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Valentino IM, Llivicota-Guaman JG, Dao TP, Mulvey EO, Lehman AM, Galagedera SKK, Mallon EL, Castañeda CA, Kraut DA. Phase separation of polyubiquitinated proteins in UBQLN2 condensates controls substrate fate. Proc Natl Acad Sci U S A 2024; 121:e2405964121. [PMID: 39121161 DOI: 10.1073/pnas.2405964121] [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: 03/22/2024] [Accepted: 06/26/2024] [Indexed: 08/11/2024] Open
Abstract
Ubiquitination is one of the most common posttranslational modifications in eukaryotic cells. Depending on the architecture of polyubiquitin chains, substrate proteins can meet different cellular fates, but our understanding of how chain linkage controls protein fate remains limited. UBL-UBA shuttle proteins, such as UBQLN2, bind to ubiquitinated proteins and to the proteasome or other protein quality control machinery elements and play a role in substrate fate determination. Under physiological conditions, UBQLN2 forms biomolecular condensates through phase separation, a physicochemical phenomenon in which multivalent interactions drive the formation of a macromolecule-rich dense phase. Ubiquitin and polyubiquitin chains modulate UBQLN2's phase separation in a linkage-dependent manner, suggesting a possible link to substrate fate determination, but polyubiquitinated substrates have not been examined directly. Using sedimentation assays and microscopy we show that polyubiquitinated substrates induce UBQLN2 phase separation and incorporate into the resulting condensates. This substrate effect is strongest with K63-linked substrates, intermediate with mixed-linkage substrates, and weakest with K48-linked substrates. Proteasomes can be recruited to these condensates, but proteasome activity toward K63-linked and mixed linkage substrates is inhibited in condensates. Substrates are also protected from deubiquitinases by UBQLN2-induced phase separation. Our results suggest that phase separation could regulate the fate of ubiquitinated substrates in a chain-linkage-dependent manner, thus serving as an interpreter of the ubiquitin code.
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Affiliation(s)
| | | | - Thuy P Dao
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Erin O Mulvey
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Andrew M Lehman
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Sarasi K K Galagedera
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Erica L Mallon
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Carlos A Castañeda
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Daniel A Kraut
- Department of Chemistry, Villanova University, Villanova, PA 19085
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2
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Onwunma J, Binsabaan S, Allen SP, Sankaran B, Wohlever ML. The structural and biophysical basis of substrate binding to the hydrophobic groove in Ubiquilin Sti1 domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602902. [PMID: 39026758 PMCID: PMC11257586 DOI: 10.1101/2024.07.10.602902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Ubiquilins are a family of cytosolic proteins that ferry ubiquitinated substrates to the proteasome for degradation. Recent work has demonstrated that Ubiquilins can also act as molecular chaperones, utilizing internal Sti1 domains to directly bind to hydrophobic sequences. Ubiquilins are associated with several neurodegenerative diseases with point mutations in UBQLN2 causing dominant, X-linked Amyotrophic Lateral Sclerosis (ALS). The molecular basis of Ubiquilin chaperone activity and how ALS mutations in the Sti1 domains affect Ubiquilin activity are poorly understood. This study presents the first crystal structure of the Sti1 domain from a fungal Ubiquilin homolog bound to a transmembrane domain (TMD). The structure reveals that two Sti1 domains form a head-to-head dimer, creating a hydrophobic cavity that accommodates two TMDs. Mapping the UBQLN2 sequence onto the structure shows that several ALS mutations are predicted to disrupt the hydrophobic groove. Using a newly developed competitive binding assay, we show that Ubiquilins preferentially bind to hydrophobic substrates with low helical propensity, motifs that are enriched in both substrates and in Ubiquilins. This study provides insights into the molecular and structural basis for Ubiquilin substrate binding, with broad implications for the role of the Sti1 domain in phase separation and ALS.
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Affiliation(s)
- Joan Onwunma
- Previously at University of Toledo, Department of Chemistry & Biochemistry
| | | | - Shawn P Allen
- Previously at University of Toledo, Department of Chemistry & Biochemistry
- University of Pittsburgh, Department of Cell Biology
| | - Banumathi Sankaran
- Lawrence Berkley National Lab, Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging
| | - Matthew L Wohlever
- Previously at University of Toledo, Department of Chemistry & Biochemistry
- University of Pittsburgh, Department of Cell Biology
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3
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Valentino IM, Llivicota-Guaman JG, Dao TP, Mulvey EO, Lehman AM, Galagedera SKK, Mallon EL, Castañeda CA, Kraut DA. Phase separation of polyubiquitinated proteins in UBQLN2 condensates controls substrate fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585243. [PMID: 38559018 PMCID: PMC10980000 DOI: 10.1101/2024.03.15.585243] [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: 04/04/2024]
Abstract
Ubiquitination is one of the most common post-translational modifications in eukaryotic cells. Depending on the architecture of polyubiquitin chains, substrate proteins can meet different cellular fates, but our understanding of how chain linkage controls protein fate remains limited. UBL-UBA shuttle proteins, such as UBQLN2, bind to ubiquitinated proteins and to the proteasome or other protein quality control machinery elements and play a role in substrate fate determination. Under physiological conditions, UBQLN2 forms biomolecular condensates through phase separation, a physicochemical phenomenon in which multivalent interactions drive the formation of a macromolecule-rich dense phase. Ubiquitin and polyubiquitin chains modulate UBQLN2's phase separation in a linkage-dependent manner, suggesting a possible link to substrate fate determination, but polyubiquitinated substrates have not been examined directly. Using sedimentation assays and microscopy we show that polyubiquitinated substrates induce UBQLN2 phase separation and incorporate into the resulting condensates. This substrate effect is strongest with K63-linked substrates, intermediate with mixed-linkage substrates, and weakest with K48-linked substrates. Proteasomes can be recruited to these condensates, but proteasome activity towards K63-linked and mixed linkage substrates is inhibited in condensates. Substrates are also protected from deubiquitinases by UBQLN2-induced phase separation. Our results suggest that phase separation could regulate the fate of ubiquitinated substrates in a chain-linkage dependent manner, thus serving as an interpreter of the ubiquitin code.
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Affiliation(s)
| | | | - Thuy P. Dao
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Erin O. Mulvey
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Andrew M. Lehman
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Sarasi K. K. Galagedera
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Erica L. Mallon
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Carlos A. Castañeda
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Daniel A. Kraut
- Department of Chemistry, Villanova University, Villanova, PA 19085
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4
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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: 3] [Impact Index Per Article: 3.0] [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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5
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Mukherjee S, Poudyal M, Dave K, Kadu P, Maji SK. Protein misfolding and amyloid nucleation through liquid-liquid phase separation. Chem Soc Rev 2024; 53:4976-5013. [PMID: 38597222 DOI: 10.1039/d3cs01065a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.
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Affiliation(s)
- Semanti Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manisha Poudyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Kritika Dave
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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6
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Nementzik LR, Thumbadoo KM, Murray HC, Gordon D, Yang S, Blair IP, Turner C, Faull RLM, Curtis MA, McLean C, Nicholson GA, Swanson MEV, Scotter EL. Distribution of ubiquilin 2 and TDP-43 aggregates throughout the CNS in UBQLN2 p.T487I-linked amyotrophic lateral sclerosis and frontotemporal dementia. Brain Pathol 2024; 34:e13230. [PMID: 38115557 PMCID: PMC11007053 DOI: 10.1111/bpa.13230] [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: 09/25/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023] Open
Abstract
Mutations in the UBQLN2 gene cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The neuropathology of such UBQLN2-linked cases of ALS/FTD is characterised by aggregates of the ubiquilin 2 protein in addition to aggregates of the transactive response DNA-binding protein of 43 kDa (TDP-43). ALS and FTD without UBQLN2 mutations are also characterised by TDP-43 aggregates, that may or may not colocalise with wildtype ubiquilin 2. Despite this, the relative contributions of TDP-43 and ubiquilin 2 to disease pathogenesis remain largely under-characterised, as does their relative deposition as aggregates across the central nervous system (CNS). Here we conducted multiplex immunohistochemistry of three UBQLN2 p.T487I-linked ALS/FTD cases, three non-UBQLN2-linked (sporadic) ALS cases, and 8 non-neurodegenerative disease controls, covering 40 CNS regions. We then quantified ubiquilin 2 aggregates, TDP-43 aggregates and aggregates containing both proteins in regions of interest to determine how UBQLN2-linked and non-UBQLN2-linked proteinopathy differ. We find that ubiquilin 2 aggregates that are negative for TDP-43 are predominantly small and punctate and are abundant in the hippocampal formation, spinal cord, all tested regions of neocortex, medulla and substantia nigra in UBQLN2-linked ALS/FTD but not sporadic ALS. Curiously, the striatum harboured small punctate ubiquilin 2 aggregates in all cases examined, while large diffuse striatal ubiquilin 2 aggregates were specific to UBQLN2-linked ALS/FTD. Overall, ubiquilin 2 is mainly deposited in clinically unaffected regions throughout the CNS such that symptomology in UBQLN2-linked cases maps best to the aggregation of TDP-43.
