1
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Keyport Kik S, Christopher D, Glauninger H, Hickernell CW, Bard JAM, Lin KM, Squires AH, Ford M, Sosnick TR, Drummond DA. An adaptive biomolecular condensation response is conserved across environmentally divergent species. Nat Commun 2024; 15:3127. [PMID: 38605014 PMCID: PMC11009240 DOI: 10.1038/s41467-024-47355-9] [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: 07/30/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide a remarkable view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.
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Affiliation(s)
- Samantha Keyport Kik
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Dana Christopher
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Hendrik Glauninger
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Caitlin Wong Hickernell
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jared A M Bard
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Kyle M Lin
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Allison H Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | | | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA.
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2
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Daskivich GJ, Brodsky JL. The generation of detergent-insoluble clipped fragments from an ERAD substrate in mammalian cells. Sci Rep 2023; 13:21508. [PMID: 38057493 PMCID: PMC10700608 DOI: 10.1038/s41598-023-48769-z] [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: 07/28/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
Proteostasis ensures the proper synthesis, folding, and trafficking of proteins and is required for cellular and organellar homeostasis. This network also oversees protein quality control within the cell and prevents accumulation of aberrant proteins, which can lead to cellular dysfunction and disease. For example, protein aggregates irreversibly disrupt proteostasis and can exert gain-of-function toxic effects. Although this process has been examined in detail for cytosolic proteins, how endoplasmic reticulum (ER)-tethered, aggregation-prone proteins are handled is ill-defined. To determine how a membrane protein with a cytoplasmic aggregation-prone domain is routed for ER-associated degradation (ERAD), we analyzed a new model substrate, TM-Ubc9ts. In yeast, we previously showed that TM-Ubc9ts ERAD requires Hsp104, which is absent in higher cells. In transient and stable HEK293 cells, we now report that TM-Ubc9ts degradation is largely proteasome-dependent, especially at elevated temperatures. In contrast to yeast, clipped TM-Ubc9ts polypeptides, which are stabilized upon proteasome inhibition, accumulate and are insoluble at elevated temperatures. TM-Ubc9ts cleavage is independent of the intramembrane protease RHBDL4, which clips other classes of ERAD substrates. These studies highlight an unappreciated mechanism underlying the degradation of aggregation-prone substrates in the ER and invite further work on other proteases that contribute to ERAD.
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Affiliation(s)
- Grant J Daskivich
- A320 Langley Hall, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jeffrey L Brodsky
- A320 Langley Hall, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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3
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Clay KJ, Yang Y, Clark C, Petrascheck M. Proteostasis is differentially modulated by inhibition of translation initiation or elongation. eLife 2023; 12:e76465. [PMID: 37795690 PMCID: PMC10581687 DOI: 10.7554/elife.76465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/29/2023] [Indexed: 10/06/2023] Open
Abstract
Recent work has revealed an increasingly important role for mRNA translation in maintaining proteostasis. Here, we use chemical inhibitors targeting discrete steps of translation to compare how lowering the concentration of all or only translation initiation-dependent proteins rescues Caenorhabditis elegans from proteotoxic stress. We systematically challenge proteostasis and show that pharmacologically inhibiting translation initiation or elongation elicits a distinct protective profile. Inhibiting elongation protects from heat and proteasome dysfunction independently from HSF-1 but does not protect from age-associated protein aggregation. Conversely, inhibition of initiation protects from heat and age-associated protein aggregation and increases lifespan, dependent on hsf-1, but does not protect from proteotoxicity caused by proteasome dysfunction. Surprisingly, we find that the ability of the translation initiation machinery to control the concentration of newly synthesized proteins depends on HSF-1. Inhibition of translation initiation in wild-type animals reduces the concentration of newly synthesized proteins but increases it in hsf-1 mutants. Our findings suggest that the HSF-1 pathway is not only a downstream target of translation but also directly cooperates with the translation initiation machinery to control the concentration of newly synthesized proteins to restore proteostasis.
