar brain proteomic signatures in Alzheimer's disease and epilepsy. Acta Neuropathol 2024; 147:27. [PMID: 38289539 PMCID: PMC10827928 DOI: 10.1007/s00401-024-02683-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024]
Abstract
The prevalence of epilepsy is increased among Alzheimer's Disease (AD) patients and cognitive impairment is common among people with epilepsy. Epilepsy and AD are linked but the shared pathophysiological changes remain poorly defined. We aim to identify protein differences associated with epilepsy and AD using published proteomics datasets. We observed a highly significant overlap in protein differences in epilepsy and AD: 89% (689/777) of proteins altered in the hippocampus of epilepsy patients were significantly altered in advanced AD. Of the proteins altered in both epilepsy and AD, 340 were altered in the same direction, while 216 proteins were altered in the opposite direction. Synapse and mitochondrial proteins were markedly decreased in epilepsy and AD, suggesting common disease mechanisms. In contrast, ribosome proteins were increased in epilepsy but decreased in AD. Notably, many of the proteins altered in epilepsy interact with tau or are regulated by tau expression. This suggests that tau likely mediates common protein changes in epilepsy and AD. Immunohistochemistry for Aβ and multiple phosphorylated tau species (pTau396/404, pTau217, pTau231) showed a trend for increased intraneuronal pTau217 and pTau231 but no phosphorylated tau aggregates or amyloid plaques in epilepsy hippocampal sections. Our results provide insights into common mechanisms in epilepsy and AD and highlights the potential role of tau in mediating common pathological protein changes in epilepsy and AD.
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Affiliation(s)
- Dominique Leitner
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, 10016, USA
| | - Geoffrey Pires
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
| | - Tomas Kavanagh
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Evgeny Kanshin
- Proteomics Laboratory, Division of Advanced Research Technologies and Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, 10016, USA
| | | | - Beatrix Ueberheide
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies and Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, 10016, USA
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, 10016, USA
| | - Thomas Wisniewski
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA.
| | - Eleanor Drummond
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA.
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia.
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44
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Merta H, Isogai T, Paul B, Danuser G, Henne WM. Spatial proteomics of ER tubules reveals CLMN, an ER-actin tether at focal adhesions that promotes cell migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577043. [PMID: 38328045 PMCID: PMC10849733 DOI: 10.1101/2024.01.24.577043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The endoplasmic reticulum (ER) is structurally and functionally diverse, yet how its functions are organized within morphological subdomains is incompletely understood. Utilizing TurboID-based proximity labeling and CRISPR knock-in technologies, here we map the proteomic landscape of the human ER and nuclear envelope. Spatial proteomics reveals enrichments of proteins into ER tubules, sheets, and nuclear envelope. We uncover an ER-enriched actin-binding protein, Calmin (CLMN), and define it as an ER-actin tether that localizes to focal adhesions adjacent to ER tubules. CLMN depletion perturbs focal adhesion disassembly, actin dynamics, and cell movement. Mechanistically, CLMN-depleted cells also exhibit defects in calcium signaling near ER-actin interfaces, suggesting CLMN promotes calcium signaling near adhesions to facilitate their disassembly. Collectively, we map the sub-organelle proteome landscape of the ER, identify CLMN as an ER-actin tether, and describe a non-canonical mechanism by which ER tubules engage actin to regulate cell migration.
