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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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Kandasamy J, Li R, Vamesu BM, Olave N, Halloran B, Jilling T, Ballinger SW, Ambalavanan N. Mitochondrial DNA Variations Modulate Alveolar Epithelial Mitochondrial Function and Oxidative Stress in Newborn Mice Exposed to Hyperoxia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541177. [PMID: 37292719 PMCID: PMC10245974 DOI: 10.1101/2023.05.17.541177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Oxidative stress is an important contributor to bronchopulmonary dysplasia (BPD), a form of chronic lung disease that is the most common morbidity in very preterm infants. Mitochondrial functional differences due to inherited and acquired mutations influence the pathogenesis of disorders in which oxidative stress plays a critical role. We previously showed using mitochondrial-nuclear exchange (MNX) mice that mitochondrial DNA (mtDNA) variations modulate hyperoxia-induced lung injury severity in a model of BPD. In this study, we studied the effects of mtDNA variations on mitochondrial function including mitophagy in alveolar epithelial cells (AT2) from MNX mice. We also investigated oxidant and inflammatory stress as well as transcriptomic profiles in lung tissue in mice and expression of proteins such as PINK1, Parkin and SIRT3 in infants with BPD. Our results indicate that AT2 from mice with C57 mtDNA had decreased mitochondrial bioenergetic function and inner membrane potential, increased mitochondrial membrane permeability and were exposed to higher levels of oxidant stress during hyperoxia compared to AT2 from mice with C3H mtDNA. Lungs from hyperoxia-exposed mice with C57 mtDNA also had higher levels of pro-inflammatory cytokines compared to lungs from mice with C3H mtDNA. We also noted changes in KEGG pathways related to inflammation, PPAR and glutamatergic signaling, and mitophagy in mice with certain mito-nuclear combinations but not others. Mitophagy was decreased by hyperoxia in all mice strains, but to a greater degree in AT2 and neonatal mice lung fibroblasts from hyperoxia-exposed mice with C57 mtDNA compared to C3H mtDNA. Finally, mtDNA haplogroups vary with ethnicity, and Black infants with BPD had lower levels of PINK1, Parkin and SIRT3 expression in HUVEC at birth and tracheal aspirates at 28 days of life when compared to White infants with BPD. These results indicate that predisposition to neonatal lung injury may be modulated by variations in mtDNA and mito-nuclear interactions need to be investigated to discover novel pathogenic mechanisms for BPD.
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Goiran T, Eldeeb MA, Zorca CE, Fon EA. Hallmarks and Molecular Tools for the Study of Mitophagy in Parkinson’s Disease. Cells 2022; 11:cells11132097. [PMID: 35805181 PMCID: PMC9265644 DOI: 10.3390/cells11132097] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 01/27/2023] Open
Abstract
The best-known hallmarks of Parkinson’s disease (PD) are the motor deficits that result from the degeneration of dopaminergic neurons in the substantia nigra. Dopaminergic neurons are thought to be particularly susceptible to mitochondrial dysfunction. As such, for their survival, they rely on the elaborate quality control mechanisms that have evolved in mammalian cells to monitor mitochondrial function and eliminate dysfunctional mitochondria. Mitophagy is a specialized type of autophagy that mediates the selective removal of damaged mitochondria from cells, with the net effect of dampening the toxicity arising from these dysfunctional organelles. Despite an increasing understanding of the molecular mechanisms that regulate the removal of damaged mitochondria, the detailed molecular link to PD pathophysiology is still not entirely clear. Herein, we review the fundamental molecular pathways involved in PINK1/Parkin-mediated and receptor-mediated mitophagy, the evidence for the dysfunction of these pathways in PD, and recently-developed state-of-the art assays for measuring mitophagy in vitro and in vivo.
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