1
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Wei L, Gok MO, Svoboda JD, Kozul KL, Forny M, Friedman JR, Niemi NM. Dual-localized PPTC7 limits mitophagy through proximal and dynamic interactions with BNIP3 and NIX. Life Sci Alliance 2024; 7:e202402765. [PMID: 38991726 PMCID: PMC11239977 DOI: 10.26508/lsa.202402765] [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: 04/11/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 07/13/2024] Open
Abstract
PPTC7 is a mitochondrial-localized phosphatase that suppresses BNIP3- and NIX-mediated mitophagy, but the mechanisms underlying this regulation remain ill-defined. Here, we demonstrate that loss of PPTC7 upregulates BNIP3 and NIX post-transcriptionally and independent of HIF-1α stabilization. Loss of PPTC7 prolongs the half-life of BNIP3 and NIX while blunting their accumulation in response to proteasomal inhibition, suggesting that PPTC7 promotes the ubiquitin-mediated turnover of BNIP3 and NIX. Consistently, overexpression of PPTC7 limits the accumulation of BNIP3 and NIX protein levels, which requires an intact catalytic motif but is surprisingly independent of its targeting to mitochondria. Consistently, we find that PPTC7 is dual-localized to the outer mitochondrial membrane and the matrix. Importantly, anchoring PPTC7 to the outer mitochondrial membrane is sufficient to blunt BNIP3 and NIX accumulation, and proximity labeling and fluorescence co-localization experiments demonstrate that PPTC7 dynamically associates with BNIP3 and NIX within the native cellular environment. Collectively, these data reveal that a fraction of PPTC7 localizes to the outer mitochondrial membrane to promote the proteasomal turnover of BNIP3 and NIX, limiting basal mitophagy.
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Affiliation(s)
- Lianjie Wei
- https://ror.org/04cf69335 Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Mehmet Oguz Gok
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jordyn D Svoboda
- https://ror.org/04cf69335 Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Keri-Lyn Kozul
- https://ror.org/04cf69335 Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Merima Forny
- https://ror.org/04cf69335 Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Jonathan R Friedman
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Natalie M Niemi
- https://ror.org/04cf69335 Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
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2
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Nguyen-Dien GT, Townsend B, Kulkarni PG, Kozul KL, Ooi SS, Eldershaw DN, Weeratunga S, Liu M, Jones MJ, Millard SS, Ng DC, Pagano M, Bonfim-Melo A, Schneider T, Komander D, Lazarou M, Collins BM, Pagan JK. PPTC7 antagonizes mitophagy by promoting BNIP3 and NIX degradation via SCF FBXL4. EMBO Rep 2024; 25:3324-3347. [PMID: 38992176 PMCID: PMC11316107 DOI: 10.1038/s44319-024-00181-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 07/13/2024] Open
Abstract
Mitophagy must be carefully regulated to ensure that cells maintain appropriate numbers of functional mitochondria. The SCFFBXL4 ubiquitin ligase complex suppresses mitophagy by controlling the degradation of BNIP3 and NIX mitophagy receptors, and FBXL4 mutations result in mitochondrial disease as a consequence of elevated mitophagy. Here, we reveal that the mitochondrial phosphatase PPTC7 is an essential cofactor for SCFFBXL4-mediated destruction of BNIP3 and NIX, suppressing both steady-state and induced mitophagy. Disruption of the phosphatase activity of PPTC7 does not influence BNIP3 and NIX turnover. Rather, a pool of PPTC7 on the mitochondrial outer membrane acts as an adaptor linking BNIP3 and NIX to FBXL4, facilitating the turnover of these mitophagy receptors. PPTC7 accumulates on the outer mitochondrial membrane in response to mitophagy induction or the absence of FBXL4, suggesting a homoeostatic feedback mechanism that attenuates high levels of mitophagy. We mapped critical residues required for PPTC7-BNIP3/NIX and PPTC7-FBXL4 interactions and their disruption interferes with both BNIP3/NIX degradation and mitophagy suppression. Collectively, these findings delineate a complex regulatory mechanism that restricts BNIP3/NIX-induced mitophagy.