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Affiliation(s)
- Khalyd J Clay
- Department of Molecular Medicine, Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Yongzhi Yang
- Department of Molecular Medicine, Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Christina Clark
- Department of Molecular Medicine, Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Michael Petrascheck
- Department of Molecular Medicine, Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
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4
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Kik SK, Christopher D, Glauninger H, Hickernell CW, Bard JAM, Ford M, Sosnick TR, Drummond DA. An adaptive biomolecular condensation response is conserved across environmentally divergent species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551061. [PMID: 37546789 PMCID: PMC10402146 DOI: 10.1101/2023.07.28.551061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide an unprecedented view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.
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Affiliation(s)
- Samantha Keyport Kik
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL
| | - Dana Christopher
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Hendrik Glauninger
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL
| | | | - Jared A. M. Bard
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | | | - Tobin R. Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL
| | - D. Allan Drummond
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL
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5
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Huiting W, Dekker SL, van der Lienden JCJ, Mergener R, Musskopf MK, Furtado GV, Gerrits E, Coit D, Oghbaie M, Di Stefano LH, Schepers H, van Waarde-Verhagen MAWH, Couzijn S, Barazzuol L, LaCava J, Kampinga HH, Bergink S. Targeting DNA topoisomerases or checkpoint kinases results in an overload of chaperone systems, triggering aggregation of a metastable subproteome. eLife 2022; 11:e70726. [PMID: 35200138 PMCID: PMC8871389 DOI: 10.7554/elife.70726] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/07/2022] [Indexed: 02/07/2023] Open
Abstract
A loss of the checkpoint kinase ataxia telangiectasia mutated (ATM) leads to impairments in the DNA damage response, and in humans causes cerebellar neurodegeneration, and an increased risk of cancer. A loss of ATM is also associated with increased protein aggregation. The relevance and characteristics of this aggregation are still incompletely understood. Moreover, it is unclear to what extent other genotoxic conditions can trigger protein aggregation as well. Here, we show that targeting ATM, but also ATR or DNA topoisomerases, results in the widespread aggregation of a metastable, disease-associated subfraction of the proteome. Aggregation-prone model substrates, including Huntingtin exon 1 containing an expanded polyglutamine repeat, aggregate faster under these conditions. This increased aggregation results from an overload of chaperone systems, which lowers the cell-intrinsic threshold for proteins to aggregate. In line with this, we find that inhibition of the HSP70 chaperone system further exacerbates the increased protein aggregation. Moreover, we identify the molecular chaperone HSPB5 as a cell-specific suppressor of it. Our findings reveal that various genotoxic conditions trigger widespread protein aggregation in a manner that is highly reminiscent of the aggregation occurring in situations of proteotoxic stress and in proteinopathies.
