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Konstantinidis G, Tavernarakis N. Nucleophagy: A two-step exit with the help of an outsider. Curr Biol 2025; 35:R342-R344. [PMID: 40328221 DOI: 10.1016/j.cub.2025.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2025]
Abstract
Maintenance of nuclear surveillance and quality control is paramount to a cell's long-term survival and function. A new study reveals how nucleophagy achieves the selective recycling of nuclear components via the autophagic pathway in the cytoplasm without compromising the integrity of the nuclear envelope.
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Affiliation(s)
- Georgios Konstantinidis
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, Crete, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, Crete, Greece; Department of Basic Sciences, School of Medicine, University of Crete, Crete, Greece.
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2
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Machado IF, Palmeira CM, Rolo AP. Sestrin2 is a central regulator of mitochondrial stress responses in disease and aging. Ageing Res Rev 2025; 109:102762. [PMID: 40320152 DOI: 10.1016/j.arr.2025.102762] [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: 01/08/2025] [Revised: 04/09/2025] [Accepted: 04/30/2025] [Indexed: 05/08/2025]
Abstract
Mitochondria supply most of the energy for cellular functions and coordinate numerous cellular pathways. Their dynamic nature allows them to adjust to stress and cellular metabolic demands, thus ensuring the preservation of cellular homeostasis. Loss of normal mitochondrial function compromises cell survival and has been implicated in the development of many diseases and in aging. Although exposure to continuous or severe stress has adverse effects on cells, mild mitochondrial stress enhances mitochondrial function and potentially extends health span through mitochondrial adaptive responses. Over the past few decades, sestrin2 (SESN2) has emerged as a pivotal regulator of stress responses. For instance, SESN2 responds to genotoxic, oxidative, and metabolic stress, promoting cellular defense against stress-associated damage. Here, we focus on recent findings that establish SESN2 as an orchestrator of mitochondrial stress adaptation, which is supported by its involvement in the integrated stress response, mitochondrial biogenesis, and mitophagy. Additionally, we discuss the integral role of SESN2 in mediating the health benefits of exercise as well as its impact on skeletal muscle, liver and heart injury, and aging.
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Affiliation(s)
- Ivo F Machado
- CNC-UC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; CiBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal; Institute of Interdisciplinary Research, Doctoral Program in Experimental Biology and Biomedicine (PDBEB), University of Coimbra, Coimbra, Portugal
| | - Carlos M Palmeira
- CNC-UC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; CiBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal; Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Anabela P Rolo
- CNC-UC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; CiBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal; Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
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3
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Lee-Glover LP, Picard M, Shutt TE. Mitochondria - the CEO of the cell. J Cell Sci 2025; 138:jcs263403. [PMID: 40310473 PMCID: PMC12070065 DOI: 10.1242/jcs.263403] [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] [Indexed: 05/02/2025] Open
Abstract
As we have learned more about mitochondria over the past decades, including about their essential cellular roles and how altered mitochondrial biology results in disease, it has become apparent that they are not just powerplants pumping out ATP at the whim of the cell. Rather, mitochondria are dynamic information and energy processors that play crucial roles in directing dozens of cellular processes and behaviors. They provide instructions to enact programs that regulate various cellular operations, such as complex metabolic networks, signaling and innate immunity, and even control cell fate, dictating when cells should divide, differentiate or die. To help current and future generations of cell biologists incorporate the dynamic, multifaceted nature of mitochondria and assimilate modern discoveries into their scientific framework, mitochondria need a 21st century 'rebranding'. In this Opinion article, we argue that mitochondria should be considered as the 'Chief Executive Organelle' - the CEO - of the cell.
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Affiliation(s)
- Laurie P. Lee-Glover
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, 10032, USA
- Department of Neurology, H. Houston Merritt Center for Neuromuscular and Mitochondrial Disorders, Columbia University Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, 10032, USA
- New York State Psychiatric Institute, New York, 10032, USA
- Robert N Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, 10032, USA
| | - Timothy E. Shutt
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada
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4
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Amador-Martínez I, Aranda-Rivera AK, Martínez-Castañeda MR, Pedraza-Chaverri J. Mitochondrial quality control and stress signaling pathways in the pathophysiology of cardio-renal diseases. Mitochondrion 2025; 84:102040. [PMID: 40252890 DOI: 10.1016/j.mito.2025.102040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 04/05/2025] [Accepted: 04/16/2025] [Indexed: 04/21/2025]
Abstract
Mitochondria are essential organelles for cellular function and have become a broad field of study. In cardio-renal diseases, it has been established that mitochondrial dysfunction is a primary mechanism leading to these pathologies. Under stress, mitochondria can develop stress response mechanisms to maintain mitochondrial quality control (MQC) and functions. In contrast, the perturbation of these mechanisms has been associated with the pathogenesis of several diseases. Thus, targeting specific pathways within MQC could offer a therapeutic avenue for protecting mitochondrial integrity. However, the mechanisms related to MQC and mitochondrial stress signaling in the cardio-renal axis have been poorly explored. The primary limitations include the lack of reproducibility in the experimental models of cardio-renal disease, the incomplete knowledge of molecules that generate bidirectional damage, and the temporality of the study models. Therefore, we believe that integration of all of those limitations, along with recent advances in MQC mechanisms (i.e., mitophagy), stress signaling pathways (e.g., integrated stress response, mitochondrial unfolded protein response, and mitochondrial protein import), associated pharmacology, and targeted therapeutic approaches could reveal what the deregulation of these mechanisms is like and provide ideas for generating strategies that seek to avoid the progression of cardio-renal diseases.
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Affiliation(s)
- Isabel Amador-Martínez
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, C.P. 04510, CDMX, Mexico; Department of Biology, Faculty of Chemistry, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Ana Karina Aranda-Rivera
- Department of Biology, Faculty of Chemistry, National Autonomous University of Mexico, Mexico City 04510, Mexico; Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Mauricio Raziel Martínez-Castañeda
- Department of Biology, Faculty of Chemistry, National Autonomous University of Mexico, Mexico City 04510, Mexico; Programa de Doctorado en Ciencias Biomédicas, Unidad de Posgrado, Edificio B - 101, 1° Piso, Circuito de Posgrado, Ciudad Universitaria, Coyoacán, C.P. 04510, CDMX, Mexico
| | - José Pedraza-Chaverri
- Department of Biology, Faculty of Chemistry, National Autonomous University of Mexico, Mexico City 04510, Mexico.
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5
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McKenna MJ, Kraus F, Coelho JP, Vasandani M, Zhang J, Adams BM, Paulo JA, Harper JW, Shao S. ARMC1 partitions between distinct complexes and assembles MIRO with MTFR to control mitochondrial distribution. SCIENCE ADVANCES 2025; 11:eadu5091. [PMID: 40203102 PMCID: PMC11980836 DOI: 10.1126/sciadv.adu5091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2024] [Accepted: 03/04/2025] [Indexed: 04/11/2025]
Abstract
Maintaining an optimal mitochondrial distribution is critical to ensure an adequate supply of energy and metabolites to support important cellular functions. How cells balance dynamic mitochondrial processes to achieve homeostasis is incompletely understood. Here, we show that ARMC1 partitioning between distinct mitochondrial protein complexes is a key determinant of mitochondrial distribution. In one complex, the mitochondrial trafficking adaptor MIRO recruits ARMC1, which mediates the assembly of a mitochondrial fission regulator (MTFR). MTFR stability depends on ARMC1, and MIRO-MTFR complexes specifically antagonize retrograde mitochondrial movement. In another complex, DNAJC11 facilitates ARMC1 release from mitochondria. Disrupting MIRO-MTFR assembly fails to rescue aberrant mitochondrial distributions clustered in the perinuclear area observed with ARMC1 deletion, while disrupting ARMC1 interaction with DNAJC11 leads to excessive mitochondrially localized ARMC1 and distinct mitochondrial defects. Thus, the abundance and trafficking impact of MIRO-MTFR complexes require ARMC1, whose mito-cytoplasmic shuttling balanced by DNAJC11 tunes steady-state mitochondrial distributions.
