1
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Lyu J, Zhang H, Wang C, Pan M. New insight in treating autoimmune diseases by targeting autophagy. Autoimmunity 2024; 57:2351872. [PMID: 38739691 DOI: 10.1080/08916934.2024.2351872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/28/2024] [Indexed: 05/16/2024]
Abstract
Autophagy is a highly conserved biological process in eukaryotes, which degrades cellular misfolded proteins, damaged organelles and invasive pathogens in the lysosome-dependent manner. Autoimmune diseases caused by genetic elements, environments and aberrant immune responses severely impact patients' living quality and even threaten life. Recently, numerous studies have reported autophagy can regulate immune responses, and play an important role in autoimmune diseases. In this review, we summarised the features of autophagy and autophagy-related genes, enumerated some autophagy-related genes involved in autoimmune diseases, and further overviewed how to treat autoimmune diseases through targeting autophagy. Finally, we outlooked the prospect of relieving and curing autoimmune diseases by targeting autophagy pathway.
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Affiliation(s)
- Jiao Lyu
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Hongqian Zhang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Chaoyang Wang
- The Key Medical Laboratory for Chemical Poison Detection of Henan Province, The Third People's Hospital of Henan Province, Zhengzhou, China
- Department of Biomedical Science, City University of Hong Kong, Hong Kong, China
| | - Mingyu Pan
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
- Department of Biomedical Science, City University of Hong Kong, Hong Kong, China
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2
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Lacombe A, Scorrano L. The interplay between mitochondrial dynamics and autophagy: From a key homeostatic mechanism to a driver of pathology. Semin Cell Dev Biol 2024; 161-162:1-19. [PMID: 38430721 DOI: 10.1016/j.semcdb.2024.02.001] [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: 11/06/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024]
Abstract
The complex relationship between mitochondrial dynamics and autophagy illustrates how two cellular housekeeping processes are intimately linked, illuminating fundamental principles of cellular homeostasis and shedding light on disparate pathological conditions including several neurodegenerative disorders. Here we review the basic tenets of mitochondrial dynamics i.e., the concerted balance between fusion and fission of the organelle, and its interplay with macroautophagy and selective mitochondrial autophagy, also dubbed mitophagy, in the maintenance of mitochondrial quality control and ultimately in cell viability. We illustrate how conditions of altered mitochondrial dynamics reverberate on autophagy and vice versa. Finally, we illustrate how altered interplay between these two key cellular processes participates in the pathogenesis of human disorders affecting multiple organs and systems.
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Affiliation(s)
- Alice Lacombe
- Dept. of Biology, University of Padova, Padova, Italy
| | - Luca Scorrano
- Dept. of Biology, University of Padova, Padova, Italy; Veneto Institute of Molecular Medicine, Padova, Italy.
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3
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Tábara LC, Burr SP, Frison M, Chowdhury SR, Paupe V, Nie Y, Johnson M, Villar-Azpillaga J, Viegas F, Segawa M, Anand H, Petkevicius K, Chinnery PF, Prudent J. MTFP1 controls mitochondrial fusion to regulate inner membrane quality control and maintain mtDNA levels. Cell 2024; 187:3619-3637.e27. [PMID: 38851188 DOI: 10.1016/j.cell.2024.05.017] [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: 09/22/2023] [Revised: 03/19/2024] [Accepted: 05/09/2024] [Indexed: 06/10/2024]
Abstract
Mitochondrial dynamics play a critical role in cell fate decisions and in controlling mtDNA levels and distribution. However, the molecular mechanisms linking mitochondrial membrane remodeling and quality control to mtDNA copy number (CN) regulation remain elusive. Here, we demonstrate that the inner mitochondrial membrane (IMM) protein mitochondrial fission process 1 (MTFP1) negatively regulates IMM fusion. Moreover, manipulation of mitochondrial fusion through the regulation of MTFP1 levels results in mtDNA CN modulation. Mechanistically, we found that MTFP1 inhibits mitochondrial fusion to isolate and exclude damaged IMM subdomains from the rest of the network. Subsequently, peripheral fission ensures their segregation into small MTFP1-enriched mitochondria (SMEM) that are targeted for degradation in an autophagic-dependent manner. Remarkably, MTFP1-dependent IMM quality control is essential for basal nucleoid recycling and therefore to maintain adequate mtDNA levels within the cell.
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Affiliation(s)
- Luis Carlos Tábara
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.
| | - Stephen P Burr
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Michele Frison
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Suvagata R Chowdhury
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Vincent Paupe
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Yu Nie
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Mark Johnson
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Jara Villar-Azpillaga
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Filipa Viegas
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Mayuko Segawa
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Hanish Anand
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Kasparas Petkevicius
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Patrick F Chinnery
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Julien Prudent
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.
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4
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Wang Y, Luo S, Su H, Wang Z, Chu L, Zhang C. BL-918 activates PINK1/Parkin signaling pathway to ameliorate the progression of Parkinson's disease. J Biol Chem 2024:107543. [PMID: 38992440 DOI: 10.1016/j.jbc.2024.107543] [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: 01/05/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024] Open
Abstract
The pathogenesis of Parkinson's disease (PD) has been associated with mitochondrial dysfunction. Given that the PINK1/Parkin pathway governs mitochondrial quality control by inducing mitophagy to remove damaged mitochondria, therapeutic approaches to activate PINK1/Parkin-mediated mitophagy have the potential in the treatment of PD. Here, we have identified a new small molecule, BL-918, as an inducer of mitophagy via activating the PINK1/Parkin pathway. BL-918 triggers PINK1 accumulation and Parkin mitochondrial translocation to initiate PINK1/Parkin-mediated mitophagy. We found that mitochondrial membrane potential and mitochondrial permeability transition (mPT) pore were involved in BL-918-induced PINK1/Parkin pathway activation. Moreover, we showed that BL-918 mitigated PD progression in MPTP-induced PD mice in a PINK1-dependent manner. Our results unravel a new activator of the PINK1/Parkin signaling pathway and provide a potential strategy for the treatment of PD and other diseases with dysfunctional mitochondria.
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Affiliation(s)
- Yi Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China; State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Siyuan Luo
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Huili Su
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China; State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhimeng Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China; State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Ling Chu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
| | - Conggang Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China; State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
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5
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Liu Y, Ma Z. Leukemia and mitophagy: a novel perspective for understanding oncogenesis and resistance. Ann Hematol 2024; 103:2185-2196. [PMID: 38282059 DOI: 10.1007/s00277-024-05635-w] [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: 11/23/2023] [Accepted: 01/19/2024] [Indexed: 01/30/2024]
Abstract
Mitophagy, the selective autophagic process that specifically degrades mitochondria, serves as a vital regulatory mechanism for eliminating damaged mitochondria and maintaining cellular balance. Emerging research underscores the central role of mitophagy in the initiation, advancement, and treatment of cancer. Mitophagy is widely acknowledged to govern mitochondrial homeostasis in hematopoietic stem cells (HSCs), influencing their metabolic dynamics. In this article, we integrate recent data to elucidate the regulatory mechanisms governing mitophagy and its intricate significance in the context of leukemia. An in-depth molecular elucidation of the processes governing mitophagy may serve as a basis for the development of pioneering approaches in targeted therapeutic interventions.
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Affiliation(s)
- Yueyao Liu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Sichuan Province, No. 20, Section 3, Renmin South Road, Chengdu, 610041, China
| | - Zhigui Ma
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Sichuan Province, No. 20, Section 3, Renmin South Road, Chengdu, 610041, China.
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6
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Tudorica DA, Basak B, Puerta Cordova AS, Khuu G, Rose K, Lazarou M, Holzbaur EL, Hurley JH. A RAB7A phosphoswitch coordinates Rubicon Homology protein regulation of Parkin-dependent mitophagy. J Cell Biol 2024; 223:e202309015. [PMID: 38728007 PMCID: PMC11090050 DOI: 10.1083/jcb.202309015] [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: 09/05/2023] [Revised: 01/12/2024] [Accepted: 04/05/2024] [Indexed: 05/15/2024] Open
Abstract
Activation of PINK1 and Parkin in response to mitochondrial damage initiates a response that includes phosphorylation of RAB7A at Ser72. Rubicon is a RAB7A binding negative regulator of autophagy. The structure of the Rubicon:RAB7A complex suggests that phosphorylation of RAB7A at Ser72 would block Rubicon binding. Indeed, in vitro phosphorylation of RAB7A by TBK1 abrogates Rubicon:RAB7A binding. Pacer, a positive regulator of autophagy, has an RH domain with a basic triad predicted to bind an introduced phosphate. Consistent with this, Pacer-RH binds to phosho-RAB7A but not to unphosphorylated RAB7A. In cells, mitochondrial depolarization reduces Rubicon:RAB7A colocalization whilst recruiting Pacer to phospho-RAB7A-positive puncta. Pacer knockout reduces Parkin mitophagy with little effect on bulk autophagy or Parkin-independent mitophagy. Rescue of Parkin-dependent mitophagy requires the intact pRAB7A phosphate-binding basic triad of Pacer. Together these structural and functional data support a model in which the TBK1-dependent phosphorylation of RAB7A serves as a switch, promoting mitophagy by relieving Rubicon inhibition and favoring Pacer activation.
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Affiliation(s)
- Dan A. Tudorica
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Bishal Basak
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Alexia S. Puerta Cordova
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Grace Khuu
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Kevin Rose
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michael Lazarou
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Erika L.F. Holzbaur
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - James H. Hurley
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
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7
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Saha B, Olsvik H, Williams GL, Oh S, Evjen G, Sjøttem E, Mandell MA. TBK1 is ubiquitinated by TRIM5α to assemble mitophagy machinery. Cell Rep 2024; 43:114294. [PMID: 38814780 PMCID: PMC11216866 DOI: 10.1016/j.celrep.2024.114294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 04/05/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024] Open
Abstract
Ubiquitination of mitochondrial proteins provides a basis for the downstream recruitment of mitophagy machinery, yet whether ubiquitination of the machinery itself contributes to mitophagy is unknown. Here, we show that K63-linked polyubiquitination of the key mitophagy regulator TBK1 is essential for its mitophagy functions. This modification is catalyzed by the ubiquitin ligase TRIM5α and is required for TBK1 to interact with and activate a set of ubiquitin-binding autophagy adaptors including NDP52, p62/SQSTM1, and NBR1. Autophagy adaptors, along with TRIM27, enable TRIM5α to engage with TBK1 following mitochondrial damage. TRIM5α's ubiquitin ligase activity is required for the accumulation of active TBK1 on damaged mitochondria in Parkin-dependent and Parkin-independent mitophagy pathways. Our data support a model in which TRIM5α provides a mitochondria-localized, ubiquitin-based, self-amplifying assembly platform for TBK1 and mitophagy adaptors that is ultimately necessary for the recruitment of the core autophagy machinery.
