1
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Wang J, Zhu H, Tian R, Zhang Q, Zhang H, Hu J, Wang S. Physiological and pathological effects of phase separation in the central nervous system. J Mol Med (Berl) 2024; 102:599-615. [PMID: 38441598 PMCID: PMC11055734 DOI: 10.1007/s00109-024-02435-7] [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: 05/01/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 04/28/2024]
Abstract
Phase separation, also known as biomolecule condensate, participates in physiological processes such as transcriptional regulation, signal transduction, gene expression, and DNA damage repair by creating a membrane-free compartment. Phase separation is primarily caused by the interaction of multivalent non-covalent bonds between proteins and/or nucleic acids. The strength of molecular multivalent interaction can be modified by component concentration, the potential of hydrogen, posttranslational modification, and other factors. Notably, phase separation occurs frequently in the cytoplasm of mitochondria, the nucleus, and synapses. Phase separation in vivo is dynamic or stable in the normal physiological state, while abnormal phase separation will lead to the formation of biomolecule condensates, speeding up the disease progression. To provide candidate suggestions for the clinical treatment of nervous system diseases, this review, based on existing studies, carefully and systematically represents the physiological roles of phase separation in the central nervous system and its pathological mechanism in neurodegenerative diseases.
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Affiliation(s)
- Jiaxin Wang
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, People's Republic of China
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Hongrui Zhu
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, People's Republic of China.
- Core Facility Center, The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Hefei, China.
| | - Ruijia Tian
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Qian Zhang
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Haoliang Zhang
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Jin Hu
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Sheng Wang
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, People's Republic of China.
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2
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Kim SH, Nichols KD, Anderson EN, Liu Y, Ramesh N, Jia W, Kuerbis CJ, Scalf M, Smith LM, Pandey UB, Tibbetts RS. Axon guidance genes modulate neurotoxicity of ALS-associated UBQLN2. eLife 2023; 12:e84382. [PMID: 37039476 PMCID: PMC10147378 DOI: 10.7554/elife.84382] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
Mutations in the ubiquitin (Ub) chaperone Ubiquilin 2 (UBQLN2) cause X-linked forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) through unknown mechanisms. Here, we show that aggregation-prone, ALS-associated mutants of UBQLN2 (UBQLN2ALS) trigger heat stress-dependent neurodegeneration in Drosophila. A genetic modifier screen implicated endolysosomal and axon guidance genes, including the netrin receptor, Unc-5, as key modulators of UBQLN2 toxicity. Reduced gene dosage of Unc-5 or its coreceptor Dcc/frazzled diminished neurodegenerative phenotypes, including motor dysfunction, neuromuscular junction defects, and shortened lifespan, in flies expressing UBQLN2ALS alleles. Induced pluripotent stem cells (iPSCs) harboring UBQLN2ALS knockin mutations exhibited lysosomal defects while inducible motor neurons (iMNs) expressing UBQLN2ALS alleles exhibited cytosolic UBQLN2 inclusions, reduced neurite complexity, and growth cone defects that were partially reversed by silencing of UNC5B and DCC. The combined findings suggest that altered growth cone dynamics are a conserved pathomechanism in UBQLN2-associated ALS/FTD.
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Affiliation(s)
- Sang Hwa Kim
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Kye D Nichols
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Yining Liu
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Nandini Ramesh
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Weiyan Jia
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Connor J Kuerbis
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Randal S Tibbetts
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
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3
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Black HH, Hanson JL, Roberts JE, Leslie SN, Campodonico W, Ebmeier CC, Holling GA, Tay JW, Matthews AM, Ung E, Lau CI, Whiteley AM. UBQLN2 restrains the domesticated retrotransposon PEG10 to maintain neuronal health in ALS. eLife 2023; 12:e79452. [PMID: 36951542 PMCID: PMC10076021 DOI: 10.7554/elife.79452] [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: 04/13/2022] [Accepted: 03/15/2023] [Indexed: 03/24/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive motor neuron dysfunction and loss. A portion of ALS cases are caused by mutation of the proteasome shuttle factor Ubiquilin 2 (UBQLN2), but the molecular pathway leading from UBQLN2 dysfunction to disease remains unclear. Here, we demonstrate that UBQLN2 regulates the domesticated gag-pol retrotransposon 'paternally expressed gene 10 (PEG10)' in human cells and tissues. In cells, the PEG10 gag-pol protein cleaves itself in a mechanism reminiscent of retrotransposon self-processing to generate a liberated 'nucleocapsid' fragment, which uniquely localizes to the nucleus and changes the expression of genes involved in axon remodeling. In spinal cord tissue from ALS patients, PEG10 gag-pol is elevated compared to healthy controls. These findings implicate the retrotransposon-like activity of PEG10 as a contributing mechanism in ALS through the regulation of gene expression, and restraint of PEG10 as a primary function of UBQLN2.