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Affiliation(s)
- Laura R. Nementzik
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
- Centre for Brain ResearchUniversity of AucklandAucklandNew Zealand
| | - Kyrah M. Thumbadoo
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
- Centre for Brain ResearchUniversity of AucklandAucklandNew Zealand
| | - Helen C. Murray
- Centre for Brain ResearchUniversity of AucklandAucklandNew Zealand
- Department of Anatomy and Medical ImagingUniversity of AucklandAucklandNew Zealand
| | - David Gordon
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
- Centre for Brain ResearchUniversity of AucklandAucklandNew Zealand
| | - Shu Yang
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
| | - Ian P. Blair
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
| | - Clinton Turner
- Centre for Brain ResearchUniversity of AucklandAucklandNew Zealand
- Department of Anatomy and Medical ImagingUniversity of AucklandAucklandNew Zealand
- Department of Anatomical Pathology, LabPlusAuckland City HospitalAucklandNew Zealand
| | - Richard L. M. Faull
- Centre for Brain ResearchUniversity of AucklandAucklandNew Zealand
- Department of Anatomy and Medical ImagingUniversity of AucklandAucklandNew Zealand
| | - Maurice A. Curtis
- Centre for Brain ResearchUniversity of AucklandAucklandNew Zealand
- Department of Anatomy and Medical ImagingUniversity of AucklandAucklandNew Zealand
| | - Catriona McLean
- Department of Anatomical PathologyAlfred HealthMelbourneVictoriaAustralia
| | - Garth A. Nicholson
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health, and Human SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
- Northcott Neuroscience LaboratoryANZAC Research InstituteSydneyAustralia
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyAustralia
| | - Molly E. V. Swanson
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
- Centre for Brain ResearchUniversity of AucklandAucklandNew Zealand
| | - Emma L. Scotter
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
- Centre for Brain ResearchUniversity of AucklandAucklandNew Zealand
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7
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Safren N, Dao TP, Mohan HM, Huang C, Trotter B, Castañeda CA, Paulson H, Barmada S, Sharkey LM. Pathogenic mutations in UBQLN2 exhibit diverse aggregation propensity and neurotoxicity. Sci Rep 2024; 14:6049. [PMID: 38472280 PMCID: PMC10933299 DOI: 10.1038/s41598-024-55582-9] [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: 11/02/2023] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The ubiquitin-adaptor protein UBQLN2 promotes degradation of several aggregate-prone proteins implicated in neurodegenerative diseases. Missense UBQLN2 mutations also cause X-linked amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Previously we demonstrated that the liquid-like properties of UBQLN2 molecular assemblies are altered by a specific pathogenic mutation, P506T, and that the propensity of UBQLN2 to aggregate correlated with neurotoxicity. Here, we systematically assess the effects of multiple, spatially distinct ALS/FTD-linked missense mutations on UBQLN2 aggregation propensity, neurotoxicity, phase separation, and autophagic flux. In contrast to what we observed for the P506T mutation, no other tested pathogenic mutant exhibited a clear correlation between aggregation propensity and neurotoxicity. These results emphasize the unique nature of pathogenic UBQLN2 mutations and argue against a generalizable link between aggregation propensity and neurodegeneration in UBQLN2-linked ALS/FTD.
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Affiliation(s)
- 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.
| | - Thuy P Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY, 13244, USA
| | - Harihar Milaganur Mohan
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Camellia Huang
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Bryce Trotter
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY, 13244, USA
| | - Henry 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
| | - Sami Barmada
- 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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8
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Parra AS, Johnston CA. Phase Separation as a Driver of Stem Cell Organization and Function during Development. J Dev Biol 2023; 11:45. [PMID: 38132713 PMCID: PMC10743522 DOI: 10.3390/jdb11040045] [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: 11/07/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
A properly organized subcellular composition is essential to cell function. The canonical organizing principle within eukaryotic cells involves membrane-bound organelles; yet, such structures do not fully explain cellular complexity. Furthermore, discrete non-membrane-bound structures have been known for over a century. Liquid-liquid phase separation (LLPS) has emerged as a ubiquitous mode of cellular organization without the need for formal lipid membranes, with an ever-expanding and diverse list of cellular functions that appear to be regulated by this process. In comparison to traditional organelles, LLPS can occur across wider spatial and temporal scales and involves more distinct protein and RNA complexes. In this review, we discuss the impacts of LLPS on the organization of stem cells and their function during development. Specifically, the roles of LLPS in developmental signaling pathways, chromatin organization, and gene expression will be detailed, as well as its impacts on essential processes of asymmetric cell division. We will also discuss how the dynamic and regulated nature of LLPS may afford stem cells an adaptable mode of organization throughout the developmental time to control cell fate. Finally, we will discuss how aberrant LLPS in these processes may contribute to developmental defects and disease.
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9
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Namitz KEW, Showalter SA, Cosgrove MS. Phase separation promotes a highly active oligomeric scaffold of the MLL1 core complex for regulation of histone H3K4 methylation. J Biol Chem 2023; 299:105204. [PMID: 37660926 PMCID: PMC10551905 DOI: 10.1016/j.jbc.2023.105204] [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: 07/05/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023] Open
Abstract
Enzymes that regulate the degree of histone H3 lysine 4 (H3K4) methylation are crucial for proper cellular differentiation and are frequently mutated in cancer. The Mixed lineage leukemia (MLL) family of enzymes deposit H3K4 mono-, di-, or trimethylation at distinct genomic locations, requiring precise spatial and temporal control. Despite evidence that the degree of H3K4 methylation is controlled in part by a hierarchical assembly pathway with key subcomplex components, we previously found that the assembled state of the MLL1 core complex is not favored at physiological temperature. To better understand this paradox, we tested the hypothesis that increasing the concentration of subunits in a biomolecular condensate overcomes this thermodynamic barrier via mass action. Here, we demonstrate that MLL1 core complex phase separation stimulates enzymatic activity up to 60-fold but not primarily by concentrating subunits into droplets. Instead, we found that stimulated activity is largely due to the formation of an altered oligomeric scaffold that greatly reduces substrate Km. We posit that phase separation-induced scaffolding of the MLL1 core complex is a potential "switch-like" mechanism for spatiotemporal control of H3K4 methylation through the rapid formation or dissolution of biomolecular condensates within RNA Pol II transcription factories.
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Affiliation(s)
- Kevin E W Namitz
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA
| | - Scott A Showalter
- Department of Chemistry, Penn State University, University Park, Pennsylvania, USA
| | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA.
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10
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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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11
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Guo G, Wang X, Zhang Y, Li T. Sequence variations of phase-separating proteins and resources for studying biomolecular condensates. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1119-1132. [PMID: 37464880 PMCID: PMC10423696 DOI: 10.3724/abbs.2023131] [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: 04/13/2023] [Accepted: 06/06/2023] [Indexed: 07/20/2023] Open
Abstract
Phase separation (PS) is an important mechanism underlying the formation of biomolecular condensates. Physiological condensates are associated with numerous biological processes, such as transcription, immunity, signaling, and synaptic transmission. Changes in particular amino acids or segments can disturb the protein's phase behavior and interactions with other biomolecules in condensates. It is thus presumed that variations in the phase-separating-prone domains can significantly impact the properties and functions of condensates. The dysfunction of condensates contributes to a number of pathological processes. Pharmacological perturbation of these condensates is proposed as a promising way to restore physiological states. In this review, we characterize the variations observed in PS proteins that lead to aberrant biomolecular compartmentalization. We also showcase recent advancements in bioinformatics of membraneless organelles (MLOs), focusing on available databases useful for screening PS proteins and describing endogenous condensates, guiding researchers to seek the underlying pathogenic mechanisms of biomolecular condensates.
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Affiliation(s)
- Gaigai Guo
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
| | - Xinxin Wang
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
| | - Yi Zhang
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
| | - Tingting Li
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
- Key Laboratory for NeuroscienceMinistry of Education/National Health Commission of ChinaPeking UniversityBeijing100191China
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12
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Idera A, Sharkey LM, Kurauchi Y, Kadoyama K, Paulson HL, Katsuki H, Seki T. Wild-type and pathogenic forms of ubiquilin 2 differentially modulate components of the autophagy-lysosome pathways. J Pharmacol Sci 2023; 152:182-192. [PMID: 37257946 DOI: 10.1016/j.jphs.2023.05.002] [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: 03/01/2023] [Revised: 04/14/2023] [Accepted: 05/08/2023] [Indexed: 06/02/2023] Open
Abstract
Missense mutations of ubiquilin 2 (UBQLN2) have been identified to cause X-linked amyotrophic lateral sclerosis (ALS). Proteasome-mediated protein degradation is reported to be impaired by ALS-associated mutations of UBQLN2. However, it remains unknown how these mutations affect autophagy-lysosome protein degradation, which consists of macroautophagy (MA), microautophagy (mA), and chaperone-mediated autophagy (CMA). Using a CMA/mA fluorescence reporter we found that overexpression of wild-type UBQLN2 impairs CMA. Conversely, knockdown of endogenous UBQLN2 increases CMA activity, suggesting that normally UBQLN2 negatively regulates CMA. ALS-associated mutant forms of UBQLN2 exacerbate this impairment of CMA. Using cells stably transfected with wild-type or ALS-associated mutant UBQLN2, we further determined that wild-type UBQLN2 increased the ratio of LAMP2A (a CMA-related protein) to LAMP1 (a lysosomal protein). This could represent a compensatory reaction to the impairment of CMA by wild-type UBQLN2. However, ALS-associated mutant UBQLN2 failed to show this compensation, exacerbating the impairment of CMA by mutant UBQLN2. We further demonstrated that ALS-associated mutant forms of UBQLN2 also impair MA, but wild-type UBQLN2 does not. These results support the view that ALS-associated mutant forms of UBQLN2 impair both CMA and MA which may contribute to the neurodegeneration observed in patients with UBQLN2-mediated ALS.