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Affiliation(s)
- Bhaskar Saha
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Hallvard Olsvik
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Geneva L Williams
- Biomedical Sciences Graduate Program, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Seeun Oh
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Gry Evjen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Eva Sjøttem
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Michael A Mandell
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; Autophagy, Inflammation, and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
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8
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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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9
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Eickhorst C, Babic R, Rush-Kittle J, Lucya L, Imam FL, Sánchez-Martín P, Hollenstein DM, Michaelis J, Münch C, Meisinger C, Slade D, Gámez-Díaz L, Kraft C. FIP200 Phosphorylation Regulates Late Steps in Mitophagy. J Mol Biol 2024:168631. [PMID: 38821350 DOI: 10.1016/j.jmb.2024.168631] [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: 01/27/2024] [Revised: 05/18/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
Mitophagy is a specific type of autophagy responsible for the selective elimination of dysfunctional or superfluous mitochondria, ensuring the maintenance of mitochondrial quality control. The initiation of mitophagy is coordinated by the ULK1 kinase complex, which engages mitophagy receptors via its FIP200 subunit. Whether FIP200 performs additional functions in the subsequent later phases of mitophagy beyond this initial step and how its regulation occurs, remains unclear. Our findings reveal that multiple phosphorylation events on FIP200 differentially control the early and late stages of mitophagy. Furthermore, these phosphorylation events influence FIP200's interaction with ATG16L1. In summary, our results highlight the necessity for precise and dynamic regulation of FIP200, underscoring its importance in the progression of mitophagy.
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Affiliation(s)
- Christopher Eickhorst
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Riccardo Babic
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jorrell Rush-Kittle
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany; Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Leon Lucya
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Fatimah Lami Imam
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Pablo Sánchez-Martín
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - David M Hollenstein
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Department for Biochemistry and Cell Biology, University of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria; Mass Spectrometry Facility, Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Jonas Michaelis
- Institute of Molecular Systems Medicine, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Christian Münch
- Institute of Molecular Systems Medicine, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Chris Meisinger
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria; Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Laura Gámez-Díaz
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, University Medical Center Freiburg, 79106 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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10
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Takeda E, Isoda T, Hosokawa S, Oikawa Y, Hotta-Ren S, May AI, Ohsumi Y. Receptor-mediated cargo hitchhiking on bulk autophagy. EMBO J 2024:10.1038/s44318-024-00091-8. [PMID: 38755257 DOI: 10.1038/s44318-024-00091-8] [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: 08/22/2023] [Revised: 02/24/2024] [Accepted: 02/28/2024] [Indexed: 05/18/2024] Open
Abstract
While the molecular mechanism of autophagy is well studied, the cargoes delivered by autophagy remain incompletely characterized. To examine the selectivity of autophagy cargo, we conducted proteomics on isolated yeast autophagic bodies, which are intermediate structures in the autophagy process. We identify a protein, Hab1, that is highly preferentially delivered to vacuoles. The N-terminal 42 amino acid region of Hab1 contains an amphipathic helix and an Atg8-family interacting motif, both of which are necessary and sufficient for the preferential delivery of Hab1 by autophagy. We find that fusion of this region with a cytosolic protein results in preferential delivery of this protein to the vacuole. Furthermore, attachment of this region to an organelle allows for autophagic delivery in a manner independent of canonical autophagy receptor or scaffold proteins. We propose a novel mode of selective autophagy in which a receptor, in this case Hab1, binds directly to forming isolation membranes during bulk autophagy.
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Affiliation(s)
- Eigo Takeda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
| | - Takahiro Isoda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
- Frontier Research Center, POLA Chemical Industries Inc., Yokohama, Japan
| | - Sachiko Hosokawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yu Oikawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Shukun Hotta-Ren
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Alexander I May
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
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11
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Ma W, Lu Y, Jin X, Lin N, Zhang L, Song Y. Targeting selective autophagy and beyond: From underlying mechanisms to potential therapies. J Adv Res 2024:S2090-1232(24)00199-1. [PMID: 38750694 DOI: 10.1016/j.jare.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/26/2024] [Accepted: 05/08/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Autophagy is an evolutionarily conserved turnover process for intracellular substances in eukaryotes, relying on lysosomal (in animals) or vacuolar (in yeast and plants) mechanisms. In the past two decades, emerging evidence suggests that, under specific conditions, autophagy can target particular macromolecules or organelles for degradation, a process termed selective autophagy. Recently, accumulating studies have demonstrated that the abnormality of selective autophagy is closely associated with the occurrence and progression of many human diseases, including neurodegenerative diseases, cancers, metabolic diseases, and cardiovascular diseases. AIM OF REVIEW This review aims at systematically and comprehensively introducing selective autophagy and its role in various diseases, while unravelling the molecular mechanisms of selective autophagy. By providing a theoretical basis for the development of related small-molecule drugs as well as treating related human diseases, this review seeks to contribute to the understanding of selective autophagy and its therapeutic potential. KEY SCIENTIFIC CONCEPTS OF REVIEW In this review, we systematically introduce and dissect the major categories of selective autophagy that have been discovered. We also focus on recent advances in understanding the molecular mechanisms underlying both classical and non-classical selective autophagy. Moreover, the current situation of small-molecule drugs targeting different types of selective autophagy is further summarized, providing valuable insights into the discovery of more candidate small-molecule drugs targeting selective autophagy in the future. On the other hand, we also reveal clinically relevant implementations that are potentially related to selective autophagy, such as predictive approaches and treatments tailored to individual patients.
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Affiliation(s)
- Wei Ma
- Department of Breast Surgery, Department of Ultrasound, Department of Hematology and Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yingying Lu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Xin Jin
- Department of Breast Surgery, Department of Ultrasound, Department of Hematology and Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang 110001, China
| | - Na Lin
- Department of Breast Surgery, Department of Ultrasound, Department of Hematology and Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang 110001, China.
| | - Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Yaowen Song
- Department of Breast Surgery, Department of Ultrasound, Department of Hematology and Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang 110001, China.
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12
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Schmid M, Fischer P, Engl M, Widder J, Kerschbaum-Gruber S, Slade D. The interplay between autophagy and cGAS-STING signaling and its implications for cancer. Front Immunol 2024; 15:1356369. [PMID: 38660307 PMCID: PMC11039819 DOI: 10.3389/fimmu.2024.1356369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Autophagy is an intracellular process that targets various cargos for degradation, including members of the cGAS-STING signaling cascade. cGAS-STING senses cytosolic double-stranded DNA and triggers an innate immune response through type I interferons. Emerging evidence suggests that autophagy plays a crucial role in regulating and fine-tuning cGAS-STING signaling. Reciprocally, cGAS-STING pathway members can actively induce canonical as well as various non-canonical forms of autophagy, establishing a regulatory network of feedback mechanisms that alter both the cGAS-STING and the autophagic pathway. The crosstalk between autophagy and the cGAS-STING pathway impacts a wide variety of cellular processes such as protection against pathogenic infections as well as signaling in neurodegenerative disease, autoinflammatory disease and cancer. Here we provide a comprehensive overview of the mechanisms involved in autophagy and cGAS-STING signaling, with a specific focus on the interactions between the two pathways and their importance for cancer.
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Affiliation(s)
- Maximilian Schmid
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- MedAustron Ion Therapy Center, Wiener Neustadt, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Patrick Fischer
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- MedAustron Ion Therapy Center, Wiener Neustadt, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Magdalena Engl
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Joachim Widder
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Sylvia Kerschbaum-Gruber
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- MedAustron Ion Therapy Center, Wiener Neustadt, Austria
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- MedAustron Ion Therapy Center, Wiener Neustadt, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
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13
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Liu L, Matsumoto M, Watanabe-Matsui M, Nakagawa T, Nagasawa Y, Pang J, Callens BKK, Muto A, Ochiai K, Takekawa H, Alam M, Nishizawa H, Shirouzu M, Shima H, Nakayama K, Igarashi K. TANK Binding Kinase 1 Promotes BACH1 Degradation through Both Phosphorylation-Dependent and -Independent Mechanisms without Relying on Heme and FBXO22. Int J Mol Sci 2024; 25:4141. [PMID: 38673728 PMCID: PMC11050367 DOI: 10.3390/ijms25084141] [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: 02/20/2024] [Revised: 03/26/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
BTB and CNC homology 1 (BACH1) represses the expression of genes involved in the metabolism of iron, heme and reactive oxygen species. While BACH1 is rapidly degraded when it is bound to heme, it remains unclear how BACH1 degradation is regulated under other conditions. We found that FBXO22, a ubiquitin ligase previously reported to promote BACH1 degradation, polyubiquitinated BACH1 only in the presence of heme in a highly purified reconstitution assay. In parallel to this regulatory mechanism, TANK binding kinase 1 (TBK1), a protein kinase that activates innate immune response and regulates iron metabolism via ferritinophagy, was found to promote BACH1 degradation when overexpressed in 293T cells. While TBK1 phosphorylated BACH1 at multiple serine and threonine residues, BACH1 degradation was observed with not only the wild-type TBK1 but also catalytically impaired TBK1. The BACH1 degradation in response to catalytically impaired TBK1 was not dependent on FBXO22 but involved both autophagy-lysosome and ubiquitin-proteasome pathways judging from its suppression by using inhibitors of lysosome and proteasome. Chemical inhibition of TBK1 in hepatoma Hepa1 cells showed that TBK1 was not required for the heme-induced BACH1 degradation. Its inhibition in Namalwa B lymphoma cells increased endogenous BACH1 protein. These results suggest that TBK1 promotes BACH1 degradation in parallel to the FBXO22- and heme-dependent pathway, placing BACH1 as a downstream effector of TBK1 in iron metabolism or innate immune response.
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Affiliation(s)
- Liang Liu
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan (H.T.); (M.A.)
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mitsuyo Matsumoto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan (H.T.); (M.A.)
- Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan
| | - Miki Watanabe-Matsui
- Department of Neurochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan
| | - Tadashi Nakagawa
- Division of Cell Proliferation, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan; (T.N.); (K.N.)
- Department of Clinical Pharmacology, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo-Onoda 756-0884, Japan
| | - Yuko Nagasawa
- Division of Cell Proliferation, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan; (T.N.); (K.N.)
| | - Jingyao Pang
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan (H.T.); (M.A.)
| | - Bert K. K. Callens
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan (H.T.); (M.A.)
- Faculty of Health, Medicine and Life Sciences, Maastricht University, 6229 GT Maastricht, The Netherlands
| | - Akihiko Muto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan (H.T.); (M.A.)
| | - Kyoko Ochiai
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan (H.T.); (M.A.)
| | - Hirotaka Takekawa
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan (H.T.); (M.A.)
| | - Mahabub Alam
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan (H.T.); (M.A.)
- Department of Animal Science and Nutrition, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram 4225, Bangladesh
| | - Hironari Nishizawa
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan (H.T.); (M.A.)
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama 305-0074, Japan
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan (H.T.); (M.A.)
- Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan; (T.N.); (K.N.)
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan (H.T.); (M.A.)
- Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan
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14
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Lee KW, Ryu KJ, Kim M, Lim S, Kim J, Kim JY, Hwangbo C, Yoo J, Cho YY, Kim KD. RCHY1 and OPTN are required for melanophagy, selective autophagy of melanosomes. Proc Natl Acad Sci U S A 2024; 121:e2318039121. [PMID: 38536750 PMCID: PMC10998605 DOI: 10.1073/pnas.2318039121] [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: 10/24/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024] Open
Abstract
Melanosomes are specific organelles dedicated to melanin synthesis and accumulation in melanocytes. Autophagy is suggestively involved in melanosome degradation, although the potential underlying molecular mechanisms remain elusive. In selective autophagy, autophagy receptors and E3-ligases are the key factors conferring cargo selectivity. In B16F10 cells, β-mangostin efficiently induced melanosome degradation without affecting other organelles such as mitochondria, peroxisomes, and the endoplasmic reticulum. Among various autophagy receptors, optineurin (OPTN) contributes TANK-binding kinase 1 (TBK1)-dependently to melanosome degradation and its knockdown inhibited β-mangostin-mediated melanosome degradation. OPTN translocation to melanosomes was dependent on its ubiquitin-binding domain. Moreover, OPTN-mediated TBK1 activation and subsequent TBK1-mediated S187 OPTN phosphorylation were essential for melanosome degradation. β-mangostin increased K63-linked melanosome ubiquitination. Finally, the E3-ligase RCHY1 knockdown inhibited the melanosome ubiquitination required for OPTN- and TBK1-phosphorylation as well as melanosome degradation. This study suggests that melanophagy, melanosome-selective autophagy, contributes to melanosome degradation, and OPTN and RCHY1 are an essential autophagy receptor and a E3-ligase, respectively, conferring cargo selectivity in melanophagy.
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Affiliation(s)
- Ki Won Lee
- Anti-aging Bio Cell factory Regional Leading Research Center, Gyeongsang National University, Jinju52828, South Korea
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
| | - Ki-jun Ryu
- Research Institute of Life Sciences, Gyeongsang National University, Jinju52828, South Korea
| | - Minju Kim
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
| | - Seyeon Lim
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
| | - Jisu Kim
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
| | - Jeong Yoon Kim
- Department of Pharmaceutical Engineering, Gyeongsang National University, Jinju52725, South Korea
| | - Cheol Hwangbo
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
- Division of Life Science, Gyeongsang National University, Jinju52828, South Korea
| | - Jiyun Yoo
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
- Division of Life Science, Gyeongsang National University, Jinju52828, South Korea
| | - Yong-Yeon Cho
- College of Pharmacy, The Catholic University of Korea, Wonmi-Gu, Bucheon-si, Gyeonggi-Do14662, South Korea
| | - Kwang Dong Kim
- Anti-aging Bio Cell factory Regional Leading Research Center, Gyeongsang National University, Jinju52828, South Korea
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
- Division of Life Science, Gyeongsang National University, Jinju52828, South Korea
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju52828, South Korea
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15
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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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16
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Russo T, Kolisnyk B, B. S. A, Plessis‐Belair J, Kim TW, Martin J, Ni J, Pearson JA, Park EJ, Sher RB, Studer L, Riessland M. The SATB1-MIR22-GBA axis mediates glucocerebroside accumulation inducing a cellular senescence-like phenotype in dopaminergic neurons. Aging Cell 2024; 23:e14077. [PMID: 38303548 PMCID: PMC11019121 DOI: 10.1111/acel.14077] [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: 08/03/2023] [Revised: 12/01/2023] [Accepted: 12/19/2023] [Indexed: 02/03/2024] Open
Abstract
Idiopathic Parkinson's disease (PD) is characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta, which is associated with neuroinflammation and reactive gliosis. The underlying cause of PD and the concurrent neuroinflammation are not well understood. In this study, we utilize human and murine neuronal lines, stem cell-derived dopaminergic neurons, and mice to demonstrate that three previously identified genetic risk factors for PD, namely SATB1, MIR22HG, and GBA, are components of a single gene regulatory pathway. Our findings indicate that dysregulation of this pathway leads to the upregulation of glucocerebrosides (GluCer), which triggers a cellular senescence-like phenotype in dopaminergic neurons. Specifically, we discovered that downregulation of the transcriptional repressor SATB1 results in the derepression of the microRNA miR-22-3p, leading to decreased GBA expression and subsequent accumulation of GluCer. Furthermore, our results demonstrate that an increase in GluCer alone is sufficient to impair lysosomal and mitochondrial function, thereby inducing cellular senescence. Dysregulation of the SATB1-MIR22-GBA pathway, observed in both PD patients and normal aging, leads to lysosomal and mitochondrial dysfunction due to the GluCer accumulation, ultimately resulting in a cellular senescence-like phenotype in dopaminergic neurons. Therefore, our study highlights a novel pathway involving three genetic risk factors for PD and provides a potential mechanism for the senescence-induced neuroinflammation and reactive gliosis observed in both PD and normal aging.
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Affiliation(s)
- Taylor Russo
- Department of Neurobiology and BehaviorStony Brook UniversityStony BrookNew YorkUSA
- Center for Nervous System DisordersStony Brook UniversityStony BrookNew YorkUSA
| | - Benjamin Kolisnyk
- Laboratory of Molecular and Cellular NeuroscienceThe Rockefeller UniversityNew YorkNew YorkUSA
| | - Aswathy B. S.
- Department of Neurobiology and BehaviorStony Brook UniversityStony BrookNew YorkUSA
- Center for Nervous System DisordersStony Brook UniversityStony BrookNew YorkUSA
| | - Jonathan Plessis‐Belair
- Department of Neurobiology and BehaviorStony Brook UniversityStony BrookNew YorkUSA
- Center for Nervous System DisordersStony Brook UniversityStony BrookNew YorkUSA
| | - Tae Wan Kim
- Center for Stem Cell BiologyMemorial Sloan‐Kettering Cancer CenterNew YorkNew YorkUSA
- Developmental Biology ProgramMemorial Sloan‐Kettering Cancer CenterNew YorkNew YorkUSA
| | - Jacqueline Martin
- Department of Neurobiology and BehaviorStony Brook UniversityStony BrookNew YorkUSA
- Center for Nervous System DisordersStony Brook UniversityStony BrookNew YorkUSA
| | - Jason Ni
- Laboratory of Molecular and Cellular NeuroscienceThe Rockefeller UniversityNew YorkNew YorkUSA
| | - Jordan A. Pearson
- Medical Scientist Training Program, Stony Brook University Renaissance School of MedicineStony Brook UniversityStony BrookNew YorkUSA
| | - Emily J. Park
- Stem Cells and Regenerative Medicine, Center for Cell and Gene Therapy, Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer CenterBaylor College of MedicineHoustonTexasUSA
| | - Roger B. Sher
- Department of Neurobiology and BehaviorStony Brook UniversityStony BrookNew YorkUSA
- Center for Nervous System DisordersStony Brook UniversityStony BrookNew YorkUSA
| | - Lorenz Studer
- Center for Stem Cell BiologyMemorial Sloan‐Kettering Cancer CenterNew YorkNew YorkUSA
- Developmental Biology ProgramMemorial Sloan‐Kettering Cancer CenterNew YorkNew YorkUSA
| | - Markus Riessland
- Department of Neurobiology and BehaviorStony Brook UniversityStony BrookNew YorkUSA
- Center for Nervous System DisordersStony Brook UniversityStony BrookNew YorkUSA
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17
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Zou T, Xie R, Huang S, Lu D, Liu J. Potential role of modulating autophagy levels in sensorineural hearing loss. Biochem Pharmacol 2024; 222:116115. [PMID: 38460910 DOI: 10.1016/j.bcp.2024.116115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/20/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
In recent years, extensive research has been conducted on the pathogenesis of sensorineural hearing loss (SNHL). Apoptosis and necrosis have been identified to play important roles in hearing loss, but they cannot account for all hearing loss. Autophagy, a cellular process responsible for cell self-degradation and reutilization, has emerged as a significant factor contributing to hearing loss, particularly in cases of autophagy deficiency. Autophagy plays a crucial role in maintaining cell health by exerting cytoprotective and metabolically homeostatic effects in organisms. Consequently, modulating autophagy levels can profoundly impact the survival, death, and regeneration of cells in the inner ear, including hair cells (HCs) and spiral ganglion neurons (SGNs). Abnormal mitochondrial autophagy has been demonstrated in animal models of SNHL. These findings indicate the profound significance of comprehending autophagy while suggesting that our perspective on this cellular process holds promise for advancing the treatment of SNHL. Thus, this review aims to clarify the pathogenic mechanisms of SNHL and the role of autophagy in the developmental processes of various cochlear structures, including the greater epithelial ridge (GER), SGNs, and the ribbon synapse. The pathogenic mechanisms of age-related hearing loss (ARHL), also known as presbycusis, and the latest research on autophagy are also discussed. Furthermore, we underscore recent findings on the modulation of autophagy in SNHL induced by ototoxic drugs. Additionally, we suggest further research that might illuminate the complete potential of autophagy in addressing SNHL, ultimately leading to the formulation of pioneering therapeutic strategies and approaches for the treatment of deafness.
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Affiliation(s)
- Ting Zou
- Department of Otorhinolaryngology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Renwei Xie
- Department of Otorhinolaryngology, Renhe Hospital, Baoshan District, Shanghai, China
| | - Sihan Huang
- Department of Otorhinolaryngology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dingkun Lu
- Cardiac Arrhythmia Center, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jun Liu
- Department of Otorhinolaryngology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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18
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Chakrabarty Y, Yang Z, Chen H, Chan DC. The HRI branch of the integrated stress response selectively triggers mitophagy. Mol Cell 2024; 84:1090-1100.e6. [PMID: 38340717 PMCID: PMC11062084 DOI: 10.1016/j.molcel.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 08/31/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
To maintain mitochondrial homeostasis, damaged or excessive mitochondria are culled in coordination with the physiological state of the cell. The integrated stress response (ISR) is a signaling network that recognizes diverse cellular stresses, including mitochondrial dysfunction. Because the four ISR branches converge to common outputs, it is unclear whether mitochondrial stress detected by this network can regulate mitophagy, the autophagic degradation of mitochondria. Using a whole-genome screen, we show that the heme-regulated inhibitor (HRI) branch of the ISR selectively induces mitophagy. Activation of the HRI branch results in mitochondrial localization of phosphorylated eukaryotic initiation factor 2, which we show is sufficient to induce mitophagy. The HRI mitophagy pathway operates in parallel with the mitophagy pathway controlled by the Parkinson's disease related genes PINK1 and PARKIN and is mechanistically distinct. Therefore, HRI repurposes machinery that is normally used for translational initiation to trigger mitophagy in response to mitochondrial damage.
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Affiliation(s)
- Yogaditya Chakrabarty
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zheng Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hsiuchen Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - David C Chan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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19
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Dine E, Youle RJ. Integrating the response to stressed mitochondria. Mol Cell 2024; 84:995-997. [PMID: 38518749 DOI: 10.1016/j.molcel.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/24/2024]
Abstract
Chakrabarty et al.1 demonstrate that phospho-EIF2α (pEIF2α), the translation initiation factor that mediates the integrated stress response (ISR), is necessary and sufficient for the autophagic degradation of mitochondria following the addition of mitochondrial stressors.