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Affiliation(s)
- Michael J. McKenna
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
| | - Felix Kraus
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
| | - João P.L. Coelho
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Muskaan Vasandani
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
| | - Jiuchun Zhang
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
| | - Benjamin M. Adams
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
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6
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Ruzza A, Zaltron E, Vianello F, Celotti I, Scavezzon M, Severin F, Leanza L. HSPA8 and HSPA9: Two prognostic and therapeutic targets in breast, colon, and kidney cancers? Biochim Biophys Acta Mol Basis Dis 2025; 1871:167827. [PMID: 40189113 DOI: 10.1016/j.bbadis.2025.167827] [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: 11/28/2024] [Revised: 03/24/2025] [Accepted: 03/31/2025] [Indexed: 04/17/2025]
Abstract
The process of protein folding is important to ensure the efficient functioning of cells. The capacity of a protein to attain the three-dimensional native conformation can impact its structure and function. Errors in this process result in the accumulation of misfolded proteins, which can contribute to the development of various diseases, including cancer. To prevent the pileup of misfolded proteins, a number of control systems have been developed over the course of evolution. In this scenario, a pivotal function has been attributed to molecular chaperones and the ubiquitin-proteasome degradation system. In this paper, we concentrate on molecular chaperones, with a particular focus on a family of heat shock proteins (HSPs), to highlight any potential correlation between their expression and function and the development of cancer. Hence, we have collected data from various public databases regarding the HSP70 protein family. By employing mRNA expression signatures, prognostic value analysis, and differentially expressed gene ontology analysis, we have elucidated the tumor-specific role of two members of the HSP70 family, namely HSPA8 and HSPA9, in kidney renal clear cell carcinoma (KIRC), colon adenocarcinoma (COAD), and breast invasive carcinoma (BRCA). Our research shed light on the controversial and tumor-specific role of HSP70s. More in detail, we have identified HSPA8 and HSPA9 as potential prognostic and therapeutic targets involved in several biological processes leading to tumorigenesis, including nucleic acid maturation, cell signaling, vesicle trafficking, mitochondrial structure and function, and protein maturation.
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Affiliation(s)
- Alessia Ruzza
- Department of Biology, University of Padua, 35131 Padua, Italy.
| | | | | | - Ilaria Celotti
- Department of Biology, University of Padua, 35131 Padua, Italy.
| | | | - Filippo Severin
- Department of Biology, University of Padua, 35131 Padua, Italy.
| | - Luigi Leanza
- Department of Biology, University of Padua, 35131 Padua, Italy.
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7
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Antico O, Thompson PW, Hertz NT, Muqit MMK, Parton LE. Targeting mitophagy in neurodegenerative diseases. Nat Rev Drug Discov 2025; 24:276-299. [PMID: 39809929 DOI: 10.1038/s41573-024-01105-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2024] [Indexed: 01/16/2025]
Abstract
Mitochondrial dysfunction is a hallmark of idiopathic neurodegenerative diseases, including Parkinson disease, amyotrophic lateral sclerosis, Alzheimer disease and Huntington disease. Familial forms of Parkinson disease and amyotrophic lateral sclerosis are often characterized by mutations in genes associated with mitophagy deficits. Therefore, enhancing the mitophagy pathway may represent a novel therapeutic approach to targeting an underlying pathogenic cause of neurodegenerative diseases, with the potential to deliver neuroprotection and disease modification, which is an important unmet need. Accumulating genetic, molecular and preclinical model-based evidence now supports targeting mitophagy in neurodegenerative diseases. Despite clinical development challenges, small-molecule-based approaches for selective mitophagy enhancement - namely, USP30 inhibitors and PINK1 activators - are entering phase I clinical trials for the first time.
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Affiliation(s)
- Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Paul W Thompson
- Mission Therapeutics Ltd, Babraham Research Campus, Cambridge, UK
| | | | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Laura E Parton
- Mission Therapeutics Ltd, Babraham Research Campus, Cambridge, UK.
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8
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Salmonowicz H, Szczepanowska K. The fate of mitochondrial respiratory complexes in aging. Trends Cell Biol 2025:S0962-8924(25)00042-X. [PMID: 40148160 DOI: 10.1016/j.tcb.2025.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Revised: 01/31/2025] [Accepted: 02/14/2025] [Indexed: 03/29/2025]
Abstract
While mitochondrial dysfunction is one of the canonical hallmarks of aging, it remains only vaguely defined. Its core feature embraces defects in energy-producing molecular machinery, the mitochondrial respiratory complexes (MRCs). The causes and consequences of these defects hold research attention. In this review, we assess the lifecycle of respiratory complexes, from biogenesis to degradation, and look closely at the mechanisms that could underpin their dysfunction in aged cells. We discuss how these processes could be altered by aging and expand on the fate of MRCs in age-associated pathologies. Given the complexity behind MRC maintenance and functionality, several traits could contribute to the phenomenon known as age-associated mitochondrial dysfunction. New advances will help us better understand the fate of this machinery in aging and age-related diseases.
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Affiliation(s)
- Hanna Salmonowicz
- IMol Polish Academy of Sciences, 02-247 Warsaw, Poland; Remedy International Research Agenda Unit, IMol Polish Academy of Sciences, 02-247 Warsaw, Poland
| | - Karolina Szczepanowska
- IMol Polish Academy of Sciences, 02-247 Warsaw, Poland; Remedy International Research Agenda Unit, IMol Polish Academy of Sciences, 02-247 Warsaw, Poland.
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9
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Pollock L, Georgiou IC, Rusilowicz-Jones EV, Clague MJ, Urbé S. A long-lived pool of PINK1 imparts a molecular memory of depolarization-induced activity. SCIENCE ADVANCES 2025; 11:eadr1938. [PMID: 40020067 PMCID: PMC11870087 DOI: 10.1126/sciadv.adr1938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 01/24/2025] [Indexed: 03/03/2025]
Abstract
The Parkinson's disease-linked kinase, PINK1, is a short-lived protein that undergoes cleavage upon mitochondrial import leading to its proteasomal degradation. Under depolarizing conditions, it accumulates on mitochondria where it becomes activated, phosphorylating both ubiquitin and the ubiquitin E3 ligase Parkin, at Ser65. Our experiments reveal that in retinal pigment epithelial cells, only a fraction of PINK1 becomes stabilized after depolarization by electron transport chain inhibitors. Furthermore, the observed accrual of PINK1 cannot be completely accounted for without an accompanying increase in biosynthesis. We have used a ubiquitylation inhibitor TAK-243 to accumulate cleaved PINK1. Under these conditions, generation of unconjugated "free" phospho-ubiquitin serves as a proxy readout for PINK1 activity. This has enabled us to find a preconditioning phenomenon, whereby an initial depolarizing treatment leaves a residual pool of active PINK1 that remains competent to seed the activation of nascent cleaved PINK1 following a 16-hour recovery period.
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Affiliation(s)
- Liam Pollock
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 3BX, UK
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany
| | - Ioanna Ch. Georgiou
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 3BX, UK
| | - Emma V. Rusilowicz-Jones
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 3BX, UK
| | - Michael J. Clague
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 3BX, UK
| | - Sylvie Urbé
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 3BX, UK
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10
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Thayer JA, Petersen JD, Huang X, Hawrot J, Ramos DM, Sekine S, Li Y, Ward ME, Narendra DP. Novel reporter of the PINK1-Parkin mitophagy pathway identifies its damage sensor in the import gate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.19.639160. [PMID: 40027798 PMCID: PMC11870511 DOI: 10.1101/2025.02.19.639160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Damaged mitochondria can be cleared from the cell by mitophagy, using a pathway formed by the recessive Parkinson's disease genes PINK1 and Parkin. How mitochondrial damage is sensed by the PINK1-Parkin pathway, however, remains uncertain. Here, using a Parkin substrate-based reporter in genome-wide screens, we identified that diverse forms of mitochondrial damage converge on loss of mitochondrial membrane potential (MMP) to activate PINK1. Consistently, the MMP but not the presequence translocase-associated motor (PAM) import motor provided the essential driving force for endogenous PINK1 import through the inner membrane translocase TIM23. In the absence of TIM23, PINK1 arrested in the translocase of the outer membrane (TOM) during import. The energy-state outside of the mitochondria further modulated the pathway by controlling the rate of new PINK1 synthesis. Our results identify separation of PINK1 from TOM by the MMP, as the key damage-sensing switch in the PINK1-Parkin mitophagy pathway. Highlights MFN2-Halo is a quantitative single-cell reporter of PINK1-Parkin activation.Diverse forms of mitochondrial damage, identified in whole-genome screens, activate the PINK1-Parkin pathway by disrupting the mitochondrial membrane potential (MMP).The primary driving force for endogenous PINK1 import through the TIM23 translocase is the MMP with the PAM import motor playing a supporting role.Loss of TIM23 is sufficient to stabilize PINK1 in the TOM complex and activate Parkin.
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Affiliation(s)
- Julia A. Thayer
- Mitochondrial Biology and Neurodegeneration Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer D. Petersen
- Mitochondrial Biology and Neurodegeneration Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- Equal-author contribution
| | - Xiaoping Huang
- Mitochondrial Biology and Neurodegeneration Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- Equal-author contribution
| | - James Hawrot
- Inherited Neurodegenerative Diseases Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Neuroscience, Brown University, Providence, RI 02912,USA
| | - Daniel M. Ramos
- iPSC Neurodegenerative Disease Initiative, National Institute of Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shiori Sekine
- Aging Institute, Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael E. Ward
- Inherited Neurodegenerative Diseases Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Derek P. Narendra
- Mitochondrial Biology and Neurodegeneration Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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11
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Clague MJ, Urbé S. Diverse routes to mitophagy governed by ubiquitylation and mitochondrial import. Trends Cell Biol 2025:S0962-8924(25)00003-0. [PMID: 39922712 DOI: 10.1016/j.tcb.2025.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Revised: 01/07/2025] [Accepted: 01/08/2025] [Indexed: 02/10/2025]
Abstract
The selective removal of mitochondria by mitophagy proceeds via multiple mechanisms and is essential for human well-being. The PINK1/Parkin and NIX/BNIP3 pathways are strongly linked to mitochondrial dysfunction and hypoxia, respectively. Both are regulated by ubiquitylation and mitochondrial import. Recent studies have elucidated how the ubiquitin kinase PINK1 acts as a sensor of mitochondrial import stress through stable interaction with a mitochondrial import supercomplex. The stability of BNIP3 and NIX is regulated by the SCFFBXL4 ubiquitin ligase complex. Substrate recognition requires an adaptor molecule, PPTC7, whose availability is limited by mitochondrial import. Unravelling the functional implications of each mode of mitophagy remains a critical challenge. We propose that mitochondrial import stress prompts a switch between these two pathways.