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Affiliation(s)
- Holly Merta
- Department of Cell Biology, UT Southwestern Medical Center, Dallas TX 75390
| | - Tadamoto Isogai
- Lyda Hill Department of Bioinformatics and Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas TX 75390
| | - Blessy Paul
- Department of Cell Biology, UT Southwestern Medical Center, Dallas TX 75390
| | - Gaudenz Danuser
- Department of Cell Biology, UT Southwestern Medical Center, Dallas TX 75390
- Lyda Hill Department of Bioinformatics and Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas TX 75390
| | - W Mike Henne
- Department of Cell Biology, UT Southwestern Medical Center, Dallas TX 75390
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45
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Quiñones LS, Gonzalez FS, Darden C, Khan M, Tripathi A, Smith JT, Davis J, Misra S, Chaudhuri M. Unique Interactions of the Small Translocases of the Mitochondrial Inner Membrane (Tims) in Trypanosoma brucei. Int J Mol Sci 2024; 25:1415. [PMID: 38338692 PMCID: PMC10855554 DOI: 10.3390/ijms25031415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
The infectious agent for African trypanosomiasis, Trypanosoma brucei, possesses a unique and essential translocase of the mitochondrial inner membrane, known as the TbTIM17 complex. TbTim17 associates with six small TbTims (TbTim9, TbTim10, TbTim11, TbTim12, TbTim13, and TbTim8/13). However, the interaction patterns of these smaller TbTims with each other and TbTim17 are not clear. Through yeast two-hybrid (Y2H) and co-immunoprecipitation analyses, we demonstrate that all six small TbTims interact with each other. Stronger interactions were found among TbTim8/13, TbTim9, and TbTim10. However, TbTim10 shows weaker associations with TbTim13, which has a stronger connection with TbTim17. Each of the small TbTims also interacts strongly with the C-terminal region of TbTim17. RNAi studies indicated that among all small TbTims, TbTim13 is most crucial for maintaining the steady-state levels of the TbTIM17 complex. Further analysis of the small TbTim complexes by size exclusion chromatography revealed that each small TbTim, except for TbTim13, is present in ~70 kDa complexes, possibly existing in heterohexameric forms. In contrast, TbTim13 is primarily present in the larger complex (>800 kDa) and co-fractionates with TbTim17. Altogether, our results demonstrate that, relative to other eukaryotes, the architecture and function of the small TbTim complexes are specific to T. brucei.
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Affiliation(s)
- Linda S. Quiñones
- Department of Microbiology, Immunology, and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA; (L.S.Q.); (F.S.G.); (M.K.); (A.T.)
| | - Fidel Soto Gonzalez
- Department of Microbiology, Immunology, and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA; (L.S.Q.); (F.S.G.); (M.K.); (A.T.)
| | - Chauncey Darden
- Department of Biochemistry, Cancer Biology, Neuroscience, and Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA; (C.D.); (J.D.)
| | - Muhammad Khan
- Department of Microbiology, Immunology, and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA; (L.S.Q.); (F.S.G.); (M.K.); (A.T.)
| | - Anuj Tripathi
- Department of Microbiology, Immunology, and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA; (L.S.Q.); (F.S.G.); (M.K.); (A.T.)
| | - Joseph T. Smith
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA;
| | - Jamaine Davis
- Department of Biochemistry, Cancer Biology, Neuroscience, and Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA; (C.D.); (J.D.)
| | - Smita Misra
- Department of Biomedical Science, School of Graduate Studies, Meharry Medical College, Nashville, TN 37208, USA;
| | - Minu Chaudhuri
- Department of Microbiology, Immunology, and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA; (L.S.Q.); (F.S.G.); (M.K.); (A.T.)
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46
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Leon Kropf V, Albany CJ, Zoccarato A, Green HLH, Yang Y, Brewer AC. TET3 is a positive regulator of mitochondrial respiration in Neuro2A cells. PLoS One 2024; 19:e0294187. [PMID: 38227585 PMCID: PMC10790995 DOI: 10.1371/journal.pone.0294187] [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: 08/19/2023] [Accepted: 10/26/2023] [Indexed: 01/18/2024] Open
Abstract
Ten-Eleven-Translocase (TET) enzymes contribute to the regulation of the methylome via successive oxidation of 5-methyl cytosine (5mC) to derivatives which can be actively removed by base-excision-repair (BER) mechanisms in the absence of cell division. This is particularly important in post-mitotic neurons where changes in DNA methylation are known to associate with changes in neural function. TET3, specifically, is a critical regulator of both neuronal differentiation in development and mediates dynamic changes in the methylome of adult neurons associated with cognitive function. While DNA methylation is understood to regulate transcription, little is known of the specific targets of TET3-dependent catalytic activity in neurons. We report the results of an unbiased transcriptome analysis of the neuroblastoma-derived cell line; Neuro2A, in which Tet3 was silenced. Oxidative phosphorylation (OxPhos) was identified as the most significantly down-regulated functional canonical pathway, and these findings were confirmed by measurements of oxygen consumption rate in the Seahorse bioenergetics analyser. The mRNA levels of both nuclear- and mitochondrial-encoded OxPhos genes were reduced by Tet3-silencing, but we found no evidence for differential (hydroxy)methylation deposition at these gene loci. However, the mRNA expression of genes known to be involved in mitochondrial quality control were also shown to be significantly downregulated in the absence of TET3. One of these genes; EndoG, was identified as a direct target of TET3-catalytic activity at non-CpG methylated sites within its gene body. Accordingly, we propose that aberrant mitochondrial homeostasis may contribute to the decrease in OxPhos, observed upon Tet3-downregulation in Neuro2A cells.