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Affiliation(s)
- Elliot Dine
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Richard J Youle
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
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20
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Zhang M, Wang Y, Gong X, Wang Y, Zhang Y, Tang Y, Zhou X, Liu H, Huang Y, Zhang J, Pan L. Mechanistic insights into the interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins. Proc Natl Acad Sci U S A 2024; 121:e2315550121. [PMID: 38437556 PMCID: PMC10945755 DOI: 10.1073/pnas.2315550121] [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: 09/11/2023] [Accepted: 02/02/2024] [Indexed: 03/06/2024] Open
Abstract
TAX1BP1, a multifunctional autophagy adaptor, plays critical roles in different autophagy processes. As an autophagy receptor, TAX1BP1 can interact with RB1CC1, NAP1, and mammalian ATG8 family proteins to drive selective autophagy for relevant substrates. However, the mechanistic bases underpinning the specific interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins remain elusive. Here, we find that there are two distinct binding sites between TAX1BP1 and RB1CC1. In addition to the previously reported TAX1BP1 SKICH (skeletal muscle and kidney enriched inositol phosphatase (SKIP) carboxyl homology)/RB1CC1 coiled-coil interaction, the first coiled-coil domain of TAX1BP1 can directly bind to the extreme C-terminal coiled-coil and Claw region of RB1CC1. We determine the crystal structure of the TAX1BP1 SKICH/RB1CC1 coiled-coil complex and unravel the detailed binding mechanism of TAX1BP1 SKICH with RB1CC1. Moreover, we demonstrate that RB1CC1 and NAP1 are competitive in binding to the TAX1BP1 SKICH domain, but the presence of NAP1's FIP200-interacting region (FIR) motif can stabilize the ternary TAX1BP1/NAP1/RB1CC1 complex formation. Finally, we elucidate the molecular mechanism governing the selective interactions of TAX1BP1 with ATG8 family members by solving the structure of GABARAP in complex with the non-canonical LIR (LC3-interacting region) motif of TAX1BP1, which unveils a unique binding mode between LIR and ATG8 family protein. Collectively, our findings provide mechanistic insights into the interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins and are valuable for further understanding the working mode and function of TAX1BP1 in autophagy.
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Affiliation(s)
- Mingfang Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Yingli Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Xinyu Gong
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Yaru Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
| | - Yuchao Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Yubin Tang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Xindi Zhou
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Haobo Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Yichao Huang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Jing Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, Sichuan610068, China
| | - Lifeng Pan
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, Sichuan610068, China
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21
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Yamamoto H, Matsui T. Molecular Mechanisms of Macroautophagy, Microautophagy, and Chaperone-Mediated Autophagy. J NIPPON MED SCH 2024; 91:2-9. [PMID: 37271546 DOI: 10.1272/jnms.jnms.2024_91-102] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Autophagy is a self-digestive process that is conserved in eukaryotic cells and responsible for maintaining cellular homeostasis through proteolysis. By this process, cells break down their own components in lysosomes. Autophagy can be classified into three categories: macroautophagy, microautophagy, and chaperone-mediated autophagy (CMA). Macroautophagy involves membrane elongation and microautophagy involves membrane internalization, and both pathways undergo selective or non-selective processes that transport cytoplasmic components into lysosomes to be degraded. CMA, however, involves selective incorporation of cytosolic materials into lysosomes without membrane deformation. All three categories of autophagy have attracted much attention due to their involvement in various biological phenomena and their relevance to human diseases, such as neurodegenerative diseases and cancer. Clarification of the molecular mechanisms behind these processes is key to understanding autophagy and recent studies have made major progress in this regard, especially for the mechanisms of initiation and membrane elongation in macroautophagy and substrate recognition in microautophagy and CMA. Furthermore, it is becoming evident that the three categories of autophagy are related to each other despite their implementation by different sets of proteins and the involvement of completely different membrane dynamics. In this review, recent progress in macroautophagy, microautophagy, and CMA are summarized.
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Affiliation(s)
- Hayashi Yamamoto
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School
| | - Takahide Matsui
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School
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22
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Jiang M, Wu W, Xiong Z, Yu X, Ye Z, Wu Z. Targeting autophagy drug discovery: Targets, indications and development trends. Eur J Med Chem 2024; 267:116117. [PMID: 38295689 DOI: 10.1016/j.ejmech.2023.116117] [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: 11/20/2023] [Revised: 12/30/2023] [Accepted: 12/31/2023] [Indexed: 02/25/2024]
Abstract
Autophagy plays a vital role in sustaining cellular homeostasis and its alterations have been implicated in the etiology of many diseases. Drugs development targeting autophagy began decades ago and hundreds of agents were developed, some of which are licensed for the clinical usage. However, no existing intervention specifically aimed at modulating autophagy is available. The obstacles that prevent drug developments come from the complexity of the actual impact of autophagy regulators in disease scenarios. With the development and application of new technologies, several promising categories of compounds for autophagy-based therapy have emerged in recent years. In this paper, the autophagy-targeted drugs based on their targets at various hierarchical sites of the autophagic signaling network, e.g., the upstream and downstream of the autophagosome and the autophagic components with enzyme activities are reviewed and analyzed respectively, with special attention paid to those at preclinical or clinical trials. The drugs tailored to specific autophagy alone and combination with drugs/adjuvant therapies widely used in clinical for various diseases treatments are also emphasized. The emerging drug design and development targeting selective autophagy receptors (SARs) and their related proteins, which would be expected to arrest or reverse the progression of disease in various cancers, inflammation, neurodegeneration, and metabolic disorders, are critically reviewed. And the challenges and perspective in clinically developing autophagy-targeted drugs and possible combinations with other medicine are considered in the review.
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Affiliation(s)
- Mengjia Jiang
- Department of Pharmacology and Pharmacy, China Jiliang University, China
| | - Wayne Wu
- College of Osteopathic Medicine, New York Institute of Technology, USA
| | - Zijie Xiong
- Department of Pharmacology and Pharmacy, China Jiliang University, China
| | - Xiaoping Yu
- Department of Biology, China Jiliang University, China
| | - Zihong Ye
- Department of Biology, China Jiliang University, China
| | - Zhiping Wu
- Department of Pharmacology and Pharmacy, China Jiliang University, China.
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23
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Yamano K, Sawada M, Kikuchi R, Nagataki K, Kojima W, Endo R, Kinefuchi H, Sugihara A, Fujino T, Watanabe A, Tanaka K, Hayashi G, Murakami H, Matsuda N. Optineurin provides a mitophagy contact site for TBK1 activation. EMBO J 2024; 43:754-779. [PMID: 38287189 PMCID: PMC10907724 DOI: 10.1038/s44318-024-00036-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
Tank-binding kinase 1 (TBK1) is a Ser/Thr kinase that is involved in many intracellular processes, such as innate immunity, cell cycle, and apoptosis. TBK1 is also important for phosphorylating the autophagy adaptors that mediate the selective autophagic removal of damaged mitochondria. However, the mechanism by which PINK1-Parkin-mediated mitophagy activates TBK1 remains largely unknown. Here, we show that the autophagy adaptor optineurin (OPTN) provides a unique platform for TBK1 activation. Both the OPTN-ubiquitin and the OPTN-pre-autophagosomal structure (PAS) interaction axes facilitate assembly of the OPTN-TBK1 complex at a contact sites between damaged mitochondria and the autophagosome formation sites. At this assembly point, a positive feedback loop for TBK1 activation is initiated that accelerates hetero-autophosphorylation of the protein. Expression of monobodies engineered here to bind OPTN impaired OPTN accumulation at contact sites, as well as the subsequent activation of TBK1, thereby inhibiting mitochondrial degradation. Taken together, these data show that a positive and reciprocal relationship between OPTN and TBK1 initiates autophagosome biogenesis on damaged mitochondria.
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Affiliation(s)
- Koji Yamano
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
| | - Momoha Sawada
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Reika Kikuchi
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Kafu Nagataki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Waka Kojima
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Ryu Endo
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hiroki Kinefuchi
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Atsushi Sugihara
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Aiko Watanabe
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Keiji Tanaka
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Noriyuki Matsuda
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
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24
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Yeo SK, Haas M, Manupati K, Hao M, Yang F, Chen S, Guan JL. AZI2 mediates TBK1 activation at unresolved selective autophagy cargo receptor complexes with implications for CD8 T-cell infiltration in breast cancer. Autophagy 2024; 20:525-540. [PMID: 37733921 PMCID: PMC10936636 DOI: 10.1080/15548627.2023.2259775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
Most breast cancers do not respond to immune checkpoint inhibitors and there is an urgent need to identify novel sensitization strategies. Herein, we uncovered that activation of the TBK-IFN pathway that is mediated by the TBK1 adapter protein AZI2 is a potent strategy for this purpose. Our initial observations showed that RB1CC1 depletion leads to accumulation of AZI2, in puncta along with selective macroautophagy/autophagy cargo receptors, which are both required for TBK1 activation. Specifically, disrupting the selective autophagy function of RB1CC1 was sufficient to sustain AZI2 puncta accumulation and TBK1 activation. AZI2 then mediates downstream activation of DDX3X, increasing its interaction with IRF3 for transcription of pro-inflammatory chemokines. Consequently, we performed a screen to identify inhibitors that can induce the AZI2-TBK1 pathway, and this revealed Lys05 as a pharmacological agent that induced pro-inflammatory chemokine expression and CD8+ T cell infiltration into tumors. Overall, we have identified a distinct AZI2-TBK1-IFN signaling pathway that is responsive to selective autophagy blockade and can be activated to make breast cancers more immunogenic.Abbreviations: AZI2/NAP1: 5-azacytidine induced 2; CALCOCO2: calcium binding and coiled-coil domain 2; DDX3X: DEAD-box helicase 3 X-linked; FCCP: carbonyl cyanide p-triflouromethoxyphenylhydrazone; a protonophore that depolarizes the mitochondrial inner membrane; ICI: immune checkpoint inhibitor; IFN: interferon; NBR1: NBR1 autophagy cargo receptor; OPTN: optineurin; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SQSTM1/p62: sequestosome 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1.
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Affiliation(s)
- Syn Kok Yeo
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Michael Haas
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kanakaraju Manupati
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Mingang Hao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Fuchun Yang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Song Chen
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Translational Research Institute, Henan Provincial People’s Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jun-Lin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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25
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Choudhury D, Rong N, Senthil Kumar HV, Swedick S, Samuel RZ, Mehrotra P, Toftegaard J, Rajabian N, Thiyagarajan R, Podder AK, Wu Y, Shahini S, Seldeen KL, Troen B, Lei P, Andreadis ST. Proline restores mitochondrial function and reverses aging hallmarks in senescent cells. Cell Rep 2024; 43:113738. [PMID: 38354087 DOI: 10.1016/j.celrep.2024.113738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/04/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024] Open
Abstract
Mitochondrial dysfunction is a hallmark of cellular senescence, with the loss of mitochondrial function identified as a potential causal factor contributing to senescence-associated decline in cellular functions. Our recent findings revealed that ectopic expression of the pluripotency transcription factor NANOG rejuvenates dysfunctional mitochondria of senescent cells by rewiring metabolic pathways. In this study, we report that NANOG restores the expression of key enzymes, PYCR1 and PYCR2, in the proline biosynthesis pathway. Additionally, senescent mesenchymal stem cells manifest severe mitochondrial respiratory impairment, which is alleviated through proline supplementation. Proline induces mitophagy by activating AMP-activated protein kinase α and upregulating Parkin expression, enhancing mitochondrial clearance and ultimately restoring cell metabolism. Notably, proline treatment also mitigates several aging hallmarks, including DNA damage, senescence-associated β-galactosidase, inflammatory cytokine expressions, and impaired myogenic differentiation capacity. Overall, this study highlights the role of proline in mitophagy and its potential in reversing senescence-associated mitochondrial dysfunction and aging hallmarks.