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Affiliation(s)
- Michael J Clague
- Department of Biochemistry, Cell, and Systems Biology, Institute of Systems, Molecular, and Integrative Biology (ISMIB), University of Liverpool, Liverpool L69 3BX, UK.
| | - Sylvie Urbé
- Department of Biochemistry, Cell, and Systems Biology, Institute of Systems, Molecular, and Integrative Biology (ISMIB), University of Liverpool, Liverpool L69 3BX, UK
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12
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Pfanner N, den Brave F, Becker T. Mitochondrial protein import stress. Nat Cell Biol 2025; 27:188-201. [PMID: 39843636 DOI: 10.1038/s41556-024-01590-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Accepted: 12/06/2024] [Indexed: 01/24/2025]
Abstract
Mitochondria have to import a large number of precursor proteins from the cytosol. Chaperones keep these proteins in a largely unfolded state and guide them to the mitochondrial import sites. Premature folding, mitochondrial stress and import defects can cause clogging of import sites and accumulation of non-imported precursors, representing a critical burden for cellular proteostasis. Here we discuss how cells respond to mitochondrial protein import stress by regenerating clogged import sites and inducing stress responses. The mitochondrial protein import machinery has a dual role by serving as sensor for detecting mitochondrial dysfunction and inducing stress-response pathways. The production of chaperones that fold or sequester precursor proteins in deposits is induced and the proteasomal activity is increased to remove the excess precursor proteins. Together, these pathways reveal how mitochondria are tightly integrated into a cellular proteostasis and stress response network to maintain cell viability.
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Affiliation(s)
- Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMB, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany.
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13
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López-Cánovas JL, Naranjo-Martínez B, Diaz-Ruiz A. Fasting in combination with the cocktail Sorafenib:Metformin blunts cellular plasticity and promotes liver cancer cell death via poly-metabolic exhaustion. Cell Oncol (Dordr) 2025; 48:161-182. [PMID: 38990489 PMCID: PMC11850423 DOI: 10.1007/s13402-024-00966-2] [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] [Accepted: 05/31/2024] [Indexed: 07/12/2024] Open
Abstract
PURPOSE Dual-Interventions targeting glucose and oxidative metabolism are receiving increasing attention in cancer therapy. Sorafenib (S) and Metformin (M), two gold-standards in liver cancer, are known for their mitochondrial inhibitory capacity. Fasting, a glucose-limiting strategy, is also emerging as chemotherapy adjuvant. Herein, we explore the anti-carcinogenic response of nutrient restriction in combination with sorafenib:metformin (NR-S:M). RESULTS Our data demonstrates that, independently of liver cancer aggressiveness, fasting synergistically boosts the anti-proliferative effects of S:M co-treatment. Metabolic and Cellular plasticity was determined by the examination of mitochondrial and glycolytic activity, cell cycle modulation, activation of cellular apoptosis, and regulation of key signaling and metabolic enzymes. Under NR-S:M conditions, early apoptotic events and the pro-apoptotic Bcl-xS/Bcl-xL ratio were found increased. NR-S:M induced the highest retention in cellular SubG1 phase, consistent with the presence of DNA fragments from cellular apoptosis. Mitochondrial functionality, Mitochondrial ATP-linked respiration, Maximal respiration and Spare respiratory capacity, were all found blunted under NR-S:M conditions. Basal Glycolysis, Glycolytic reserve, and glycolytic capacity, together with the expression of glycogenic (PKM), gluconeogenic (PCK1 and G6PC3), and glycogenolytic enzymes (PYGL, PGM1, and G6PC3), were also negatively impacted by NR-S:M. Lastly, a TMT-proteomic approach corroborated the synchronization of liver cancer metabolic reprogramming with the activation of molecular pathways to drive a quiescent-like status of energetic-collapse and cellular death. CONCLUSION Altogether, we show that the energy-based polytherapy NR-S:M blunts cellular, metabolic and molecular plasticity of liver cancer. Notwithstanding the in vitro design of this study, it holds a promising therapeutic tool worthy of exploration for this tumor pathology.
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Affiliation(s)
- Juan L López-Cánovas
- Laboratory of Cellular and Molecular Gerontology, Precision Nutrition and Aging Program, Institute IMDEA Food (CEI UAM+CSIC), Crta. de Canto Blanco nº 8, Madrid, E-28049, Spain
| | - Beatriz Naranjo-Martínez
- Laboratory of Cellular and Molecular Gerontology, Precision Nutrition and Aging Program, Institute IMDEA Food (CEI UAM+CSIC), Crta. de Canto Blanco nº 8, Madrid, E-28049, Spain
| | - Alberto Diaz-Ruiz
- Laboratory of Cellular and Molecular Gerontology, Precision Nutrition and Aging Program, Institute IMDEA Food (CEI UAM+CSIC), Crta. de Canto Blanco nº 8, Madrid, E-28049, Spain.
- CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), Córdoba, Spain.
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14
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El Fissi N, Rosenberger FA, Chang K, Wilhalm A, Barton-Owen T, Hansen FM, Golder Z, Alsina D, Wedell A, Mann M, Chinnery PF, Freyer C, Wredenberg A. Preventing excessive autophagy protects from the pathology of mtDNA mutations in Drosophila melanogaster. Nat Commun 2024; 15:10719. [PMID: 39715749 PMCID: PMC11666730 DOI: 10.1038/s41467-024-55559-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 12/16/2024] [Indexed: 12/25/2024] Open
Abstract
Aberration of mitochondrial function is a shared feature of many human pathologies, characterised by changes in metabolic flux, cellular energetics, morphology, composition, and dynamics of the mitochondrial network. While some of these changes serve as compensatory mechanisms to maintain cellular homeostasis, their chronic activation can permanently affect cellular metabolism and signalling, ultimately impairing cell function. Here, we use a Drosophila melanogaster model expressing a proofreading-deficient mtDNA polymerase (POLγexo-) in a genetic screen to find genes that mitigate the harmful accumulation of mtDNA mutations. We identify critical pathways associated with nutrient sensing, insulin signalling, mitochondrial protein import, and autophagy that can rescue the lethal phenotype of the POLγexo- flies. Rescued flies, hemizygous for dilp1, atg2, tim14 or melted, normalise their autophagic flux and proteasome function and adapt their metabolism. Mutation frequencies remain high with the exception of melted-rescued flies, suggesting that melted may act early in development. Treating POLγexo- larvae with the autophagy activator rapamycin aggravates their lethal phenotype, highlighting that excessive autophagy can significantly contribute to the pathophysiology of mitochondrial diseases. Moreover, we show that the nucleation process of autophagy is a critical target for intervention.
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Affiliation(s)
- Najla El Fissi
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Florian A Rosenberger
- Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Kai Chang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Alissa Wilhalm
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Tom Barton-Owen
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge, UK
| | - Fynn M Hansen
- Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Zoe Golder
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge, UK
| | - David Alsina
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Anna Wedell
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Matthias Mann
- Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
- Faculty of Health Sciences, NNF Centre for Protein Research, University of Copenhagen, Copenhagen, 2200, Denmark
| | - 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, Cambridge Biomedical Campus, Cambridge, UK
| | - Christoph Freyer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65, Stockholm, Sweden.
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden.
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65, Stockholm, Sweden.
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden.
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15
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Yang M, Mo Z, Walsh K, Liu W, Guo X. The Integrated Stress Response Suppresses PINK1-dependent Mitophagy by Preserving Mitochondrial Import Efficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.16.617214. [PMID: 39463933 PMCID: PMC11507992 DOI: 10.1101/2024.10.16.617214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
Mitophagy is crucial for maintaining mitochondrial health, but how its levels adjust to different stress conditions remains unclear. In this study, we investigated the role of the DELE1-HRI axis of integrated stress response (ISR) in regulating mitophagy, a key mitochondrial stress pathway. Our findings show that the ISR suppresses mitophagy under non-depolarizing mitochondrial stress by positively regulating mitochondrial protein import, independent of ATF4 activation. Mitochondrial protein import is regulated by the rate of protein synthesis under both depolarizing and non-depolarizing stress. Without ISR, increased protein synthesis overwhelms the mitochondrial import machinery, reducing its efficiency. Under depolarizing stress, mitochondrial import is heavily impaired even with active ISR, leading to significant PINK1 accumulation. In contrast, non-depolarizing stress allows more efficient protein import in the presence of ISR, resulting in lower mitophagy. Without ISR, mitochondrial protein import becomes severely compromised, causing PINK1 accumulation to reach the threshold necessary to trigger mitophagy. These findings reveal a novel link between ISR-regulated protein synthesis, mitochondrial import, and mitophagy, offering potential therapeutic targets for diseases associated with mitochondrial dysfunction.