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Affiliation(s)
- Wouter Huiting
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Suzanne L Dekker
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Joris CJ van der Lienden
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Rafaella Mergener
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Maiara K Musskopf
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Gabriel V Furtado
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Emma Gerrits
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - David Coit
- Laboratory of Cellular and Structural Biology, The Rockefeller UniversityNew YorkUnited States
| | - Mehrnoosh Oghbaie
- Laboratory of Cellular and Structural Biology, The Rockefeller UniversityNew YorkUnited States
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Luciano H Di Stefano
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Hein Schepers
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Maria AWH van Waarde-Verhagen
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Suzanne Couzijn
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Lara Barazzuol
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of GroningenGroningenNetherlands
- Department of Radiation Oncology, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller UniversityNew YorkUnited States
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Harm H Kampinga
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Steven Bergink
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of GroningenGroningenNetherlands
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6
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Sierra-Fonseca JA, Hamdan JN, Cohen AA, Cardenas SM, Saucedo S, Lodoza GA, Gosselink KL. Neonatal Maternal Separation Modifies Proteostasis Marker Expression in the Adult Hippocampus. Front Mol Neurosci 2021; 14:661993. [PMID: 34447296 PMCID: PMC8383781 DOI: 10.3389/fnmol.2021.661993] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 07/05/2021] [Indexed: 01/01/2023] Open
Abstract
Exposure to early-life stress (ELS) can persistently modify neuronal circuits and functions, and contribute to the expression of misfolded and aggregated proteins that are hallmarks of several neurodegenerative diseases. The healthy brain is able to clear dysfunctional proteins through the ubiquitin-proteasome system (UPS) and the autophagy-lysosomal pathway (ALP). Accumulating evidence indicates that impairment of these pathways contributes to enhanced protein aggregation and neurodegeneration. While stress is a known precipitant of neurological decline, few specific mechanistic links underlying this relationship have been identified. We hypothesized that neonatal maternal separation (MatSep), a well-established model of ELS, has the ability to alter the levels of UPS and ALP components in the brain, and thus has the potential to disrupt proteostasis. The expression of proteostasis-associated protein markers was evaluated by immunoblotting in the hippocampus and cortex of adult Wistar rats that were previously subjected to MatSep. We observed multiple sex- and MatSep-specific changes in the expression of proteins in the ALP, mitophagy, and UPS pathways, particularly in the hippocampus of adult animals. In contrast, MatSep had limited influence on proteostasis marker expression in the cortex of adult animals. Our results indicate that MatSep can selectively modify the intracellular protein degradation machinery in ways that may impact the development and progression of neurodegenerative disease.
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Affiliation(s)
- Jorge A Sierra-Fonseca
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Jameel N Hamdan
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Alexis A Cohen
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States.,Neuroscience Program, Smith College, Northampton, MA, United States
| | - Sonia M Cardenas
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Sigifredo Saucedo
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Gabriel A Lodoza
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Kristin L Gosselink
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States.,Department of Physiology and Pathology, Burrell College of Osteopathic Medicine, Las Cruces, NM, United States
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7
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8
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Jagaraj CJ, Parakh S, Atkin JD. Emerging Evidence Highlighting the Importance of Redox Dysregulation in the Pathogenesis of Amyotrophic Lateral Sclerosis (ALS). Front Cell Neurosci 2021; 14:581950. [PMID: 33679322 PMCID: PMC7929997 DOI: 10.3389/fncel.2020.581950] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/21/2020] [Indexed: 12/20/2022] Open
Abstract
The cellular redox state, or balance between cellular oxidation and reduction reactions, serves as a vital antioxidant defence system that is linked to all important cellular activities. Redox regulation is therefore a fundamental cellular process for aerobic organisms. Whilst oxidative stress is well described in neurodegenerative disorders including amyotrophic lateral sclerosis (ALS), other aspects of redox dysfunction and their contributions to pathophysiology are only just emerging. ALS is a fatal neurodegenerative disease affecting motor neurons, with few useful treatments. Hence there is an urgent need to develop more effective therapeutics in the future. Here, we discuss the increasing evidence for redox dysregulation as an important and primary contributor to ALS pathogenesis, which is associated with multiple disease mechanisms. Understanding the connection between redox homeostasis, proteins that mediate redox regulation, and disease pathophysiology in ALS, may facilitate a better understanding of disease mechanisms, and lead to the design of better therapeutic strategies.