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Affiliation(s)
- Akiko Idera
- Department of Chemico-Pharmacological Sciences, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Lisa M Sharkey
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Yuki Kurauchi
- Department of Chemico-Pharmacological Sciences, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Keiichi Kadoyama
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Japan
| | - Henry L Paulson
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Hiroshi Katsuki
- Department of Chemico-Pharmacological Sciences, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takahiro Seki
- Department of Chemico-Pharmacological Sciences, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan; Department of Pharmacology, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Japan.
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13
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Robb CG, Dao TP, Ujma J, Castañeda CA, Beveridge R. Ion Mobility Mass Spectrometry Unveils Global Protein Conformations in Response to Conditions that Promote and Reverse Liquid-Liquid Phase Separation. J Am Chem Soc 2023. [PMID: 37276246 DOI: 10.1021/jacs.3c00756] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Liquid-liquid phase separation (LLPS) is a process by which biomacromolecules, particularly proteins, condense into a dense phase that resembles liquid droplets. Dysregulation of LLPS is implicated in disease, yet the relationship between protein conformational changes and LLPS remains difficult to discern. This is due to the high flexibility and disordered nature of many proteins that phase separate under physiological conditions and their tendency to oligomerize. Here, we demonstrate that ion mobility mass spectrometry (IM-MS) overcomes these limitations. We used IM-MS to investigate the conformational states of full-length ubiquilin-2 (UBQLN2) protein, LLPS of which is driven by high-salt concentration and reversed by noncovalent interactions with ubiquitin (Ub). IM-MS revealed that UBQLN2 exists as a mixture of monomers and dimers and that increasing salt concentration causes the UBQLN2 dimers to undergo a subtle shift toward extended conformations. UBQLN2 binds to Ub in 2:1 and 2:2 UBQLN2/Ub complexes, which have compact geometries compared to free UBQLN2 dimers. Together, these results suggest that extended conformations of UBQLN2 are correlated with UBQLN2's ability to phase separate. Overall, delineating protein conformations that are implicit in LLPS will greatly increase understanding of the phase separation process, both in normal cell physiology and disease states.
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Affiliation(s)
- Christina Glen Robb
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, U.K
| | - Thuy P Dao
- Departments of Biology and Chemistry, BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States
| | - Jakub Ujma
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, U.K
| | - Carlos A Castañeda
- Departments of Biology and Chemistry, BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States
| | - Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, U.K
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14
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Kampmeyer C, Grønbæk-Thygesen M, Oelerich N, Tatham MH, Cagiada M, Lindorff-Larsen K, Boomsma W, Hofmann K, Hartmann-Petersen R. Lysine deserts prevent adventitious ubiquitylation of ubiquitin-proteasome components. Cell Mol Life Sci 2023; 80:143. [PMID: 37160462 PMCID: PMC10169902 DOI: 10.1007/s00018-023-04782-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 05/11/2023]
Abstract
In terms of its relative frequency, lysine is a common amino acid in the human proteome. However, by bioinformatics we find hundreds of proteins that contain long and evolutionarily conserved stretches completely devoid of lysine residues. These so-called lysine deserts show a high prevalence in intrinsically disordered proteins with known or predicted functions within the ubiquitin-proteasome system (UPS), including many E3 ubiquitin-protein ligases and UBL domain proteasome substrate shuttles, such as BAG6, RAD23A, UBQLN1 and UBQLN2. We show that introduction of lysine residues into the deserts leads to a striking increase in ubiquitylation of some of these proteins. In case of BAG6, we show that ubiquitylation is catalyzed by the E3 RNF126, while RAD23A is ubiquitylated by E6AP. Despite the elevated ubiquitylation, mutant RAD23A appears stable, but displays a partial loss of function phenotype in fission yeast. In case of UBQLN1 and BAG6, introducing lysine leads to a reduced abundance due to proteasomal degradation of the proteins. For UBQLN1 we show that arginine residues within the lysine depleted region are critical for its ability to form cytosolic speckles/inclusions. We propose that selective pressure to avoid lysine residues may be a common evolutionary mechanism to prevent unwarranted ubiquitylation and/or perhaps other lysine post-translational modifications. This may be particularly relevant for UPS components as they closely and frequently encounter the ubiquitylation machinery and are thus more susceptible to nonspecific ubiquitylation.
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Affiliation(s)
- Caroline Kampmeyer
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Martin Grønbæk-Thygesen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Nicole Oelerich
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Michael H Tatham
- Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK
| | - Matteo Cagiada
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany.
| | - Rasmus Hartmann-Petersen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark.
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15
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Choi HJ, Lee JY, Kim K. Glutathionylation on RNA-binding proteins: a regulator of liquid‒liquid phase separation in the pathogenesis of amyotrophic lateral sclerosis. Exp Mol Med 2023; 55:735-744. [PMID: 37009800 PMCID: PMC10167235 DOI: 10.1038/s12276-023-00978-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 04/04/2023] Open
Abstract
RNA-binding proteins (RBPs) containing low-sequence complexity domains mediate the formation of cellular condensates and membrane-less organelles with biological functions via liquid‒liquid phase separation (LLPS). However, the abnormal phase transition of these proteins induces the formation of insoluble aggregates. Aggregates are pathological hallmarks of neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS). The molecular mechanisms underlying aggregate formation by ALS-associated RPBs remain largely unknown. This review highlights emerging studies on various posttranslational modifications (PTMs) related to protein aggregation. We begin with the introduction of several ALS-associated RBPs that form aggregates induced by phase separation. In addition, we highlight our recent discovery of a new PTM involved in the phase transition during the pathogenesis of fused-in-sarcoma (FUS)-associated ALS. We suggest a molecular mechanism through which LLPS mediates glutathionylation in FUS-linked ALS. This review aims to provide a detailed overview of the key molecular mechanisms of LLPS-mediated aggregate formation by PTMs, which will help further the understanding of the pathogenesis and development of ALS therapeutics.
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Affiliation(s)
- Hyun-Jun Choi
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
- Department of Integrated Biomedical Sciences, Soonchunhyang University, Cheonan, 31151, Korea
| | - Ji Young Lee
- Department of Medical Biotechnology, Soonchunhyang University, Asan, 31538, Korea
- Department of Medical Science, Soonchunhyang University, Asan, 31538, Korea
| | - Kiyoung Kim
- Department of Medical Science, Soonchunhyang University, Asan, 31538, Korea.
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16
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Goel S, Oliva R, Jeganathan S, Bader V, Krause LJ, Kriegler S, Stender ID, Christine CW, Nakamura K, Hoffmann JE, Winter R, Tatzelt J, Winklhofer KF. Linear ubiquitination induces NEMO phase separation to activate NF-κB signaling. Life Sci Alliance 2023; 6:e202201607. [PMID: 36720498 PMCID: PMC9889916 DOI: 10.26508/lsa.202201607] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 02/02/2023] Open
Abstract
The NF-κB essential modulator NEMO is the core regulatory component of the inhibitor of κB kinase complex, which is a critical checkpoint in canonical NF-κB signaling downstream of innate and adaptive immune receptors. In response to various stimuli, such as TNF or IL-1β, NEMO binds to linear or M1-linked ubiquitin chains generated by LUBAC, promoting its oligomerization and subsequent activation of the associated kinases. Here we show that M1-ubiquitin chains induce phase separation of NEMO and the formation of NEMO assemblies in cells after exposure to IL-1β. Phase separation is promoted by both binding of NEMO to linear ubiquitin chains and covalent linkage of M1-ubiquitin to NEMO and is essential but not sufficient for its phase separation. Supporting the functional relevance of NEMO phase separation in signaling, a pathogenic NEMO mutant, which is impaired in both binding and linkage to linear ubiquitin chains, does not undergo phase separation and is defective in mediating IL-1β-induced NF-κB activation.
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Affiliation(s)
- Simran Goel
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Rosario Oliva
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Sadasivam Jeganathan
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Laura J Krause
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Simon Kriegler
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Isabelle D Stender
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Ken Nakamura
- Department of Neurology, UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Jörg Tatzelt
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
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17
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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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18
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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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19
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Piol D, Robberechts T, Da Cruz S. Lost in local translation: TDP-43 and FUS in axonal/neuromuscular junction maintenance and dysregulation in amyotrophic lateral sclerosis. Neuron 2023; 111:1355-1380. [PMID: 36963381 DOI: 10.1016/j.neuron.2023.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/21/2022] [Accepted: 02/16/2023] [Indexed: 03/26/2023]
Abstract
Key early features of amyotrophic lateral sclerosis (ALS) are denervation of neuromuscular junctions and axonal degeneration. Motor neuron homeostasis relies on local translation through controlled regulation of axonal mRNA localization, transport, and stability. Yet the composition of the local transcriptome, translatome (mRNAs locally translated), and proteome during health and disease remains largely unexplored. This review covers recent discoveries on axonal translation as a critical mechanism for neuronal maintenance/survival. We focus on two RNA binding proteins, transactive response DNA binding protein-43 (TDP-43) and fused in sarcoma (FUS), whose mutations cause ALS and frontotemporal dementia (FTD). Emerging evidence points to their essential role in the maintenance of axons and synapses, including mRNA localization, transport, and local translation, and whose dysfunction may contribute to ALS. Finally, we describe recent advances in omics-based approaches mapping compartment-specific local RNA and protein compositions, which will be invaluable to elucidate fundamental local processes and identify key targets for therapy development.