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16
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Medhavy A, Athanasopoulos V, Bassett K, He Y, Stanley M, Enosi Tuipulotu D, Cappello J, Brown GJ, Gonzalez-Figueroa P, Turnbull C, Shanmuganandam S, Tummala P, Hart G, Lea-Henry T, Wang H, Nambadan S, Shen Q, Roco JA, Burgio G, Wu P, Cho E, Andrews TD, Field MA, Wu X, Ding H, Guo Q, Shen N, Man SM, Jiang SH, Cook MC, Vinuesa CG. A TNIP1-driven systemic autoimmune disorder with elevated IgG4. Nat Immunol 2024; 25:1678-1691. [PMID: 39060650 PMCID: PMC11362012 DOI: 10.1038/s41590-024-01902-0] [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: 01/31/2023] [Accepted: 06/18/2024] [Indexed: 07/28/2024]
Abstract
Whole-exome sequencing of two unrelated kindreds with systemic autoimmune disease featuring antinuclear antibodies with IgG4 elevation uncovered an identical ultrarare heterozygous TNIP1Q333P variant segregating with disease. Mice with the orthologous Q346P variant developed antinuclear autoantibodies, salivary gland inflammation, elevated IgG2c, spontaneous germinal centers and expansion of age-associated B cells, plasma cells and follicular and extrafollicular helper T cells. B cell phenotypes were cell-autonomous and rescued by ablation of Toll-like receptor 7 (TLR7) or MyD88. The variant increased interferon-β without altering nuclear factor kappa-light-chain-enhancer of activated B cells signaling, and impaired MyD88 and IRAK1 recruitment to autophagosomes. Additionally, the Q333P variant impaired TNIP1 localization to damaged mitochondria and mitophagosome formation. Damaged mitochondria were abundant in the salivary epithelial cells of Tnip1Q346P mice. These findings suggest that TNIP1-mediated autoimmunity may be a consequence of increased TLR7 signaling due to impaired recruitment of downstream signaling molecules and damaged mitochondria to autophagosomes and may thus respond to TLR7-targeted therapeutics.
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Affiliation(s)
- Arti Medhavy
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Vicki Athanasopoulos
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Katharine Bassett
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Yuke He
- China Australia Center for Personalized Immunology, Shanghai Renji Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Maurice Stanley
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Daniel Enosi Tuipulotu
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jean Cappello
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Grant J Brown
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Paula Gonzalez-Figueroa
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Cynthia Turnbull
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Somasundhari Shanmuganandam
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Padmaja Tummala
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Gemma Hart
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Tom Lea-Henry
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Hao Wang
- Francis Crick Institute, London, UK
| | - Sonia Nambadan
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | | | - Jonathan A Roco
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Gaetan Burgio
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Phil Wu
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eun Cho
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - T Daniel Andrews
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matt A Field
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Center for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Xiaoqian Wu
- China Australia Center for Personalized Immunology, Shanghai Renji Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Huihua Ding
- Department of Rheumatology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Qiang Guo
- Department of Rheumatology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Nan Shen
- China Australia Center for Personalized Immunology, Shanghai Renji Hospital, Shanghai Jiaotong University, Shanghai, China
- Department of Rheumatology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Si Ming Man
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Simon H Jiang
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matthew C Cook
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Carola G Vinuesa
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.
- China Australia Center for Personalized Immunology, Shanghai Renji Hospital, Shanghai Jiaotong University, Shanghai, China.
- Francis Crick Institute, London, UK.
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17
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Bozkurt S, Parmar BS, Münch C. Quantifying mitochondrial protein import by mePROD mt proteomics. Methods Enzymol 2024; 706:449-474. [PMID: 39455229 DOI: 10.1016/bs.mie.2024.07.017] [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] [Indexed: 10/28/2024]
Abstract
Mitochondrial protein import is crucial for maintaining cellular health and homeostasis. Disruptions in this process have been linked to various diseases. Traditional methods for studying mitochondrial protein import predominantly focus on individual proteins and lack the dynamic resolution needed to fully appreciate the complexity of mitochondrial proteostasis and protein trafficking. To address these limitations, we developed a technique called mitochondria-specific multiplexed enhanced protein dynamics (mePRODmt). This method is a novel application of the mePROD methodology and utilizes pulsed stable isotope labeling with amino acids in cell culture (pSILAC)-based proteomics approach to study transient mitochondrial protein import. This chapter outlines the mePRODmt protocol, which includes the preparation of heavy SILAC-labeled peptides for boosting overall mitochondrial peptide signals (booster), SILAC labeling of cultured cells under experimental conditions, mitochondria isolation, sample preparation for multiplex proteomics using tandem mass tags (TMT) for isobaric labeling, recommended liquid chromatography-mass spectrometry (LC-MS) settings for reporter ion quantitation and a data analysis pipeline to analyze pSILAC-TMT data.
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Affiliation(s)
- Süleyman Bozkurt
- Institute of Molecular Systems Medicine, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Bhavesh S Parmar
- Institute of Molecular Systems Medicine, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Molecular Systems Medicine, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Cardio-Pulmonary Institute, Frankfurt am Main, Germany.
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18
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Sutandy FXR. Monitoring mitochondrial protein import by live cell imaging. Methods Enzymol 2024; 706:437-447. [PMID: 39455228 DOI: 10.1016/bs.mie.2024.07.027] [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] [Indexed: 10/28/2024]
Abstract
The majority of mitochondrial proteins are synthesized in the cytosol and must be imported into mitochondria to attain their mature forms and execute their functions. Disruption of mitochondrial functions, whether caused by external or internal stress, may compromise mitochondrial protein import. Therefore, monitoring mitochondrial protein import has become a standard approach to assess mitochondrial health and gain insights into mitochondrial biology, especially during stress. This chapter describes a detailed protocol for monitoring mitochondrial import in live cells using microscopy. Co-localization between mitochondria and a genetic reporter of mitochondrially targeted enhanced GFP (eGFP) is employed to evaluate mitochondrial protein import efficiency under different physiological conditions. Overall, this technique provides a simple and robust approach to assess mitochondrial protein import efficiency within its native cellular environment.
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Affiliation(s)
- F X Reymond Sutandy
- Institute of Molecular Systems Medicine, Goethe University Frankfurt, Faculty of Medicine, Frankfurt am Main, Germany.
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19
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Clausen L, Okarmus J, Voutsinos V, Meyer M, Lindorff-Larsen K, Hartmann-Petersen R. PRKN-linked familial Parkinson's disease: cellular and molecular mechanisms of disease-linked variants. Cell Mol Life Sci 2024; 81:223. [PMID: 38767677 PMCID: PMC11106057 DOI: 10.1007/s00018-024-05262-8] [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: 02/27/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024]
Abstract
Parkinson's disease (PD) is a common and incurable neurodegenerative disorder that arises from the loss of dopaminergic neurons in the substantia nigra and is mainly characterized by progressive loss of motor function. Monogenic familial PD is associated with highly penetrant variants in specific genes, notably the PRKN gene, where homozygous or compound heterozygous loss-of-function variants predominate. PRKN encodes Parkin, an E3 ubiquitin-protein ligase important for protein ubiquitination and mitophagy of damaged mitochondria. Accordingly, Parkin plays a central role in mitochondrial quality control but is itself also subject to a strict protein quality control system that rapidly eliminates certain disease-linked Parkin variants. Here, we summarize the cellular and molecular functions of Parkin, highlighting the various mechanisms by which PRKN gene variants result in loss-of-function. We emphasize the importance of high-throughput assays and computational tools for the clinical classification of PRKN gene variants and how detailed insights into the pathogenic mechanisms of PRKN gene variants may impact the development of personalized therapeutics.
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Affiliation(s)
- Lene Clausen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Justyna Okarmus
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5230, Odense, Denmark
| | - Vasileios Voutsinos
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Morten Meyer
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5230, Odense, Denmark
- Department of Neurology, Odense University Hospital, 5000, Odense, Denmark
- Department of Clinical Research, BRIDGE, Brain Research Inter Disciplinary Guided Excellence, University of Southern Denmark, 5230, Odense, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rasmus Hartmann-Petersen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark.