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Affiliation(s)
- Cyril Jones Jagaraj
- Department of Biomedical Sciences, Macquarie University Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sonam Parakh
- Department of Biomedical Sciences, Macquarie University Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Julie D Atkin
- Department of Biomedical Sciences, Macquarie University Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
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9
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Xu G, Fromholt SE, Chakrabarty P, Zhu F, Liu X, Pace MC, Koh J, Golde TE, Levites Y, Lewis J, Borchelt DR. Diversity in Aβ deposit morphology and secondary proteome insolubility across models of Alzheimer-type amyloidosis. Acta Neuropathol Commun 2020; 8:43. [PMID: 32252825 PMCID: PMC7137436 DOI: 10.1186/s40478-020-00911-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 12/30/2022] Open
Abstract
A hallmark pathology of Alzheimer's disease (AD) is the formation of amyloid β (Aβ) deposits that exhibit diverse localization and morphologies, ranging from diffuse to cored-neuritic deposits in brain parenchyma, with cerebral vascular deposition in leptomeningeal and parenchymal compartments. Most AD brains exhibit the full spectrum of pathologic Aβ morphologies. In the course of studies to model AD amyloidosis, we have generated multiple transgenic mouse models that vary in the nature of the transgene constructs that are expressed; including the species origin of Aβ peptides, the levels and length of Aβ that is deposited, and whether mutant presenilin 1 (PS1) is co-expressed. These models recapitulate features of human AD amyloidosis, but interestingly some models can produce pathology in which one type of Aβ morphology dominates. In prior studies of mice that primarily develop cored-neuritic deposits, we determined that Aβ deposition is associated with changes in cytosolic protein solubility in which a subset of proteins become detergent-insoluble, indicative of secondary proteome instability. Here, we survey changes in cytosolic protein solubility across seven different transgenic mouse models that exhibit a range of Aβ deposit morphologies. We find a surprisingly diverse range of changes in proteome solubility across these models. Mice that deposit human Aβ40 and Aβ42 in cored-neuritic plaques had the most robust changes in proteome solubility. Insoluble cytosolic proteins were also detected in the brains of mice that develop diffuse Aβ42 deposits but to a lesser extent. Notably, mice with cored deposits containing only Aβ42 had relatively few proteins that became detergent-insoluble. Our data provide new insight into the diversity of biological effects that can be attributed to different types of Aβ pathology and support the view that fibrillar cored-neuritic plaque pathology is the more disruptive Aβ pathology in the Alzheimer's cascade.
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Affiliation(s)
- Guilian Xu
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Susan E Fromholt
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Paramita Chakrabarty
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Fanchao Zhu
- The Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL, 32610, USA
| | - Xuefei Liu
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Michael C Pace
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Jin Koh
- The Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL, 32610, USA
| | - Todd E Golde
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Yona Levites
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Jada Lewis
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - David R Borchelt
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
- SantaFe Healthcare Alzheimer's Disease Research Center, Gainesville, FL, USA.
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10
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Baron DM, Matheny T, Lin YC, Leszyk JD, Kenna K, Gall KV, Santos DP, Tischbein M, Funes S, Hayward LJ, Kiskinis E, Landers JE, Parker R, Shaffer SA, Bosco DA. Quantitative proteomics identifies proteins that resist translational repression and become dysregulated in ALS-FUS. Hum Mol Genet 2020; 28:2143-2160. [PMID: 30806671 DOI: 10.1093/hmg/ddz048] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/01/2019] [Accepted: 02/07/2019] [Indexed: 12/13/2022] Open
Abstract
Aberrant translational repression is a feature of multiple neurodegenerative diseases. The association between disease-linked proteins and stress granules further implicates impaired stress responses in neurodegeneration. However, our knowledge of the proteins that evade translational repression is incomplete. It is also unclear whether disease-linked proteins influence the proteome under conditions of translational repression. To address these questions, a quantitative proteomics approach was used to identify proteins that evade stress-induced translational repression in arsenite-treated cells expressing either wild-type or amyotrophic lateral sclerosis (ALS)-linked mutant FUS. This study revealed hundreds of proteins that are actively synthesized during stress-induced translational repression, irrespective of FUS genotype. In addition to proteins involved in RNA- and protein-processing, proteins associated with neurodegenerative diseases such as ALS were also actively synthesized during stress. Protein synthesis under stress was largely unperturbed by mutant FUS, although several proteins were found to be differentially expressed between mutant and control cells. One protein in particular, COPBI, was downregulated in mutant FUS-expressing cells under stress. COPBI is the beta subunit of the coat protein I (COPI), which is involved in Golgi to endoplasmic reticulum (ER) retrograde transport. Further investigation revealed reduced levels of other COPI subunit proteins and defects in COPBI-relatedprocesses in cells expressing mutant FUS. Even in the absence of stress, COPBI localization was altered in primary and human stem cell-derived neurons expressing ALS-linked FUS variants. Our results suggest that Golgi to ER retrograde transport may be important under conditions of stress and is perturbed upon the expression of disease-linked proteins such as FUS.
