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Dao TP, Rajendran A, Galagedera SKK, Haws W, Castañeda CA. Short disordered termini and proline-rich domain are major regulators of UBQLN1/2/4 phase separation. Biophys J 2024; 123:1449-1457. [PMID: 38041404 PMCID: PMC11163289 DOI: 10.1016/j.bpj.2023.11.3401] [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: 09/30/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/03/2023] Open
Abstract
Highly homologous ubiquitin-binding shuttle proteins UBQLN1, UBQLN2, and UBQLN4 differ in both their specific protein quality control functions and their propensities to localize to stress-induced condensates, cellular aggregates, and aggresomes. We previously showed that UBQLN2 phase separates in vitro, and that the phase separation propensities of UBQLN2 deletion constructs correlate with their ability to form condensates in cells. Here, we demonstrated that full-length UBQLN1, UBQLN2, and UBQLN4 exhibit distinct phase behaviors in vitro. Strikingly, UBQLN4 phase separates at a much lower saturation concentration than UBQLN1. However, neither UBQLN1 nor UBQLN4 phase separates with a strong temperature dependence, unlike UBQLN2. We determined that the temperature-dependent phase behavior of UBQLN2 stems from its unique proline-rich region, which is absent in the other UBQLNs. We found that the short N-terminal disordered regions of UBQLN1, UBQLN2, and UBQLN4 inhibit UBQLN phase separation via electrostatics interactions. Charge variants of the N-terminal regions exhibit altered phase behaviors. Consistent with the sensitivity of UBQLN phase separation to the composition of the N-terminal regions, epitope tags placed on the N-termini of the UBQLNs tune phase separation. Overall, our in vitro results have important implications for studies of UBQLNs in cells, including the identification of phase separation as a potential mechanism to distinguish the cellular roles of UBQLNs and the need to apply caution when using epitope tags to prevent experimental artifacts.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York
| | - Anitha Rajendran
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York
| | | | - William Haws
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York
| | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York; Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, New York; BioInspired Institute, Syracuse University, Syracuse, New York.
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2
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Huang TN, Shih YT, Yen TL, Hsueh YP. Vcp overexpression and leucine supplementation extend lifespan and ameliorate neuromuscular junction phenotypes of a SOD1G93A-ALS mouse model. Hum Mol Genet 2024; 33:935-944. [PMID: 38382647 PMCID: PMC11102594 DOI: 10.1093/hmg/ddae022] [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: 11/23/2023] [Revised: 01/12/2024] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
Many genes with distinct molecular functions have been linked to genetically heterogeneous amyotrophic lateral sclerosis (ALS), including SuperOxide Dismutase 1 (SOD1) and Valosin-Containing Protein (VCP). SOD1 converts superoxide to oxygen and hydrogen peroxide. VCP acts as a chaperon to regulate protein degradation and synthesis and various other cellular responses. Although the functions of these two genes differ, in the current report we show that overexpression of wild-type VCP in mice enhances lifespan and maintains the size of neuromuscular junctions (NMJs) of both male and female SOD1G93A mice, a well-known ALS mouse model. Although VCP exerts multiple functions, its regulation of ER formation and consequent protein synthesis has been shown to play the most important role in controlling dendritic spine formation and social and memory behaviors. Given that SOD1 mutation results in protein accumulation and aggregation, it may direct VCP to the protein degradation pathway, thereby impairing protein synthesis. Since we previously showed that the protein synthesis defects caused by Vcp deficiency can be improved by leucine supplementation, to confirm the role of the VCP-protein synthesis pathway in SOD1-linked ALS, we applied leucine supplementation to SOD1G93A mice and, similar to Vcp overexpression, we found that it extends SOD1G93A mouse lifespan. In addition, the phenotypes of reduced muscle strength and fewer NMJs of SOD1G93A mice are also improved by leucine supplementation. These results support the existence of crosstalk between SOD1 and VCP and suggest a critical role for protein synthesis in ASL. Our study also implies a potential therapeutic treatment for ALS.
