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Bertgen L, Bökenkamp JE, Schneckmann T, Koch C, Räschle M, Storchová Z, Herrmann JM. Distinct types of intramitochondrial protein aggregates protect mitochondria against proteotoxic stress. Cell Rep 2024; 43:114018. [PMID: 38551959 DOI: 10.1016/j.celrep.2024.114018] [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: 10/02/2023] [Revised: 02/27/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
Mitochondria consist of hundreds of proteins, most of which are inaccessible to the proteasomal quality control system of the cytosol. How cells stabilize the mitochondrial proteome during challenging conditions remains poorly understood. Here, we show that mitochondria form spatially defined protein aggregates as a stress-protecting mechanism. Two different types of intramitochondrial protein aggregates can be distinguished. The mitoribosomal protein Var1 (uS3m) undergoes a stress-induced transition from a soluble, chaperone-stabilized protein that is prevalent under benign conditions to an insoluble, aggregated form upon acute stress. The formation of Var1 bodies stabilizes mitochondrial proteostasis, presumably by sequestration of aggregation-prone proteins. The AAA chaperone Hsp78 is part of a second type of intramitochondrial aggregate that transiently sequesters proteins and promotes their folding or Pim1-mediated degradation. Thus, mitochondrial proteins actively control the formation of distinct types of intramitochondrial protein aggregates, which cooperate to stabilize the mitochondrial proteome during proteotoxic stress conditions.
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Affiliation(s)
- Lea Bertgen
- Cell Biology, University of Kaiserslautern, RPTU, Erwin-Schrödinger-Strasse 13, 67663 Kaiserslautern, Germany
| | - Jan-Eric Bökenkamp
- Molecular Genetics, University of Kaiserslautern, RPTU, Paul-Ehrlich-Strasse 24, 67663 Kaiserslautern, Germany
| | - Tim Schneckmann
- Cell Biology, University of Kaiserslautern, RPTU, Erwin-Schrödinger-Strasse 13, 67663 Kaiserslautern, Germany
| | - Christian Koch
- Cell Biology, University of Kaiserslautern, RPTU, Erwin-Schrödinger-Strasse 13, 67663 Kaiserslautern, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, RPTU, Paul-Ehrlich-Strasse 24, 67663 Kaiserslautern, Germany
| | - Zuzana Storchová
- Molecular Genetics, University of Kaiserslautern, RPTU, Paul-Ehrlich-Strasse 24, 67663 Kaiserslautern, Germany
| | - Johannes M Herrmann
- Cell Biology, University of Kaiserslautern, RPTU, Erwin-Schrödinger-Strasse 13, 67663 Kaiserslautern, Germany.
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2
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Chowdhury S, Sarkar N. Exploring the potential of amyloids in biomedical applications: A review. Biotechnol Bioeng 2024; 121:26-38. [PMID: 37822225 DOI: 10.1002/bit.28569] [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: 04/19/2023] [Revised: 08/31/2023] [Accepted: 09/24/2023] [Indexed: 10/13/2023]
Abstract
Amyloid is defined as a fibrous quaternary structure formed by assembling protein or peptide monomers into intermolecularly hydrogen linked β-sheets. There is a prevalent issue with protein aggregation and the buildup of amyloid molecules, which results in human neurological illnesses including Alzheimer's and Parkinson's. But it is now evident that many organisms, like bacteria, fungi as well as humans, use the same fibrillar structure to carry out a variety of biological functions, such as structure and protection supporting interface transitions and cell-cell recognition, protein control and storage, epigenetic inheritance, and memory. Recent discoveries of self-assembling amyloidogenic peptides and proteins, based on the amyloid core structure, give rise to interesting biomaterials with potential uses in numerous industries. These functions dramatically diverge from the initial conception of amyloid fibrils as intrinsically diseased entities. Apart from the natural ability of amyloids to spontaneously arrange themselves and their exceptional material characteristics, this aspect has prompted extensive research into engineering artificial amyloids for generating various nanostructures, molecular substances, and combined materials. Here, we discuss significant developments in the artificial design of useful amyloids as well as how amyloid materials serve as examples of how function emerges from protein self-assembly at various length scales.
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Affiliation(s)
- Srijita Chowdhury
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Nandini Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, Odisha, India
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3
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Hall D. MIL-CELL: a tool for multi-scale simulation of yeast replication and prion transmission. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:673-704. [PMID: 37670150 PMCID: PMC10682183 DOI: 10.1007/s00249-023-01679-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 09/07/2023]
Abstract
The single-celled baker's yeast, Saccharomyces cerevisiae, can sustain a number of amyloid-based prions, the three most prominent examples being [URE3], [PSI+], and [PIN+]. In the laboratory, haploid S. cerevisiae cells of a single mating type can acquire an amyloid prion in one of two ways (i) spontaneous nucleation of the prion within the yeast cell, and (ii) receipt via mother-to-daughter transmission during the cell division cycle. Similarly, prions can be lost due to (i) dissolution of the prion amyloid by its breakage into non-amyloid monomeric units, or (ii) preferential donation/retention of prions between the mother and daughter during cell division. Here we present a computational tool (Monitoring Induction and Loss of prions in Cells; MIL-CELL) for modelling these four general processes using a multiscale approach describing both spatial and kinetic aspects of the yeast life cycle and the amyloid-prion behavior. We describe the workings of the model, assumptions upon which it is based and some interesting simulation results pertaining to the wave-like spread of the epigenetic prion elements through the yeast population. MIL-CELL is provided as a stand-alone GUI executable program for free download with the paper. MIL-CELL is equipped with a relational database allowing all simulated properties to be searched, collated and graphed. Its ability to incorporate variation in heritable properties means MIL-CELL is also capable of simulating loss of the isogenic nature of a cell population over time. The capability to monitor both chronological and reproductive age also makes MIL-CELL potentially useful in studies of cell aging.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa, 920-1164, Japan.
