1
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Hoffmann ME, Jacomin AC, Popovic D, Kalina D, Covarrubias-Pinto A, Dikic I. TBC1D2B undergoes phase separation and mediates autophagy initiation. J Cell Biochem 2024; 125:e30481. [PMID: 38226533 DOI: 10.1002/jcb.30481] [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: 02/08/2023] [Revised: 08/28/2023] [Accepted: 09/17/2023] [Indexed: 01/17/2024]
Abstract
Small ubiquitin-like modifiers from the ATG8 family regulate autophagy initiation and progression in mammalian cells. Their interaction with LC3-interacting region (LIR) containing proteins promotes cargo sequestration, phagophore assembly, or even fusion between autophagosomes and lysosomes. Previously, we have shown that RabGAP proteins from the TBC family directly bind to LC3/GABARAP proteins. In the present study, we focus on the function of TBC1D2B. We show that TBC1D2B contains a functional canonical LIR motif and acts at an early stage of autophagy by binding to both LC3/GABARAP and ATG12 conjugation complexes. Subsequently, TBC1D2B is degraded by autophagy. TBC1D2B condensates into liquid droplets upon autophagy induction. Our study suggests that phase separation is an underlying mechanism of TBC1D2B-dependent autophagy induction.
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Affiliation(s)
- Marina E Hoffmann
- Molecular Signaling Group, Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
| | - Anne-Claire Jacomin
- Molecular Signaling Group, Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
| | - Doris Popovic
- Molecular Signaling Group, Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
| | - Daniel Kalina
- Molecular Signaling Group, Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
- Biomedical Research Laboratory, Department of Internal Medicine, Goethe University Clinic Frankfurt, Frankfurt, Germany
| | - Adriana Covarrubias-Pinto
- Molecular Signaling Group, Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
| | - Ivan Dikic
- Molecular Signaling Group, Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
- Molecular Signaling Group, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Frankfurt, Germany
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2
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Kurusu R, Morishita H, Komatsu M. p62 bodies: cytosolic zoning by phase separation. J Biochem 2024; 175:141-146. [PMID: 37948628 DOI: 10.1093/jb/mvad089] [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: 09/07/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
Cellular zoning or partitioning is critical in preventing macromolecules from random diffusion and orchestrating the spatiotemporal dynamics of biochemical reactions. Along with membranous organelles, membraneless organelles contribute to the precise regulation of biochemical reactions inside cells. In response to environmental cues, membraneless organelles rapidly form through liquid-liquid phase separation, sequester certain proteins and RNAs, mediate specific reactions and dissociate. Among membraneless organelles, ubiquitin-positive condensates, namely, p62 bodies, maintain cellular homeostasis through selective autophagy of themselves to contribute to intracellular quality control. p62 bodies also activate the anti-oxidative stress response regulated by the KEAP1-NRF2 system. In this review, we present an overview of recent advancements in cellular and molecular biology related to p62 bodies, highlighting their dynamic nature and functions.
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Affiliation(s)
- Reo Kurusu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Hideaki Morishita
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
- Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
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3
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Hatanaka A, Nakada S, Matsumoto G, Satoh K, Aketa I, Watanabe A, Hirakawa T, Tsujita T, Waku T, Kobayashi A. The transcription factor NRF1 (NFE2L1) activates aggrephagy by inducing p62 and GABARAPL1 after proteasome inhibition to maintain proteostasis. Sci Rep 2023; 13:14405. [PMID: 37658135 PMCID: PMC10474156 DOI: 10.1038/s41598-023-41492-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023] Open
Abstract
The ubiquitin‒proteasome system (UPS) and autophagy are the two primary cellular pathways of misfolded or damaged protein degradation that maintain cellular proteostasis. When the proteasome is dysfunctional, cells compensate for impaired protein clearance by activating aggrephagy, a type of selective autophagy, to eliminate ubiquitinated protein aggregates; however, the molecular mechanisms by which impaired proteasome function activates aggrephagy remain poorly understood. Here, we demonstrate that activation of aggrephagy is transcriptionally induced by the transcription factor NRF1 (NFE2L1) in response to proteasome dysfunction. Although NRF1 has been previously shown to induce the expression of proteasome genes after proteasome inhibition (i.e., the proteasome bounce-back response), our genome-wide transcriptome analyses identified autophagy-related p62/SQSTM1 and GABARAPL1 as genes directly targeted by NRF1. Intriguingly, NRF1 was also found to be indispensable for the formation of p62-positive puncta and their colocalization with ULK1 and TBK1, which play roles in p62 activation via phosphorylation. Consistently, NRF1 knockdown substantially reduced the phosphorylation rate of Ser403 in p62. Finally, NRF1 selectively upregulated the expression of GABARAPL1, an ATG8 family gene, to induce the clearance of ubiquitinated proteins. Our findings highlight the discovery of an activation mechanism underlying NRF1-mediated aggrephagy through gene regulation when proteasome activity is impaired.