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Affiliation(s)
- Tzyy-Nan Huang
- Institute of Molecular Biology, Academia Sinica, 128 Sec 2, Academia Rd, Taipei, 11529, Taiwan, ROC
| | - Yu-Tzu Shih
- Institute of Molecular Biology, Academia Sinica, 128 Sec 2, Academia Rd, Taipei, 11529, Taiwan, ROC
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Tzu-Li Yen
- Institute of Molecular Biology, Academia Sinica, 128 Sec 2, Academia Rd, Taipei, 11529, Taiwan, ROC
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, 128 Sec 2, Academia Rd, Taipei, 11529, Taiwan, ROC
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3
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Shang Z, Zhang S, Wang J, Zhou L, Zhang X, Billadeau DD, Yang P, Zhang L, Zhou F, Bai P, Jia D. TRIM25 predominately associates with anti-viral stress granules. Nat Commun 2024; 15:4127. [PMID: 38750080 PMCID: PMC11096359 DOI: 10.1038/s41467-024-48596-4] [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: 07/02/2023] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Stress granules (SGs) are induced by various environmental stressors, resulting in their compositional and functional heterogeneity. SGs play a crucial role in the antiviral process, owing to their potent translational repressive effects and ability to trigger signal transduction; however, it is poorly understood how these antiviral SGs differ from SGs induced by other environmental stressors. Here we identify that TRIM25, a known driver of the ubiquitination-dependent antiviral innate immune response, is a potent and critical marker of the antiviral SGs. TRIM25 undergoes liquid-liquid phase separation (LLPS) and co-condenses with the SG core protein G3BP1 in a dsRNA-dependent manner. The co-condensation of TRIM25 and G3BP1 results in a significant enhancement of TRIM25's ubiquitination activity towards multiple antiviral proteins, which are mainly located in SGs. This co-condensation is critical in activating the RIG-I signaling pathway, thus restraining RNA virus infection. Our studies provide a conceptual framework for better understanding the heterogeneity of stress granule components and their response to distinct environmental stressors.
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Affiliation(s)
- Zehua Shang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Sitao Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Jinrui Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Lili Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215000, China
| | - Xinyue Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Daniel D Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Peiguo Yang
- School of Life Sciences, Westlake University, Hangzhou, 310024, 310030, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 100850, Beijing, China
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215000, China
| | - Peng Bai
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China.
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Fakim H, Vande Velde C. The implications of physiological biomolecular condensates in amyotrophic lateral sclerosis. Semin Cell Dev Biol 2024; 156:176-189. [PMID: 37268555 DOI: 10.1016/j.semcdb.2023.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023]
Abstract
In recent years, there has been an emphasis on the role of phase-separated biomolecular condensates, especially stress granules, in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). This is largely due to several ALS-associated mutations occurring in genes involved in stress granule assembly and observations that pathological inclusions detected in ALS patient neurons contain stress granule proteins, including the ALS-linked proteins TDP-43 and FUS. However, protein components of stress granules are also found in numerous other phase-separated biomolecular condensates under physiological conditions which are inadequately discussed in the context of ALS. In this review, we look beyond stress granules and describe the roles of TDP-43 and FUS in physiological condensates occurring in the nucleus and neurites, such as the nucleolus, Cajal bodies, paraspeckles and neuronal RNA transport granules. We also discuss the consequences of ALS-linked mutations in TDP-43 and FUS on their ability to phase separate into these stress-independent biomolecular condensates and perform their respective functions. Importantly, biomolecular condensates sequester multiple overlapping protein and RNA components, and their dysregulation could contribute to the observed pleiotropic effects of both sporadic and familial ALS on RNA metabolism.
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Affiliation(s)
- Hana Fakim
- Department of Neurosciences, Université de Montréal, and CHUM Research Center, Montréal, QC, Canada
| | - Christine Vande Velde
- Department of Neurosciences, Université de Montréal, and CHUM Research Center, Montréal, QC, Canada.
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Jagaraj CJ, Shadfar S, Kashani SA, Saravanabavan S, Farzana F, Atkin JD. Molecular hallmarks of ageing in amyotrophic lateral sclerosis. Cell Mol Life Sci 2024; 81:111. [PMID: 38430277 PMCID: PMC10908642 DOI: 10.1007/s00018-024-05164-9] [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: 12/05/2023] [Revised: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, severely debilitating and rapidly progressing disorder affecting motor neurons in the brain, brainstem, and spinal cord. Unfortunately, there are few effective treatments, thus there remains a critical need to find novel interventions that can mitigate against its effects. Whilst the aetiology of ALS remains unclear, ageing is the major risk factor. Ageing is a slowly progressive process marked by functional decline of an organism over its lifespan. However, it remains unclear how ageing promotes the risk of ALS. At the molecular and cellular level there are specific hallmarks characteristic of normal ageing. These hallmarks are highly inter-related and overlap significantly with each other. Moreover, whilst ageing is a normal process, there are striking similarities at the molecular level between these factors and neurodegeneration in ALS. Nine ageing hallmarks were originally proposed: genomic instability, loss of telomeres, senescence, epigenetic modifications, dysregulated nutrient sensing, loss of proteostasis, mitochondrial dysfunction, stem cell exhaustion, and altered inter-cellular communication. However, these were recently (2023) expanded to include dysregulation of autophagy, inflammation and dysbiosis. Hence, given the latest updates to these hallmarks, and their close association to disease processes in ALS, a new examination of their relationship to pathophysiology is warranted. In this review, we describe possible mechanisms by which normal ageing impacts on neurodegenerative mechanisms implicated in ALS, and new therapeutic interventions that may arise from this.