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4
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Roy M, Fleisher RC, Alexandrov AI, Horovitz A. Reduced ADP off-rate by the yeast CCT2 double mutation T394P/R510H which causes Leber congenital amaurosis in humans. Commun Biol 2023; 6:888. [PMID: 37644231 PMCID: PMC10465592 DOI: 10.1038/s42003-023-05261-8] [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: 04/02/2023] [Accepted: 08/20/2023] [Indexed: 08/31/2023] Open
Abstract
The CCT/TRiC chaperonin is found in the cytosol of all eukaryotic cells and assists protein folding in an ATP-dependent manner. The heterozygous double mutation T400P and R516H in subunit CCT2 is known to cause Leber congenital amaurosis (LCA), a hereditary congenital retinopathy. This double mutation also renders the function of subunit CCT2, when it is outside of the CCT/TRiC complex, to be defective in promoting autophagy. Here, we show using steady-state and transient kinetic analysis that the corresponding double mutation in subunit CCT2 from Saccharomyces cerevisiae reduces the off-rate of ADP during ATP hydrolysis by CCT/TRiC. We also report that the ATPase activity of CCT/TRiC is stimulated by a non-folded substrate. Our results suggest that the closed state of CCT/TRiC is stabilized by the double mutation owing to the slower off-rate of ADP, thereby impeding the exit of CCT2 from the complex that is required for its function in autophagy.
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Affiliation(s)
- Mousam Roy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Rachel C Fleisher
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Alexander I Alexandrov
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Amnon Horovitz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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Howell-Bray T, Byrne L. The effect of prions on cellular metabolism: The metabolic impact of the [RNQ +] prion and potential role of native Rnq1p. RESEARCH SQUARE 2023:rs.3.rs-2511186. [PMID: 36909567 PMCID: PMC10002837 DOI: 10.21203/rs.3.rs-2511186/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Within the field of amyloid and prion disease there is a need for a more comprehensive understanding of the fundamentals of disease biology. In order to facilitate the progression treatment and underpin comprehension of toxicity, fundamental understanding of the disruption to normal cellular biochemistry and trafficking is needed. Here, by removing the complex biochemistry of the brain, we have utilised known prion forming strains of Saccharomyces cerevisiae carrying different conformational variants of the Rnq1p to obtain Liquid Chromatography-Mass Spectrometry (LC-MS) metabolic profiles and identify key perturbations of prion presence. These studies reveal that prion containing [RNQ+] cells display a significant reduction in amino acid biosynthesis and distinct perturbations in sphingolipid metabolism, with significant downregulation in metabolites within these pathways. Moreover, that native Rnq1p appears to downregulate ubiquinone biosynthesis pathways within cells, suggesting that Rnq1p may play a lipid/mevalonate-based cytoprotective role as a regulator of ubiquinone production. These findings contribute to the understanding of how prion proteins interact in vivo in both their prion and non-prion confirmations and indicate potential targets for the mitigation of these effects. We demonstrate specific sphingolipid centred metabolic disruptions due to prion presence and give insight into a potential cytoprotective role of the native Rnq1 protein. This provides evidence of metabolic similarities between yeast and mammalian cells as a consequence of prion presence and establishes the application of metabolomics as a tool to investigate prion/amyloid-based phenomena.
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Xia Q, Li Y, Xu W, Wu C, Zheng H, Liu L, Dong L. Enhanced liquidity of p62 droplets mediated by Smurf1 links Nrf2 activation and autophagy. Cell Biosci 2023; 13:37. [PMID: 36810259 PMCID: PMC9945626 DOI: 10.1186/s13578-023-00978-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 02/02/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Macro-autophagy/Autophagy is an evolutionarily well-conserved recycling process to maintain the balance through precise spatiotemporal regulation. However, the regulatory mechanisms of biomolecular condensates by the key adaptor protein p62 via liquid-liquid phase separation (LLPS) remain obscure. RESULTS In this study, we showed that E3 ligase Smurf1 enhanced Nrf2 activation and promoted autophagy by increasing p62 phase separation capability. Specifically, the Smurf1/p62 interaction improved the formation and material exchange of liquid droplets compared with p62 single puncta. Additionally, Smurf1 promoted the competitive binding of p62 with Keap1 to increase Nrf2 nuclear translocation in p62 Ser349 phosphorylation-dependent manner. Mechanistically, overexpressed Smurf1 increased the activation of mTORC1 (mechanistic target of rapamycin complex 1), in turn leading to p62 Ser349 phosphorylation. Nrf2 activation increased the mRNA levels of Smurf1, p62, and NBR1, further promoting the droplet liquidity to enhance oxidative stress response. Importantly, we showed that Smurf1 maintained cellular homeostasis by promoting cargo degradation through the p62/LC3 autophagic pathway. CONCLUSIONS These findings revealed the complex interconnected role among Smurf1, p62/Nrf2/NBR1, and p62/LC3 axis in determining Nrf2 activation and subsequent clearance of condensates through LLPS mechanism.