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Affiliation(s)
- Holly H Black
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Jessica L Hanson
- Institute for Behavioral Genetics, University of Colorado BoulderBoulderUnited States
| | - Julia E Roberts
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Shannon N Leslie
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Will Campodonico
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | | | - G Aaron Holling
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Jian Wei Tay
- Biofrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Autumn M Matthews
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Elizabeth Ung
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Cristina I Lau
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
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4
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Sandoval-Pistorius SS, Gerson JE, Liggans N, Ryou JH, Oak K, Li X, Negron-Rios KY, Fischer S, Barsh H, Crowley EV, Skinner ME, Sharkey LM, Barmada SJ, Paulson HL. Ubiquilin-2 regulates pathological alpha-synuclein. Sci Rep 2023; 13:293. [PMID: 36609661 PMCID: PMC9823102 DOI: 10.1038/s41598-022-26899-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/21/2022] [Indexed: 01/08/2023] Open
Abstract
The key protein implicated in Parkinson's disease and other synucleinopathies is α-synuclein, and a post-translationally modified form of the protein, phosphorylated at serine 129 (pS129), is a principal component in Lewy bodies, a pathological hallmark of PD. While altered proteostasis has been implicated in the etiology of Parkinson's disease, we still have a limited understanding of how α-synuclein is regulated in the nervous system. The protein quality control protein Ubiquilin-2 (UBQLN2) is known to accumulate in synucleinopathies, but whether it directly regulates α-synuclein is unknown. Using cellular and mouse models, we find that UBQLN2 decreases levels of α-synuclein, including the pS129 phosphorylated isoform. Pharmacological inhibition of the proteasome revealed that, while α-synuclein may be cleared by parallel and redundant quality control pathways, UBQLN2 preferentially targets pS129 for proteasomal degradation. Moreover, in brain tissue from human PD and transgenic mice expressing pathogenic α-synuclein (A53T), native UBQLN2 becomes more insoluble. Collectively, our studies support a role for UBQLN2 in directly regulating pathological forms of α-synuclein and indicate that UBQLN2 dysregulation in disease may contribute to α-synuclein-mediated toxicity.
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Affiliation(s)
- Stephanie S. Sandoval-Pistorius
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA ,grid.214458.e0000000086837370Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109 USA
| | - Julia E. Gerson
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA
| | - Nyjerus Liggans
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA
| | - Jaimie H. Ryou
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA
| | - Kulin Oak
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA
| | - Xingli Li
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA
| | - Keyshla Y. Negron-Rios
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA
| | - Svetlana Fischer
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA
| | - Henry Barsh
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA
| | - Emily V. Crowley
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA
| | - Mary E. Skinner
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA
| | - Lisa M. Sharkey
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA
| | - Sami J. Barmada
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA
| | - Henry L. Paulson
- grid.214458.e0000000086837370Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 USA
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5
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Protein interactions: anything new? Essays Biochem 2022; 66:821-830. [PMID: 36416856 PMCID: PMC9760424 DOI: 10.1042/ebc20220044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022]
Abstract
How do proteins interact in the cellular environment? Which interactions stabilize liquid-liquid phase separated condensates? Are the concepts, which have been developed for specific protein complexes also applicable to higher-order assemblies? Recent discoveries prompt for a universal framework for protein interactions, which can be applied across the scales of protein communities. Here, we discuss how our views on protein interactions have evolved from rigid structures to conformational ensembles of proteins and discuss the open problems, in particular related to biomolecular condensates. Protein interactions have evolved to follow changes in the cellular environment, which manifests in multiple modes of interactions between the same partners. Such cellular context-dependence requires multiplicity of binding modes (MBM) by sampling multiple minima of the interaction energy landscape. We demonstrate that the energy landscape framework of protein folding can be applied to explain this phenomenon, opening a perspective toward a physics-based, universal model for cellular protein behaviors.