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Affiliation(s)
- Giang Thanh Nguyen-Dien
- Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia
- Department of Biotechnology, School of Biotechnology, Viet Nam National University-International University, Ho Chi Minh City, Vietnam
| | - Brendan Townsend
- Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Prajakta Gosavi Kulkarni
- Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Keri-Lyn Kozul
- Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, MO, 63110, St Louis, USA
| | - Soo Siang Ooi
- Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Denaye N Eldershaw
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD, 4072, Australia
| | - Saroja Weeratunga
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD, 4072, Australia
| | - Meihan Liu
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD, 4072, Australia
| | - Mathew Jk Jones
- The University of Queensland Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, 4102, Australia
- School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - S Sean Millard
- Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Dominic Ch Ng
- Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, 10065, USA
| | - Alexis Bonfim-Melo
- The University of Queensland Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, 4102, Australia
| | - Tobias Schneider
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3068, Australia
| | - David Komander
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3068, Australia
| | - Michael Lazarou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3068, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3068, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Brett M Collins
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD, 4072, Australia.
| | - Julia K Pagan
- Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia.
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3
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Adriaenssens E, Nguyen TN, Sawa-Makarska J, Khuu G, Schuschnig M, Shoebridge S, Skulsuppaisarn M, Watts EM, Csalyi KD, Padman BS, Lazarou M, Martens S. Control of mitophagy initiation and progression by the TBK1 adaptors NAP1 and SINTBAD. Nat Struct Mol Biol 2024:10.1038/s41594-024-01338-y. [PMID: 38918639 DOI: 10.1038/s41594-024-01338-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 05/22/2024] [Indexed: 06/27/2024]
Abstract
Mitophagy preserves overall mitochondrial fitness by selectively targeting damaged mitochondria for degradation. The regulatory mechanisms that prevent PTEN-induced putative kinase 1 (PINK1) and E3 ubiquitin ligase Parkin (PINK1/Parkin)-dependent mitophagy and other selective autophagy pathways from overreacting while ensuring swift progression once initiated are largely elusive. Here, we demonstrate how the TBK1 (TANK-binding kinase 1) adaptors NAP1 (NAK-associated protein 1) and SINTBAD (similar to NAP1 TBK1 adaptor) restrict the initiation of OPTN (optineurin)-driven mitophagy by competing with OPTN for TBK1. Conversely, they promote the progression of nuclear dot protein 52 (NDP52)-driven mitophagy by recruiting TBK1 to NDP52 and stabilizing its interaction with FIP200. Notably, OPTN emerges as the primary recruiter of TBK1 during mitophagy initiation, which in return boosts NDP52-mediated mitophagy. Our results thus define NAP1 and SINTBAD as cargo receptor rheostats, elevating the threshold for mitophagy initiation by OPTN while promoting the progression of the pathway once set in motion by supporting NDP52. These findings shed light on the cellular strategy to prevent pathway hyperactivity while still ensuring efficient progression.
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Affiliation(s)
- Elias Adriaenssens
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Thanh Ngoc Nguyen
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Justyna Sawa-Makarska
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Grace Khuu
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Martina Schuschnig
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria
| | - Stephen Shoebridge
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Marvin Skulsuppaisarn
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Emily Maria Watts
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Kitti Dora Csalyi
- Max Perutz Labs BioOptics FACS Facility, Max Perutz Labs, University of Vienna, Vienna BioCenter Campus (VBC), Vienna, Austria
| | - Benjamin Scott Padman
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, The University of Western Australia, Nedlands, Western Australia, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Michael Lazarou
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
| | - Sascha Martens
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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4
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Benej M, Papandreou I, Denko NC. Hypoxic adaptation of mitochondria and its impact on tumor cell function. Semin Cancer Biol 2024; 100:28-38. [PMID: 38556040 PMCID: PMC11320707 DOI: 10.1016/j.semcancer.2024.03.004] [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: 01/09/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
Mitochondria are the major sink for oxygen in the cell, consuming it during ATP production. Therefore, when environmental oxygen levels drop in the tumor, significant adaptation is required. Mitochondrial activity is also a major producer of biosynthetic precursors and a regulator of cellular oxidative and reductive balance. Because of the complex biochemistry, mitochondrial adaptation to hypoxia occurs through multiple mechanisms and has significant impact on other cellular processes such as macromolecule synthesis and gene regulation. In tumor hypoxia, mitochondria shift their location in the cell and accelerate the fission and quality control pathways. Hypoxic mitochondria also undergo significant changes to fundamental metabolic pathways of carbon metabolism and electron transport. These metabolic changes further impact the nuclear epigenome because mitochondrial metabolites are used as enzymatic substrates for modifying chromatin. This coordinated response delivers physiological flexibility and increased tumor cell robustness during the environmental stress of low oxygen.