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Affiliation(s)
- Qin Xia
- grid.43555.320000 0000 8841 6246School of Life Science, Beijing Institute of Technology, No. 5, South Street, Zhongguancun, Haidian District, Beijing, China
| | - Yang Li
- grid.43555.320000 0000 8841 6246School of Life Science, Beijing Institute of Technology, No. 5, South Street, Zhongguancun, Haidian District, Beijing, China
| | - Wanting Xu
- grid.43555.320000 0000 8841 6246School of Life Science, Beijing Institute of Technology, No. 5, South Street, Zhongguancun, Haidian District, Beijing, China
| | - Chengwei Wu
- grid.43555.320000 0000 8841 6246School of Life Science, Beijing Institute of Technology, No. 5, South Street, Zhongguancun, Haidian District, Beijing, China
| | - Hanfei Zheng
- grid.43555.320000 0000 8841 6246School of Life Science, Beijing Institute of Technology, No. 5, South Street, Zhongguancun, Haidian District, Beijing, China
| | - Liqun Liu
- grid.43555.320000 0000 8841 6246School of Life Science, Beijing Institute of Technology, No. 5, South Street, Zhongguancun, Haidian District, Beijing, China
| | - Lei Dong
- School of Life Science, Beijing Institute of Technology, No. 5, South Street, Zhongguancun, Haidian District, Beijing, China.
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7
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Castro E Costa AR, Mysore S, Paruchuri P, Chen KY, Liu AY. PolyQ-Expanded Mutant Huntingtin Forms Inclusion Body Following Transient Cold Shock in a Two-Step Aggregation Mechanism. ACS Chem Neurosci 2023; 14:277-288. [PMID: 36574489 DOI: 10.1021/acschemneuro.2c00585] [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] [Indexed: 12/28/2022] Open
Abstract
Age-dependent formation of insoluble protein aggregates is a hallmark of many neurodegenerative diseases. We are interested in the cell chemistry that drives the aggregation of polyQ-expanded mutant Huntingtin (mHtt) protein into insoluble inclusion bodies (IBs). Using an inducible cell model of Huntington's disease, we show that a transient cold shock (CS) at 4 °C followed by recovery incubation at temperatures of 25-37 °C strongly and rapidly induces the compaction of diffuse polyQ-expanded HuntingtinExon1-enhanced green fluorescent protein chimera protein (mHtt) into round, micron size, cytosolic IBs. This transient CS-induced mHtt IB formation is independent of microtubule integrity or de novo protein synthesis. The addition of millimolar concentrations of sodium chloride accelerates, whereas urea suppresses this transient CS-induced mHtt IB formation. These results suggest that the low temperature of CS constrains the conformation dynamics of the intrinsically disordered mHtt into labile intermediate structures to facilitate de-solvation and hydrophobic interaction for IB formation at the higher recovery temperature. This work, along with our previous observation of the effects of heat shock protein chaperones and osmolytes in driving mHtt IB formation, underscores the primacy of mHtt structuring and rigidification for H-bond-mediated cross-linking in a two-step mechanism of mHtt IB formation in living cells.
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Affiliation(s)
- Ana Raquel Castro E Costa
- Department of Cell Biology and Neuroscience, Nelson Biology Laboratory, Rutgers State University of New Jersey, 604 Allison Road, Piscataway, New Jersey 08854, United States
| | - Sachin Mysore
- Department of Cell Biology and Neuroscience, Nelson Biology Laboratory, Rutgers State University of New Jersey, 604 Allison Road, Piscataway, New Jersey 08854, United States
| | - Praneet Paruchuri
- Department of Cell Biology and Neuroscience, Nelson Biology Laboratory, Rutgers State University of New Jersey, 604 Allison Road, Piscataway, New Jersey 08854, United States
| | - Kuang Yu Chen
- Department of Chemistry and Chemical Biology, Wright-Rieman Chemistry Laboratory, Rutgers State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Alice Y Liu
- Department of Cell Biology and Neuroscience, Nelson Biology Laboratory, Rutgers State University of New Jersey, 604 Allison Road, Piscataway, New Jersey 08854, United States
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8
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Abstract
Cellular homeostasis and stress survival requires maintenance of the proteome and suppression of proteotoxicity. Molecular chaperones promote cell survival through repair of misfolded proteins and cooperation with protein degradation machines to discard terminally damaged proteins. Hsp70 family members play an essential role in cellular protein metabolism by binding and releasing non-native proteins to facilitate protein folding, refolding, and degradation. Hsp40 (DnaJ-like proteins) family members are Hsp70 co-chaperones that determine the fate of Hsp70 clients by facilitating protein folding, assembly, and degradation. Hsp40s select substrates for Hsp70 via use of an intrinsic chaperone activity to bind non-native regions of proteins. During delivery of bound cargo Hsp40s employ a conserved J-domain to stimulate Hsp70 ATPase activity and thereby stabilize complexes between Hsp70 and non-native proteins. This review describes the mechanisms by which different Hsp40s use specialized sub-domains to direct clients of Hsp70 for triage between folding versus degradation.