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Affiliation(s)
- Diana Piol
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Tessa Robberechts
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Sandrine Da Cruz
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium.
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20
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Li Y, Chen T, You K, Peng T, Li T. Sequence determinants and solution conditions underlying liquid to solid phase transition. Am J Physiol Cell Physiol 2023; 324:C236-C246. [PMID: 36503242 DOI: 10.1152/ajpcell.00280.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Life consists of numberless functional biomolecules that exist in various states. Besides well-dissolved phases, biomolecules especially proteins and nucleic acids can form liquid droplets through liquid-liquid phase separation (LLPS). Stronger interactions promote a solid-like state of biomolecular condensates, which are also formerly referred to as detergent-insoluble aggregates. Solid-like condensates exist in vivo physiologically and pathologically, and their formation has not been fully understood. Recently, more and more research has proven that liquid to solid phase transition (LST) is an essential way to form solid condensates. In this review, we summarized the regions in the sequence that have different impacts on phase transition and emphasized that the LST is affected by its sequence characteristics. Moreover, increasing evidence unveiled that LST is affected by various solution conditions. We discussed solution conditions like protein concentration, pH, ATP, ions, and small molecules in a solution. Methods have been established to study these solid phase components. Here, we summarized low-throughput experimental techniques and high-throughput omics methods in the study of the LST.
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Affiliation(s)
- Yuxuan Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
| | - Taoyu Chen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
| | - Kaiqing You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Happy Life Technology, Beijing, China
| | - Tao Peng
- Happy Life Technology, Beijing, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
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21
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A liquid-to-solid phase transition of Cu/Zn superoxide dismutase 1 initiated by oxidation and disease mutation. J Biol Chem 2023; 299:102857. [PMID: 36592929 PMCID: PMC9898760 DOI: 10.1016/j.jbc.2022.102857] [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: 04/23/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 01/01/2023] Open
Abstract
Cu/Zn superoxide dismutase 1 (SOD1) has a high propensity to misfold and form abnormal aggregates when it is subjected to oxidative stress or carries mutations associated with amyotrophic lateral sclerosis. However, the transition from functional soluble SOD1 protein to aggregated SOD1 protein is not completely clear. Here, we propose that liquid-liquid phase separation (LLPS) represents a biophysical process that converts soluble SOD1 into aggregated SOD1. We determined that SOD1 undergoes LLPS in vitro and cells under oxidative stress. Abnormal oxidation of SOD1 induces maturation of droplets formed by LLPS, eventually leading to protein aggregation and fibrosis, and involves residues Cys111 and Trp32. Additionally, we found that pathological mutations in SOD1 associated with ALS alter the morphology and material state of the droplets and promote the transformation of SOD1 to solid-like oligomers which are toxic to nerve cells. Furthermore, the fibrous aggregates formed by both pathways have a concentration-dependent toxicity effect on nerve cells. Thus, these combined results strongly indicate that LLPS may play a major role in pathological SOD1 aggregation, contributing to pathogenesis in ALS.
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22
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Phung TH, Tatman M, Monteiro MJ. UBQLN2 undergoes a reversible temperature-induced conformational switch that regulates binding with HSPA1B: ALS/FTD mutations cripple the switch but do not destroy HSPA1B binding. Biochim Biophys Acta Gen Subj 2023; 1867:130284. [PMID: 36423739 PMCID: PMC9792439 DOI: 10.1016/j.bbagen.2022.130284] [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: 07/15/2022] [Revised: 10/23/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022]
Abstract
Here we present evidence, based on alterations of its intrinsic tryptophan fluorescence, that UBQLN2 protein undergoes a conformational switch when the temperature is raised from 37 °C to 42 °C. The switch is reset on restoration of the temperature. We speculate that the switch regulates UBQLN2 function in the heat shock response because elevation of the temperature from 37 °C to 42 °C dramatically increased in vitro binding between UBQLN2 and HSPA1B. Furthermore, restoration of the temperature to 37 °C decreased HSPA1B binding. By comparison to wild type (WT) UBQLN2, we found that all five ALS/FTD mutant UBQLN2 proteins we examined had attenuated alterations in tryptophan fluorescence when shifted to 42 °C, suggesting that the conformational switch is crippled in the mutants. Paradoxically, all five mutants bound similar amounts of HSPA1B compared to WT UBQLN2 protein at 42 °C, suggesting that either the conformational switch is not instrumental for HSPA1B binding, or that, although damaged, it is still functional. Comparison of the poly-ubiquitin chain binding revealed that WT UBQLN2 binds more avidly with K63 than with K48 chains. The avidity may explain the involvement of UBQLN2 in autophagy and cell signaling. Consistent with its function in autophagy, we found UBQLN2 binds directly with LC3, the autophagosomal-specific membrane-tethered protein. Finally, we provide evidence that WT UBQLN2 can homodimerize, and heterodimerize with WT UBQLN1. We show that ALS mutant P497S-UBQLN2 protein can oligomerize with either WT UBQLN1 or 2, providing a possible mechanism for how mutant UBQLN2 proteins could bind and inactivate UBQLN proteins, causing loss of function.
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Affiliation(s)
- 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
| | - Micaela Tatman
- 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
- 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.
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23
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Sato Y, Terawaki S, Oikawa D, Shimizu K, Okina Y, Ito H, Tokunaga F. Involvement of heterologous ubiquitination including linear ubiquitination in Alzheimer's disease and amyotrophic lateral sclerosis. Front Mol Biosci 2023; 10:1089213. [PMID: 36726375 PMCID: PMC9884707 DOI: 10.3389/fmolb.2023.1089213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
In neurodegenerative diseases such as Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS), the progressive accumulation of ubiquitin-positive cytoplasmic inclusions leads to proteinopathy and neurodegeneration. Along with the seven types of Lys-linked ubiquitin chains, the linear ubiquitin chain assembly complex (LUBAC)-mediated Met1-linked linear ubiquitin chain, which activates the canonical NF-κB pathway, is also involved in cytoplasmic inclusions of tau in AD and TAR DNA-binding protein 43 in ALS. Post-translational modifications, including heterologous ubiquitination, affect proteasomal and autophagic degradation, inflammatory responses, and neurodegeneration. Single nucleotide polymorphisms (SNPs) in SHARPIN and RBCK1 (which encodes HOIL-1L), components of LUBAC, were recently identified as genetic risk factors of AD. A structural biological simulation suggested that most of the SHARPIN SNPs that cause an amino acid replacement affect the structure and function of SHARPIN. Thus, the aberrant LUBAC activity is related to AD. Protein ubiquitination and ubiquitin-binding proteins, such as ubiquilin 2 and NEMO, facilitate liquid-liquid phase separation (LLPS), and linear ubiquitination seems to promote efficient LLPS. Therefore, the development of therapeutic approaches that target ubiquitination, such as proteolysis-targeting chimeras (PROTACs) and inhibitors of ubiquitin ligases, including LUBAC, is expected to be an additional effective strategy to treat neurodegenerative diseases.
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Affiliation(s)
- Yusuke Sato
- Center for Research on Green Sustainable Chemistry, Graduate School of Engineering, Tottori University, Tottori, Japan,Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Seigo Terawaki
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan,Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Japan
| | - Daisuke Oikawa
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Kouhei Shimizu
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yoshinori Okina
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Hidefumi Ito
- Department of Neurology, Wakayama Medical University, Wakayama, Japan
| | - Fuminori Tokunaga
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan,*Correspondence: Fuminori Tokunaga,
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24
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Raymond-Smiedy P, Bucknor B, Yang Y, Zheng T, Castañeda CA. A Spectrophotometric Turbidity Assay to Study Liquid-Liquid Phase Separation of UBQLN2 In Vitro. Methods Mol Biol 2023; 2551:515-541. [PMID: 36310223 DOI: 10.1007/978-1-0716-2597-2_32] [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] [Indexed: 06/16/2023]
Abstract
Liquid-liquid phase separation (LLPS) is hypothesized to be the underlying mechanism for how membraneless organelles or biomolecular condensates form inside both prokaryotic and eukaryotic cells. Protein LLPS is a biophysical process during which proteins demix from homogeneous solution to form protein-dense droplets with liquid-like properties. Disruptions to LLPS, such as changes to material properties of condensates or physicochemical parameters for LLPS onset, are implicated in neurodegenerative diseases and cancer. Therefore, it is essential to determine the physicochemical parameters that promote protein LLPS. Here, we present our UV-Vis spectrophotometric turbidity assay to characterize the temperature and concentration dependence of LLPS for UBQLN2, a protein that undergoes LLPS via homotypic interactions in vitro and forms stress-induced condensates in cells. Mutations in UBQLN2 cause amyotrophic lateral sclerosis (ALS) and disrupt UBQLN2 LLPS. We present a detailed expression and purification protocol for a C-terminal construct of UBQLN2 and how we use microscopy to image UBQLN2 LLPS. We use our UV-Vis assay to construct temperature-concentration phase diagrams for wild-type and mutant UBQLN2 constructs to determine the effects of domain deletions and/or mutations on UBQLN2 phase separation.