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Affiliation(s)
- Martin Benej
- Department of Radiation Oncology, OSU Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Ohio State University, Columbus, OH, USA
| | - Ioanna Papandreou
- Department of Radiation Oncology, OSU Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Ohio State University, Columbus, OH, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Nicholas C Denko
- Department of Radiation Oncology, OSU Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Ohio State University, Columbus, OH, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
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5
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Yamashita SI, Sugiura Y, Matsuoka Y, Maeda R, Inoue K, Furukawa K, Fukuda T, Chan DC, Kanki T. Mitophagy mediated by BNIP3 and NIX protects against ferroptosis by downregulating mitochondrial reactive oxygen species. Cell Death Differ 2024; 31:651-661. [PMID: 38519771 PMCID: PMC11094013 DOI: 10.1038/s41418-024-01280-y] [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: 08/22/2023] [Revised: 03/12/2024] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Mitophagy plays an important role in the maintenance of mitochondrial homeostasis and can be categorized into two types: ubiquitin-mediated and receptor-mediated pathways. During receptor-mediated mitophagy, mitophagy receptors facilitate mitophagy by tethering the isolation membrane to mitochondria. Although at least five outer mitochondrial membrane proteins have been identified as mitophagy receptors, their individual contribution and interrelationship remain unclear. Here, we show that HeLa cells lacking BNIP3 and NIX, two of the five receptors, exhibit a complete loss of mitophagy in various conditions. Conversely, cells deficient in the other three receptors show normal mitophagy. Using BNIP3/NIX double knockout (DKO) cells as a model, we reveal that mitophagy deficiency elevates mitochondrial reactive oxygen species (mtROS), which leads to activation of the Nrf2 antioxidant pathway. Notably, BNIP3/NIX DKO cells are highly sensitive to ferroptosis when Nrf2-driven antioxidant enzymes are compromised. Moreover, the sensitivity of BNIP3/NIX DKO cells is fully rescued upon the introduction of wild-type BNIP3 and NIX, but not the mutant forms incapable of facilitating mitophagy. Consequently, our results demonstrate that BNIP3 and NIX-mediated mitophagy plays a role in regulating mtROS levels and protects cells from ferroptosis.
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Affiliation(s)
- Shun-Ichi Yamashita
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 950-8510, Japan.
| | - Yuki Sugiura
- Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan
| | - Yuta Matsuoka
- Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan
| | - Rae Maeda
- Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan
| | - Keiichi Inoue
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 950-8510, Japan
| | - Kentaro Furukawa
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 950-8510, Japan
| | - Tomoyuki Fukuda
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 950-8510, Japan
| | - David C Chan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Tomotake Kanki
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 950-8510, Japan.