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Affiliation(s)
- Douglas M Cyr
- Department of Cell Biology and Physiology, School of Medicine University of North Carolina, Chapel Hill, NC, USA.
| | - Carlos H Ramos
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil.
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9
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Furutani N, Izawa S. Adaptability of wine yeast to ethanol-induced protein denaturation. FEMS Yeast Res 2022; 22:6831633. [PMID: 36385376 DOI: 10.1093/femsyr/foac059] [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: 08/31/2022] [Revised: 10/28/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
This year marks the 200th anniversary of the birth of Dr Louis Pasteur (1822-1895), who revealed that alcoholic fermentation is performed by yeast cells. Subsequently, details of the mechanisms of alcoholic fermentation and glycolysis in yeast cells have been elucidated. However, the mechanisms underlying the high tolerance and adaptability of yeast cells to ethanol are not yet fully understood. This review presents the response and adaptability of yeast cells to ethanol-induced protein denaturation. Herein, we describe the adverse effects of severe ethanol stress on intracellular proteins and the responses of yeast cells. Furthermore, recent findings on the acquired resistance of wine yeast cells to severe ethanol stress that causes protein denaturation are discussed, not only under laboratory conditions, but also during the fermentation process at 15°C to mimic the vinification process of white wine.
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Affiliation(s)
- Noboru Furutani
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan
| | - Shingo Izawa
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan
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10
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Gropp MHM, Klaips CL, Hartl FU. Formation of toxic oligomers of polyQ-expanded Huntingtin by prion-mediated cross-seeding. Mol Cell 2022; 82:4290-4306.e11. [PMID: 36272412 DOI: 10.1016/j.molcel.2022.09.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/22/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022]
Abstract
Manifestation of aggregate pathology in Huntington's disease is thought to be facilitated by a preferential vulnerability of affected brain cells to age-dependent proteostatic decline. To understand how specific cellular backgrounds may facilitate pathologic aggregation, we utilized the yeast model in which polyQ-expanded Huntingtin forms aggregates only when the endogenous prion-forming protein Rnq1 is in its amyloid-like prion [PIN+] conformation. We employed optogenetic clustering of polyQ protein as an orthogonal method to induce polyQ aggregation in prion-free [pin-] cells. Optogenetic aggregation circumvented the prion requirement for the formation of detergent-resistant polyQ inclusions but bypassed the formation of toxic polyQ oligomers, which accumulated specifically in [PIN+] cells. Reconstitution of aggregation in vitro suggested that these polyQ oligomers formed through direct templating on Rnq1 prions. These findings shed light on the mechanism of prion-mediated formation of oligomers, which may play a role in triggering polyQ pathology in the patient brain.
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Affiliation(s)
- Michael H M Gropp
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Courtney L Klaips
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Biomedical Sciences of Cells & Systems, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV Groningen, the Netherlands.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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11
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Wine Yeast Cells Acquire Resistance to Severe Ethanol Stress and Suppress Insoluble Protein Accumulation during Alcoholic Fermentation. Microbiol Spectr 2022; 10:e0090122. [PMID: 36040149 PMCID: PMC9603993 DOI: 10.1128/spectrum.00901-22] [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] [Indexed: 12/30/2022] Open
Abstract
Under laboratory conditions, acute 10% (vol/vol) ethanol stress causes protein denaturation and accumulation of insoluble proteins in yeast cells. However, yeast cells can acquire resistance to severe ethanol stress by pretreatment with mild ethanol stress (6% vol/vol) and mitigate insoluble protein accumulation under subsequent exposure to 10% (vol/vol) ethanol. On the other hand, protein quality control (PQC) of yeast cells during winemaking remains poorly understood. Ethanol concentrations in the grape must increase gradually, rather than acutely, to more than 10% (vol/vol) during the winemaking process. Gradual increases in ethanol evoke two possibilities for yeast PQC under high ethanol concentrations in the must: suppression of insoluble protein accumulation through the acquisition of resistance or the accumulation of denatured insoluble proteins. We examined these two possibilities by conducting alcoholic fermentation tests at 15°C that mimic white winemaking using synthetic grape must (SGM). The results obtained revealed the negligible accumulation of insoluble proteins in wine yeast cells throughout the fermentation process. Furthermore, wine yeast cells in fermenting SGM did not accumulate insoluble proteins when transferred to synthetic defined (SD) medium containing 10% (vol/vol) ethanol. Conversely, yeast cells cultured in SD medium accumulated insoluble proteins when transferred to fermented SGM containing 9.8% (vol/vol) ethanol. Thus, wine yeast cells acquire resistance to the cellular impact of severe ethanol stress during fermentation and mitigate the accumulation of insoluble proteins. This study provides novel insights into the PQC and robustness of wine yeast during winemaking. IMPORTANCE Winemaking is a dynamic and complex process in which ethanol concentrations gradually increase to reach >10% (vol/vol) through alcoholic fermentation. However, there is little information on protein damage in wine yeast during winemaking. We investigated the insoluble protein levels of wine yeast under laboratory conditions in SD medium and during fermentation in SGM. Under laboratory conditions, wine yeast cells, as well as laboratory strain cells, accumulated insoluble proteins under acute 10% (vol/vol) ethanol stress, and this accumulation was suppressed by pretreatment with 6% (vol/vol) ethanol. During the fermentation process, insoluble protein levels were maintained at low levels in wine yeast even when the SGM ethanol concentration exceeded 10% (vol/vol). These results indicate that the progression of wine yeast through fermentation in SGM results in stress tolerance, similar to the pretreatment of cells with mild ethanol stress. These findings further the understanding of yeast cell physiology during winemaking.