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Affiliation(s)
- Cyril Jones Jagaraj
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sina Shadfar
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sara Assar Kashani
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sayanthooran Saravanabavan
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Fabiha Farzana
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Julie D Atkin
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia.
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6
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Dao TP, Rajendran A, Galagedera SKK, Haws W, Castañeda CA. Short N-terminal disordered regions and the proline-rich domain are major regulators of phase transitions for full-length UBQLN1, UBQLN2 and UBQLN4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559790. [PMID: 37808720 PMCID: PMC10557701 DOI: 10.1101/2023.09.27.559790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Highly homologous ubiquitin-binding shuttle proteins UBQLN1, UBQLN2 and UBQLN4 differ in both their specific protein quality control functions and their propensities to localize to stress-induced condensates, cellular aggregates and aggresomes. We previously showed that UBQLN2 phase separates in vitro, and that the phase separation propensities of UBQLN2 deletion constructs correlate with their ability to form condensates in cells. Here, we demonstrated that full-length UBQLN1, UBQLN2 and UBQLN4 exhibit distinct phase behaviors in vitro. Strikingly, UBQLN4 phase separates at a much lower saturation concentration than UBQLN1. However, neither UBQLN1 nor UBQLN4 phase separates with a strong temperature dependence, unlike UBQLN2. We determined that the temperature-dependent phase behavior of UBQLN2 stems from its unique proline-rich (Pxx) region, which is absent in the other UBQLNs. We found that the short N-terminal disordered regions of UBQLN1, UBQLN2 and UBQLN4 inhibit UBQLN phase separation via electrostatics interactions. Charge variants of the N-terminal regions exhibit altered phase behaviors. Consistent with the sensitivity of UBQLN phase separation to the composition of the N-terminal regions, epitope tags placed on the N-termini of the UBQLNs tune phase separation. Overall, our in vitro results have important implications for studies of UBQLNs in cells, including the identification of phase separation as a potential mechanism to distinguish the cellular roles of UBQLNs, and the need to apply caution when using epitope tags to prevent experimental artifacts.
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Affiliation(s)
- Thuy P. Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Anitha Rajendran
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | | | - William Haws
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Carlos A. Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
- Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244, USA
- BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
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7
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Ma Y, Farny NG. Connecting the Dots: Neuronal Senescence, Stress Granules, and Neurodegeneration. Gene 2023; 871:147437. [PMID: 37084987 DOI: 10.1016/j.gene.2023.147437] [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: 02/03/2023] [Revised: 04/09/2023] [Accepted: 04/14/2023] [Indexed: 04/23/2023]
Abstract
Cellular senescence increases with aging. While senescence is associated with an exit of the cell cycle, there is ample evidence that post-mitotic cells including neurons can undergo senescence as the brain ages, and that senescence likely contributes significantly to the progression of neurodegenerative diseases (ND) such as Alzheimer's Disease (AD) and Amyotrophic Lateral Sclerosis (ALS). Stress granules (SGs) are stress-induced cytoplasmic biomolecular condensates of RNA and proteins, which have been linked to the development of AD and ALS. The SG seeding hypothesis of NDs proposes that chronic stress in aging neurons results in static SGs that progress into pathological aggregates Alterations in SG dynamics have also been linked to senescence, though studies that link SGs and senescence in the context of NDs and the aging brain have not yet been performed. In this Review, we summarize the literature on senescence, and explore the contribution of senescence to the aging brain. We describe senescence phenotypes in aging neurons and glia, and their links to neuroinflammation and the development of AD and ALS. We further examine the relationships of SGs to senescence and to ND. We propose a new hypothesis that neuronal senescence may contribute to the mechanism of SG seeding in ND by altering SG dynamics in aged cells, thereby providing additional aggregation opportunities within aged neurons.
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Affiliation(s)
- Yizhe Ma
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Natalie G Farny
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA.
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