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Affiliation(s)
| | - Barrington Bucknor
- Department of Biology, Syracuse University, Syracuse, NY, USA
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
- Program in Neuroscience, Syracuse University, Syracuse, NY, USA
| | - Yiran Yang
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Tongyin Zheng
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Carlos A Castañeda
- Department of Biology, Syracuse University, Syracuse, NY, USA.
- Department of Chemistry, Syracuse University, Syracuse, NY, USA.
- Program in Neuroscience, Syracuse University, Syracuse, NY, USA.
- BioInspired Institute, Syracuse University, Syracuse, NY, USA.
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25
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Safren N, Sharkey LM, Barmada SJ. Neuronal Puncta/Aggregate Formation by WT and Mutant UBQLN2. Methods Mol Biol 2023; 2551:561-573. [PMID: 36310225 PMCID: PMC10519613 DOI: 10.1007/978-1-0716-2597-2_34] [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] [Indexed: 06/16/2023]
Abstract
Protein aggregates are a common feature of nearly all neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis (ALS). Here we describe a method to quickly and accurately measure protein aggregation in cells expressing a fluorescently tagged aggregation-prone protein. This unbiased method obviates the need for manual scoring and facilitates the identification of factors governing protein self-assembly and its downstream consequences for cell heath.
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Affiliation(s)
- Nathaniel Safren
- Department of Neurology, University of Michigan Health System, Ann Arbor, MI, USA
| | - Lisa M Sharkey
- Department of Neurology, University of Michigan Health System, Ann Arbor, MI, USA
| | - Sami J Barmada
- Department of Neurology, University of Michigan Health System, Ann Arbor, MI, USA.
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26
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Molecular and environmental determinants of biomolecular condensate formation. Nat Chem Biol 2022; 18:1319-1329. [DOI: 10.1038/s41589-022-01175-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 09/15/2022] [Indexed: 11/21/2022]
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27
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Strohm L, Hu Z, Suk Y, Rühmkorf A, Sternburg E, Gattringer V, Riemenschneider H, Berutti R, Graf E, Weishaupt JH, Brill MS, Harbauer AB, Dormann D, Dengjel J, Edbauer D, Behrends C. Multi-omics profiling identifies a deregulated FUS-MAP1B axis in ALS/FTD-associated UBQLN2 mutants. Life Sci Alliance 2022; 5:5/11/e202101327. [PMID: 35777956 PMCID: PMC9258132 DOI: 10.26508/lsa.202101327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 11/24/2022] Open
Abstract
Analysis of ALS patient-derived and engineered cells revealed that mutant UBQLN2 increases mRNA and protein of MAP1B which is mediated by dephosphorylation of FUS within its RNA-binding domain. Ubiquilin-2 (UBQLN2) is a ubiquitin-binding protein that shuttles ubiquitinated proteins to proteasomal and autophagic degradation. UBQLN2 mutations are genetically linked to the neurodegenerative disorders amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). However, it remains elusive how UBQLN2 mutations cause ALS/FTD. Here, we systematically examined proteomic and transcriptomic changes in patient-derived lymphoblasts and CRISPR/Cas9–engineered HeLa cells carrying ALS/FTD UBQLN2 mutations. This analysis revealed a strong up-regulation of the microtubule-associated protein 1B (MAP1B) which was also observed in UBQLN2 knockout cells and primary rodent neurons depleted of UBQLN2, suggesting that a UBQLN2 loss-of-function mechanism is responsible for the elevated MAP1B levels. Consistent with MAP1B’s role in microtubule binding, we detected an increase in total and acetylated tubulin. Furthermore, we uncovered that UBQLN2 mutations result in decreased phosphorylation of MAP1B and of the ALS/FTD–linked fused in sarcoma (FUS) protein at S439 which is critical for regulating FUS-RNA binding and MAP1B protein abundance. Together, our findings point to a deregulated UBQLN2-FUS-MAP1B axis that may link protein homeostasis, RNA metabolism, and cytoskeleton dynamics, three molecular pathomechanisms of ALS/FTD.
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Affiliation(s)
- Laura Strohm
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany
| | - Zehan Hu
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Yongwon Suk
- Institute for Molecular Physiology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Alina Rühmkorf
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Erin Sternburg
- Institute for Molecular Physiology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Vanessa Gattringer
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany
| | - Henrick Riemenschneider
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany.,German Center for Neurodegenerative Diseases Munich, Munich, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Elisabeth Graf
- Institut für Humangenetik, Klinikum Rechts der Isar der Technischen Universität München, Munich, Germany
| | - Jochen H Weishaupt
- Division of Neurodegenerative Disorders, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, Mannheim, Germany
| | | | - Angelika B Harbauer
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany.,Max Planck Institute of Neurobiology, Martinsried, Germany.,Munich Cluster for Systems Neurology, Munich, Germany
| | - Dorothee Dormann
- Institute for Molecular Physiology, Johannes Gutenberg-University Mainz, Mainz, Germany.,Institute of Molecule Biology, Mainz, Germany
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Dieter Edbauer
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany.,German Center for Neurodegenerative Diseases Munich, Munich, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany
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28
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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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29
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Abstract
Condensed states of proteins, including liquid-like membraneless organelles and solid-like aggregates, contribute in fundamental ways to the organisation and function of the cell. Perturbations of these states can lead to a variety of diseases through mechanisms that we are now beginning to understand. We define protein condensation diseases as conditions caused by the disruption of the normal behaviour of the condensed states of proteins. We analyze the problem of the identification of targets for pharmacological interventions for these diseases and explore opportunities for the regulation of the formation and organisation of aberrant condensed states of proteins. In this review, the authors define protein condensation diseases as conditions caused by aberrant liquid-like or solid-like states of proteins, and describe opportunities for therapeutic interventions to restore the normal phase behaviour of proteins. The review accompanies the related collection of articles published in Nature Communications focusing on possible therapeutic approaches involving liquid-liquid phase separation.
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30
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ALS mutations in the TIA-1 prion-like domain trigger highly condensed pathogenic structures. Proc Natl Acad Sci U S A 2022; 119:e2122523119. [PMID: 36112647 PMCID: PMC9499527 DOI: 10.1073/pnas.2122523119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
T cell intracellular antigen-1 (TIA-1) plays a central role in stress granule (SG) formation by self-assembly via the prion-like domain (PLD). In the TIA-1 PLD, amino acid mutations associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) or Welander distal myopathy (WDM), have been identified. However, how these mutations affect PLD self-assembly properties has remained elusive. In this study, we uncovered the implicit pathogenic structures caused by the mutations. NMR analysis indicated that the dynamic structures of the PLD are synergistically determined by the physicochemical properties of amino acids in units of five residues. Molecular dynamics simulations and three-dimensional electron crystallography, together with biochemical assays, revealed that the WDM mutation E384K attenuated the sticky properties, whereas the ALS mutations P362L and A381T enhanced the self-assembly by inducing β-sheet interactions and highly condensed assembly, respectively. These results suggest that the P362L and A381T mutations increase the likelihood of irreversible amyloid fibrillization after phase-separated droplet formation, and this process may lead to pathogenicity.
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31
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Li Z, Liu X, Liu M. Stress Granule Homeostasis, Aberrant Phase Transition, and Amyotrophic Lateral Sclerosis. ACS Chem Neurosci 2022; 13:2356-2370. [PMID: 35905138 DOI: 10.1021/acschemneuro.2c00262] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. In recent years, a large number of ALS-related mutations have been discovered to have a strong link to stress granules (SGs). SGs are cytoplasmic ribonucleoprotein condensates mediated by liquid-liquid phase separation (LLPS) of biomacromolecules. They help cells cope with stress. The normal physiological functions of SGs are dependent on three key aspects of SG "homeostasis": SG assembly, disassembly, and SG components. Any of these three aspects can be disrupted, resulting in abnormalities in the cellular stress response and leading to cytotoxicity. Several ALS-related pathogenic mutants have abnormal LLPS abilities that disrupt SG homeostasis, and some of them can even cause aberrant phase transitions. As a result, ALS-related mutants may disrupt various aspects of SG homeostasis by directly disturbing the intermolecular interactions or affecting core SG components, thus disrupting the phase equilibrium of the cytoplasm during stress. Considering that the importance of the "global view" of SG homeostasis in ALS pathogenesis has not received enough attention, we first systematically summarize the physiological regulatory mechanism of SG homeostasis based on LLPS and then examine ALS pathogenesis from the perspective of disrupted SG homeostasis and aberrant phase transition of biomacromolecules.
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Affiliation(s)
- Zhanxu Li
- Xiangya School of Medicine, Central South University, Changsha 410078, Hunan, China
| | - Xionghao Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, Hunan, China
| | - Mujun Liu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410078, Hunan, China
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32
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Crosstalk between Biomolecular Condensates and Proteostasis. Cells 2022; 11:cells11152415. [PMID: 35954258 PMCID: PMC9368065 DOI: 10.3390/cells11152415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 12/23/2022] Open
Abstract
Proper homeostasis of the proteome, referred to as proteostasis, is maintained by chaperone-dependent refolding of misfolded proteins and by protein degradation via the ubiquitin-proteasome system and the autophagic machinery. This review will discuss a crosstalk between biomolecular condensates and proteostasis, whereby the crowding of proteostasis factors into macromolecular assemblies is often established by phase separation of membraneless biomolecular condensates. Specifically, ubiquitin and other posttranslational modifications come into play as agents of phase separation, essential for the formation of condensates and for ubiquitin-proteasome system activity. Furthermore, an intriguing connection associates malfunction of the same pathways to the accumulation of misfolded and ubiquitinated proteins in aberrant condensates, the formation of protein aggregates, and finally, to the pathogenesis of neurodegenerative diseases. The crosstalk between biomolecular condensates and proteostasis is an emerging theme in cellular and disease biology and further studies will focus on delineating specific molecular pathways involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases.