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12
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J Proteins Counteract Amyloid Propagation and Toxicity in Yeast. BIOLOGY 2022; 11:biology11091292. [PMID: 36138771 PMCID: PMC9495310 DOI: 10.3390/biology11091292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 12/02/2022]
Abstract
Simple Summary Dozens of diseases are associated with misfolded proteins that accumulate in highly ordered fibrous aggregates called amyloids. Protein quality control (PQC) factors keep cells healthy by helping maintain the integrity of the cell’s proteins and physiological processes. Yeast has been used widely for years to study how amyloids cause toxicity to cells and how PQC factors help protect cells from amyloid toxicity. The so-called J-domain proteins (JDPs) are PQC factors that are particularly effective at providing such protection. We discuss how PQC factors protect animals, human cells, and yeast from amyloid toxicity, focusing on yeast and human JDPs. Abstract The accumulation of misfolded proteins as amyloids is associated with pathology in dozens of debilitating human disorders, including diabetes, Alzheimer’s, Parkinson’s, and Huntington’s diseases. Expressing human amyloid-forming proteins in yeast is toxic, and yeast prions that propagate as infectious amyloid forms of cellular proteins are also harmful. The yeast system, which has been useful for studying amyloids and their toxic effects, has provided much insight into how amyloids affect cells and how cells respond to them. Given that an amyloid is a protein folding problem, it is unsurprising that the factors found to counteract the propagation or toxicity of amyloids in yeast involve protein quality control. Here, we discuss such factors with an emphasis on J-domain proteins (JDPs), which are the most highly abundant and diverse regulators of Hsp70 chaperones. The anti-amyloid effects of JDPs can be direct or require interaction with Hsp70.
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13
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Differential Interactions of Molecular Chaperones and Yeast Prions. J Fungi (Basel) 2022; 8:jof8020122. [PMID: 35205876 PMCID: PMC8877571 DOI: 10.3390/jof8020122] [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: 01/04/2022] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 02/01/2023] Open
Abstract
Baker’s yeast Saccharomyces cerevisiae is an important model organism that is applied to study various aspects of eukaryotic cell biology. Prions in yeast are self-perpetuating heritable protein aggregates that can be leveraged to study the interaction between the protein quality control (PQC) machinery and misfolded proteins. More than ten prions have been identified in yeast, of which the most studied ones include [PSI+], [URE3], and [PIN+]. While all of the major molecular chaperones have been implicated in propagation of yeast prions, many of these chaperones differentially impact propagation of different prions and/or prion variants. In this review, we summarize the current understanding of the life cycle of yeast prions and systematically review the effects of different chaperone proteins on their propagation. Our analysis clearly shows that Hsp40 proteins play a central role in prion propagation by determining the fate of prion seeds and other amyloids. Moreover, direct prion-chaperone interaction seems to be critically important for proper recruitment of all PQC components to the aggregate. Recent results also suggest that the cell asymmetry apparatus, cytoskeleton, and cell signaling all contribute to the complex network of prion interaction with the yeast cell.
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14
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Dong L, Liu L, Li Y, Li W, Zhou L, Xia Q. E3 ligase Smurf1 protects against misfolded SOD1 in neuronal cells by promoting its K63 ubiquitylation and aggresome formation. Hum Mol Genet 2022; 31:2035-2048. [PMID: 35022748 DOI: 10.1093/hmg/ddac008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 11/15/2022] Open
Abstract
K63-linked polyubiquitination of the neurodegenerative disease-associated misfolded protein copper-zinc superoxide dismutase (SOD1) is associated with the formation of inclusion bodies. Highly expressed E3 ligase Smurf1 promotes cellular homostasis through the enhanced capability of aggregate degradation. However, it is not well explored the role of Smurf1 in the dynamics of SOD1 aggresomes. In this study, we report that Smurf1 promotes the recruitment of SOD1 to form aggresomes. Mechanistically, Smurf1 interacts with mutant SOD1 to promote aggresome formation by modification of its K63-linked polyubiquitination. Moreover, overexpressed Smurf1 enhances mutant SOD1 aggresome formation and autophagic degradation to prevent cell death. Thus, our data suggest that Smurf1 plays an important role in attenuating protein misfolding-induced cell toxicity by both driving the sequestration of misfolded SOD1 into aggresomes and autophagic degradation.