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Affiliation(s)
- Desiree M Baron
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Tyler Matheny
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
| | - Yen-Chen Lin
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - John D Leszyk
- Department of Biochemistry and Molecular Pharmacology, Worcester, MA, USA.,Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA, USA
| | - Kevin Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Katherine V Gall
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - David P Santos
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Maeve Tischbein
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Salome Funes
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lawrence J Hayward
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Scott A Shaffer
- Department of Biochemistry and Molecular Pharmacology, Worcester, MA, USA.,Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA, USA
| | - Daryl A Bosco
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Biochemistry and Molecular Pharmacology, Worcester, MA, USA
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11
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Owyong TC, Subedi P, Deng J, Hinde E, Paxman JJ, White JM, Chen W, Heras B, Wong WWH, Hong Y. A Molecular Chameleon for Mapping Subcellular Polarity in an Unfolded Proteome Environment. Angew Chem Int Ed Engl 2020; 59:10129-10135. [DOI: 10.1002/anie.201914263] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Tze Cin Owyong
- ARC Centre of Excellence in Exciton Science School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Pramod Subedi
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Jieru Deng
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Elizabeth Hinde
- School of Physics Department of Biochemistry and Molecular Biology Bio21 Institute The University of Melbourne Melbourne VIC 3010 Australia
| | - Jason J. Paxman
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Jonathan M. White
- ARC Centre of Excellence in Exciton Science School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
| | - Weisan Chen
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Begoña Heras
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Wallace W. H. Wong
- ARC Centre of Excellence in Exciton Science School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
| | - Yuning Hong
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
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12
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Owyong TC, Subedi P, Deng J, Hinde E, Paxman JJ, White JM, Chen W, Heras B, Wong WWH, Hong Y. A Molecular Chameleon for Mapping Subcellular Polarity in an Unfolded Proteome Environment. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914263] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tze Cin Owyong
- ARC Centre of Excellence in Exciton Science School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Pramod Subedi
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Jieru Deng
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Elizabeth Hinde
- School of Physics Department of Biochemistry and Molecular Biology Bio21 Institute The University of Melbourne Melbourne VIC 3010 Australia
| | - Jason J. Paxman
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Jonathan M. White
- ARC Centre of Excellence in Exciton Science School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
| | - Weisan Chen
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Begoña Heras
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Wallace W. H. Wong
- ARC Centre of Excellence in Exciton Science School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
| | - Yuning Hong
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
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13
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Jayaraj GG, Hipp MS, Hartl FU. Functional Modules of the Proteostasis Network. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a033951. [PMID: 30833457 DOI: 10.1101/cshperspect.a033951] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cells invest in an extensive network of factors to maintain protein homeostasis (proteostasis) and prevent the accumulation of potentially toxic protein aggregates. This proteostasis network (PN) comprises the machineries for the biogenesis, folding, conformational maintenance, and degradation of proteins with molecular chaperones as central coordinators. Here, we review recent progress in understanding the modular architecture of the PN in mammalian cells and how it is modified during cell differentiation. We discuss the capacity and limitations of the PN in maintaining proteome integrity in the face of proteotoxic stresses, such as aggregate formation in neurodegenerative diseases. Finally, we outline various pharmacological interventions to ameliorate proteostasis imbalance.