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6
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Filograna R, Gerlach J, Choi HN, Rigoni G, Barbaro M, Oscarson M, Lee S, Tiklova K, Ringnér M, Koolmeister C, Wibom R, Riggare S, Nennesmo I, Perlmann T, Wredenberg A, Wedell A, Motori E, Svenningsson P, Larsson NG. PARKIN is not required to sustain OXPHOS function in adult mammalian tissues. NPJ Parkinsons Dis 2024; 10:93. [PMID: 38684669 PMCID: PMC11058849 DOI: 10.1038/s41531-024-00707-0] [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: 09/12/2023] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
Loss-of-function variants in the PRKN gene encoding the ubiquitin E3 ligase PARKIN cause autosomal recessive early-onset Parkinson's disease (PD). Extensive in vitro and in vivo studies have reported that PARKIN is involved in multiple pathways of mitochondrial quality control, including mitochondrial degradation and biogenesis. However, these findings are surrounded by substantial controversy due to conflicting experimental data. In addition, the existing PARKIN-deficient mouse models have failed to faithfully recapitulate PD phenotypes. Therefore, we have investigated the mitochondrial role of PARKIN during ageing and in response to stress by employing a series of conditional Parkin knockout mice. We report that PARKIN loss does not affect oxidative phosphorylation (OXPHOS) capacity and mitochondrial DNA (mtDNA) levels in the brain, heart, and skeletal muscle of aged mice. We also demonstrate that PARKIN deficiency does not exacerbate the brain defects and the pro-inflammatory phenotype observed in mice carrying high levels of mtDNA mutations. To rule out compensatory mechanisms activated during embryonic development of Parkin-deficient mice, we generated a mouse model where loss of PARKIN was induced in adult dopaminergic (DA) neurons. Surprisingly, also these mice did not show motor impairment or neurodegeneration, and no major transcriptional changes were found in isolated midbrain DA neurons. Finally, we report a patient with compound heterozygous PRKN pathogenic variants that lacks PARKIN and has developed PD. The PARKIN deficiency did not impair OXPHOS activities or induce mitochondrial pathology in skeletal muscle from the patient. Altogether, our results argue that PARKIN is dispensable for OXPHOS function in adult mammalian tissues.
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Affiliation(s)
- Roberta Filograna
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Jule Gerlach
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hae-Na Choi
- Institute for Biochemistry, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Giovanni Rigoni
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Michela Barbaro
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Mikael Oscarson
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Seungmin Lee
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Katarina Tiklova
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Markus Ringnér
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rolf Wibom
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Sara Riggare
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Inger Nennesmo
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Perlmann
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wedell
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Elisa Motori
- Institute for Biochemistry, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Nils-Göran Larsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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7
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Gao K, Xu X, Wang C. FBXL4 mutation-caused mitochondrial DNA depletion syndrome is driven by BNIP3/BNIP3L-dependent excessive mitophagy. Trends Mol Med 2024; 30:113-116. [PMID: 38123379 DOI: 10.1016/j.molmed.2023.11.017] [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] [Received: 11/05/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
Encephalomyopathic mitochondrial DNA (mtDNA) depletion syndrome 13 (MTDPS13) is an autosomal recessive disorder arising from biallelic F-box and leucine-rich repeat (LRR) protein 4 (FBXL4) gene mutations. Recent advances have shown that excessive BCL2 interacting protein 3 (BNIP3)/ BCL2 interacting protein 3 like (BNIP3L)-dependent mitophagy underlies the molecular pathogenesis of MTDPS13. Here, we provide an overview of these groundbreaking findings and discuss potential therapeutic strategies for this fatal disease.
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Affiliation(s)
- Kun Gao
- Department of Clinical Laboratory, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Xiayun Xu
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, China
| | - Chenji Wang
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, China.