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20
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Speck SL, Wei X, Semenkovich CF. Depalmitoylation and cell physiology: APT1 as a mediator of metabolic signals. Am J Physiol Cell Physiol 2024; 326:C1034-C1041. [PMID: 38344800 PMCID: PMC11193526 DOI: 10.1152/ajpcell.00542.2023] [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: 10/16/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 03/13/2024]
Abstract
More than half of the global population is obese or overweight, especially in Western countries, and this excess adiposity disrupts normal physiology to cause chronic diseases. Diabetes, an adiposity-associated epidemic disease, affects >500 million people, and cases are projected to exceed 1 billion before 2050. Lipid excess can impact physiology through the posttranslational modification of proteins, including the reversible process of S-palmitoylation. Dynamic palmitoylation cycling requires the S-acylation of proteins by acyltransferases and the depalmitoylation of these proteins mediated in part by acyl-protein thioesterases (APTs) such as APT1. Emerging evidence points to tissue-specific roles for the depalmitoylase APT1 in maintaining homeostasis in the vasculature, pancreatic islets, and liver. These recent findings raise the possibility that APT1 substrates can be therapeutically targeted to treat the complications of metabolic diseases.
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Affiliation(s)
- Sarah L Speck
- Division of Endocrinology, Metabolism and Lipid Research, Washington University in St. Louis, St. Louis, Missouri, United States
| | - Xiaochao Wei
- Division of Endocrinology, Metabolism and Lipid Research, Washington University in St. Louis, St. Louis, Missouri, United States
| | - Clay F Semenkovich
- Division of Endocrinology, Metabolism and Lipid Research, Washington University in St. Louis, St. Louis, Missouri, United States
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21
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Lee-Glover LP, Shutt TE. Mitochondrial quality control pathways sense mitochondrial protein import. Trends Endocrinol Metab 2024; 35:308-320. [PMID: 38103974 DOI: 10.1016/j.tem.2023.11.004] [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: 10/18/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
Mitochondrial quality control (MQC) mechanisms are required to maintain a functional proteome, which enables mitochondria to perform a myriad of important cellular functions from oxidative phosphorylation to numerous other metabolic pathways. Mitochondrial protein homeostasis begins with the import of over 1000 nuclear-encoded mitochondrial proteins and the synthesis of 13 mitochondrial DNA-encoded proteins. A network of chaperones and proteases helps to fold new proteins and degrade unnecessary, damaged, or misfolded proteins, whereas more extensive damage can be removed by mitochondrial-derived vesicles (MDVs) or mitochondrial autophagy (mitophagy). Here, focusing on mechanisms in mammalian cells, we review the importance of mitochondrial protein import as a sentinel of mitochondrial function that activates multiple MQC mechanisms when impaired.
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Affiliation(s)
- Laurie P Lee-Glover
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Timothy E Shutt
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Alberta, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Alberta, Canada; Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada; Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada.
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22
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Campbell D, Zuryn S. The mechanisms and roles of mitochondrial dynamics in C. elegans. Semin Cell Dev Biol 2024; 156:266-275. [PMID: 37919144 DOI: 10.1016/j.semcdb.2023.10.006] [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: 06/18/2023] [Revised: 10/15/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023]
Abstract
If mitochondria are the powerhouses of the cell, then mitochondrial dynamics are the power grid that regulates how that energy output is directed and maintained in response to unique physiological demands. Fission and fusion dynamics are highly regulated processes that fine-tune the mitochondrial networks of cells to enable appropriate responses to intrinsic and extrinsic stimuli, thereby maintaining cellular and organismal homeostasis. These dynamics shape many aspects of an organism's healthspan including development, longevity, stress resistance, immunity, and response to disease. In this review, we discuss the latest findings regarding the mechanisms and roles of mitochondrial dynamics by focussing on the nematode Caenorhabditis elegans. Whole live-animal studies in C. elegans have enabled a true organismal-level understanding of the impact that mitochondrial dynamics play in homeostasis over a lifetime.
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Affiliation(s)
- Daniel Campbell
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Steven Zuryn
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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23
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Singh F, Wilhelm L, Prescott AR, Ostacolo K, Zhao JF, Ogmundsdottir MH, Ganley IG. PINK1 regulated mitophagy is evident in skeletal muscles. AUTOPHAGY REPORTS 2024; 3:2326402. [PMID: 38988500 PMCID: PMC7616148 DOI: 10.1080/27694127.2024.2326402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 07/12/2024]
Abstract
PINK1, mutated in familial forms of Parkinson's disease, initiates mitophagy following mitochondrial depolarization. However, it is difficult to monitor this pathway physiologically in mice as loss of PINK1 does not alter basal mitophagy levels in most tissues. To further characterize this pathway in vivo, we used mito-QC mice in which loss of PINK1 was combined with the mitochondrial-associated POLGD257A mutation. We focused on skeletal muscle as gene expression data indicates that this tissue has the highest PINK1 levels. We found that loss of PINK1 in oxidative hindlimb muscle significantly reduced mitophagy. Of interest, the presence of the POLGD257A mutation, while having a minor effect in most tissues, restored levels of muscle mitophagy caused by the loss of PINK1. Although our observations highlight that multiple mitophagy pathways operate within a single tissue, we identify skeletal muscle as a tissue of choice for the study of PINK1-dependant mitophagy under basal conditions.
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Affiliation(s)
- Francois Singh
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Department of Physiology, Biomedical Center, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Lea Wilhelm
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Alan R. Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee, UK
| | - Kevin Ostacolo
- Department of Anatomy, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jin-Feng Zhao
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Margret H. Ogmundsdottir
- Department of Anatomy, Biomedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Ian G. Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
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24
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Delgado JM, Shepard LW, Lamson SW, Liu SL, Shoemaker CJ. The ER membrane protein complex restricts mitophagy by controlling BNIP3 turnover. EMBO J 2024; 43:32-60. [PMID: 38177312 PMCID: PMC10883272 DOI: 10.1038/s44318-023-00006-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 01/06/2024] Open
Abstract
Lysosomal degradation of autophagy receptors is a common proxy for selective autophagy. However, we find that two established mitophagy receptors, BNIP3 and BNIP3L/NIX, are constitutively delivered to lysosomes in an autophagy-independent manner. This alternative lysosomal delivery of BNIP3 accounts for nearly all its lysosome-mediated degradation, even upon mitophagy induction. To identify how BNIP3, a tail-anchored protein in the outer mitochondrial membrane, is delivered to lysosomes, we performed a genome-wide CRISPR screen for factors influencing BNIP3 flux. This screen revealed both known modifiers of BNIP3 stability as well as a pronounced reliance on endolysosomal components, including the ER membrane protein complex (EMC). Importantly, the endolysosomal system and the ubiquitin-proteosome system regulated BNIP3 independently. Perturbation of either mechanism is sufficient to modulate BNIP3-associated mitophagy and affect underlying cellular physiology. More broadly, these findings extend recent models for tail-anchored protein quality control and install endosomal trafficking and lysosomal degradation in the canon of pathways that tightly regulate endogenous tail-anchored protein localization.
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Affiliation(s)
- Jose M Delgado
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Logan Wallace Shepard
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Sarah W Lamson
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Samantha L Liu
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Christopher J Shoemaker
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.
- Dartmouth Cancer Center, Lebanon, NH, USA.
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25
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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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26
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Ma J, Liu L, Song L, Liu J, Yang L, Chen Q, Wu JY, Zhu L. Integration of FUNDC1-associated mitochondrial protein import and mitochondrial quality control contributes to TDP-43 degradation. Cell Death Dis 2023; 14:735. [PMID: 37951930 PMCID: PMC10640645 DOI: 10.1038/s41419-023-06261-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/20/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
Though TDP-43 protein can be translocated into mitochondria and causes mitochondrial damage in TDP-43 proteinopathy, little is known about how TDP-43 is imported into mitochondria. In addition, whether mitochondrial damage is caused by mitochondrial mislocalization of TDP-43 or a side effect of mitochondria-mediated TDP-43 degradation remains to be investigated. Here, our bioinformatical analyses reveal that mitophagy receptor gene FUNDC1 is co-expressed with TDP-43, and both TDP-43 and FUNDC1 expression is correlated with genes associated with mitochondrial protein import pathway in brain samples of patients diagnosed with TDP-43 proteinopathy. FUNDC1 promotes mitochondrial translocation of TDP-43 possibly by promoting TDP-43-TOM70 and DNAJA2-TOM70 interactions, which is independent of the LC3 interacting region of FUNDC1 in cellular experiments. In the transgenic fly model of TDP-43 proteinopathy, overexpressing FUNDC1 enhances TDP-43 induced mitochondrial damage, whereas down-regulating FUNDC1 reverses TDP-43 induced mitochondrial damage. FUNDC1 regulates mitochondria-mediated TDP-43 degradation not only by regulating mitochondrial TDP-43 import, but also by increasing LONP1 level and by activating mitophagy, which plays important roles in cytosolic TDP-43 clearance. Together, this study not only uncovers the mechanism of mitochondrial TDP-43 import, but also unravels the active role played by mitochondria in regulating TDP-43 homeostasis.