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Affiliation(s)
- Lei Dong
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Liqun Liu
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yang Li
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Wenxuan Li
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Liying Zhou
- Beijing Tide Pharmaceutical CO., LTD, Beijing, 100000, China
| | - Qin Xia
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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15
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Acquired Resistance to Severe Ethanol Stress in Saccharomyces cerevisiae Protein Quality Control. Appl Environ Microbiol 2021; 87:AEM.02353-20. [PMID: 33361368 DOI: 10.1128/aem.02353-20] [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: 09/23/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Acute severe ethanol stress (10% [vol/vol]) damages proteins and causes the intracellular accumulation of insoluble proteins in Saccharomyces cerevisiae On the other hand, a pretreatment with mild stress increases tolerance to subsequent severe stress, which is called acquired stress resistance. It currently remains unclear whether the accumulation of insoluble proteins under severe ethanol stress may be mitigated by increasing protein quality control (PQC) activity in cells pretreated with mild stress. In the present study, we examined the induction of resistance to severe ethanol stress in PQC and confirmed that a pretreatment with 6% (vol/vol) ethanol or mild thermal stress at 37°C significantly reduced insoluble protein levels and the aggregation of Lsg1, which is prone to denaturation and aggregation by stress, in yeast cells under 10% (vol/vol) ethanol stress. The induction of this stress resistance required the new synthesis of proteins; the expression of proteins comprising the bichaperone system (Hsp104, Ssa3, and Fes1), Sis1, and Hsp42 was upregulated during the pretreatment and maintained under subsequent severe ethanol stress. Since the pretreated cells of deficient mutants in the bichaperone system (fes1Δ hsp104Δ and ssa2Δ ssa3Δ ssa4Δ) failed to sufficiently reduce insoluble protein levels and Lsg1 aggregation, the enhanced activity of the bichaperone system appears to be important for the induction of adequate stress resistance. In contrast, the importance of proteasomes and aggregases (Btn2 and Hsp42) in the induction of stress resistance has not been confirmed. These results provide further insights into the PQC activity of yeast cells under severe ethanol stress, including the brewing process.IMPORTANCE Although the budding yeast S. cerevisiae, which is used in the production of alcoholic beverages and bioethanol, is highly tolerant of ethanol, high concentrations of ethanol are also stressful to the yeast and cause various adverse effects, including protein denaturation. A pretreatment with mild stress improves the ethanol tolerance of yeast cells; however, it currently remains unclear whether it increases PQC activity and reduces the levels of denatured proteins. In the present study, we found that a pretreatment with mild ethanol upregulated the expression of proteins involved in PQC and mitigated the accumulation of insoluble proteins, even under severe ethanol stress. These results provide novel insights into ethanol tolerance and the adaptive capacity of yeast. They may also contribute to research on the physiology of yeast cells during the brewing process, in which the concentration of ethanol gradually increases.
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16
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Ayala Mariscal SM, Kirstein J. J-domain proteins interaction with neurodegenerative disease-related proteins. Exp Cell Res 2021; 399:112491. [PMID: 33460589 DOI: 10.1016/j.yexcr.2021.112491] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 12/28/2022]
Abstract
HSP70 chaperones, J-domain proteins (JDPs) and nucleotide exchange factors (NEF) form functional networks that have the ability to prevent and reverse the aggregation of proteins associated with neurodegenerative diseases. JDPs can interact with specific substrate proteins, hold them in a refolding-competent conformation and target them to specific HSP70 chaperones for remodeling. Thereby, JDPs select specific substrates and constitute an attractive target for pharmacological intervention of neurodegenerative diseases. This, under the condition that the exact mechanism of JDPs interaction with specific substrates is unveiled. In this review, we provide an overview of the structural and functional variety of JDPs that interact with neurodegenerative disease-associated proteins and we highlight those studies that identified specific residues, domains or regions of JDPs that are crucial for substrate binding.
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Affiliation(s)
- Sara María Ayala Mariscal
- Leibniz Research Institute for Molecular Pharmacology Im Forschungsverbund Berlin e.V., R.-Roessle-Strasse 10, 13125, Berlin, Germany
| | - Janine Kirstein
- Leibniz Research Institute for Molecular Pharmacology Im Forschungsverbund Berlin e.V., R.-Roessle-Strasse 10, 13125, Berlin, Germany; University of Bremen, Faculty 2, Cell Biology, Leobener Strasse, 28359, Bremen, Germany.
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17
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Jalal D, Chalissery J, Hassan AH. Irc20 Regulates the Yeast Endogenous 2-μm Plasmid Levels by Controlling Flp1. Front Mol Biosci 2020; 7:221. [PMID: 33330615 PMCID: PMC7710549 DOI: 10.3389/fmolb.2020.00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 08/07/2020] [Indexed: 12/03/2022] Open
Abstract
The endogenous yeast 2-μm plasmid while innocuous to the host, needs to be properly regulated to avoid a toxic increase in copy number. The plasmid copy number control system is under the control of the plasmid encoded recombinase, Flp1. In case of a drop in 2-μm plasmid levels due to rare plasmid mis-segregation events, the Flp1 recombinase together with the cell’s homologous recombination machinery, produce multiple copies of the 2-μm plasmid that are spooled during DNA replication. The 2-μm plasmid copy number is tightly regulated by controlled expression of Flp1 as well as its ubiquitin and SUMO modification. Here, we identify a novel regulator of the 2-μm plasmid, the ATPase, ubiquitin ligase, Irc20. Irc20 was initially identified as a homologous recombination regulator, and here we uncover a new role for Irc20 in maintaining the 2-μm plasmid copy number and segregation through regulating Flp1 protein levels in the cell.