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33
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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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34
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Banani SF, Afeyan LK, Hawken SW, Henninger JE, Dall'Agnese A, Clark VE, Platt JM, Oksuz O, Hannett NM, Sagi I, Lee TI, Young RA. Genetic variation associated with condensate dysregulation in disease. Dev Cell 2022; 57:1776-1788.e8. [PMID: 35809564 PMCID: PMC9339523 DOI: 10.1016/j.devcel.2022.06.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 03/11/2022] [Accepted: 06/14/2022] [Indexed: 12/18/2022]
Abstract
A multitude of cellular processes involve biomolecular condensates, which has led to the suggestion that diverse pathogenic mutations may dysregulate condensates. Although proof-of-concept studies have identified specific mutations that cause condensate dysregulation, the full scope of the pathological genetic variation that affects condensates is not yet known. Here, we comprehensively map pathogenic mutations to condensate-promoting protein features in putative condensate-forming proteins and find over 36,000 pathogenic mutations that plausibly contribute to condensate dysregulation in over 1,200 Mendelian diseases and 550 cancers. This resource captures mutations presently known to dysregulate condensates, and experimental tests confirm that additional pathological mutations do indeed affect condensate properties in cells. These findings suggest that condensate dysregulation may be a pervasive pathogenic mechanism underlying a broad spectrum of human diseases, provide a strategy to identify proteins and mutations involved in pathologically altered condensates, and serve as a foundation for mechanistic insights into disease and therapeutic hypotheses.
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Affiliation(s)
- Salman F Banani
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lena K Afeyan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Susana W Hawken
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Program of Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Victoria E Clark
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jesse M Platt
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ozgur Oksuz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ido Sagi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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35
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Kuechler ER, Jacobson M, Mayor T, Gsponer J. GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents. Nucleic Acids Res 2022; 50:W384-W391. [PMID: 35474477 PMCID: PMC9252806 DOI: 10.1093/nar/gkac279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/27/2022] [Accepted: 04/09/2022] [Indexed: 01/30/2023] Open
Abstract
Phase separation-based condensate formation is a novel working paradigm in biology, helping to rationalize many important cellular phenomena including the assembly of membraneless organelles. Uncovering the functional impact of cellular condensates requires a better knowledge of these condensates’ constituents. Herein, we introduce the webserver GraPES (Granule Protein Enrichment Server), a user-friendly online interface containing the MaGS and MaGSeq predictors, which provide propensity scores for proteins’ localization into cellular condensates. Our webpage contains models trained on human (Homo sapiens) and yeast (Saccharomyces cerevisiae) stress granule proteins. MaGS utilizes experimentally-based protein features for prediction, whereas MaGSeq is an entirely protein sequence-based implementation. GraPES is implemented in HTML/CSS and Javascript and is freely available for public use at https://grapes.msl.ubc.ca/. Documentation for using the provided webtools, descriptions of their methodology, and implementation notes can be found on the webpage.
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Affiliation(s)
- Erich R Kuechler
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Matthew Jacobson
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
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36
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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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Babl L, Giacomelli G, Ramm B, Gelmroth AK, Bramkamp M, Schwille P. CTP-controlled liquid-liquid phase separation of ParB. J Mol Biol 2022; 434:167401. [PMID: 34902429 DOI: 10.1016/j.jmb.2021.167401] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/11/2021] [Accepted: 12/07/2021] [Indexed: 12/30/2022]
Abstract
The ParABS system is supposed to be responsible for plasmid partitioning and chromosome segregation in bacteria. ParABS ensures a high degree of fidelity in inheritance by dividing the genetic material equally between daughter cells during cell division. However, the molecular mechanisms underlying the assembly of the partition complex, representing the core of the ParABS system, are still far from being understood. Here we demonstrate that the partition complex is formed via liquid-liquid phase separation. Assembly of the partition complex is initiated by the formation of oligomeric ParB species, which in turn are regulated by CTP-binding. Phase diagrams and in vivo analysis show how the partition complex can further be spatially regulated by parS. By investigating the phylogenetic variation in phase separation and its regulation by CTP, we find a high degree of evolutionary conservation among distantly related prokaryotes. These results advance the understanding of partition complex formation and regulation in general, by confirming and extending recently proposed models.
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Affiliation(s)
- Leon Babl
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany
| | - Giacomo Giacomelli
- Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Beatrice Ramm
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany
| | - Ann-Kathrin Gelmroth
- Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Marc Bramkamp
- Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Petra Schwille
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany.
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Nel M, Mahungu AC, Monnakgotla N, Botha GR, Mulder NJ, Wu G, Rampersaud E, van Blitterswijk M, Wuu J, Cooley A, Myers J, Rademakers R, Taylor JP, Benatar M, Heckmann JM. Revealing the Mutational Spectrum in Southern Africans With Amyotrophic Lateral Sclerosis. Neurol Genet 2022; 8:e654. [PMID: 35047667 PMCID: PMC8756565 DOI: 10.1212/nxg.0000000000000654] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/08/2021] [Indexed: 11/15/2022]
Abstract
Background and Objectives To perform the first screen of 44 amyotrophic lateral sclerosis (ALS) genes in a cohort of African genetic ancestry individuals with ALS using whole-genome sequencing (WGS) data. Methods One hundred three consecutive cases with probable/definite ALS (using the revised El Escorial criteria), and self-categorized as African genetic ancestry, underwent WGS using various Illumina platforms. As population controls, 238 samples from various African WGS data sets were included. Our analysis was restricted to 44 ALS genes, which were curated for rare sequence variants and classified according to the American College of Medical Genetics guidelines as likely benign, uncertain significance, likely pathogenic, or pathogenic variants. Results Thirteen percent of 103 ALS cases harbored pathogenic variants; 5 different SOD1 variants (N87S, G94D, I114T, L145S, and L145F) in 5 individuals (5%, 1 familial case), pathogenic C9orf72 repeat expansions in 7 individuals (7%, 1 familial case) and a likely pathogenic ANXA11 (G38R) variant in 1 individual. Thirty individuals (29%) harbored ≥1 variant of uncertain significance; 10 of these variants had limited pathogenic evidence, although this was insufficient to permit confident classification as pathogenic. Discussion Our findings show that known ALS genes can be expected to identify a genetic cause of disease in >11% of sporadic ALS cases of African genetic ancestry. Similar to European cohorts, the 2 most frequent genes harboring pathogenic variants in this population group are C9orf72 and SOD1.
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Affiliation(s)
- Melissa Nel
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - Amokelani C Mahungu
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - Nomakhosazana Monnakgotla
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - Gerrit R Botha
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - Nicola J Mulder
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - Gang Wu
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - Evadnie Rampersaud
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - Marka van Blitterswijk
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - Joanne Wuu
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - Anne Cooley
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - Jason Myers
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - Rosa Rademakers
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - J Paul Taylor
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - Michael Benatar
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
| | - Jeannine M Heckmann
- Neurology Research Group (M.N., A.C.M., N.M., J.M.H.), Neuroscience Institute, University of Cape Town; Computational Biology Division (M.N., A.C.M., N.M., G.R.B., N.J.M.), Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa; Center for Applied Bioinformatics (G.W., E.R., J.M.), St. Jude Children's Research Hospital, Memphis, TN; Department of Neuroscience (M.v.B.), Mayo Clinic, Jacksonville, FL; Department of Neurology (J.W., A.C., M.B.), University of Miami, FL; Center for Molecular Neurology (R.R.), University of Antwerp, Belguim; Department of Cell and Molecular Biology (J.P.T.), St. Jude Children's Research Hospital, Memphis, TN; and Neurology (J.M.H.), Department of Medicine, University of Cape Town, South Africa
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Therapeutics-how to treat phase separation-associated diseases. Emerg Top Life Sci 2021; 4:307-318. [PMID: 32364240 PMCID: PMC7733670 DOI: 10.1042/etls20190176] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/16/2022]
Abstract
Liquid-liquid phase separation has drawn attention as many neurodegeneration or cancer-associated proteins are able to form liquid membraneless compartments (condensates) by liquid-liquid phase separation. Furthermore, there is rapidly growing evidence that disease-associated mutation or post-translational modification of these proteins causes aberrant location, composition or physical properties of the condensates. It is ambiguous whether aberrant condensates are always causative in disease mechanisms, however they are likely promising potential targets for therapeutics. The conceptual framework of liquid-liquid phase separation provides opportunities for novel therapeutic approaches. This review summarises how the extensive recent advances in understanding control of nucleation, growth and composition of condensates by protein post-translational modification has revealed many possibilities for intervention by conventional small molecule enzyme inhibitors. This includes the first proof-of-concept examples. However, understanding membraneless organelle formation as a physical chemistry process also highlights possible physicochemical mechanisms of intervention. There is huge demand for innovation in drug development, especially for challenging diseases of old age including neurodegeneration and cancer. The conceptual framework of liquid-liquid phase separation provides a new paradigm for thinking about modulating protein function and is very different from enzyme lock-and-key or structured binding site concepts and presents new opportunities for innovation.