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Affiliation(s)
- Jinfa Ma
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lu Song
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianghong Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lingyao Yang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Quan Chen
- Interdisciplinary Center of Cell Response, State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jane Y Wu
- Department of Neurology, Center for Genetic Medicine, Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
| | - Li Zhu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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27
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Münch C, Kirstein J. Protein quality control: from molecular mechanisms to therapeutic intervention-EMBO workshop, May 21-26 2023, Srebreno, Croatia. Cell Stress Chaperones 2023; 28:631-640. [PMID: 37731161 PMCID: PMC10746685 DOI: 10.1007/s12192-023-01383-4] [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: 09/06/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
Protein quality control pathways ensure a functional proteome and rely on a complex proteostasis network (PN) that is composed of molecular chaperones and proteases. Failures in the PN can lead to a broad spectrum of diseases, including neurodegenerative disorders like Alzheimer's, Parkinson's, and a range of motor neuron diseases. The EMBO workshop "Protein quality control: from molecular mechanisms to therapeutic intervention" covered all aspects of protein quality control from underlying molecular mechanisms of chaperones and proteases to stress signaling pathways and medical implications. This report summarizes the workshop and highlights selected presentations.
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Affiliation(s)
- Christian Münch
- Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Janine Kirstein
- Friedrich-Schiller-Universität Jena, Jena, Germany.
- Leibniz-Institute on Aging/Fritz-Lipmann Institute, Jena, Germany.
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28
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Uoselis L, Lindblom R, Lam WK, Küng CJ, Skulsuppaisarn M, Khuu G, Nguyen TN, Rudler DL, Filipovska A, Schittenhelm RB, Lazarou M. Temporal landscape of mitochondrial proteostasis governed by the UPR mt. SCIENCE ADVANCES 2023; 9:eadh8228. [PMID: 37738349 PMCID: PMC10516501 DOI: 10.1126/sciadv.adh8228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023]
Abstract
Breakdown of mitochondrial proteostasis activates quality control pathways including the mitochondrial unfolded protein response (UPRmt) and PINK1/Parkin mitophagy. However, beyond the up-regulation of chaperones and proteases, we have a limited understanding of how the UPRmt remodels and restores damaged mitochondrial proteomes. Here, we have developed a functional proteomics framework, termed MitoPQ (Mitochondrial Proteostasis Quantification), to dissect the UPRmt's role in maintaining proteostasis during stress. We find essential roles for the UPRmt in both protecting and repairing proteostasis, with oxidative phosphorylation metabolism being a central target of the UPRmt. Transcriptome analyses together with MitoPQ reveal that UPRmt transcription factors drive independent signaling arms that act in concert to maintain proteostasis. Unidirectional interplay between the UPRmt and PINK1/Parkin mitophagy was found to promote oxidative phosphorylation recovery when the UPRmt failed. Collectively, this study defines the network of proteostasis mediated by the UPRmt and highlights the value of functional proteomics in decoding stressed proteomes.
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Affiliation(s)
- Louise Uoselis
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Runa Lindblom
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Wai Kit Lam
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Catharina J. Küng
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Marvin Skulsuppaisarn
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Grace Khuu
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Thanh N. Nguyen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Danielle L. Rudler
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, Nedlands, Western Australia, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, Nedlands, Western Australia, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, Nedlands, Western Australia, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, Nedlands, Western Australia, Australia
| | - Ralf B. Schittenhelm
- Monash Proteomics and Metabolomics Facility, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Michael Lazarou
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD 20185, USA
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
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Jiménez-Loygorri JI, Benítez-Fernández R, Viedma-Poyatos Á, Zapata-Muñoz J, Villarejo-Zori B, Gómez-Sintes R, Boya P. Mitophagy in the retina: Viewing mitochondrial homeostasis through a new lens. Prog Retin Eye Res 2023; 96:101205. [PMID: 37454969 DOI: 10.1016/j.preteyeres.2023.101205] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Mitochondrial function is key to support metabolism and homeostasis in the retina, an organ that has one of the highest metabolic rates body-wide and is constantly exposed to photooxidative damage and external stressors. Mitophagy is the selective autophagic degradation of mitochondria within lysosomes, and can be triggered by distinct stimuli such as mitochondrial damage or hypoxia. Here, we review the importance of mitophagy in retinal physiology and pathology. In the developing retina, mitophagy is essential for metabolic reprogramming and differentiation of retina ganglion cells (RGCs). In basal conditions, mitophagy acts as a quality control mechanism, maintaining a healthy mitochondrial pool to meet cellular demands. We summarize the different autophagy- and mitophagy-deficient mouse models described in the literature, and discuss the potential role of mitophagy dysregulation in retinal diseases such as glaucoma, diabetic retinopathy, retinitis pigmentosa, and age-related macular degeneration. Finally, we provide an overview of methods used to monitor mitophagy in vitro, ex vivo, and in vivo. This review highlights the important role of mitophagy in sustaining visual function, and its potential as a putative therapeutic target for retinal and other diseases.
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Affiliation(s)
- Juan Ignacio Jiménez-Loygorri
- Autophagy Lab, Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain.
| | - Rocío Benítez-Fernández
- Autophagy Lab, Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain; Departament of Neuroscience and Movement Science, Faculty of Science and Medicine, University of Fribourg, 1700, Fribourg, Switzerland
| | - Álvaro Viedma-Poyatos
- Autophagy Lab, Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Juan Zapata-Muñoz
- Autophagy Lab, Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Beatriz Villarejo-Zori
- Autophagy Lab, Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Raquel Gómez-Sintes
- Autophagy Lab, Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Patricia Boya
- Autophagy Lab, Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain; Departament of Neuroscience and Movement Science, Faculty of Science and Medicine, University of Fribourg, 1700, Fribourg, Switzerland.
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30
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Han Y, Liu D, Cheng Y, Ji Q, Liu M, Zhang B, Zhou S. Maintenance of mitochondrial homeostasis for Alzheimer's disease: Strategies and challenges. Redox Biol 2023; 63:102734. [PMID: 37159984 PMCID: PMC10189488 DOI: 10.1016/j.redox.2023.102734] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/11/2023] Open
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative diseases, and its early onset is closely related to mitochondrial energy metabolism. The brain is only 2% of body weight, but consumes 20% of total energy needs. Mitochondria are responsible for providing energy in cells, and maintaining their homeostasis ensures an adequate supply of energy to the brain. Mitochondrial homeostasis is constituted by mitochondrial quantity and quality control, which is dynamically regulated by mitochondrial energy metabolism, mitochondrial dynamics and mitochondrial quality control. Impaired energy metabolism of brain cells occurs early in AD, and maintaining mitochondrial homeostasis is a promising therapeutic target in the future. We summarized the mechanism of mitochondrial homeostasis in AD, its influence on the pathogenesis of early AD, strategies for maintaining mitochondrial homeostasis, and mitochondrial targeting strategies. This review concludes with the authors' opinions on future research and development for mitochondrial homeostasis of early AD.
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Affiliation(s)
- Ying Han
- Department of Pharmaceutics, School of Pharmacy, Air Force Medical University, Changle West Road 169, Xi'an, 710032, Shaanxi, China
| | - Daozhou Liu
- Department of Pharmaceutics, School of Pharmacy, Air Force Medical University, Changle West Road 169, Xi'an, 710032, Shaanxi, China
| | - Ying Cheng
- Department of Pharmaceutics, School of Pharmacy, Air Force Medical University, Changle West Road 169, Xi'an, 710032, Shaanxi, China
| | - Qifeng Ji
- Department of Pharmaceutics, School of Pharmacy, Air Force Medical University, Changle West Road 169, Xi'an, 710032, Shaanxi, China
| | - Miao Liu
- Department of Pharmaceutics, School of Pharmacy, Air Force Medical University, Changle West Road 169, Xi'an, 710032, Shaanxi, China
| | - Bangle Zhang
- Department of Pharmaceutics, School of Pharmacy, Air Force Medical University, Changle West Road 169, Xi'an, 710032, Shaanxi, China
| | - Siyuan Zhou
- Department of Pharmaceutics, School of Pharmacy, Air Force Medical University, Changle West Road 169, Xi'an, 710032, Shaanxi, China.