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Affiliation(s)
- Deena Jalal
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Jisha Chalissery
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Ahmed H Hassan
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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18
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Klaips CL, Gropp MHM, Hipp MS, Hartl FU. Sis1 potentiates the stress response to protein aggregation and elevated temperature. Nat Commun 2020; 11:6271. [PMID: 33293525 PMCID: PMC7722728 DOI: 10.1038/s41467-020-20000-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
Cells adapt to conditions that compromise protein conformational stability by activating various stress response pathways, but the mechanisms used in sensing misfolded proteins remain unclear. Moreover, aggregates of disease proteins often fail to induce a productive stress response. Here, using a yeast model of polyQ protein aggregation, we identified Sis1, an essential Hsp40 co-chaperone of Hsp70, as a critical sensor of proteotoxic stress. At elevated levels, Sis1 prevented the formation of dense polyQ inclusions and directed soluble polyQ oligomers towards the formation of permeable condensates. Hsp70 accumulated in a liquid-like state within this polyQ meshwork, resulting in a potent activation of the HSF1 dependent stress response. Sis1, and the homologous DnaJB6 in mammalian cells, also regulated the magnitude of the cellular heat stress response, suggesting a general role in sensing protein misfolding. Sis1/DnaJB6 functions as a limiting regulator to enable a dynamic stress response and avoid hypersensitivity to environmental changes.
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Affiliation(s)
- Courtney L Klaips
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Michael H M Gropp
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Mark S Hipp
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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19
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Vecchi G, Sormanni P, Mannini B, Vandelli A, Tartaglia GG, Dobson CM, Hartl FU, Vendruscolo M. Proteome-wide observation of the phenomenon of life on the edge of solubility. Proc Natl Acad Sci U S A 2020; 117:1015-1020. [PMID: 31892536 PMCID: PMC6969518 DOI: 10.1073/pnas.1910444117] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
To function effectively proteins must avoid aberrant aggregation, and hence they are expected to be expressed at concentrations safely below their solubility limits. By analyzing proteome-wide mass spectrometry data of Caenorhabditis elegans, however, we show that the levels of about three-quarters of the nearly 4,000 proteins analyzed in adult animals are close to their intrinsic solubility limits, indeed exceeding them by about 10% on average. We next asked how aging and functional self-assembly influence these solubility limits. We found that despite the fact that the total quantity of proteins within the cellular environment remains approximately constant during aging, protein aggregation sharply increases between days 6 and 12 of adulthood, after the worms have reproduced, as individual proteins lose their stoichiometric balances and the cellular machinery that maintains solubility undergoes functional decline. These findings reveal that these proteins are highly prone to undergoing concentration-dependent phase separation, which on aging is rationalized in a decrease of their effective solubilities, in particular for proteins associated with translation, growth, reproduction, and the chaperone system.
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Affiliation(s)
- Giulia Vecchi
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Andrea Vandelli
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
- CRG, BIST, 08003 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avancats (ICREA), 08010 Barcelona, Spain
- Department of Biology "Charles Darwin," Sapienza University of Rome, 00185 Rome, Italy
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom;
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20
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Huang YM, Hong XZ, Shen J, Geng LJ, Pan YH, Ling W, Zhao HL. Amyloids in Site-Specific Autoimmune Reactions and Inflammatory Responses. Front Immunol 2020; 10:2980. [PMID: 31993048 PMCID: PMC6964640 DOI: 10.3389/fimmu.2019.02980] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022] Open
Abstract
Amyloid deposition is a histological hallmark of common human disorders including Alzheimer's disease (AD) and type 2 diabetes. Although some reports highlight that amyloid fibrils might activate the innate immunity system via pattern recognition receptors, here, we provide multiple lines of evidence for the protection by site-specific amyloid protein analogs and fibrils against autoimmune attacks: (1) strategies targeting clearance of the AD-related brain amyloid plaque induce high risk of deadly autoimmune destructions in subjects with cognitive dysfunction; (2) administration of amyloidogenic peptides with either full length or core hexapeptide structure consistently ameliorates signs of experimental autoimmune encephalomyelitis; (3) experimental autoimmune encephalomyelitis is exacerbated following genetic deletion of amyloid precursor proteins; (4) absence of islet amyloid coexists with T-cell-mediated insulitis in autoimmune diabetes and autoimmune polyendocrine syndrome; (5) use of islet amyloid polypeptide agonists rather than antagonists improves diabetes care; and (6) common suppressive signaling pathways by regulatory T cells are activated in both local and systemic amyloidosis. These findings indicate dual modulation activity mediated by amyloid protein monomers, oligomers, and fibrils to maintain immune homeostasis. The protection from autoimmune destruction by amyloid proteins offers a novel therapeutic approach to regenerative medicine for common degenerative diseases.