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Affiliation(s)
- Debanik Choudhury
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Na Rong
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | | | - Sydney Swedick
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Ronel Z Samuel
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Pihu Mehrotra
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - John Toftegaard
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Nika Rajabian
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Ramkumar Thiyagarajan
- Department of Medicine, Division of Geriatrics and Palliative Medicine, Buffalo, NY 14203, USA
| | - Ashis K Podder
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Yulun Wu
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Shahryar Shahini
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Kenneth L Seldeen
- Department of Medicine, Division of Geriatrics and Palliative Medicine, Buffalo, NY 14203, USA
| | - Bruce Troen
- Department of Medicine, Division of Geriatrics and Palliative Medicine, Buffalo, NY 14203, USA
| | - Pedro Lei
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Stelios T Andreadis
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY 14260, USA; Department of Biomedical Engineering, University at Buffalo, Buffalo, NY 14260, USA; Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14263, USA; Center for Cell, Gene and Tissue Engineering (CGTE), University at Buffalo, Buffalo, NY 14260, USA.
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26
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Maruyama T, Hama Y, Noda NN. Mechanisms of mitochondrial reorganization. J Biochem 2024; 175:167-178. [PMID: 38016932 DOI: 10.1093/jb/mvad098] [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: 08/30/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/30/2023] Open
Abstract
The cytoplasm of eukaryotes is dynamically zoned by membrane-bound and membraneless organelles. Cytoplasmic zoning allows various biochemical reactions to take place at the right time and place. Mitochondrion is a membrane-bound organelle that provides a zone for intracellular energy production and metabolism of lipids and iron. A key feature of mitochondria is their high dynamics: mitochondria constantly undergo fusion and fission, and excess or damaged mitochondria are selectively eliminated by mitophagy. Therefore, mitochondria are appropriate model systems to understand dynamic cytoplasmic zoning by membrane organelles. In this review, we summarize the molecular mechanisms of mitochondrial fusion and fission as well as mitophagy unveiled through studies using yeast and mammalian models.
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Affiliation(s)
- Tatsuro Maruyama
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Yutaro Hama
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
- Institute for Genetic Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo 060-0815, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
- Institute for Genetic Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo 060-0815, Japan
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27
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Ma L, Han T, Zhan YA. Mechanism and role of mitophagy in the development of severe infection. Cell Death Discov 2024; 10:88. [PMID: 38374038 PMCID: PMC10876966 DOI: 10.1038/s41420-024-01844-4] [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: 10/23/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
Mitochondria produce adenosine triphosphate and potentially contribute to proinflammatory responses and cell death. Mitophagy, as a conservative phenomenon, scavenges waste mitochondria and their components in the cell. Recent studies suggest that severe infections develop alongside mitochondrial dysfunction and mitophagy abnormalities. Restoring mitophagy protects against excessive inflammation and multiple organ failure in sepsis. Here, we review the normal mitophagy process, its interaction with invading microorganisms and the immune system, and summarize the mechanism of mitophagy dysfunction during severe infection. We highlight critical role of normal mitophagy in preventing severe infection.
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Affiliation(s)
- Lixiu Ma
- Department of Respiratory and Critical Care Medicine, the 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Tianyu Han
- Jiangxi Institute of Respiratory Disease, the 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yi-An Zhan
- Department of Respiratory and Critical Care Medicine, the 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China.
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28
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Sasaki T, Kushida Y, Norizuki T, Kosako H, Sato K, Sato M. ALLO-1- and IKKE-1-dependent positive feedback mechanism promotes the initiation of paternal mitochondrial autophagy. Nat Commun 2024; 15:1460. [PMID: 38368448 PMCID: PMC10874384 DOI: 10.1038/s41467-024-45863-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 02/06/2024] [Indexed: 02/19/2024] Open
Abstract
Allophagy is responsible for the selective removal of paternally inherited organelles, including mitochondria, in Caenorhabditis elegans embryos, thereby facilitating the maternal inheritance of mitochondrial DNA. We previously identified two key factors in allophagy: an autophagy adaptor allophagy-1 (ALLO-1) and TBK1/IKKε family kinase IKKE-1. However, the precise mechanisms by which ALLO-1 and IKKE-1 regulate local autophagosome formation remain unclear. In this study, we identify two ALLO-1 isoforms with different substrate preferences during allophagy. Live imaging reveals a stepwise mechanism of ALLO-1 localization with rapid cargo recognition, followed by ALLO-1 accumulation around the cargo. In the ikke-1 mutant, the accumulation of ALLO-1, and not the recognition of cargo, is impaired, resulting in the failure of isolation membrane formation. Our results also suggest a feedback mechanism for ALLO-1 accumulation via EPG-7/ATG-11, a worm homolog of FIP200, which is a candidate for IKKE-1-dependent phosphorylation. This feedback mechanism may underlie the ALLO-1-dependent initiation and progression of autophagosome formation around paternal organelles.
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Affiliation(s)
- Taeko Sasaki
- Laboratory of Molecular Membrane Biology, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, 371-8512, Japan
- Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, 371-8512, Japan
| | - Yasuharu Kushida
- Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, 371-8512, Japan
| | - Takuya Norizuki
- Laboratory of Molecular Membrane Biology, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, 371-8512, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Ken Sato
- Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, 371-8512, Japan.
| | - Miyuki Sato
- Laboratory of Molecular Membrane Biology, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, 371-8512, Japan.
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29
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Phelan JD, Scheich S, Choi J, Wright GW, Häupl B, Young RM, Rieke SA, Pape M, Ji Y, Urlaub H, Bolomsky A, Doebele C, Zindel A, Wotapek T, Kasbekar M, Collinge B, Huang DW, Coulibaly ZA, Morris VM, Zhuang X, Enssle JC, Yu X, Xu W, Yang Y, Zhao H, Wang Z, Tran AD, Shoemaker CJ, Shevchenko G, Hodson DJ, Shaffer AL, Staudt LM, Oellerich T. Response to Bruton's tyrosine kinase inhibitors in aggressive lymphomas linked to chronic selective autophagy. Cancer Cell 2024; 42:238-252.e9. [PMID: 38215749 DOI: 10.1016/j.ccell.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 11/10/2023] [Accepted: 12/20/2023] [Indexed: 01/14/2024]
Abstract
Diffuse large B cell lymphoma (DLBCL) is an aggressive, profoundly heterogeneous cancer, presenting a challenge for precision medicine. Bruton's tyrosine kinase (BTK) inhibitors block B cell receptor (BCR) signaling and are particularly effective in certain molecular subtypes of DLBCL that rely on chronic active BCR signaling to promote oncogenic NF-κB. The MCD genetic subtype, which often acquires mutations in the BCR subunit, CD79B, and in the innate immune adapter, MYD88L265P, typically resists chemotherapy but responds exceptionally to BTK inhibitors. However, the underlying mechanisms of response to BTK inhibitors are poorly understood. Herein, we find a non-canonical form of chronic selective autophagy in MCD DLBCL that targets ubiquitinated MYD88L265P for degradation in a TBK1-dependent manner. MCD tumors acquire genetic and epigenetic alterations that attenuate this autophagic tumor suppressive pathway. In contrast, BTK inhibitors promote autophagic degradation of MYD88L265P, thus explaining their exceptional clinical benefit in MCD DLBCL.
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Affiliation(s)
- James D Phelan
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sebastian Scheich
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Goethe University Frankfurt, University Hospital, 60590 Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany; University Cancer Center (UCT) Frankfurt, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Jaewoo Choi
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - George W Wright
- Biometric Research Branch, Division of Cancer Diagnosis and Treatment, National Cancer Institute, Bethesda, MD 20850, USA
| | - Björn Häupl
- Goethe University Frankfurt, University Hospital, 60590 Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Ryan M Young
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sara A Rieke
- Goethe University Frankfurt, University Hospital, 60590 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Martine Pape
- Goethe University Frankfurt, University Hospital, 60590 Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Yanlong Ji
- Goethe University Frankfurt, University Hospital, 60590 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Arnold Bolomsky
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carmen Doebele
- Goethe University Frankfurt, University Hospital, 60590 Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany; University Cancer Center (UCT) Frankfurt, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Alena Zindel
- Goethe University Frankfurt, University Hospital, 60590 Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Tanja Wotapek
- Goethe University Frankfurt, University Hospital, 60590 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Monica Kasbekar
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brett Collinge
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC V5Z 4E6, Canada
| | - Da Wei Huang
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zana A Coulibaly
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vivian M Morris
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Johns Hopkins University Department of Biology, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Xiaoxuan Zhuang
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julius C Enssle
- Goethe University Frankfurt, University Hospital, 60590 Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany; University Cancer Center (UCT) Frankfurt, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Xin Yu
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Weihong Xu
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yandan Yang
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hong Zhao
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhuo Wang
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andy D Tran
- CCR Microscopy Core, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher J Shoemaker
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Galina Shevchenko
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| | - Daniel J Hodson
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| | - Arthur L Shaffer
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Louis M Staudt
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Thomas Oellerich
- Goethe University Frankfurt, University Hospital, 60590 Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany; University Cancer Center (UCT) Frankfurt, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany.
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30
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Paul S, Sarraf SA, Nam KH, Zavar L, DeFoor N, Biswas SR, Fritsch LE, Yaron TM, Johnson JL, Huntsman EM, Cantley LC, Ordureau A, Pickrell AM. NAK-associated protein 1/NAP1 activates TBK1 to ensure accurate mitosis and cytokinesis. J Cell Biol 2024; 223:e202303082. [PMID: 38059900 PMCID: PMC10702366 DOI: 10.1083/jcb.202303082] [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: 03/20/2023] [Revised: 10/03/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023] Open
Abstract
Subcellular location and activation of Tank Binding Kinase 1 (TBK1) govern precise progression through mitosis. Either loss of activated TBK1 or its sequestration from the centrosomes causes errors in mitosis and growth defects. Yet, what regulates its recruitment and activation on the centrosomes is unknown. We identified that NAK-associated protein 1 (NAP1) is essential for mitosis, binding to and activating TBK1, which both localize to centrosomes. Loss of NAP1 causes several mitotic and cytokinetic defects due to inactivation of TBK1. Our quantitative phosphoproteomics identified numerous TBK1 substrates that are not only confined to the centrosomes but are also associated with microtubules. Substrate motifs analysis indicates that TBK1 acts upstream of other essential cell cycle kinases like Aurora and PAK kinases. We also identified NAP1 as a TBK1 substrate phosphorylating NAP1 at S318 to promote its degradation by the ubiquitin proteasomal system. These data uncover an important distinct function for the NAP1-TBK1 complex during cell division.