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31
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Gong P, Yue S, Shi F, Yang W, Yao W, Chen F, Guo Y. Protective Effect of Astragaloside IV against Cadmium-Induced Damage on Mouse Renal Podocytes (MPC5). Molecules 2023; 28:4897. [PMID: 37446560 DOI: 10.3390/molecules28134897] [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: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
In this study, we investigated the protective effect of Astragaloside IV (Ast) on mouse podocytes and its possible mechanism of action by constructing a cadmium-induced mouse renal podocytes model. We investigated the effects of cadmium (Cd) toxicity on cell number, morphology, the mitochondrial status of subcellular organelles, protein and gene levels, and the protective effects of Ast by constructing a model of Cd-induced damage to mouse renal podocytes (MPC5) and giving Ast protection at the same time. The results showed that exposure of MPC5 cells to CdCl2 culture medium containing 6.25 μM concentration acted with low cell mortality, but the mortality of MPC5 cells increased with the prolongation of cadmium exposure time. Given Ast, the death rate in the low dose group (12.5 μM) was significantly reduced, while the death rate in the medium dose group (25 μM) was extremely significantly reduced. In comparison to the control group, the Cd-exposed group exhibited a significant increase of 166.7% in malondialdehyde (MDA) content and a significant decrease of 17.1% in SOD activity. The mitochondrial membrane potential was also reduced to varying degrees. However, in the Ast-protected group compared to the Cd-exposed group, the MDA content significantly decreased by 20.8%, the SOD activity decreased by 7.14%, and the mitochondrial membrane potential showed a significant increase. Fluorescence staining of mitochondrial membrane potential indicated that Cd exposure caused mitochondrial apoptosis. In the 12-h cadmium-exposed group, the protein expression of Nephrin in mice significantly decreased by 33.4%. However, the expression of the Desmin protein significantly increased by 67.8%, and the expression of the autophagy protein LC3-II significantly increased by 55.5%. Meanwhile, the expression of PINK1, a mitochondrial autophagy pathway protein, was significantly increased in the 12 h and 24 h cadmium exposure groups. The mRNA level of PINK1 was significantly increased, and that of Parkin was decreased in the 48 h cadmium exposure group. Compared to the Cd-exposed group, the Ast group showed more significant improvements in the expression of podocyte structure, functional proteins, and mitochondrial autophagy pathway proteins. The immunological assay of mitochondrial autophagic pathway proteins further indicated that Cd-induced damage to MPC5 cells might be associated with the dysregulation of mitochondrial autophagy.
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Affiliation(s)
- Pin Gong
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
- School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Shan Yue
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
- School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Fuxiong Shi
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
- School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Wenjuan Yang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
- School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Wenbo Yao
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
- School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Fuxin Chen
- School of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, Xi'an 710054, China
| | - Yuxi Guo
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
- School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an 710021, China
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32
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Eldeeb MA, Soumbasis A, Fon EA. How does mitochondrial import machinery fine-tune mitophagy? Different paths and one destination. Trends Endocrinol Metab 2023:S1043-2760(23)00107-8. [PMID: 37321958 DOI: 10.1016/j.tem.2023.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023]
Abstract
Given their polyvalent roles, an intrinsic challenge that mitochondria face is the continuous exposure to various stressors including mitochondrial import defects, which leads to their dysfunction. Recent work has unveiled a presequence translocase-associated import motor (PAM) complex-dependent quality control pathway whereby misfolded proteins mitigate mitochondrial protein import and subsequently elicit mitophagy without the loss of mitochondrial membrane potential.
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Affiliation(s)
- Mohamed A Eldeeb
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.
| | - Andrea Soumbasis
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Edward A Fon
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.
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33
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Sutandy FXR, Gößner I, Tascher G, Münch C. A cytosolic surveillance mechanism activates the mitochondrial UPR. Nature 2023:10.1038/s41586-023-06142-0. [PMID: 37286597 DOI: 10.1038/s41586-023-06142-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023]
Abstract
The mitochondrial unfolded protein response (UPRmt) is essential to safeguard mitochondria from proteotoxic damage by activating a dedicated transcriptional response in the nucleus to restore proteostasis1,2. Yet, it remains unclear how the information on mitochondria misfolding stress (MMS) is signalled to the nucleus as part of the human UPRmt (refs. 3,4). Here, we show that UPRmt signalling is driven by the release of two individual signals in the cytosol-mitochondrial reactive oxygen species (mtROS) and accumulation of mitochondrial protein precursors in the cytosol (c-mtProt). Combining proteomics and genetic approaches, we identified that MMS causes the release of mtROS into the cytosol. In parallel, MMS leads to mitochondrial protein import defects causing c-mtProt accumulation. Both signals integrate to activate the UPRmt; released mtROS oxidize the cytosolic HSP40 protein DNAJA1, which leads to enhanced recruitment of cytosolic HSP70 to c-mtProt. Consequently, HSP70 releases HSF1, which translocates to the nucleus and activates transcription of UPRmt genes. Together, we identify a highly controlled cytosolic surveillance mechanism that integrates independent mitochondrial stress signals to initiate the UPRmt. These observations reveal a link between mitochondrial and cytosolic proteostasis and provide molecular insight into UPRmt signalling in human cells.
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Affiliation(s)
- F X Reymond Sutandy
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ines Gößner
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany.
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34
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Groh C, Haberkant P, Stein F, Filbeck S, Pfeffer S, Savitski MM, Boos F, Herrmann JM. Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins. Life Sci Alliance 2023; 6:e202201805. [PMID: 36941057 PMCID: PMC10027898 DOI: 10.26508/lsa.202201805] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/23/2023] Open
Abstract
Cellular functionality relies on a well-balanced, but highly dynamic proteome. Dysfunction of mitochondrial protein import leads to the cytosolic accumulation of mitochondrial precursor proteins which compromise cellular proteostasis and trigger a mitoprotein-induced stress response. To dissect the effects of mitochondrial dysfunction on the cellular proteome as a whole, we developed pre-post thermal proteome profiling. This multiplexed time-resolved proteome-wide thermal stability profiling approach with isobaric peptide tags in combination with a pulsed SILAC labelling elucidated dynamic proteostasis changes in several dimensions: In addition to adaptations in protein abundance, we observed rapid modulations of the thermal stability of individual cellular proteins. Different functional groups of proteins showed characteristic response patterns and reacted with group-specific kinetics, allowing the identification of functional modules that are relevant for mitoprotein-induced stress. Thus, our new pre-post thermal proteome profiling approach uncovered a complex response network that orchestrates proteome homeostasis in eukaryotic cells by time-controlled adaptations of the abundance and the conformation of proteins.
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Affiliation(s)
- Carina Groh
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | | | | | | | - Felix Boos
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany;
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35
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Zhang L, Zhang H, Du S, Song X, Hu D. In Vitro Transcriptional Response of Eimeria tenella to Toltrazuril Reveals That Oxidative Stress and Autophagy Contribute to Its Anticoccidial Effect. Int J Mol Sci 2023; 24:ijms24098370. [PMID: 37176073 PMCID: PMC10179680 DOI: 10.3390/ijms24098370] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/16/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Intestinal coccidiosis is a common parasitic disease in livestock, caused by the infection of Eimeria and Cystoisospora parasites, which results in great economic losses to animal husbandry. Triazine compounds, such as toltrazuril and diclazuril, are widely used in the treatment and chemoprophylaxis of coccidiosis. Unfortunately, widespread drug resistance has compromised their effectiveness. Most studies have focused on prophylaxis and therapeutics with toltrazuril in flocks, while a comprehensive understanding of how toltrazuril treatment alters the transcriptome of E. tenella remains unknown. In this study, merozoites of E. tenella were treated in vitro with 0.5 μg/mL toltrazuril for 0, 1, 2 and 4 h, respectively. The gene transcription profiles were then compared by high-throughput sequencing. Our results showed that protein hydrolysis genes were significantly upregulated after drug treatment, while cell cycle-related genes were significantly downregulated, suggesting that toltrazuril may affect parasite division. The expression of redox-related genes was upregulated and elevated levels of ROS and autophagosomes were detected in the parasite after toltrazuril treatment, suggesting that toltrazuril may cause oxidative stress to parasite cells and lead to its autophagy. Our results provide basic knowledge of the response of Eimeria genes to toltrazuril and further analysis of the identified transcriptional changes can provide useful information for a better understanding of the mechanism of action of toltrazuril against Eimeria.
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Affiliation(s)
- Lei Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Hongtao Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Shiqi Du
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Xingju Song
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning 530004, China
| | - Dandan Hu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning 530004, China
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36
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Trempe JF, Gehring K. Structural mechanisms of mitochondrial quality control mediated by PINK1 and parkin. J Mol Biol 2023:168090. [PMID: 37054910 DOI: 10.1016/j.jmb.2023.168090] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease and represents a looming public health crisis as the global population ages. While the etiology of the more common, idiopathic form of the disease remains unknown, the last ten years have seen a breakthrough in our understanding of the genetic forms related to two proteins that regulate a quality control system for the removal of damaged or non-functional mitochondria. Here, we review the structure of these proteins, PINK1, a protein kinase, and parkin, a ubiquitin ligase with an emphasis on the molecular mechanisms responsible for their recognition of dysfunctional mitochondria and control of the subsequent ubiquitination cascade. Recent atomic structures have revealed the basis of PINK1 substrate specificity and the conformational changes responsible for activation of PINK1 and parkin catalytic activity. Progress in understanding the molecular basis of mitochondrial quality control promises to open new avenues for therapeutic interventions in PD.