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Affiliation(s)
- Gopal G Jayaraj
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Mark S Hipp
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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14
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Marinko J, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Chem Rev 2019; 119:5537-5606. [PMID: 30608666 PMCID: PMC6506414 DOI: 10.1021/acs.chemrev.8b00532] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Indexed: 12/13/2022]
Abstract
Advances over the past 25 years have revealed much about how the structural properties of membranes and associated proteins are linked to the thermodynamics and kinetics of membrane protein (MP) folding. At the same time biochemical progress has outlined how cellular proteostasis networks mediate MP folding and manage misfolding in the cell. When combined with results from genomic sequencing, these studies have established paradigms for how MP folding and misfolding are linked to the molecular etiologies of a variety of diseases. This emerging framework has paved the way for the development of a new class of small molecule "pharmacological chaperones" that bind to and stabilize misfolded MP variants, some of which are now in clinical use. In this review, we comprehensively outline current perspectives on the folding and misfolding of integral MPs as well as the mechanisms of cellular MP quality control. Based on these perspectives, we highlight new opportunities for innovations that bridge our molecular understanding of the energetics of MP folding with the nuanced complexity of biological systems. Given the many linkages between MP misfolding and human disease, we also examine some of the exciting opportunities to leverage these advances to address emerging challenges in the development of therapeutics and precision medicine.
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Affiliation(s)
- Justin
T. Marinko
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Hui Huang
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Wesley D. Penn
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - John A. Capra
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37245, United States
| | - Jonathan P. Schlebach
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Charles R. Sanders
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
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15
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Huang C, Wagner-Valladolid S, Stephens AD, Jung R, Poudel C, Sinnige T, Lechler MC, Schlörit N, Lu M, Laine RF, Michel CH, Vendruscolo M, Kaminski CF, Kaminski Schierle GS, David DC. Intrinsically aggregation-prone proteins form amyloid-like aggregates and contribute to tissue aging in Caenorhabditis elegans. eLife 2019; 8:e43059. [PMID: 31050339 PMCID: PMC6524967 DOI: 10.7554/elife.43059] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 05/02/2019] [Indexed: 12/13/2022] Open
Abstract
Reduced protein homeostasis leading to increased protein instability is a common molecular feature of aging, but it remains unclear whether this is a cause or consequence of the aging process. In neurodegenerative diseases and other amyloidoses, specific proteins self-assemble into amyloid fibrils and accumulate as pathological aggregates in different tissues. More recently, widespread protein aggregation has been described during normal aging. Until now, an extensive characterization of the nature of age-dependent protein aggregation has been lacking. Here, we show that age-dependent aggregates are rapidly formed by newly synthesized proteins and have an amyloid-like structure resembling that of protein aggregates observed in disease. We then demonstrate that age-dependent protein aggregation accelerates the functional decline of different tissues in C. elegans. Together, these findings imply that amyloid-like aggregates contribute to the aging process and therefore could be important targets for strategies designed to maintain physiological functions in the late stages of life.