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Affiliation(s)
- Valeria Leon Kropf
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Caraugh J. Albany
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Anna Zoccarato
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Hannah L. H. Green
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Youwen Yang
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Alison C. Brewer
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
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47
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Baker ZN, Forny P, Pagliarini DJ. Mitochondrial proteome research: the road ahead. Nat Rev Mol Cell Biol 2024; 25:65-82. [PMID: 37773518 PMCID: PMC11378943 DOI: 10.1038/s41580-023-00650-7] [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] [Accepted: 08/08/2023] [Indexed: 10/01/2023]
Abstract
Mitochondria are multifaceted organelles with key roles in anabolic and catabolic metabolism, bioenergetics, cellular signalling and nutrient sensing, and programmed cell death processes. Their diverse functions are enabled by a sophisticated set of protein components encoded by the nuclear and mitochondrial genomes. The extent and complexity of the mitochondrial proteome remained unclear for decades. This began to change 20 years ago when, driven by the emergence of mass spectrometry-based proteomics, the first draft mitochondrial proteomes were established. In the ensuing decades, further technological and computational advances helped to refine these 'maps', with current estimates of the core mammalian mitochondrial proteome ranging from 1,000 to 1,500 proteins. The creation of these compendia provided a systemic view of an organelle previously studied primarily in a reductionist fashion and has accelerated both basic scientific discovery and the diagnosis and treatment of human disease. Yet numerous challenges remain in understanding mitochondrial biology and translating this knowledge into the medical context. In this Roadmap, we propose a path forward for refining the mitochondrial protein map to enhance its discovery and therapeutic potential. We discuss how emerging technologies can assist the detection of new mitochondrial proteins, reveal their patterns of expression across diverse tissues and cell types, and provide key information on proteoforms. We highlight the power of an enhanced map for systematically defining the functions of its members. Finally, we examine the utility of an expanded, functionally annotated mitochondrial proteome in a translational setting for aiding both diagnosis of mitochondrial disease and targeting of mitochondria for treatment.
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Affiliation(s)
- Zakery N Baker
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick Forny
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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48
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Mukhtar M, Thakkur K, Chacinska A, Bragoszewski P. Mechanisms of stress management in mitochondrial protein import. Biochem Soc Trans 2023; 51:2117-2126. [PMID: 37987513 DOI: 10.1042/bst20230377] [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: 10/07/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Mitochondria are vital to the functions of eukaryotic cells. Most mitochondrial proteins are transported into the organelle following their synthesis by cytoplasmic ribosomes. However, precise protein targeting is complex because the two diverse lipid membranes encase mitochondria. Efficient protein translocation across membranes and accurate sorting to specific sub-compartments require the cooperation of multiple factors. Any failure in mitochondrial protein import can disrupt organelle fitness. Proteins intended for mitochondria make up a significant portion of all proteins produced in the cytosol. Therefore, import defects causing their mislocalization can significantly stress cellular protein homeostasis. Recognition of this phenomenon has increased interest in molecular mechanisms that respond to import-related stress and restore proteostasis, which is the focus of this review. Significantly, disruptions in protein homeostasis link strongly to the pathology of several degenerative disorders highly relevant in ageing societies. A comprehensive understanding of protein import quality control will allow harnessing this machinery in therapeutic approaches.