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Affiliation(s)
- Atsushi Hatanaka
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto, 610-0394, Japan
- Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan
| | - Sota Nakada
- Laboratory for Genetic Code, Department of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, Japan
| | - Gen Matsumoto
- Department of Anatomy and Neurobiology, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Katsuya Satoh
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto, 610-0394, Japan
| | - Iori Aketa
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto, 610-0394, Japan
| | - Akira Watanabe
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoaki Hirakawa
- Laboratory of Biochemistry, Faculty of Agriculture, Saga University, Saga, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Tadayuki Tsujita
- Laboratory of Biochemistry, Faculty of Agriculture, Saga University, Saga, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Tsuyoshi Waku
- Laboratory for Genetic Code, Department of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, Japan
| | - Akira Kobayashi
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto, 610-0394, Japan.
- Laboratory for Genetic Code, Department of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, Japan.
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4
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Kurusu R, Fujimoto Y, Morishita H, Noshiro D, Takada S, Yamano K, Tanaka H, Arai R, Kageyama S, Funakoshi T, Komatsu-Hirota S, Taka H, Kazuno S, Miura Y, Koike M, Wakai T, Waguri S, Noda NN, Komatsu M. Integrated proteomics identifies p62-dependent selective autophagy of the supramolecular vault complex. Dev Cell 2023:S1534-5807(23)00191-0. [PMID: 37192622 DOI: 10.1016/j.devcel.2023.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/13/2023] [Accepted: 04/25/2023] [Indexed: 05/18/2023]
Abstract
In addition to membranous organelles, autophagy selectively degrades biomolecular condensates, in particular p62/SQSTM1 bodies, to prevent diseases including cancer. Evidence is growing regarding the mechanisms by which autophagy degrades p62 bodies, but little is known about their constituents. Here, we established a fluorescence-activated-particle-sorting-based purification method for p62 bodies using human cell lines and determined their constituents by mass spectrometry. Combined with mass spectrometry of selective-autophagy-defective mouse tissues, we identified vault, a large supramolecular complex, as a cargo within p62 bodies. Mechanistically, major vault protein directly interacts with NBR1, a p62-interacting protein, to recruit vault into p62 bodies for efficient degradation. This process, named vault-phagy, regulates homeostatic vault levels in vivo, and its impairment may be associated with non-alcoholic-steatohepatitis-derived hepatocellular carcinoma. Our study provides an approach to identifying phase-separation-mediated selective autophagy cargoes, expanding our understanding of the role of phase separation in proteostasis.
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Affiliation(s)
- Reo Kurusu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Yuki Fujimoto
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Hideaki Morishita
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan.
| | - Daisuke Noshiro
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Shuhei Takada
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Koji Yamano
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hideaki Tanaka
- Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ritsuko Arai
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukushima 960-1295, Japan
| | - Shun Kageyama
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Tomoko Funakoshi
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Satoko Komatsu-Hirota
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Hikari Taka
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Saiko Kazuno
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Yoshiki Miura
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Masato Koike
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata City, Niigata 951-8510, Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukushima 960-1295, Japan
| | - Nobuo N Noda
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan.