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Affiliation(s)
- Jean-François Trempe
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada; Centre de Recherche en Biologie Structurale
| | - Kalle Gehring
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada; Centre de Recherche en Biologie Structurale
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Delgado JM, Wallace Shepard L, Lamson SW, Liu SL, Shoemaker CJ. The ER membrane protein complex governs lysosomal turnover of a mitochondrial tail-anchored protein, BNIP3, to restrict mitophagy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533681. [PMID: 36993512 PMCID: PMC10055395 DOI: 10.1101/2023.03.22.533681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Lysosomal degradation of autophagy receptors is a common proxy for selective autophagy. However, we find that two established mitophagy receptors, BNIP3 and BNIP3L/NIX, violate this assumption. Rather, BNIP3 and NIX are constitutively delivered to lysosomes in an autophagy-independent manner. This alternative lysosomal delivery of BNIP3 accounts for nearly all of its lysosome-mediated degradation, even upon mitophagy induction. To identify how BNIP3, a tail-anchored protein in the outer mitochondrial membrane, is delivered to lysosomes, we performed a genome-wide CRISPR screen for factors influencing BNIP3 flux. By this approach, we revealed both known modifiers of BNIP3 stability as well as a pronounced reliance on endolysosomal components, including the ER membrane protein complex (EMC). Importantly, the endolysosomal system regulates BNIP3 alongside, but independent of, the ubiquitin-proteosome system (UPS). Perturbation of either mechanism is sufficient to modulate BNIP3-associated mitophagy and affect underlying cellular physiology. In short, while BNIP3 can be cleared by parallel and partially compensatory quality control pathways, non-autophagic lysosomal degradation of BNIP3 is a strong post-translational modifier of BNIP3 function. More broadly, these data reveal an unanticipated connection between mitophagy and TA protein quality control, wherein the endolysosomal system provides a critical axis for regulating cellular metabolism. Moreover, these findings extend recent models for tail-anchored protein quality control and install endosomal trafficking and lysosomal degradation in the canon of pathways that ensure tight regulation of endogenous TA protein localization.
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Affiliation(s)
- Jose M Delgado
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Logan Wallace Shepard
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Sarah W Lamson
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Samantha L Liu
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Christopher J Shoemaker
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH
- Dartmouth Cancer Center, Lebanon, NH, USA
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38
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Schäfer JA, Sutandy FXR, Münch C. Omics-based approaches for the systematic profiling of mitochondrial biology. Mol Cell 2023; 83:911-926. [PMID: 36931258 DOI: 10.1016/j.molcel.2023.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Mitochondria are essential for cellular functions such as metabolism and apoptosis. They dynamically adapt to the changing environmental demands by adjusting their protein, nucleic acid, metabolite, and lipid contents. In addition, the mitochondrial components are modulated on different levels in response to changes, including abundance, activity, and interaction. A wide range of omics-based approaches has been developed to be able to explore mitochondrial adaptation and how mitochondrial function is compromised in disease contexts. Here, we provide an overview of the omics methods that allow us to systematically investigate the different aspects of mitochondrial biology. In addition, we show examples of how these methods have provided new biological insights. The emerging use of these toolboxes provides a more comprehensive understanding of the processes underlying mitochondrial function.
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Affiliation(s)
- Jasmin Adriana Schäfer
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany
| | - F X Reymond Sutandy
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany.
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Busch JD, Fielden LF, Pfanner N, Wiedemann N. Mitochondrial protein transport: Versatility of translocases and mechanisms. Mol Cell 2023; 83:890-910. [PMID: 36931257 DOI: 10.1016/j.molcel.2023.02.020] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/17/2023]
Abstract
Biogenesis of mitochondria requires the import of approximately 1,000 different precursor proteins into and across the mitochondrial membranes. Mitochondria exhibit a wide variety of mechanisms and machineries for the translocation and sorting of precursor proteins. Five major import pathways that transport proteins to their functional intramitochondrial destination have been elucidated; these pathways range from the classical amino-terminal presequence-directed pathway to pathways using internal or even carboxy-terminal targeting signals in the precursors. Recent studies have provided important insights into the structural organization of membrane-embedded preprotein translocases of mitochondria. A comparison of the different translocases reveals the existence of at least three fundamentally different mechanisms: two-pore-translocase, β-barrel switching, and transport cavities open to the lipid bilayer. In addition, translocases are physically engaged in dynamic interactions with respiratory chain complexes, metabolite transporters, quality control factors, and machineries controlling membrane morphology. Thus, mitochondrial preprotein translocases are integrated into multi-functional networks of mitochondrial and cellular machineries.
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Affiliation(s)
- Jakob D Busch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Laura F Fielden
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, 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.
| | - Nils Wiedemann
- 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.
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40
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Wang Q, Liu J, Yang X, Zhou H, Li Y. Gold nanoparticles enhance proliferation and osteogenic differentiation of periodontal ligament stem cells by PINK1-mediated mitophagy. Arch Oral Biol 2023; 150:105692. [PMID: 37004436 DOI: 10.1016/j.archoralbio.2023.105692] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023]
Abstract
OBJECTIVE Evidence suggests that gold nanoparticles (AuNPs) improve osteogenic differentiation of periodontal ligament stem cells (PDLSCs), PTEN-induced putative kinase 1 (PINK1) dependent mitophagy modulates inter-clonal communication among PDLSCs with osteogenic heterogeneity, but the mechanism remains vague. Therefore, the current research assessed the influence of AuNPs on proliferation, osteogenic differentiation and mitophagy of PDLSCs and the potential mechanism was analyzed. METHODS Gold nanospheres with a diameter of 5, 10, 20, 40, and 80 nm were synthesized and characterized through transmission electron microscopy, and rat PDLSCs were isolated using flow sorting. Next, PDLSCs were treated with AuNPs or PINK1 lentivirus to obtain its overexpression or suppression. Proliferation and osteogenic differentiation were evaluated by CCK-8, ALP staining, ARS staining, and immunoblotting of OCN, OPN, RUNX2, ALP, BMP2, and COL1. Mitochondrial quality, homeostasis and quantity were assessed though JC-1 staining, immunoblotting of Tom20, Tim23 and HSP60 and mitochondrial ROS detection. PINK1, Parkin, Beclin1 and LC3 expression was quantified to investigate mitophagy, using RT-qPCR and immunoblotting and the formation of RFP-GFP-LC3-labeled autophagosomes were also measured. RESULTS The proliferation ability of PDLSCs almost reached the maximum under 20 nm AuNPs for 24 h. AuNPs enhanced the proliferation and osteogenic differentiation of PDLSCs, improved mitochondrial quality and homeostasis as well as attenuated mitochondrial quantity. Additionally, mitophagy was enhanced by PDLSCs. Activation of PINK1 synergistically enhanced AuNPs-mediated mitophagy, mitochondrial quality, homeostasis and osteogenic differentiation in PDLSCs, obtaining opposite effects when PINK1 was suppressed. CONCLUSION AuNPs enhance proliferation and osteogenic differentiation of PDLSCs through PINK1-mediated mitophagy.
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41
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Michaelis JB, Bozkurt S, Schäfer JA, Münch C. Monitoring Mitochondrial Protein Import Using Mitochondrial Targeting Sequence (MTS)-eGFP. Bio Protoc 2022; 12:e4578. [PMID: 36618095 PMCID: PMC9797355 DOI: 10.21769/bioprotoc.4578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/19/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Mitochondria are cellular organelles essential for the function and survival of eukaryotic cells. Nearly all mitochondrial proteins are nuclear-encoded and require mitochondrial import upon their synthesis in the cytosol. Various approaches have been described to study mitochondrial protein import, such as monitoring the entry of radiolabeled proteins into purified mitochondria or quantifying newly synthesized proteins within mitochondria by proteomics. Here, we provide a detailed protocol for a commonly used and straightforward assay that quantitatively examines mitochondrial protein import by monitoring the co-localization of mitochondrially targeted enhanced green fluorescent protein (eGFP) with the mitochondrial fluorescence dye MitoTracker TM Deep Red FM by live cell imaging. We describe the preparation and use of a stable mammalian cell line inducibly expressing a mitochondrial targeting sequence (MTS)-eGFP, followed by quantitative image analysis using an open-source ImageJ-based plugin. This inducible expression system avoids the need for transient transfection while enabling titration of MTS-eGFP expression and thereby avoiding protein folding stress. Overall, the assay provides a simple and robust approach to assess mitochondrial import capacity of cells in various disease-related settings. This protocol was validated in: Mol Cell (2021), DOI: 10.1016/j.molcel.2021.11.004 Graphical abstract.
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Affiliation(s)
- Jonas B. Michaelis
- Institute of Biochemistry II, Goethe University Frankfurt, Faculty of Medicine, Theodor-Stern-Kai 7, Haus 75 60590 Frankfurt am Main, Germany
| | - Süleyman Bozkurt
- Institute of Biochemistry II, Goethe University Frankfurt, Faculty of Medicine, Theodor-Stern-Kai 7, Haus 75 60590 Frankfurt am Main, Germany
| | - Jasmin A. Schäfer
- Institute of Biochemistry II, Goethe University Frankfurt, Faculty of Medicine, Theodor-Stern-Kai 7, Haus 75 60590 Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Goethe University Frankfurt, Faculty of Medicine, Theodor-Stern-Kai 7, Haus 75 60590 Frankfurt am Main, Germany
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Frankfurt Cancer Institute, Frankfurt am Main, Germany
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Cardio-Pulmonary Institute, Frankfurt am Main, Germany
,
*For correspondence:
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