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40
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Riley JF, Fioramonti PJ, Rusnock AK, Hehnly H, Castañeda CA. ALS-linked mutations impair UBQLN2 stress-induced biomolecular condensate assembly in cells. J Neurochem 2021; 159:145-155. [PMID: 34129687 DOI: 10.1111/jnc.15453] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/30/2021] [Accepted: 06/13/2021] [Indexed: 11/28/2022]
Abstract
Mutations in Ubiquilin-2 (UBQLN2), a ubiquitin-binding shuttle protein involved in several protein quality control processes, can lead to amyotrophic lateral sclerosis (ALS). We previously found that wild-type UBQLN2 forms dynamic, membraneless biomolecular condensates upon cellular stress, and undergoes liquid-liquid phase separation in vitro. However, the impact of ALS-linked mutations on UBQLN2 condensate formation in cells is unknown. Here, we employ live-cell imaging and photokinetic analysis to investigate how five patient-derived ALS-linked mutations in UBQLN2 impact stress-induced UBQLN2 condensate assembly and condensate material properties. Both wild-type and mutant UBQLN2 condensates are generally cytoplasmic and liquid-like. However, cells transfected with mutant UBQLN2 contain fewer stress-induced UBQLN2 condensates than those with wild-type UBQLN2. Most strikingly, exogenously expressed P506T UBQLN2 forms the lowest number of stress-induced condensates of all UBQLN2 mutants, and these condensates are significantly smaller than those of wild-type UBQLN2. Fluorescence recovery after photobleaching (FRAP) analysis of UBQLN2 condensates revealed higher immobile fractions for UBQLN2 mutants, especially P506T. P497S and P497H mutations differentially impact condensate properties, demonstrating that the effects of ALS-linked mutations are both position- and amino acid-dependent. Collectively, our data show that disease mutations hinder assembly and alter viscoelastic properties of stress-induced UBQLN2 condensates, potentially leading to aggregates commonly observed in ALS.
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Affiliation(s)
- Julia F Riley
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA.,Department of Chemistry, Syracuse University, Syracuse, NY, 13244, USA.,Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY, 13244, USA
| | | | - Amber K Rusnock
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA
| | - Heidi Hehnly
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA
| | - Carlos A Castañeda
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA.,Department of Chemistry, Syracuse University, Syracuse, NY, 13244, USA.,Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY, 13244, USA
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Zheng T, Galagedera SKK, Castañeda CA. Previously uncharacterized interactions between the folded and intrinsically disordered domains impart asymmetric effects on UBQLN2 phase separation. Protein Sci 2021; 30:1467-1481. [PMID: 34029402 DOI: 10.1002/pro.4128] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023]
Abstract
Shuttle protein UBQLN2 functions in protein quality control (PQC) by binding to proteasomal receptors and ubiquitinated substrates via its N-terminal ubiquitin-like (UBL) and C-terminal ubiquitin-associated (UBA) domains, respectively. Between these two folded domains are low-complexity STI1-I and STI1-II regions, connected by disordered linkers. The STI1 regions bind other components, such as HSP70, that are important to the PQC functions of UBQLN2. We recently determined that the STI1-II region enables UBQLN2 to undergo liquid-liquid phase separation (LLPS) to form liquid droplets in vitro and biomolecular condensates in cells. However, how the interplay between the folded (UBL/UBA) domains and the intrinsically disordered regions mediates phase separation is largely unknown. Using engineered domain deletion constructs, we found that removing the UBA domain inhibits UBQLN2 LLPS while removing the UBL domain enhances LLPS, suggesting that UBA and UBL domains contribute asymmetrically in modulating UBQLN2 LLPS. To explain these differential effects, we interrogated the interactions that involve the UBA and UBL domains across the entire UBQLN2 molecule using nuclear magnetic resonance spectroscopy. To our surprise, aside from well-studied canonical UBL:UBA interactions, there also exist moderate interactions between the UBL and several disordered regions, including STI1-I and residues 555-570, the latter of which is a known contributor to UBQLN2 LLPS. Our findings are essential for the understanding of both the molecular driving forces of UBQLN2 LLPS and the effects of ligand binding to UBL, UBA, or disordered regions on the phase behavior and physiological functions of UBQLN2.
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Affiliation(s)
- Tongyin Zheng
- Department of Chemistry, Syracuse University, Syracuse, New York, USA
| | | | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York, USA.,Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, New York, USA.,BioInspired Institute, Syracuse University, Syracuse, New York, USA
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Emenecker RJ, Holehouse AS, Strader LC. Sequence determinants of in cell condensate morphology, dynamics, and oligomerization as measured by number and brightness analysis. Cell Commun Signal 2021; 19:65. [PMID: 34090478 PMCID: PMC8178893 DOI: 10.1186/s12964-021-00744-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/20/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Biomolecular condensates are non-stoichiometric assemblies that are characterized by their capacity to spatially concentrate biomolecules and play a key role in cellular organization. Proteins that drive the formation of biomolecular condensates frequently contain oligomerization domains and intrinsically disordered regions (IDRs), both of which can contribute multivalent interactions that drive higher-order assembly. Our understanding of the relative and temporal contribution of oligomerization domains and IDRs to the material properties of in vivo biomolecular condensates is limited. Similarly, the spatial and temporal dependence of protein oligomeric state inside condensates has been largely unexplored in vivo. METHODS In this study, we combined quantitative microscopy with number and brightness analysis to investigate the aging, material properties, and protein oligomeric state of biomolecular condensates in vivo. Our work is focused on condensates formed by AUXIN RESPONSE FACTOR 19 (ARF19), a transcription factor integral to the auxin signaling pathway in plants. ARF19 contains a large central glutamine-rich IDR and a C-terminal Phox Bem1 (PB1) oligomerization domain and forms cytoplasmic condensates. RESULTS Our results reveal that the IDR amino acid composition can influence the morphology and material properties of ARF19 condensates. In contrast the distribution of oligomeric species within condensates appears insensitive to the IDR composition. In addition, we identified a relationship between the abundance of higher- and lower-order oligomers within individual condensates and their apparent fluidity. CONCLUSIONS IDR amino acid composition affects condensate morphology and material properties. In ARF condensates, altering the amino acid composition of the IDR did not greatly affect the oligomeric state of proteins within the condensate. Video Abstract.
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Affiliation(s)
- Ryan J. Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130 USA
- Center for Engineering Mechanobiology, Washington University, St. Louis, MO 63130 USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130 USA
| | - Lucia C. Strader
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130 USA
- Center for Engineering Mechanobiology, Washington University, St. Louis, MO 63130 USA
- Department of Biology, Duke University, Durham, NC 27708 USA
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Ruff KM, Dar F, Pappu RV. Polyphasic linkage and the impact of ligand binding on the regulation of biomolecular condensates. BIOPHYSICS REVIEWS 2021; 2:021302. [PMID: 34179888 PMCID: PMC8211317 DOI: 10.1063/5.0050059] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 12/30/2022]
Abstract
Cellular matter can be spatially and temporally organized into membraneless biomolecular condensates. The current thinking is that these condensates form and dissolve via phase transitions driven by one or more condensate-specific multivalent macromolecules known as scaffolds. Cells likely regulate condensate formation and dissolution by exerting control over the concentrations of regulatory molecules, which we refer to as ligands. Wyman and Gill introduced the framework of polyphasic linkage to explain how ligands can exert thermodynamic control over phase transitions. This review focuses on describing the concepts of polyphasic linkage and the relevance of such a mechanism for controlling condensate formation and dissolution. We describe how ligand-mediated control over scaffold phase behavior can be quantified experimentally. Further, we build on recent studies to highlight features of ligands that make them suppressors vs drivers of phase separation. Finally, we highlight areas where advances are needed to further understand ligand-mediated control of condensates in complex cellular environments. These advances include understanding the effects of networks of ligands on condensate behavior and how ligands modulate phase transitions controlled by different combinations of homotypic and heterotypic interactions among scaffold macromolecules. Insights gained from the application of polyphasic linkage concepts should be useful for designing novel pharmaceutical ligands to regulate condensates.
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Affiliation(s)
- Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Furqan Dar
- Department of Physics, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, USA
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Lei L, Wu Z, Winklhofer KF. Protein quality control by the proteasome and autophagy: A regulatory role of ubiquitin and liquid-liquid phase separation. Matrix Biol 2021; 100-101:9-22. [DOI: 10.1016/j.matbio.2020.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022]
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Saxton AD, Kraemer BC. Human Ubiquilin 2 and TDP-43 co-pathology drives neurodegeneration in transgenic C. elegans. G3-GENES GENOMES GENETICS 2021; 11:6272515. [PMID: 33963840 DOI: 10.1093/g3journal/jkab158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/01/2021] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a debilitating, fatal neurodegenerative disease that causes rapid muscle wasting. It shares a spectrum of symptoms and pathology with frontotemporal lobar degeneration (FTLD). These diseases are caused by aberrant activity of a set of proteins including TDP-43 and UBIQUILIN-2 (UBQLN2). UBQLN2 encodes an ubiquitin-like adaptor protein involved in the ubiquitin-proteasome protein degradation pathway. Mutations in the PXX domain of UBQLN2 cause familial ALS. UBQLN2 aggregates in skein-like inclusions with other ALS and FTLD associated proteins including TDP-43 and ubiquitin. To facilitate further investigation of UBQLN2-mediated mechanisms of neurodegeneration, we made Caenorhabditis elegans transgenic lines pan-neuronally expressing human UBQLN2 cDNAs carrying either the wild-type UBQLN2 sequence or UBQLN2 with ALS causing mutations. Transgenic animals exhibit motor dysfunction accompanied by neurodegeneration of GABAergic motor neurons. At low levels of UBQLN2 expression, wild-type UBQLN2 causes significant motor impairment and neurodegeneration that is exacerbated by ALS associated mutations in UBQLN2. At higher levels of UBQLN2 expression, both wild-type and ALS mutated versions of UBQLN2 cause severe impairment. Molecular genetic investigation revealed that UBQLN2 dependent locomotor defects do not require the involvement of the endogenous homolog of TDP-43 in C. elegans (tdp-1). However, co-expression of wild-type human TDP-43 exacerbates UBQLN2 deficits. This model of UBQLN2-mediated neurodegeneration may be useful for further mechanistic investigation into the molecular cascades driving neurodegeneration in ALS and ALS-FTLD.
