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Rondón Ortiz AN, Zhang L, Ash PEA, Basu A, Puri S, van der Spek SJF, Wang Z, Dorrian L, Emili A, Wolozin B. Proximity labeling reveals dynamic changes in the SQSTM1 protein network. J Biol Chem 2024:107621. [PMID: 39098523 DOI: 10.1016/j.jbc.2024.107621] [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: 01/24/2024] [Revised: 06/30/2024] [Accepted: 07/19/2024] [Indexed: 08/06/2024] Open
Abstract
Sequestosome1 (SQSTM1) is an autophagy receptor that mediates degradation of intracellular cargo, including protein aggregates, through multiple protein interactions. These interactions form the SQSTM1 protein network, and these interactions are mediated by SQSTM1 functional interaction domains, which include LIR, PB1, UBA and KIR. Technological advances in cell biology continue to expand our knowledge of the SQSTM1 protein network and of the relationship of the actions of the SQSTM1 protein network in cellular physiology and disease states. Here we apply proximity profile labeling to investigate the SQSTM1 protein interaction network by fusing TurboID with the human protein SQSTM1 (TurboID::SQSTM1). This chimeric protein displayed well-established SQSTM1 features including production of SQSTM1 intracellular bodies, binding to known SQSTM1 interacting partners, and capture of novel SQSTM1 protein interactors. Strikingly, aggregated tau protein altered the protein interaction network of SQSTM1 to include many stress-associated proteins. We demonstrate the importance of the PB1 and/or UBA domains for binding network members, including the K18 domain of tau. Overall, our work reveals the dynamic landscape of the SQSTM1 protein network and offers a resource to study SQSTM1 function in cellular physiology and disease state.
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Affiliation(s)
- Alejandro N Rondón Ortiz
- Department of Biology, Boston University, Boston, MA 02215, USA; Center for Network Systems Biology, Boston University, Boston, MA 02215, USA; Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Lushuang Zhang
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Peter E A Ash
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Avik Basu
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA; Department of Biochemistry, Boston University, Boston, MA 02115, USA; Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Sambhavi Puri
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | | | - Zihan Wang
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Luke Dorrian
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA; Department of Biochemistry, Boston University, Boston, MA 02115, USA; Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, OR 97239, USA.
| | - Benjamin Wolozin
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA; Center for Systems Neuroscience, Boston University, Boston, MA 02115, USA; Center for Neurophotonics, Boston University, Boston, MA 02115, USA; Department of Neurology, Boston University, Boston, MA 02115, USA; Department of Pharmacology, Physiology and Biophysics.
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Ortiz ANR, Zhang L, Ash PE, Basu A, Puri S, van der Spek SJ, Wang Z, Dorrian L, Emili A, Wolozin B. Proximity labeling reveals dynamic changes in the SQSTM1 protein network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571324. [PMID: 38168279 PMCID: PMC10760047 DOI: 10.1101/2023.12.12.571324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Sequestosome1 (SQSTM1) is an autophagy receptor that mediates degradation of intracellular cargo, including protein aggregates, through multiple protein interactions. These interactions form the SQSTM1 protein network, and these interactions are mediated by SQSTM1 functional interaction domains, which include LIR, PB1, UBA and KIR. Technological advances in cell biology continue to expand our knowledge of the SQSTM1 protein network and of the relationship of the actions of the SQSTM1 protein network in cellular physiology and disease states. Here we apply proximity profile labeling to investigate the SQSTM1 protein interaction network by fusing TurboID with the human protein SQSTM1 (TurboID::SQSTM1). This chimeric protein displayed well-established SQSTM1 features including production of SQSTM1 intracellular bodies, binding to known SQSTM1 interacting partners, and capture of novel SQSTM1 protein interactors. Strikingly, aggregated tau protein altered the protein interaction network of SQSTM1 to include many stress-associated proteins. We demonstrate the importance of the PB1 and/or UBA domains for binding network members, including the K18 domain of tau. Overall, our work reveals the dynamic landscape of the SQSTM1 protein network and offers a resource to study SQSTM1 function in cellular physiology and disease state.
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Affiliation(s)
- Alejandro N. Rondón Ortiz
- Department of Biology, Boston University, Boston, MA 02215, USA
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Lushuang Zhang
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Peter E.A. Ash
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Avik Basu
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biochemistry, Boston University, Boston, MA 02115, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Sambhavi Puri
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | | | - Zihan Wang
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Luke Dorrian
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biochemistry, Boston University, Boston, MA 02115, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Benjamin Wolozin
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
- Center for Systems Neuroscience, Boston University, Boston, MA 02115, USA
- Center for Neurophotonics, Boston University, Boston, MA 02115, USA
- Department of Neurology, Boston University, Boston, MA 02115, USA
- Department of Pharmacology, Physiology and Biophysics
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Văcăraş V, Vulturar R, Chiş A, Damian L. Inclusion body myositis, viral infections, and TDP-43: a narrative review. Clin Exp Med 2024; 24:91. [PMID: 38693436 PMCID: PMC11062973 DOI: 10.1007/s10238-024-01353-9] [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: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024]
Abstract
The ubiquitous RNA-processing molecule TDP-43 is involved in neuromuscular diseases such as inclusion body myositis, a late-onset acquired inflammatory myopathy. TDP-43 solubility and function are disrupted in certain viral infections. Certain viruses, high viremia, co-infections, reactivation of latent viruses, and post-acute expansion of cytotoxic T cells may all contribute to inclusion body myositis, mainly in an age-shaped immune landscape. The virally induced senescent, interferon gamma-producing cytotoxic CD8+ T cells with increased inflammatory, and cytotoxic features are involved in the occurrence of inclusion body myositis in most such cases, in a genetically predisposed host. We discuss the putative mechanisms linking inclusion body myositis, TDP-43, and viral infections untangling the links between viruses, interferon, and neuromuscular degeneration could shed a light on the pathogenesis of the inclusion body myositis and other TDP-43-related neuromuscular diseases, with possible therapeutic implications.
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Affiliation(s)
- Vitalie Văcăraş
- Department of Neurosciences, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, 43, Victor Babeş St, 400012, Cluj-Napoca, Romania
- Neurology Department of Cluj, County Emergency Hospital, 3-5, Clinicilor St, 400347, Cluj-Napoca, Romania
| | - Romana Vulturar
- Department of Molecular Sciences, "Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, 6, Pasteur St, 400349, Cluj-Napoca, Romania
- Cognitive Neuroscience Laboratory, University Babeş-Bolyai, 30, Fântânele St, 400294, Cluj-Napoca, Romania
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St, 400497, Cluj-Napoca, Romania
| | - Adina Chiş
- Department of Molecular Sciences, "Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, 6, Pasteur St, 400349, Cluj-Napoca, Romania.
- Cognitive Neuroscience Laboratory, University Babeş-Bolyai, 30, Fântânele St, 400294, Cluj-Napoca, Romania.
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St, 400497, Cluj-Napoca, Romania.
| | - Laura Damian
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St, 400497, Cluj-Napoca, Romania
- Department of Rheumatology, Centre for Rare Autoimmune and Autoinflammatory Diseases, Emergency, Clinical County Hospital Cluj, 2-4, Clinicilor St, 400006, Cluj-Napoca, Romania
- CMI Reumatologie Dr. Damian, 6-8, Petru Maior St, 400002, Cluj-Napoca, Romania
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