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Affiliation(s)
- Swagatika Paul
- Graduate Program in Biomedical and Veterinary Sciences, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | - Shireen A. Sarraf
- Biochemistry Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ki Hong Nam
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leila Zavar
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Nicole DeFoor
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Sahitya Ranjan Biswas
- Translational Biology, Medicine, and Health Graduate Program, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Lauren E. Fritsch
- Translational Biology, Medicine, and Health Graduate Program, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Tomer M. Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Emily M. Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alicia M. Pickrell
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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31
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Pareek G, Kundu M. Physiological functions of ULK1/2. J Mol Biol 2024:168472. [PMID: 38311233 DOI: 10.1016/j.jmb.2024.168472] [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: 12/19/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
UNC-51-like kinases 1 and 2 (ULK1/2) are serine/threonine kinases that are best known for their evolutionarily conserved role in the autophagy pathway. Upon sensing the nutrient status of a cell, ULK1/2 integrate signals from upstream cellular energy sensors such as mTOR and AMPK and relay them to the downstream components of the autophagy machinery. ULK1/2 also play indispensable roles in the selective autophagy pathway, removing damaged mitochondria, invading pathogens, and toxic protein aggregates. Additional functions of ULK1/2 have emerged beyond autophagy, including roles in protein trafficking, RNP granule dynamics, and signaling events impacting innate immunity, axon guidance, cellular homeostasis, and cell fate. Therefore, it is no surprise that alterations in ULK1/2 expression and activity have been linked with pathophysiological processes, including cancer, neurological disorders, and cardiovascular diseases. Growing evidence suggests that ULK1/2 function as biological rheostats, tuning cellular functions to intra and extra-cellular cues. Given their broad physiological relevance, ULK1/2 are candidate targets for small molecule activators or inhibitors that may pave the way for the development of therapeutics for the treatment of diseases in humans.
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Affiliation(s)
- Gautam Pareek
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mondira Kundu
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, TN, USA.
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32
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Mizushima N. Ubiquitin in autophagy and non-protein ubiquitination. Nat Struct Mol Biol 2024; 31:208-209. [PMID: 38366228 DOI: 10.1038/s41594-024-01217-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Affiliation(s)
- Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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33
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Germain K, So RWL, DiGiovanni LF, Watts JC, Bandsma RHJ, Kim PK. Upregulated pexophagy limits the capacity of selective autophagy. Nat Commun 2024; 15:375. [PMID: 38195640 PMCID: PMC10776696 DOI: 10.1038/s41467-023-44005-4] [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: 05/23/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
Selective autophagy is an essential process to maintain cellular homeostasis through the constant recycling of damaged or superfluous components. Over a dozen selective autophagy pathways mediate the degradation of diverse cellular substrates, but whether these pathways can influence one another remains unknown. We address this question using pexophagy, the autophagic degradation of peroxisomes, as a model. We show in cells that upregulated pexophagy impairs the selective autophagy of both mitochondria and protein aggregates by exhausting the autophagy initiation factor, ULK1. We confirm this finding in cell models of the pexophagy-mediated form of Zellweger Spectrum Disorder, a disease characterized by peroxisome dysfunction. Further, we extend the generalizability of limited selective autophagy by determining that increased protein aggregate degradation reciprocally reduces pexophagy using cell models of Parkinson's Disease and Huntington's Disease. Our findings suggest that the degradative capacity of selective autophagy can become limited by an increase in one substrate.
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Affiliation(s)
- Kyla Germain
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Raphaella W L So
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, Toronto, ON, M5T 0S8, Canada
| | - Laura F DiGiovanni
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Joel C Watts
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, Toronto, ON, M5T 0S8, Canada
| | - Robert H J Bandsma
- Translational Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1A8, Canada.
| | - Peter K Kim
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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34
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Gao A, Wang M, Tang X, Shi G, Hou K, Fang J, Zhou L, Zhou H, Jiang W, Li Y, Ouyang F. NDP52 SUMOylation contributes to low-dose X-rays-induced cardiac hypertrophy through PINK1/Parkin-mediated mitophagy via MUL1/SUMO2 signalling. J Cell Physiol 2024; 239:79-96. [PMID: 37942585 DOI: 10.1002/jcp.31145] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023]
Abstract
Radiation-induced heart damage caused by low-dose X-rays has a significant impact on tumour patients' prognosis, with cardiac hypertrophy being the most severe noncarcinogenic adverse effect. Our previous study demonstrated that mitophagy activation promoted cardiac hypertrophy, but the underlying mechanisms remained unclear. In the present study, PARL-IN-1 enhanced excessive hypertrophy of cardiomyocytes and exacerbated mitochondrial damage. Isobaric tags for relative and absolute quantification-based quantitative proteomics identified NDP52 as a crucial target mediating cardiac hypertrophy induced by low-dose X-rays. SUMOylation proteomics revealed that the SUMO E3 ligase MUL1 facilitated NDP52 SUMOylation through SUMO2. Co-IP coupled with LC-MS/MS identified a critical lysine residue at position 262 of NDP52 as the key site for SUMO2-mediated SUMOylation of NDP52. The point mutation plasmid NDP52K262R inhibited mitophagy under MUL1 overexpression, as evidenced by inhibition of LC3 interaction with NDP52, PINK1 and LAMP2A. A mitochondrial dissociation study revealed that NDP52K262R inhibited PINK1 targeting to endosomes early endosomal marker (EEA1), late/lysosome endosomal marker (LAMP2A) and recycling endosomal marker (RAB11), and laser confocal microscopy confirmed that NDP52K262R impaired the recruitment of mitochondria to the autophagic pathway through EEA1/RAB11 and ATG3, ATG5, ATG16L1 and STX17, but did not affect mitochondrial delivery to lysosomes via LAMP2A for degradation. In conclusion, our findings suggest that MUL1-mediated SUMOylation of NDP52 plays a crucial role in regulating mitophagy in the context of low-dose X-ray-induced cardiac hypertrophy. Two hundred sixty-second lysine of NDP52 is identified as a key SUMOylation site for low-dose X-ray promoting mitophagy activation and cardiac hypertrophy. Collectively, this study provides novel implications for the development of therapeutic strategies aimed at preventing the progression of cardiac hypertrophy induced by low-dose X-rays.
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Affiliation(s)
- Anbo Gao
- Hengyang Medical School, Clinical Research Institute, The Second Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Mengjie Wang
- Hengyang Medical School, Clinical Research Institute, The Second Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Xing Tang
- Hengyang Medical School, Clinical Research Institute, The Second Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Gangqing Shi
- Hengyang Medical School, Clinical Research Institute, The Second Affiliated Hospital, University of South China, Hengyang, Hunan, China
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, Cancer Research Institute, University of South China, Hengyang, Hunan, China
| | - Kai Hou
- Hengyang Medical School, Clinical Research Institute, The Second Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Jinren Fang
- Hengyang Medical School, Clinical Research Institute, The Second Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Linlin Zhou
- Hengyang Medical School, Clinical Research Institute, The Second Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Hong Zhou
- Department of Radiology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Weimin Jiang
- Department of Cardiology, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
| | - Yukun Li
- Department of Assisted Reproductive Centre, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
| | - Fan Ouyang
- Department of Cardiology, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
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35
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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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36
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Sun J, Liu C, Liu YY, Guo ZA. Mitophagy in renal interstitial fibrosis. Int Urol Nephrol 2024; 56:167-179. [PMID: 37450241 DOI: 10.1007/s11255-023-03686-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: 03/27/2023] [Accepted: 06/06/2023] [Indexed: 07/18/2023]
Abstract
As a high energy consumption organ, kidney relies on a large number of mitochondria to ensure normal physiological activities. Under specific stimulation, mitophagy and mitochondrial dynamics (fission, fusion) cooperatively regulate mitochondrial quality and participate in many life activities such as energy metabolism, inflammatory response, oxidative stress, cell senescence and death. Mitophagy plays a key role in the progression of acute kidney injury and chronic kidney disease. The early induction of oxidative stress in renal parenchyma, the activation of pro-inflammatory cytokines and TGF-β signal pathway are closely related to renal interstitial fibrosis. Macrophage reprogramming is also considered to be an important participant in the progression of kidney fibrosis. This review summarizes the molecular mechanism of mitochondrial autophagy and its relationship with the pathway of promoting fibrosis, and discusses the possibility of restoring mitophagy balance as a pharmacological target for the treatment of renal interstitial fibrosis, so as to provide new ideas for more efficient anti-fibrosis and delay the progress of chronic kidney disease.
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Affiliation(s)
- Jun Sun
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chong Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ying-Ying Liu
- Department of Nephrology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhao-An Guo
- Department of Nephrology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China.
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37
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Cui S, Xia T, Zhao J, Ren X, Wu T, Kameni M, Guo X, He L, Guo J, Duperray-Susini A, Levillayer F, Collard JM, Zhong J, Pan L, Tangy F, Vidalain PO, Zhou D, Jiu Y, Faure M, Wei Y. NDP52 mediates an antiviral response to hepatitis B virus infection through Rab9-dependent lysosomal degradation pathway. Nat Commun 2023; 14:8440. [PMID: 38114531 PMCID: PMC10730550 DOI: 10.1038/s41467-023-44201-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
Autophagy receptor NDP52 triggers bacterial autophagy against infection. However, the ability of NDP52 to protect against viral infection has not been established. We show that NDP52 binds to envelope proteins of hepatitis B virus (HBV) and triggers a degradation process that promotes HBV clearance. Inactivating NDP52 in hepatocytes results in decreased targeting of viral envelopes in the lysosome and increased levels of viral replication. NDP52 inhibits HBV at both viral entry and late replication stages. In contrast to NDP52-mediated bacterial autophagy, lysosomal degradation of HBV envelopes is independent of galectin 8 and ATG5. NDP52 forms complex with Rab9 and viral envelope proteins and links HBV to Rab9-dependent lysosomal degradation pathway. These findings reveal that NDP52 acts as a sensor for HBV infection, which mediates a unique antiviral response to eliminate the virus. This work also suggests direct roles for autophagy receptors in other lysosomal degradation pathways than canonical autophagy.
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Affiliation(s)
- Shuzhi Cui
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Tian Xia
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
- Institut Pasteur, Université Paris Cité, 28 rue du Dr. Roux, 75015, Paris, France
| | - Jianjin Zhao
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Xiaoyu Ren
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Tingtao Wu
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Mireille Kameni
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Xiaoju Guo
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Li He
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Jingao Guo
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | | | - Florence Levillayer
- Institut Pasteur, Université Paris Cité, 28 rue du Dr. Roux, 75015, Paris, France
| | - Jean-Marc Collard
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
- Institut Pasteur, Université Paris Cité, 28 rue du Dr. Roux, 75015, Paris, France
| | - Jin Zhong
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Lifeng Pan
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, 200032, Shanghai, China
| | - Frédéric Tangy
- Institut Pasteur, Université Paris Cité, 28 rue du Dr. Roux, 75015, Paris, France
| | - Pierre-Olivier Vidalain
- Institut Pasteur, Université Paris Cité, 28 rue du Dr. Roux, 75015, Paris, France
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France
| | - Dongming Zhou
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Yaming Jiu
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Mathias Faure
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France
| | - Yu Wei
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China.