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5
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Nam J, Gwon Y. Neuronal biomolecular condensates and their implications in neurodegenerative diseases. Front Aging Neurosci 2023; 15:1145420. [PMID: 37065458 PMCID: PMC10102667 DOI: 10.3389/fnagi.2023.1145420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/01/2023] [Indexed: 04/03/2023] Open
Abstract
Biomolecular condensates are subcellular organizations where functionally related proteins and nucleic acids are assembled through liquid-liquid phase separation, allowing them to develop on a larger scale without a membrane. However, biomolecular condensates are highly vulnerable to disruptions from genetic risks and various factors inside and outside the cell and are strongly implicated in the pathogenesis of many neurodegenerative diseases. In addition to the classical view of the nucleation-polymerization process that triggers the protein aggregation from the misfolded seed, the pathologic transition of biomolecular condensates can also promote the aggregation of proteins found in the deposits of neurodegenerative diseases. Furthermore, it has been suggested that several protein or protein-RNA complexes located in the synapse and along the neuronal process are neuron-specific condensates displaying liquid-like properties. As their compositional and functional modifications play a crucial role in the context of neurodegeneration, further research is needed to fully understand the role of neuronal biomolecular condensates. In this article, we will discuss recent findings that explore the pivotal role of biomolecular condensates in the development of neuronal defects and neurodegeneration.
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Affiliation(s)
| | - Youngdae Gwon
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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6
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Xu M, Yang A, Xia J, Jiang J, Liu CF, Ye Z, Ma J, Yang S. Protein glycosylation in urine as a biomarker of diseases. Transl Res 2023; 253:95-107. [PMID: 35952983 DOI: 10.1016/j.trsl.2022.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023]
Abstract
Human body fluids have become an indispensable resource for clinical research, diagnosis and prognosis. Urine is widely used to discover disease-specific glycoprotein biomarkers because of its recurrently non-invasive collection and disease-indicating properties. While urine is an unstable fluid in that its composition changes with ingested nutrients and further as it is excreted through micturition, urinary proteins are more stable and their abnormal glycosylation is associated with diseases. It is known that aberrant glycosylation can define tumor malignancy and indicate disease initiation and progression. However, a thorough and translational survey of urinary glycosylation in diseases has not been performed. In this article, we evaluate the clinical applications of urine, introduce methods for urine glycosylation analysis, and discuss urine glycoprotein biomarkers. We emphasize the importance of mining urinary glycoproteins and searching for disease-specific glycosylation in various diseases (including cancer, neurodegenerative diseases, diabetes, and viral infections). With advances in mass spectrometry-based glycomics/glycoproteomics/glycopeptidomics, characterization of disease-specific glycosylation will optimistically lead to the discovery of disease-related urinary biomarkers with better sensitivity and specificity in the near future.
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Affiliation(s)
- Mingming Xu
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Arthur Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Jun Xia
- Clinical Laboratory Center, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
| | - Junhong Jiang
- Department of Pulmonary and Critical Care Medicine, Dushu Lake Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chun-Feng Liu
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhenyu Ye
- Department of General Surgery, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, District of Columbia.
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China.
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7
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Gallagher ER, Holzbaur ELF. The selective autophagy adaptor p62/SQSTM1 forms phase condensates regulated by HSP27 that facilitate the clearance of damaged lysosomes via lysophagy. Cell Rep 2023; 42:112037. [PMID: 36701233 PMCID: PMC10366342 DOI: 10.1016/j.celrep.2023.112037] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 12/16/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
In response to lysosomal damage, cells engage several quality-control mechanisms, including the selective isolation and degradation of damaged lysosomes by lysophagy. Here, we report that the selective autophagy adaptor SQSTM1/p62 is recruited to damaged lysosomes in both HeLa cells and neurons and is required for lysophagic flux. The Phox and Bem1p (PB1) domain of p62 mediates oligomerization and is specifically required for lysophagy. Consistent with this observation, we find that p62 forms condensates on damaged lysosomes. These condensates are precisely tuned by the small heat shock protein HSP27, which is phosphorylated in response to lysosomal injury and maintains the liquidity of p62 condensates, facilitating autophagosome formation. Mutations in p62 have been identified in patients with amyotrophic lateral sclerosis (ALS); ALS-associated mutations in p62 impair lysophagy, suggesting that deficits in this pathway may contribute to neurodegeneration. Thus, p62 condensates regulated by HSP27 promote lysophagy by forming platforms for autophagosome biogenesis at damaged lysosomes.
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Affiliation(s)
- Elizabeth R Gallagher
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Erika L F Holzbaur
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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