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Affiliation(s)
- Chaolie Huang
- German Center for Neurodegenerative Diseases (DZNE)TübingenGermany
| | - Sara Wagner-Valladolid
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Amberley D Stephens
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Raimund Jung
- German Center for Neurodegenerative Diseases (DZNE)TübingenGermany
| | - Chetan Poudel
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Tessa Sinnige
- Department of ChemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - Marie C Lechler
- German Center for Neurodegenerative Diseases (DZNE)TübingenGermany
- Graduate Training Centre of NeuroscienceUniversity of TübingenTübingenGermany
| | - Nicole Schlörit
- German Center for Neurodegenerative Diseases (DZNE)TübingenGermany
- Graduate Training Centre of NeuroscienceUniversity of TübingenTübingenGermany
| | - Meng Lu
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Romain F Laine
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Claire H Michel
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Clemens F Kaminski
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Della C David
- German Center for Neurodegenerative Diseases (DZNE)TübingenGermany
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16
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Aprile-Garcia F, Tomar P, Hummel B, Khavaran A, Sawarkar R. Nascent-protein ubiquitination is required for heat shock–induced gene downregulation in human cells. Nat Struct Mol Biol 2019; 26:137-146. [DOI: 10.1038/s41594-018-0182-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022]
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17
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Pace MC, Xu G, Fromholt S, Howard J, Crosby K, Giasson BI, Lewis J, Borchelt DR. Changes in proteome solubility indicate widespread proteostatic disruption in mouse models of neurodegenerative disease. Acta Neuropathol 2018; 136:919-938. [PMID: 30140941 DOI: 10.1007/s00401-018-1895-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/02/2018] [Indexed: 12/17/2022]
Abstract
The deposition of pathologic misfolded proteins in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, frontotemporal dementia and amyotrophic lateral sclerosis is hypothesized to burden protein homeostatic (proteostatic) machinery, potentially leading to insufficient capacity to maintain the proteome. This hypothesis has been supported by previous work in our laboratory, as evidenced by the perturbation of cytosolic protein solubility in response to amyloid plaques in a mouse model of Alzheimer's amyloidosis. In the current study, we demonstrate changes in proteome solubility are a common pathology to mouse models of neurodegenerative disease. Pathological accumulations of misfolded tau, α-synuclein and mutant superoxide dismutase 1 in CNS tissues of transgenic mice were associated with changes in the solubility of hundreds of CNS proteins in each model. We observed that changes in proteome solubility were progressive and, using the rTg4510 model of inducible tau pathology, demonstrated that these changes were dependent upon sustained expression of the primary pathologic protein. In all of the models examined, changes in proteome solubility were robust, easily detected, and provided a sensitive indicator of proteostatic disruption. Interestingly, a subset of the proteins that display a shift towards insolubility were common between these different models, suggesting that a specific subset of the proteome is vulnerable to proteostatic disruption. Overall, our data suggest that neurodegenerative proteinopathies modeled in mice impose a burden on the proteostatic network that diminishes the ability of neural cells to prevent aberrant conformational changes that alter the solubility of hundreds of abundant cellular proteins.
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Affiliation(s)
- Michael C Pace
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA
| | - Guilian Xu
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA
| | - Susan Fromholt
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA
| | - John Howard
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA
| | - Keith Crosby
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA
| | - Benoit I Giasson
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA
| | - Jada Lewis
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA.
| | - David R Borchelt
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA.
- SantaFe Healthcare Alzheimer's Disease Research Center, Gainesville, FL, USA.
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18
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Solis GM, Kardakaris R, Valentine ER, Bar-Peled L, Chen AL, Blewett MM, McCormick MA, Williamson JR, Kennedy B, Cravatt BF, Petrascheck M. Translation attenuation by minocycline enhances longevity and proteostasis in old post-stress-responsive organisms. eLife 2018; 7:40314. [PMID: 30479271 PMCID: PMC6257811 DOI: 10.7554/elife.40314] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/02/2018] [Indexed: 12/12/2022] Open
Abstract