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8
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Sun Y, Cao Y, Wan H, Memetimin A, Cao Y, Li L, Wu C, Wang M, Chen S, Li Q, Ma Y, Dong M, Jiang H. A mitophagy sensor PPTC7 controls BNIP3 and NIX degradation to regulate mitochondrial mass. Mol Cell 2024; 84:327-344.e9. [PMID: 38151018 DOI: 10.1016/j.molcel.2023.11.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/15/2023] [Accepted: 11/29/2023] [Indexed: 12/29/2023]
Abstract
Mitophagy mediated by BNIP3 and NIX critically regulates mitochondrial mass. Cellular BNIP3 and NIX levels are tightly controlled by SCFFBXL4-mediated ubiquitination to prevent excessive mitochondrial loss and lethal disease. Here, we report that knockout of PPTC7, a mitochondrial matrix protein, hyperactivates BNIP3-/NIX-mediated mitophagy and causes perinatal lethality that is rescued by NIX knockout in mice. Biochemically, the PPTC7 precursor is trapped by BNIP3 and NIX to the mitochondrial outer membrane, where PPTC7 scaffolds assembly of a substrate-PPTC7-SCFFBXL4 holocomplex to degrade BNIP3 and NIX, forming a homeostatic regulatory loop. PPTC7 possesses an unusually weak mitochondrial targeting sequence to facilitate its outer membrane retention and mitophagy control. Starvation upregulates PPPTC7 expression in mouse liver to repress mitophagy, which critically maintains hepatic mitochondrial mass, bioenergetics, and gluconeogenesis. Collectively, PPTC7 functions as a mitophagy sensor that integrates homeostatic and physiological signals to dynamically control BNIP3 and NIX degradation, thereby maintaining mitochondrial mass and cellular homeostasis.
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Affiliation(s)
- Yuqiu Sun
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China; National Institute of Biological Sciences, Beijing 102206, China; Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing 102206, China
| | - Yu Cao
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China; Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing 102206, China
| | - Huayun Wan
- National Institute of Biological Sciences, Beijing 102206, China; Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing 102206, China
| | - Adalet Memetimin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yang Cao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Chongyang Wu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Meng Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Qi Li
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Yan Ma
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Mengqiu Dong
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China; National Institute of Biological Sciences, Beijing 102206, China; Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing 102206, China
| | - Hui Jiang
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China; National Institute of Biological Sciences, Beijing 102206, China; Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing 102206, China.
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9
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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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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10
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Niemi NM, Serrano LR, Muehlbauer LK, Balnis CE, Wei L, Smith AJ, Kozul KL, Forny M, Connor OM, Rashan EH, Shishkova E, Schueler KL, Keller MP, Attie AD, Friedman JR, Pagan JK, Coon JJ, Pagliarini DJ. PPTC7 maintains mitochondrial protein content by suppressing receptor-mediated mitophagy. Nat Commun 2023; 14:6431. [PMID: 37833277 PMCID: PMC10575892 DOI: 10.1038/s41467-023-42069-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
PPTC7 is a resident mitochondrial phosphatase essential for maintaining proper mitochondrial content and function. Newborn mice lacking Pptc7 exhibit aberrant mitochondrial protein phosphorylation, suffer from a range of metabolic defects, and fail to survive beyond one day after birth. Using an inducible knockout model, we reveal that loss of Pptc7 in adult mice causes marked reduction in mitochondrial mass and metabolic capacity with elevated hepatic triglyceride accumulation. Pptc7 knockout animals exhibit increased expression of the mitophagy receptors BNIP3 and NIX, and Pptc7-/- mouse embryonic fibroblasts (MEFs) display a major increase in mitophagy that is reversed upon deletion of these receptors. Our phosphoproteomics analyses reveal a common set of elevated phosphosites between perinatal tissues, adult liver, and MEFs, including multiple sites on BNIP3 and NIX, and our molecular studies demonstrate that PPTC7 can directly interact with and dephosphorylate these proteins. These data suggest that Pptc7 deletion causes mitochondrial dysfunction via dysregulation of several metabolic pathways and that PPTC7 may directly regulate mitophagy receptor function or stability. Overall, our work reveals a significant role for PPTC7 in the mitophagic response and furthers the growing notion that management of mitochondrial protein phosphorylation is essential for ensuring proper organelle content and function.