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6
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Lin BC, Higgins NR, Phung TH, Monteiro MJ. UBQLN proteins in health and disease with a focus on UBQLN2 in ALS/FTD. FEBS J 2022; 289:6132-6153. [PMID: 34273246 PMCID: PMC8761781 DOI: 10.1111/febs.16129] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/08/2021] [Accepted: 07/16/2021] [Indexed: 01/12/2023]
Abstract
Ubiquilin (UBQLN) proteins are a dynamic and versatile family of proteins found in all eukaryotes that function in the regulation of proteostasis. Besides their canonical function as shuttle factors in delivering misfolded proteins to the proteasome and autophagy systems for degradation, there is emerging evidence that UBQLN proteins play broader roles in proteostasis. New information suggests the proteins function as chaperones in protein folding, protecting proteins prior to membrane insertion, and as guardians for mitochondrial protein import. In this review, we describe the evidence for these different roles, highlighting how different domains of the proteins impart these functions. We also describe how changes in the structure and phase separation properties of UBQLNs may regulate their activity and function. Finally, we discuss the pathogenic mechanisms by which mutations in UBQLN2 cause amyotrophic lateral sclerosis and frontotemporal dementia. We describe the animal model systems made for different UBQLN2 mutations and how lessons learnt from these systems provide fundamental insight into the molecular mechanisms by which UBQLN2 mutations drive disease pathogenesis through disturbances in proteostasis.
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Affiliation(s)
- Brian C. Lin
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA,Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicole R. Higgins
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA,Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Trong H. Phung
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mervyn J. Monteiro
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA,Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA,Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
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7
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Dao TP, Yang Y, Presti MF, Cosgrove MS, Hopkins JB, Ma W, Loh SN, Castañeda CA. Mechanistic insights into enhancement or inhibition of phase separation by different polyubiquitin chains. EMBO Rep 2022; 23:e55056. [PMID: 35762418 PMCID: PMC9346500 DOI: 10.15252/embr.202255056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 12/03/2022] Open
Abstract
Ubiquitin‐binding shuttle UBQLN2 mediates crosstalk between proteasomal degradation and autophagy, likely via interactions with K48‐ and K63‐linked polyubiquitin chains, respectively. UBQLN2 comprises self‐associating regions that drive its homotypic liquid–liquid phase separation (LLPS). Specific interactions between one of these regions and ubiquitin inhibit UBQLN2 LLPS. Here, we show that, unlike ubiquitin, the effects of multivalent polyubiquitin chains on UBQLN2 LLPS are highly dependent on chain types. Specifically, K11‐Ub4 and K48‐Ub4 chains generally inhibit UBQLN2 LLPS, whereas K63‐Ub4, M1‐Ub4 chains, and a designed tetrameric ubiquitin construct significantly enhance LLPS. We demonstrate that these opposing effects stem from differences in chain conformations but not in affinities between chains and UBQLN2. Chains with extended conformations and increased accessibility to the ubiquitin‐binding surface promote UBQLN2 LLPS by enabling a switch between homotypic to partially heterotypic LLPS that is driven by both UBQLN2 self‐interactions and interactions between multiple UBQLN2 units with each polyubiquitin chain. Our study provides mechanistic insights into how the structural and conformational properties of polyubiquitin chains contribute to heterotypic LLPS with ubiquitin‐binding shuttles and adaptors.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
| | - Yiran Yang
- Department of Chemistry Syracuse University Syracuse NY USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Weikang Ma
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Carlos A Castañeda
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
- Interdisciplinary Neuroscience Program Syracuse University Syracuse NY USA
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8