Aging impairs the activation of stress signaling pathways (SSPs), preventing the induction of longevity mechanisms late in life. Here, we show that the antibiotic minocycline increases lifespan and reduces protein aggregation even in old, SSP-deficient Caenorhabditis elegans by targeting cytoplasmic ribosomes, preferentially attenuating translation of highly translated mRNAs. In contrast to most other longevity paradigms, minocycline inhibits rather than activates all major SSPs and extends lifespan in mutants deficient in the activation of SSPs, lysosomal or autophagic pathways. We propose that minocycline lowers the concentration of newly synthesized aggregation-prone proteins, resulting in a relative increase in protein-folding capacity without the necessity to induce protein-folding pathways. Our study suggests that in old individuals with incapacitated SSPs or autophagic pathways, pharmacological attenuation of cytoplasmic translation is a promising strategy to reduce protein aggregation. Altogether, it provides a geroprotecive mechanism for the many beneficial effects of tetracyclines in models of neurodegenerative disease. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Gregory M Solis
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States.,Department of Neuroscience, The Scripps Research Institute, La Jolla, United States
| | - Rozina Kardakaris
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States
| | - Elizabeth R Valentine
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Liron Bar-Peled
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Alice L Chen
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Megan M Blewett
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | | | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Brian Kennedy
- The Buck Institute for Research on Aging, Novato, United States
| | - Benjamin F Cravatt
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Michael Petrascheck
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States.,Department of Neuroscience, The Scripps Research Institute, La Jolla, United States
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19
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NEDDylation promotes nuclear protein aggregation and protects the Ubiquitin Proteasome System upon proteotoxic stress. Nat Commun 2018; 9:4376. [PMID: 30349034 PMCID: PMC6197266 DOI: 10.1038/s41467-018-06365-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 08/24/2018] [Indexed: 11/23/2022] Open
Abstract
Spatial management of stress-induced protein aggregation is an integral part of the proteostasis network. Protein modification by the ubiquitin-like molecule NEDD8 increases upon proteotoxic stress and it is characterised by the formation of hybrid NEDD8/ubiquitin conjugates. However, the biological significance of this response is unclear. Combination of quantitative proteomics with biological analysis shows that, during proteotoxic stress, NEDDylation promotes nuclear protein aggregation, including ribosomal proteins as a major group. This correlates with protection of the nuclear Ubiquitin Proteasome System from stress-induced dysfunction. Correspondingly, we show that NEDD8 compromises ubiquitination and prevents targeting and processing of substrates by the proteasome. Moreover, we identify HUWE1 as a key E3-ligase that is specifically required for NEDDylation during proteotoxic stress. The study reveals a specific role for NEDD8 in nuclear protein aggregation upon stress and is consistent with the concept that transient aggregate formation is part of a defence mechanism against proteotoxicity. Protein NEDDylation increases upon proteotoxic stress but the function of this response remains to be elucidated. Here, the authors show that NEDDylation contributes to the cellular defence against proteotoxicity by promoting nuclear protein aggregation and protecting the ubiquitin proteasome system.
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20
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Cox D, Raeburn C, Sui X, Hatters DM. Protein aggregation in cell biology: An aggregomics perspective of health and disease. Semin Cell Dev Biol 2018; 99:40-54. [PMID: 29753879 DOI: 10.1016/j.semcdb.2018.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/21/2018] [Accepted: 05/04/2018] [Indexed: 01/08/2023]
Abstract
Maintaining protein homeostasis (proteostasis) is essential for cellular health and is governed by a network of quality control machinery comprising over 800 genes. When proteostasis becomes imbalanced, proteins can abnormally aggregate or become mislocalized. Inappropriate protein aggregation and proteostasis imbalance are two of the central pathological features of common neurodegenerative diseases including Alzheimer, Parkinson, Huntington, and motor neuron diseases. How aggregation contributes to the pathogenic mechanisms of disease remains incompletely understood. Here, we integrate some of the key and emerging ideas as to how protein aggregation relates to imbalanced proteostasis with an emphasis on Huntington disease as our area of main expertise. We propose the term "aggregomics" be coined in reference to how aggregation of particular proteins concomitantly influences the spatial organization and protein-protein interactions of the surrounding proteome. Meta-analysis of aggregated interactomes from various published datasets reveals chaperones and RNA-binding proteins are common components across various disease contexts. We conclude with an examination of therapeutic avenues targeting proteostasis mechanisms.
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Affiliation(s)
- Dezerae Cox
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Australia; Bio21 Molecular Science and Biotechnology Institute, Australia
| | - Candice Raeburn
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Australia; Bio21 Molecular Science and Biotechnology Institute, Australia
| | - Xiaojing Sui
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Australia; Bio21 Molecular Science and Biotechnology Institute, Australia
| | - Danny M Hatters
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Australia; Bio21 Molecular Science and Biotechnology Institute, Australia.
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