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Affiliation(s)
- Natalie M Niemi
- Morgridge Institute for Research, Madison, WI, 53715, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Lia R Serrano
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Laura K Muehlbauer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Catherine E Balnis
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lianjie Wei
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Andrew J Smith
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Keri-Lyn Kozul
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Merima Forny
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Olivia M Connor
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Edrees H Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, 53706, USA
| | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jonathan R Friedman
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Julia K Pagan
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, 4072, Australia
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD, 4072, Australia
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, 4102, Australia
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI, 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, 53706, USA
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, WI, 53715, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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11
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Uoselis L, Nguyen TN, Lazarou M. Mitochondrial degradation: Mitophagy and beyond. Mol Cell 2023; 83:3404-3420. [PMID: 37708893 DOI: 10.1016/j.molcel.2023.08.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 08/10/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023]
Abstract
Mitochondria are central hubs of cellular metabolism that also play key roles in signaling and disease. It is therefore fundamentally important that mitochondrial quality and activity are tightly regulated. Mitochondrial degradation pathways contribute to quality control of mitochondrial networks and can also regulate the metabolic profile of mitochondria to ensure cellular homeostasis. Here, we cover the many and varied ways in which cells degrade or remove their unwanted mitochondria, ranging from mitophagy to mitochondrial extrusion. The molecular signals driving these varied pathways are discussed, including the cellular and physiological contexts under which the different degradation pathways are engaged.
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Affiliation(s)
- Louise Uoselis
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia; Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Thanh Ngoc Nguyen
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia; Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA.
| | - Michael Lazarou
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia; Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA.
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12
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Elcocks H, Brazel AJ, McCarron KR, Kaulich M, Husnjak K, Mortiboys H, Clague MJ, Urbé S. FBXL4 ubiquitin ligase deficiency promotes mitophagy by elevating NIX levels. EMBO J 2023; 42:e112799. [PMID: 37102372 PMCID: PMC10308357 DOI: 10.15252/embj.2022112799] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/17/2023] [Accepted: 04/09/2023] [Indexed: 04/28/2023] Open
Abstract
Selective autophagy of mitochondria, mitophagy, is linked to mitochondrial quality control and as such is critical to a healthy organism. We have used a CRISPR/Cas9 approach to screen human E3 ubiquitin ligases for influence on mitophagy under both basal cell culture conditions and upon acute mitochondrial depolarization. We identify two cullin-RING ligase substrate receptors, VHL and FBXL4, as the most profound negative regulators of basal mitophagy. We show that these converge, albeit via different mechanisms, on control of the mitophagy adaptors BNIP3 and BNIP3L/NIX. FBXL4 restricts NIX and BNIP3 levels via direct interaction and protein destabilization, while VHL acts through suppression of HIF1α-mediated transcription of BNIP3 and NIX. Depletion of NIX but not BNIP3 is sufficient to restore mitophagy levels. Our study contributes to an understanding of the aetiology of early-onset mitochondrial encephalomyopathy that is supported by analysis of a disease-associated mutation. We further show that the compound MLN4924, which globally interferes with cullin-RING ligase activity, is a strong inducer of mitophagy, thus providing a research tool in this context and a candidate therapeutic agent for conditions linked to mitochondrial dysfunction.
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Affiliation(s)
- Hannah Elcocks
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Ailbhe J Brazel
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
- Present address:
Department of BiologyMaynooth UniversityMaynoothIreland
| | - Katy R McCarron
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Manuel Kaulich
- Institute of Biochemistry IIGoethe University, Medical Faculty, University HospitalFrankfurt am MainGermany
- Frankfurt Cancer InstituteFrankfurt am MainGermany
| | - Koraljka Husnjak
- Institute of Biochemistry IIGoethe University, Medical Faculty, University HospitalFrankfurt am MainGermany
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Michael J Clague
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Sylvie Urbé
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
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13
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Wilhelm LP, Ganley IG. Eating your mitochondria-when too much of a good thing turns bad. EMBO J 2023; 42:e114542. [PMID: 37272260 PMCID: PMC10308347 DOI: 10.15252/embj.2023114542] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 05/25/2023] [Indexed: 06/06/2023] Open
Abstract
How mitophagy is turned on to remove damaged or excess mitochondria from cells has been well-studied, but less is known about how the pathway is turned off to avoid "over-eating" of mitochondria under basal conditions. Three new studies now reveal the disease-associated FBXL4 protein as an important negative regulator of constitutive mitophagy, controlling the stability of mitophagy receptors BNIP3 and NIX.
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Affiliation(s)
- Léa P Wilhelm
- MRC Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUK
| | - Ian G Ganley
- MRC Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUK
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