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Cozzi M, Ferrari V. Autophagy Dysfunction in ALS: from Transport to Protein Degradation. J Mol Neurosci 2022; 72:1456-1481. [PMID: 35708843 PMCID: PMC9293831 DOI: 10.1007/s12031-022-02029-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/17/2022] [Indexed: 01/18/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease affecting upper and lower motor neurons (MNs). Since the identification of the first ALS mutation in 1993, more than 40 genes have been associated with the disorder. The most frequent genetic causes of ALS are represented by mutated genes whose products challenge proteostasis, becoming unable to properly fold and consequently aggregating into inclusions that impose proteotoxic stress on affected cells. In this context, increasing evidence supports the central role played by autophagy dysfunctions in the pathogenesis of ALS. Indeed, in early stages of disease, high levels of proteins involved in autophagy are present in ALS MNs; but at the same time, with neurodegeneration progression, autophagy-mediated degradation decreases, often as a result of the accumulation of toxic protein aggregates in affected cells. Autophagy is a complex multistep pathway that has a central role in maintaining cellular homeostasis. Several proteins are involved in its tight regulation, and importantly a relevant fraction of ALS-related genes encodes products that directly take part in autophagy, further underlining the relevance of this key protein degradation system in disease onset and progression. In this review, we report the most relevant findings concerning ALS genes whose products are involved in the several steps of the autophagic pathway, from phagophore formation to autophagosome maturation and transport and finally to substrate degradation.
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Affiliation(s)
- Marta Cozzi
- Dipartimento Di Scienze Farmacologiche E Biomolecolari, Università Degli Studi Di Milano, 20133, Milan, Italy.
| | - Veronica Ferrari
- Dipartimento Di Scienze Farmacologiche E Biomolecolari, Università Degli Studi Di Milano, 20133, Milan, Italy.
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9
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Mohan HM, Trzeciakiewicz H, Pithadia A, Crowley EV, Pacitto R, Safren N, Trotter B, Zhang C, Zhou X, Zhang Y, Basrur V, Paulson HL, Sharkey LM. RTL8 promotes nuclear localization of UBQLN2 to subnuclear compartments associated with protein quality control. Cell Mol Life Sci 2022; 79:176. [PMID: 35247097 PMCID: PMC9376861 DOI: 10.1007/s00018-022-04170-z] [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: 04/19/2021] [Revised: 01/17/2022] [Accepted: 01/25/2022] [Indexed: 11/24/2022]
Abstract
The brain-expressed ubiquilins (UBQLNs) 1, 2 and 4 are a family of ubiquitin adaptor proteins that participate broadly in protein quality control (PQC) pathways, including the ubiquitin proteasome system (UPS). One family member, UBQLN2, has been implicated in numerous neurodegenerative diseases including ALS/FTD. UBQLN2 typically resides in the cytoplasm but in disease can translocate to the nucleus, as in Huntington's disease where it promotes the clearance of mutant Huntingtin. How UBQLN2 translocates to the nucleus and clears aberrant nuclear proteins, however, is not well understood. In a mass spectrometry screen to discover UBQLN2 interactors, we identified a family of small (13 kDa), highly homologous uncharacterized proteins, RTL8, and confirmed the interaction between UBQLN2 and RTL8 both in vitro using recombinant proteins and in vivo using mouse brain tissue. Under endogenous and overexpressed conditions, RTL8 localizes to nucleoli. When co-expressed with UBQLN2, RTL8 promotes nuclear translocation of UBQLN2. RTL8 also facilitates UBQLN2's nuclear translocation during heat shock. UBQLN2 and RTL8 colocalize within ubiquitin-enriched subnuclear structures containing PQC components. The robust effect of RTL8 on the nuclear translocation and subnuclear localization of UBQLN2 does not extend to the other brain-expressed ubiquilins, UBQLN1 and UBQLN4. Moreover, compared to UBQLN1 and UBQLN4, UBQLN2 preferentially stabilizes RTL8 levels in human cell lines and in mouse brain, supporting functional heterogeneity among UBQLNs. As a novel UBQLN2 interactor that recruits UBQLN2 to specific nuclear compartments, RTL8 may regulate UBQLN2 function in nuclear protein quality control.