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Affiliation(s)
- Maryam Mukhtar
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Krutika Thakkur
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | - Piotr Bragoszewski
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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49
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Ronayne CT, Jackson TD, Bennett CF, Perry EA, Kantorovic N, Puigserver P. Tetracyclines activate mitoribosome quality control and reduce ER stress to promote cell survival. EMBO Rep 2023; 24:e57228. [PMID: 37818824 DOI: 10.15252/embr.202357228] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
Mitochondrial diseases are a group of disorders defined by defects in oxidative phosphorylation caused by nuclear- or mitochondrial-encoded gene mutations. A main cellular phenotype of mitochondrial disease mutations is redox imbalances and inflammatory signaling underlying pathogenic signatures of these patients. One method to rescue this cell death vulnerability is the inhibition of mitochondrial translation using tetracyclines. However, the mechanisms whereby tetracyclines promote cell survival are unknown. Here, we show that tetracyclines inhibit the mitochondrial ribosome and promote survival through suppression of endoplasmic reticulum (ER) stress. Tetracyclines increase mitochondrial levels of the mitoribosome quality control factor MALSU1 (Mitochondrial Assembly of Ribosomal Large Subunit 1) and promote its recruitment to the mitoribosome large subunit, where MALSU1 is necessary for tetracycline-induced survival and suppression of ER stress. Glucose starvation induces ER stress to activate the unfolded protein response and IRE1α-mediated cell death that is inhibited by tetracyclines. These studies establish a new interorganelle communication whereby inhibition of the mitoribosome signals to the ER to promote survival, implicating basic mechanisms of cell survival and treatment of mitochondrial diseases.
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Affiliation(s)
- Conor T Ronayne
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Thomas D Jackson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Christopher F Bennett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Elizabeth A Perry
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Noa Kantorovic
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Pere Puigserver
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
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50
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Christie J, Anthony CM, Harish M, Mudartha D, Ud Din Farooqee SB, Venkatraman P. The interaction network of the proteasome assembly chaperone PSMD9 regulates proteostasis. FEBS J 2023; 290:5581-5604. [PMID: 37665644 DOI: 10.1111/febs.16948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/09/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Functional networks in cells are created by physical, genetic, and regulatory interactions. Mapping them and annotating their functions by available methods remains a challenge. We use affinity purification mass spectrometry (AP-MS) coupled with SLiMFinder to discern such a network involving 26S proteasome non-ATPase regulatory subunit 9 (PSMD9), a chaperone of proteasome assembly. Approximately 20% of proteins within the PSMD9 interactome carry a short linear motif (SLiM) of the type 'EXKK'. The binding of purified PSMD9 with the peptide sequence ERKK, proteins heterogeneous nuclear ribonucleoproteins A2/B1 (hnRNPA2B1; containing ERKK), and peroxiredoxin-6 (PRDX6; containing EAKK) provided proof of principle for this motif-driven network. The EXKK motif in the peptide primarily interacts with the coiled-coil N domain of PSMD9, a unique interaction not reported for any coiled-coil domain. PSMD9 knockout (KO) HEK293 cells experience endoplasmic reticulum (ER) stress and respond by increasing the unfolded protein response (UPR) and reducing the formation of aggresomes and lipid droplets. Trans-expression of PSMD9 in the KO cells rescues lipid droplet formation. Overexpression of PSMD9 in HEK293 cells results in reduced UPR, and increased lipid droplet and aggresome formation. The outcome argues for the prominent role of PSMD9 in maintaining proteostasis. Probable mechanisms involve the binding of PSMD9 to binding immunoglobulin protein (BIP/GRP78; containing EDKK), an endoplasmic reticulum chaperone and key regulator of the UPR, and fatty acid synthase (FASN; containing ELKK), involved in fatty acid synthesis/lipid biogenesis. We propose that PSMD9 acts as a buffer in the cellular milieu by moderating the UPR and enhancing aggresome formation to reduce stress-induced proteotoxicity. Akin to waves created in ponds that perpetuate to a distance, perturbing the levels of PSMD9 would cause ripples down the networks, affecting final reactions in the pathway, one of which is altered proteostasis.
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Affiliation(s)
- Joel Christie
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - C Merlyn Anthony
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Mahalakshmi Harish
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Deepti Mudartha
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Sheikh Burhan Ud Din Farooqee
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Prasanna Venkatraman
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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