- Institut Pasteur, Université Paris Cité, 28 rue du Dr. Roux, 75015, Paris, France.
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38
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Broadbent DG, McEwan CM, Tsang TM, Poole DM, Naylor BC, Price JC, Schmidt JC, Andersen JL. The formation of ubiquitin rich condensates triggers recruitment of the ATG9A lipid transfer complex to initiate basal autophagy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569058. [PMID: 38077022 PMCID: PMC10705457 DOI: 10.1101/2023.11.28.569058] [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: 12/20/2023]
Abstract
Autophagy is an essential cellular recycling process that maintains protein and organelle homeostasis. ATG9A vesicle recruitment is a critical early step in autophagy to initiate autophagosome biogenesis. The mechanisms of ATG9A vesicle recruitment are best understood in the context of starvation-induced non-selective autophagy, whereas less is known about the signals driving ATG9A vesicle recruitment to autophagy initiation sites in the absence of nutrient stress. Here we demonstrate that loss of ATG9A or the lipid transfer protein ATG2 leads to the accumulation of phosphorylated p62 aggregates in the context of basal autophagy. Furthermore, we show that p62 degradation requires the lipid scramblase activity of ATG9A. Lastly, we present evidence that poly-ubiquitin is an essential signal that recruits ATG9A and mediates autophagy foci assembly in nutrient replete cells. Together, our data support a ubiquitin-driven model of ATG9A recruitment and autophagosome formation during basal autophagy.
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Affiliation(s)
- D G Broadbent
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
- Department of Physiology, College of Natural Sciences, Michigan State University, East Lansing, MI, USA
| | - C M McEwan
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - T M Tsang
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
- Department of Physiology, College of Natural Sciences, Michigan State University, East Lansing, MI, USA
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, MI, USA
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - D M Poole
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - B C Naylor
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - J C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - J C Schmidt
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, MI, USA
| | - J L Andersen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
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Bunker EN, Le Guerroué F, Wang C, Strub M, Werner A, Tjandra N, Youle RJ. Nix interacts with WIPI2 to induce mitophagy. EMBO J 2023; 42:e113491. [PMID: 37621214 PMCID: PMC10646555 DOI: 10.15252/embj.2023113491] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 08/26/2023] Open
Abstract
Nix is a membrane-anchored outer mitochondrial protein that induces mitophagy. While Nix has an LC3-interacting (LIR) motif that binds to ATG8 proteins, it also contains a minimal essential region (MER) that induces mitophagy through an unknown mechanism. We used chemically induced dimerization (CID) to probe the mechanism of Nix-mediated mitophagy and found that both the LIR and MER are required for robust mitophagy. We find that the Nix MER interacts with the autophagy effector WIPI2 and recruits WIPI2 to mitochondria. The Nix LIR motif is also required for robust mitophagy and converts a homogeneous WIPI2 distribution on the surface of the mitochondria into puncta, even in the absence of ATG8s. Together, this work reveals unanticipated mechanisms in Nix-induced mitophagy and the elusive role of the MER, while also describing an interesting example of autophagy induction that acts downstream of the canonical initiation complexes.
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Affiliation(s)
- Eric N Bunker
- Surgical Neurology BranchNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - François Le Guerroué
- Surgical Neurology BranchNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - Chunxin Wang
- Surgical Neurology BranchNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - Marie‐Paule Strub
- Biochemistry and Biophysics CenterNational Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaMDUSA
| | - Achim Werner
- Stem Cell Biochemistry UnitNational Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMDUSA
| | - Nico Tjandra
- Biochemistry and Biophysics CenterNational Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaMDUSA
| | - Richard J Youle
- Surgical Neurology BranchNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
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40
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Atici AE, Crother TR, Noval Rivas M. Mitochondrial quality control in health and cardiovascular diseases. Front Cell Dev Biol 2023; 11:1290046. [PMID: 38020895 PMCID: PMC10657886 DOI: 10.3389/fcell.2023.1290046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Cardiovascular diseases (CVDs) are one of the primary causes of mortality worldwide. An optimal mitochondrial function is central to supplying tissues with high energy demand, such as the cardiovascular system. In addition to producing ATP as a power source, mitochondria are also heavily involved in adaptation to environmental stress and fine-tuning tissue functions. Mitochondrial quality control (MQC) through fission, fusion, mitophagy, and biogenesis ensures the clearance of dysfunctional mitochondria and preserves mitochondrial homeostasis in cardiovascular tissues. Furthermore, mitochondria generate reactive oxygen species (ROS), which trigger the production of pro-inflammatory cytokines and regulate cell survival. Mitochondrial dysfunction has been implicated in multiple CVDs, including ischemia-reperfusion (I/R), atherosclerosis, heart failure, cardiac hypertrophy, hypertension, diabetic and genetic cardiomyopathies, and Kawasaki Disease (KD). Thus, MQC is pivotal in promoting cardiovascular health. Here, we outline the mechanisms of MQC and discuss the current literature on mitochondrial adaptation in CVDs.
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Affiliation(s)
- Asli E. Atici
- Department of Pediatrics, Division of Infectious Diseases and Immunology, Guerin Children’s at Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Infectious and Immunologic Diseases Research Center (IIDRC), Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Timothy R. Crother
- Department of Pediatrics, Division of Infectious Diseases and Immunology, Guerin Children’s at Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Infectious and Immunologic Diseases Research Center (IIDRC), Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Magali Noval Rivas
- Department of Pediatrics, Division of Infectious Diseases and Immunology, Guerin Children’s at Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Infectious and Immunologic Diseases Research Center (IIDRC), Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
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41
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Xie W, Zhang C, Wang Z, Chen H, Gu T, Zhou T, Wu Y, Xia F, Li M, Wang J, Jiao R, Cui J, Jin S. ATG4B antagonizes antiviral immunity by GABARAP-directed autophagic degradation of TBK1. Autophagy 2023; 19:2853-2868. [PMID: 37434364 PMCID: PMC10549193 DOI: 10.1080/15548627.2023.2233846] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 06/15/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023] Open
Abstract
ABBREVIATIONS Baf A1: bafilomycin A1; GABARAP: GABA type A receptor-associated protein; GFP: green fluorescent protein; IFN: interferon; IKBKE/IKKi: inhibitor of nuclear factor kappa B kinase subunit epsilon; IRF3: interferon regulatory factor 3; ISG: interferon-stimulated gene; ISRE: IFN-stimulated response element; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAVS: mitochondrial antiviral signaling protein; MOI: multiplicity of infection; PAMPs: pathogen-associated molecule patterns; RIGI/DDX58: RNA sensor RIG-I; SeV: Sendai virus; siRNA: small interfering RNA; TBK1: TANK binding kinase 1; WT: wild-type; VSV: vesicular stomatitis virus.
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Affiliation(s)
- Weihong Xie
- Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Chenqiu Zhang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zheyu Wang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Hui Chen
- Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Tonghui Gu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Tao Zhou
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yaoxing Wu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Fan Xia
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Min Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jun Wang
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Renjie Jiao
- Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jun Cui
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shouheng Jin
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
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42
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Ratliffe J, Kataura T, Otten EG, Korolchuk VI. The evolution of selective autophagy as a mechanism of oxidative stress response: The evolutionarily acquired ability of selective autophagy receptors to respond to oxidative stress is beneficial for human longevity. Bioessays 2023; 45:e2300076. [PMID: 37603398 DOI: 10.1002/bies.202300076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/14/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023]
Abstract
Ageing is associated with a decline in autophagy and elevated reactive oxygen species (ROS), which can breach the capacity of antioxidant systems. Resulting oxidative stress can cause further cellular damage, including DNA breaks and protein misfolding. This poses a challenge for longevous organisms, including humans. In this review, we hypothesise that in the course of human evolution selective autophagy receptors (SARs) acquired the ability to sense and respond to localised oxidative stress. We posit that in the vicinity of protein aggregates and dysfunctional mitochondria oxidation of key cysteine residues in SARs induces their oligomerisation which initiates autophagy. The degradation of damaged cellular components thus could reduce ROS production and restore redox homeostasis. This evolutionarily acquired function of SARs may represent one of the biological adaptations that contributed to longer lifespan. Inversely, loss of this mechanism can lead to age-related diseases associated with impaired autophagy and oxidative stress.
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Affiliation(s)
- Joshua Ratliffe
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Tetsushi Kataura
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Elsje G Otten
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Viktor I Korolchuk
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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Mei L, Chen X, Wei F, Huang X, Liu L, Yao J, Chen J, Luo X, Wang Z, Yang A. Tethering ATG16L1 or LC3 induces targeted autophagic degradation of protein aggregates and mitochondria. Autophagy 2023; 19:2997-3013. [PMID: 37424101 PMCID: PMC10549199 DOI: 10.1080/15548627.2023.2234797] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) based on the ubiquitin-proteasome system have made great progress in the field of drug discovery. There is mounting evidence that the accumulation of aggregation-prone proteins or malfunctioning organelles is associated with the occurrence of various age-related neurodegenerative disorders and cancers. However, PROTACs are inefficient for the degradation of such large targets due to the narrow entrance channel of the proteasome. Macroautophagy (hereafter referred to as autophagy) is known as a self-degradative process involved in the degradation of bulk cytoplasmic components or specific cargoes that are sequestered into autophagosomes. In the present study, we report the development of a generalizable strategy for the targeted degradation of large targets. Our results suggested that tethering large target models to phagophore-associated ATG16L1 or LC3 induced targeted autophagic degradation of the large target models. Furthermore, we successfully applied this autophagy-targeting degradation strategy to the targeted degradation of HTT65Q aggregates and mitochondria. Specifically, chimeras consisting of polyQ-binding peptide 1 (QBP) and ATG16L1-binding peptide (ABP) or LC3-interacting region (LIR) induced targeted autophagic degradation of pathogenic HTT65Q aggregates; and the chimeras consisting of mitochondria-targeting sequence (MTS) and ABP or LIR promoted targeted autophagic degradation of dysfunctional mitochondria, hence ameliorating mitochondrial dysfunction in a Parkinson disease cell model and protecting cells from apoptosis induced by the mitochondrial stress agent FCCP. Therefore, this study provides a new strategy for the selective proteolysis of large targets and enrich the toolkit for autophagy-targeting degradation.Abbreviations: ABP: ATG16L1-binding peptide; ATG16L1: autophagy related 16 like 1; ATTEC: autophagy-tethering compound; AUTAC: autophagy-targeting chimera; AUTOTAC: autophagy-targeting chimera; Baf A1: bafilomycin A1; BCL2: BCL2 apoptosis regulator; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CASP3: caspase 3; CPP: cell-penetrating peptide; CQ: chloroquine phosphate; DAPI: 4',6-diamidino-2-phenylindole; DCM: dichloromethane; DMF: N,N-dimethylformamide; DMSO: dimethyl sulfoxide; EBSS: Earle's balanced salt solution; FCCP: carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone; FITC: fluorescein-5-isothiocyanate; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; HEK293: human embryonic kidney 293; HEK293T: human embryonic kidney 293T; HPLC: high-performance liquid chromatography; HRP: horseradish peroxidase; HTT: huntingtin; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MFF: mitochondrial fission factor; MTS: mitochondria-targeting sequence; NBR1: NBR1 autophagy cargo receptor; NLRX1: NLR family member X1; OPTN: optineurin; P2A: self-cleaving 2A peptide; PB1: Phox and Bem1p; PBS: phosphate-buffered saline; PE: phosphatidylethanolamine; PINK1: PTEN induced kinase 1; PRKN: parkin RBR E3 ubiquitin protein ligase; PROTACs: proteolysis-targeting chimeras; QBP: polyQ-binding peptide 1; SBP: streptavidin-binding peptide; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SPATA33: spermatogenesis associated 33; TIMM23: translocase of inner mitochondrial membrane 23; TMEM59: transmembrane protein 59; TOMM20: translocase of outer mitochondrial membrane 20; UBA: ubiquitin-associated; WT: wild type.