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Affiliation(s)
- Aleen D Saxton
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington, 98108, United States of America
| | - Brian C Kraemer
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington, 98108, United States of America; Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98104, USA; Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA; Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98195, USA
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46
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Galectin-3 N-terminal tail prolines modulate cell activity and glycan-mediated oligomerization/phase separation. Proc Natl Acad Sci U S A 2021; 118:2021074118. [PMID: 33952698 DOI: 10.1073/pnas.2021074118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Galectin-3 (Gal-3) has a long, aperiodic, and dynamic proline-rich N-terminal tail (NT). The functional role of the NT with its numerous prolines has remained enigmatic since its discovery. To provide some resolution to this puzzle, we individually mutated all 14 NT prolines over the first 68 residues and assessed their effects on various Gal-3-mediated functions. Our findings show that mutation of any single proline (especially P37A, P55A, P60A, P64A/H, and P67A) dramatically and differentially inhibits Gal-3-mediated cellular activities (i.e., cell migration, activation, endocytosis, and hemagglutination). For mechanistic insight, we investigated the role of prolines in mediating Gal-3 oligomerization, a fundamental process required for these cell activities. We showed that Gal-3 oligomerization triggered by binding to glycoproteins is a dynamic process analogous to liquid-liquid phase separation (LLPS). The composition of these heterooligomers is dependent on the concentration of Gal-3 as well as on the concentration and type of glycoprotein. LLPS-like Gal-3 oligomerization/condensation was also observed on the plasma membrane and disrupted endomembranes. Molecular- and cell-based assays indicate that glycan binding-triggered Gal-3 LLPS (or LLPS-like) is driven mainly by dynamic intermolecular interactions between the Gal-3 NT and the carbohydrate recognition domain (CRD) F-face, although NT-NT interactions appear to contribute to a lesser extent. Mutation of each proline within the NT differentially controls NT-CRD interactions, consequently affecting glycan binding, LLPS, and cellular activities. Our results unveil the role of proline polymorphisms (e.g., at P64) associated with many diseases and suggest that the function of glycosylated cell surface receptors is dynamically regulated by Gal-3.
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Darling AL, Shorter J. Combating deleterious phase transitions in neurodegenerative disease. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118984. [PMID: 33549703 PMCID: PMC7965345 DOI: 10.1016/j.bbamcr.2021.118984] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/11/2022]
Abstract
Protein aggregation is a hallmark of neurodegenerative diseases. However, the mechanism that induces pathogenic aggregation is not well understood. Recently, it has emerged that several of the pathological proteins found in an aggregated or mislocalized state in neurodegenerative diseases are also able to undergo liquid-liquid phase separation (LLPS) under physiological conditions. Although these phase transitions are likely important for various physiological functions, neurodegenerative disease-related mutations and conditions can alter the LLPS behavior of these proteins, which can elicit toxicity. Therefore, therapeutics that antagonize aberrant LLPS may be able to mitigate toxicity and aggregation that is ubiquitous in neurodegenerative disease. Here, we discuss the mechanisms by which aberrant protein phase transitions may contribute to neurodegenerative disease. We also outline potential therapeutic strategies to counter deleterious phases. State without borders: Membrane-less organelles and liquid-liquid phase transitions edited by Vladimir N Uversky.
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Affiliation(s)
- April L Darling
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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48
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Li J, Zhang Y, Chen X, Ma L, Li P, Yu H. Protein phase separation and its role in chromatin organization and diseases. Biomed Pharmacother 2021; 138:111520. [PMID: 33765580 DOI: 10.1016/j.biopha.2021.111520] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/04/2021] [Accepted: 03/14/2021] [Indexed: 12/25/2022] Open
Abstract
In the physical sciences, solid, liquid, and gas are the most familiar phase states, whose essence is their existence reflecting the different spatial distribution of molecular components. The biological molecules in the living cell also have differences in spatial distribution. The molecules organized in the form of membrane-bound organelles are well recognized. However, the biomolecules organized in membraneless compartments called biomolecular condensates remain elusive. The liquid-liquid phase separation (LLPS), as a new emerging scientific breakthrough, describes the biomolecules assembled in special distribution and appeared as membraneless condensates in the form of a new "phase" compared with the surrounding liquid milieu. LLPS provides an important theoretical basis for explaining the composition of biological molecules and related biological reactions. Mounting evidence has emerged recently that phase-separated condensates participate in various biological activities. This article reviews the occurrence of LLPS and underlying regulatory mechanisms for understanding how multivalent molecules drive phase transitions to form the biomolecular condensates. And, it also summarizes recent major progress in elucidating the roles of LLPS in chromatin organization and provides clues for the development of new innovative therapeutic strategies for related diseases.
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Affiliation(s)
- Jiaqi Li
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Yao Zhang
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Xi Chen
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Lijuan Ma
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Haijie Yu
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China.
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Gerson JE, Linton H, Xing J, Sutter AB, Kakos FS, Ryou J, Liggans N, Sharkey LM, Safren N, Paulson HL, Ivanova MI. Shared and divergent phase separation and aggregation properties of brain-expressed ubiquilins. Sci Rep 2021; 11:287. [PMID: 33431932 PMCID: PMC7801659 DOI: 10.1038/s41598-020-78775-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Abstract
The brain-expressed ubiquilins, UBQLNs 1, 2 and 4, are highly homologous proteins that participate in multiple aspects of protein homeostasis and are implicated in neurodegenerative diseases. Studies have established that UBQLN2 forms liquid-like condensates and accumulates in pathogenic aggregates, much like other proteins linked to neurodegenerative diseases. However, the relative condensate and aggregate formation of the three brain-expressed ubiquilins is unknown. Here we report that the three ubiquilins differ in aggregation propensity, revealed by in-vitro experiments, cellular models, and analysis of human brain tissue. UBQLN4 displays heightened aggregation propensity over the other ubiquilins and, like amyloids, UBQLN4 forms ThioflavinT-positive fibrils in vitro. Measuring fluorescence recovery after photobleaching (FRAP) of puncta in cells, we report that all three ubiquilins undergo liquid-liquid phase transition. UBQLN2 and 4 exhibit slower recovery than UBQLN1, suggesting the condensates formed by these brain-expressed ubiquilins have different compositions and undergo distinct internal rearrangements. We conclude that while all brain-expressed ubiquilins exhibit self-association behavior manifesting as condensates, they follow distinct courses of phase-separation and aggregation. We suggest that this variability among ubiquilins along the continuum from liquid-like to solid informs both the normal ubiquitin-linked functions of ubiquilins and their accumulation and potential contribution to toxicity in neurodegenerative diseases.
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Affiliation(s)
- Julia E Gerson
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA.
| | - Hunter Linton
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Jiazheng Xing
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Alexandra B Sutter
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
- Neuroscience Graduate Program, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Fayth S Kakos
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Jaimie Ryou
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Nyjerus Liggans
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Lisa M Sharkey
- 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
| | - Henry L Paulson
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA.
| | - Magdalena I Ivanova
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA.
- Department of Neurology, Biophysics Program, University of Michigan, Ann Arbor, MI, 48109-2200, USA.
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50
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Dao TP, Castañeda CA. Ubiquitin-Modulated Phase Separation of Shuttle Proteins: Does Condensate Formation Promote Protein Degradation? Bioessays 2020; 42:e2000036. [PMID: 32881044 PMCID: PMC7737676 DOI: 10.1002/bies.202000036] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/29/2020] [Indexed: 12/14/2022]
Abstract
Liquid-liquid phase separation (LLPS) has recently emerged as a possible mechanism that enables ubiquitin-binding shuttle proteins to facilitate the degradation of ubiquitinated substrates via distinct protein quality control (PQC) pathways. Shuttle protein LLPS is modulated by multivalent interactions among their various domains as well as heterotypic interactions with polyubiquitin chains. Here, the properties of three different shuttle proteins (hHR23B, p62, and UBQLN2) are closely examined, unifying principles for the molecular determinants of their LLPS are identified, and how LLPS is connected to their functions is discussed. Evidence supporting LLPS of other shuttle proteins is also found. In this review, it is proposed that shuttle protein LLPS leads to spatiotemporal regulation of PQC activities by mediating the recruitment of PQC machinery (including proteasomes or autophagic components) to biomolecular condensates, assembly/disassembly of condensates, selective enrichment of client proteins, and extraction of ubiquitinated proteins from condensates in cells.
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Affiliation(s)
- Thuy P Dao
- 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
- Bioinspired Institute, Syracuse University, Syracuse, NY, 13244, USA
- Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY, 13244, USA
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