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Affiliation(s)
- Harihar Milaganur Mohan
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA.,Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | | | - Amit Pithadia
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Emily V Crowley
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Regina Pacitto
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Nathaniel Safren
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA.,Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Bryce Trotter
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Xiaogen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Henry L Paulson
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA. .,Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109-2200, USA.
| | - Lisa M Sharkey
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA. .,Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109-2200, USA.
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10
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TDP-43 pathology: from noxious assembly to therapeutic removal. Prog Neurobiol 2022; 211:102229. [DOI: 10.1016/j.pneurobio.2022.102229] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/08/2021] [Accepted: 01/26/2022] [Indexed: 02/08/2023]
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11
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Vendruscolo M, Fuxreiter M. Sequence Determinants of the Aggregation of Proteins Within Condensates Generated by Liquid-liquid Phase Separation. J Mol Biol 2021; 434:167201. [PMID: 34391803 DOI: 10.1016/j.jmb.2021.167201] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/08/2021] [Accepted: 08/09/2021] [Indexed: 12/12/2022]
Abstract
The transition between the native and amyloid states of proteins can proceed via a deposition pathway via oligomeric intermediates or via a condensation pathway involving liquid droplet intermediates generated through liquid-liquid phase separation. While several computational methods are available to perform sequence-based predictions of the propensity of proteins to aggregate via the deposition pathway, much less is known about the physico-chemical principles that underlie aggregation within condensates. Here we investigate the sequence determinants of aggregation via the condensation pathway, and identify three relevant features: droplet-promoting propensity, aggregation-promoting propensity and multimodal interactions quantified by the binding mode entropy. By using this approach, we show that it is possible to predict aggregation-promoting mutations in droplet-forming proteins associated with amyotrophic lateral sclerosis (ALS). This analysis provides insights into the amino acid code for the conversion of proteins between liquid-like and solid-like condensates.
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Affiliation(s)
- Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, UK.
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Italy; Department of Biochemistry and Molecular Biology, University of Debrecen, Hungary.
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12
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Impaired 26S Proteasome Assembly Precedes Neuronal Loss in Mutant UBQLN2 Rats. Int J Mol Sci 2021; 22:ijms22094319. [PMID: 33919255 PMCID: PMC8122323 DOI: 10.3390/ijms22094319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Proteasomal dysfunction is known to be associated with amyotrophic lateral sclerosis and frontotemporal degeneration (ALS/FTD). Our previous reports have shown that a mutant form of ubiquilin-2 (UBQLN2) linked to ALS/FTD leads to neurodegeneration accompanied by accumulations of the proteasome subunit Rpt1 in transgenic rats, but the precise pathogenic mechanisms of how this mutation impairs the proteasome remains to be elucidated. Here, we reveal that this UBQLN2 mutation in rats disrupted the proteasome integrity prior to neurodegeneration, that it dissociated the 26S proteasome in vitro, and that its depletion did not affect 26S proteasome assembly. During both disease progression and in an age-dependent manner, we found that proteasome subunits were translocated to the nucleus, including both of the 20S core particles (PSMA1 and PSMB7) and the 19S regulatory particles (Rpt1 and Rpn1), suggesting that defective proteasome function may result from the proteasome-subunit mislocalization. Taken together, the present data demonstrate that impaired proteasome assembly is an early event in the pathogenesis of UBQLN2-associated neurodegeneration in mutant UBQLN2 rats.