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Affiliation(s)
- Ligang Mei
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xiaorong Chen
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Fujing Wei
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xue Huang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lu Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jia Yao
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jing Chen
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xunguang Luo
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Zhuolin Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, China
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44
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Saha B, Olsvik H, Williams GL, Oh S, Evjen G, Sjøttem E, Mandell MA. TBK1 is ubiquitinated by TRIM5α to assemble mitophagy machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563195. [PMID: 37905089 PMCID: PMC10614974 DOI: 10.1101/2023.10.19.563195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Ubiquitination of mitochondrial proteins provides a basis for the downstream recruitment of mitophagy machinery, yet whether ubiquitination of the machinery itself contributes to mitophagy is unknown. Here, we show that K63-linked polyubiquitination of the key mitophagy regulator TBK1 is essential for its mitophagy functions. This modification is catalyzed by the ubiquitin ligase TRIM5α. Mitochondrial damage triggers TRIM5α's auto-ubiquitination and its interaction with ubiquitin-binding autophagy adaptors including NDP52, optineurin, and NBR1. Autophagy adaptors, along with TRIM27, enable TRIM5α to engage with TBK1. TRIM5α with intact ubiquitination function is required for the proper accumulation of active TBK1 on damaged mitochondria in Parkin-dependent and Parkin-independent mitophagy pathways. Additionally, we show that TRIM5α can directly recruit autophagy initiation machinery to damaged mitochondria. Our data support a model in which TRIM5α provides a self-amplifying, mitochondria-localized, ubiquitin-based, assembly platform for TBK1 and mitophagy adaptors that is ultimately required to recruit the core autophagy machinery.
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Affiliation(s)
- Bhaskar Saha
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 USA
| | - Hallvard Olsvik
- Autophagy Research Group, Department of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Geneva L Williams
- Biomedical Sciences Graduate Program, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 USA
| | - Seeun Oh
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 USA
| | - Gry Evjen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Eva Sjøttem
- Autophagy Research Group, Department of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Michael A Mandell
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 USA
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center
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45
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Liu L, Li Y, Chen G, Chen Q. Crosstalk between mitochondrial biogenesis and mitophagy to maintain mitochondrial homeostasis. J Biomed Sci 2023; 30:86. [PMID: 37821940 PMCID: PMC10568841 DOI: 10.1186/s12929-023-00975-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/13/2023] [Indexed: 10/13/2023] Open
Abstract
Mitochondrial mass and quality are tightly regulated by two essential and opposing mechanisms, mitochondrial biogenesis (mitobiogenesis) and mitophagy, in response to cellular energy needs and other cellular and environmental cues. Great strides have been made to uncover key regulators of these complex processes. Emerging evidence has shown that there exists a tight coordination between mitophagy and mitobiogenesis, and their defects may cause many human diseases. In this review, we will first summarize the recent advances made in the discovery of molecular regulations of mitobiogenesis and mitophagy and then focus on the mechanism and signaling pathways involved in the simultaneous regulation of mitobiogenesis and mitophagy in the response of tissue or cultured cells to energy needs, stress, or pathophysiological conditions. Further studies of the crosstalk of these two opposing processes at the molecular level will provide a better understanding of how the cell maintains optimal cellular fitness and function under physiological and pathophysiological conditions, which holds promise for fighting aging and aging-related diseases.
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Affiliation(s)
- Lei Liu
- Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regenerative Medicine, Beijing, China.
| | - Yanjun Li
- Center of Cell Response, State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Guo Chen
- Center of Cell Response, State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Quan Chen
- Center of Cell Response, State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China.
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46
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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: 26] [Impact Index Per Article: 26.0] [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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47
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Bottone S, Joliot O, Cakil ZV, El Hajji L, Rakotoarison LM, Boncompain G, Perez F, Gautier A. A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity. Nat Methods 2023; 20:1553-1562. [PMID: 37640938 DOI: 10.1038/s41592-023-01988-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/28/2023] [Indexed: 08/31/2023]
Abstract
Molecular tools enabling the control and observation of the proximity of proteins are essential for studying the functional role of physical distance between two proteins. Here we present CATCHFIRE (chemically assisted tethering of chimera by fluorogenic-induced recognition), a chemically induced proximity technology with intrinsic fluorescence imaging and sensing capabilities. CATCHFIRE relies on genetic fusion to small dimerizing domains that interact upon addition of fluorogenic inducers of proximity that fluoresce upon formation of the ternary assembly, allowing real-time monitoring of the chemically induced proximity. CATCHFIRE is rapid and fully reversible and allows the control and tracking of protein localization, protein trafficking, organelle transport and cellular processes, opening new avenues for studying or controlling biological processes with high spatiotemporal resolution. Its fluorogenic nature allows the design of a new class of biosensors for the study of processes such as signal transduction and apoptosis.
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Affiliation(s)
- Sara Bottone
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, Paris, France
| | | | - Zeyneb Vildan Cakil
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, Paris, France
| | - Lina El Hajji
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, Paris, France
| | - Louise-Marie Rakotoarison
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, Paris, France
| | | | | | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, Paris, France.
- Institut Universitaire de France, Paris, France.
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48
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Zhang R, Feng W, Qian S, Wang F. Autophagy-mediated surveillance of Rim4-mRNA interaction safeguards programmed meiotic translation. Cell Rep 2023; 42:113051. [PMID: 37659076 PMCID: PMC10591816 DOI: 10.1016/j.celrep.2023.113051] [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: 11/30/2022] [Revised: 07/13/2023] [Accepted: 08/15/2023] [Indexed: 09/04/2023] Open
Abstract
In yeast meiosis, autophagy is active and essential. Here, we investigate the fate of Rim4, a meiosis-specific RNA-binding protein (RBP), and its associated transcripts during meiotic autophagy. We demonstrate that Rim4 employs a nuclear localization signal (NLS) to enter the nucleus, where it loads its mRNA substrates before nuclear export. Upon reaching the cytoplasm, active autophagy selectively spares the Rim4-mRNA complex. During meiotic divisions, autophagy preferentially degrades Rim4 in an Atg11-dependent manner, coinciding with the release of Rim4-bound mRNAs for translation. Intriguingly, these released mRNAs also become vulnerable to autophagy. In vitro, purified Rim4 and its RRM-motif-containing variants activate Atg1 kinase in meiotic cell lysates and in immunoprecipitated (IP) Atg1 complexes. This suggests that the conserved RNA recognition motifs (RRMs) of Rim4 are involved in stimulating Atg1 and thereby facilitating selective autophagy. Taken together, our findings indicate that autophagy surveils Rim4-mRNA interaction to ensure stage-specific translation during meiosis.
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Affiliation(s)
- Rudian Zhang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenzhi Feng
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Suhong Qian
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Fei Wang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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Harding O, Holzer E, Riley JF, Martens S, Holzbaur ELF. Damaged mitochondria recruit the effector NEMO to activate NF-κB signaling. Mol Cell 2023; 83:3188-3204.e7. [PMID: 37683611 PMCID: PMC10510730 DOI: 10.1016/j.molcel.2023.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 05/25/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
Failure to clear damaged mitochondria via mitophagy disrupts physiological function and may initiate damage signaling via inflammatory cascades, although how these pathways intersect remains unclear. We discovered that nuclear factor kappa B (NF-κB) essential regulator NF-κB effector molecule (NEMO) is recruited to damaged mitochondria in a Parkin-dependent manner in a time course similar to recruitment of the structurally related mitophagy adaptor, optineurin (OPTN). Upon recruitment, NEMO partitions into phase-separated condensates distinct from OPTN but colocalizing with p62/SQSTM1. NEMO recruitment, in turn, recruits the active catalytic inhibitor of kappa B kinase (IKK) component phospho-IKKβ, initiating NF-κB signaling and the upregulation of inflammatory cytokines. Consistent with a potential neuroinflammatory role, NEMO is recruited to mitochondria in primary astrocytes upon oxidative stress. These findings suggest that damaged, ubiquitinated mitochondria serve as an intracellular platform to initiate innate immune signaling, promoting the formation of activated IKK complexes sufficient to activate NF-κB signaling. We propose that mitophagy and NF-κB signaling are initiated as parallel pathways in response to mitochondrial stress.
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Affiliation(s)
- Olivia Harding
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Elisabeth Holzer
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA; Max Perutz Labs, Vienna Biocenter Campus, Vienna, Austria; Center for Molecular Biology, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria; Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Julia F Riley
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sascha Martens
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA; Max Perutz Labs, Vienna Biocenter Campus, Vienna, Austria; Center for Molecular Biology, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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Priem D, Huyghe J, Bertrand MJM. LC3-independent autophagy is vital to prevent TNF cytotoxicity. Autophagy 2023; 19:2585-2589. [PMID: 37014272 PMCID: PMC10392734 DOI: 10.1080/15548627.2023.2197760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/13/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
The (macro)autophagy field is facing a paradigm shift after the recent discovery that cytosolic cargoes can still be selectively targeted to phagophores (the precursors to autophagosomes) even in the absence of LC3 or other Atg8-protein family members. Several in vitro studies have indeed reported on the existence of an unconventional selective autophagic pathway that involves the in-situ formation of an autophagosome around the cargo through the direct selective autophagy receptor-mediated recruitment of RB1CC1/FIP200, thereby bypassing the requirement of LC3. In an article recently published in Science, we demonstrate the physiological importance of this unconventional autophagic pathway in the context of TNF (tumor necrosis factor) signaling. We show that it promotes the degradation of the cytotoxic TNFRSF1A/TNFR1 (TNF receptor superfamily member 1A) complex II that assembles upon TNF sensing and thereby protects mice from TNFRSF1A-driven embryonic lethality and skin inflammation.Abbreviations: ATG: autophagy related; CASP: caspase; FIR: RB1CC1/FIP200-interacting region; LIR: LC3-interacting region; M1: linear; PAS: phagophore assembly site; PtdIns3K: phosphatidylinositol 3-kinase; TNF: tumor necrosis factor; TNFRSF1A: TNF receptor superfamily member 1A.
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Affiliation(s)
- Dario Priem
- Cell Death and Inflammation Unit, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jon Huyghe
- Cell Death and Inflammation Unit, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Mathieu JM Bertrand
- Cell Death and Inflammation Unit, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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