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Whiteley AM, Prado MA, de Poot SAH, Paulo JA, Ashton M, Dominguez S, Weber M, Ngu H, Szpyt J, Jedrychowski MP, Easton A, Gygi SP, Kurz T, Monteiro MJ, Brown EJ, Finley D. Global proteomics of Ubqln2-based murine models of ALS. J Biol Chem 2020; 296:100153. [PMID: 33277362 PMCID: PMC7873701 DOI: 10.1074/jbc.ra120.015960] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/21/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022] Open
Abstract
Familial neurodegenerative diseases commonly involve mutations that result in either aberrant proteins or dysfunctional components of the proteolytic machinery that act on aberrant proteins. UBQLN2 is a ubiquitin receptor of the UBL/UBA family that binds the proteasome through its ubiquitin-like domain and is thought to deliver ubiquitinated proteins to proteasomes for degradation. UBQLN2 mutations result in familial amyotrophic lateral sclerosis (ALS)/frontotemporal dementia in humans through an unknown mechanism. Quantitative multiplexed proteomics was used to provide for the first time an unbiased and global analysis of the role of Ubqln2 in controlling the composition of the proteome. We studied several murine models of Ubqln2-linked ALS and also generated Ubqln2 null mutant mice. We identified impacts of Ubqln2 on diverse physiological pathways, most notably serotonergic signaling. Interestingly, we observed an upregulation of proteasome subunits, suggesting a compensatory response to diminished proteasome output. Among the specific proteins whose abundance is linked to UBQLN2 function, the strongest hits were the ubiquitin ligase TRIM32 and two retroelement-derived proteins, PEG10 and CXX1B. Cycloheximide chase studies using induced human neurons and HEK293 cells suggested that PEG10 and TRIM32 are direct clients. Although UBQLN2 directs the degradation of multiple proteins via the proteasome, it surprisingly conferred strong protection from degradation on the Gag-like protein CXX1B, which is expressed from the same family of retroelement genes as PEG10. In summary, this study charts the proteomic landscape of ALS-related Ubqln2 mutants and identifies candidate client proteins that are altered in vivo in disease models and whose degradation is promoted by UBQLN2.
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Affiliation(s)
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Marissa Ashton
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sara Dominguez
- Department of Neuroscience, Genentech Inc, South San Francisco, California, USA
| | - Martin Weber
- Department of Neuroscience, Genentech Inc, South San Francisco, California, USA
| | - Hai Ngu
- Department of Pathology, Genentech Inc, South San Francisco, California, USA
| | - John Szpyt
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark P Jedrychowski
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Amy Easton
- Department of Neuroscience, Genentech Inc, South San Francisco, California, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Thimo Kurz
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Mervyn J Monteiro
- Center for Biomedical Engineering and Technology, Department of Anatomy and Neurobiology, University of Maryland Medical School, Baltimore, Maryland, USA
| | - Eric J Brown
- Department of Immunology and Infectious Diseases, Genentech Inc, South San Francisco, California, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.
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14
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Johnston HE, Samant RS. Alternative systems for misfolded protein clearance: life beyond the proteasome. FEBS J 2020; 288:4464-4487. [PMID: 33135311 DOI: 10.1111/febs.15617] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/15/2020] [Accepted: 10/30/2020] [Indexed: 12/18/2022]
Abstract
Protein misfolding is a major driver of ageing-associated frailty and disease pathology. Although all cells possess multiple, well-characterised protein quality control systems to mitigate the toxicity of misfolded proteins, how they are integrated to maintain protein homeostasis ('proteostasis') in health-and how their disintegration contributes to disease-is still an exciting and fast-paced area of research. Under physiological conditions, the predominant route for misfolded protein clearance involves ubiquitylation and proteasome-mediated degradation. When the capacity of this route is overwhelmed-as happens during conditions of acute environmental stress, or chronic ageing-related decline-alternative routes for protein quality control are activated. In this review, we summarise our current understanding of how proteasome-targeted misfolded proteins are retrafficked to alternative protein quality control routes such as juxta-nuclear sequestration and selective autophagy when the ubiquitin-proteasome system is compromised. We also discuss the molecular determinants of these alternative protein quality control systems, attempt to clarify distinctions between various cytoplasmic spatial quality control inclusion bodies (e.g., Q-bodies, p62 bodies, JUNQ, aggresomes, and aggresome-like induced structures 'ALIS'), and speculate on emerging concepts in the field that we hope will spur future research-with the potential to benefit the rational development of healthy ageing strategies.
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Affiliation(s)
| | - Rahul S Samant
- Signalling Programme, The Babraham Institute, Cambridge, UK
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