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Affiliation(s)
- Yan-Mei Huang
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Center for Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, China
| | - Xue-Zhi Hong
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Department of Rheumatology and Immunology, The First Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Jian Shen
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Department of Pathology, The First Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Li-Jun Geng
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Center for Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, China
| | - Yan-Hong Pan
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Center for Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, China
| | - Wei Ling
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Department of Endocrinology, Xiangya Medical School, Central South University, Changsha, China
| | - Hai-Lu Zhao
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Center for Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, China.,Institute of Basic Medical Sciences, Faculty of Basic Medicine, Guilin Medical University, Guilin, China
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21
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Wang Y, Zhang K, Li H, Xu X, Xue H, Wang P, Fu YV. Fine-tuning the expression of target genes using a DDI2 promoter gene switch in budding yeast. Sci Rep 2019; 9:12538. [PMID: 31467340 PMCID: PMC6715627 DOI: 10.1038/s41598-019-49000-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/21/2019] [Indexed: 11/22/2022] Open
Abstract
Tuned gene expression is crucial to the proper growth and response to the environmental changes of an organism. To enable tunable gene expression as designed is desirable in both scientific research and industrial application. Here, we introduce a novel promoter switching method based on the DDI2 promoter (PDDI2) that can fine tune the expression of target genes. We constructed a recyclable cassette (PDDI2-URA3-PDDI2) and integrated it upstream of yeast target genes to replace the native promoters by DDI2 promoter without introducing any junk sequence. We found that the presence or absence of cyanamide as an inducer could turn on or off the expression of target genes. In addition, we showed that PDDI2 could act as a gene switch to linearly regulate the expression levels of target genes in vivo. We switched the original promoters of RAD18, TUP1, and CDC6 with PDDI2 as a proof-of-concept.
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Affiliation(s)
- Yong Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Kaining Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Hanfei Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huijun Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pingping Wang
- Qingdao Baihuizhiye Biotech Co.Ltd, Qingdao, 266109, China
| | - Yu V Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. .,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100101, China.
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22
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Albert B, Kos-Braun IC, Henras AK, Dez C, Rueda MP, Zhang X, Gadal O, Kos M, Shore D. A ribosome assembly stress response regulates transcription to maintain proteome homeostasis. eLife 2019; 8:45002. [PMID: 31124783 PMCID: PMC6579557 DOI: 10.7554/elife.45002] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/23/2019] [Indexed: 12/13/2022] Open
Abstract
Ribosome biogenesis is a complex and energy-demanding process requiring tight coordination of ribosomal RNA (rRNA) and ribosomal protein (RP) production. Given the extremely high level of RP synthesis in rapidly growing cells, alteration of any step in the ribosome assembly process may impact growth by leading to proteotoxic stress. Although the transcription factor Hsf1 has emerged as a central regulator of proteostasis, how its activity is coordinated with ribosome biogenesis is unknown. Here, we show that arrest of ribosome biogenesis in the budding yeast Saccharomyces cerevisiae triggers rapid activation of a highly specific stress pathway that coordinately upregulates Hsf1 target genes and downregulates RP genes. Activation of Hsf1 target genes requires neo-synthesis of RPs, which accumulate in an insoluble fraction and presumably titrate a negative regulator of Hsf1, the Hsp70 chaperone. RP aggregation is also coincident with that of the RP gene activator Ifh1, a transcription factor that is rapidly released from RP gene promoters. Our data support a model in which the levels of newly synthetized RPs, imported into the nucleus but not yet assembled into ribosomes, work to continuously balance Hsf1 and Ifh1 activity, thus guarding against proteotoxic stress during ribosome assembly. When yeast cells are growing at top speed, they can make 2,000 new ribosomes every minute. These enormous molecular assemblies are the protein-making machines of the cell. Building new ribosomes is one of the most energy-demanding parts of cell growth and, if the process goes wrong, the results can be catastrophic. The proteins that make up the ribosomes themselves are sticky. Left unattended, they start to form toxic clumps inside the compartment that houses most of the cell’s DNA, the nucleus. A protein called Heat shock factor 1, or Hsf1 for short, plays an important role in the cell's quality control systems. It helps to manage sticky proteins by switching on genes that break down protein clumps and prevent new clumps from forming. Hsf1 levels start to rise whenever cells are struggling to keep up with protein production. If it is half-finished ribosomes that are causing the problem, cells can stop making ribosome proteins. The protein in charge of this in yeast is Ifh1. It is a transcription factor that sits at the front of the genes for ribosome proteins, switching them on. When yeast cells get stressed, Ifh1 drops away from the genes within minutes, switching them off again. Yet how this happens, and how it links to Hsf1, is a mystery. To start to provide some answers, Albert et al. disrupted the production of ribosomes in yeast cells and examined the consequences. This revealed a new rescue response, that they named the “ribosome assembly stress response”. Both Hsf1 and Ifh1 are sensitive to the build-up of unfinished ribosomes in the nucleus. As expected, Hsf1 activated when ribosome proteins started to build up, and switched on the genes needed to manage the protein clumps. The effect on Isfh1, however, was unexpected. When the unassembled ribosome proteins started to build up, it was the clumps themselves that pulled the Ifh1 proteins off the genes. The unassembled ribosomes proteins seemed to be stopping their own production. Low levels of clumped ribosome proteins in the nuclei of unstressed cells also helped to keep Hsf1 active and pull Ifh1 off the ribosome genes. It is possible that this provides continual protection against a toxic protein build-up. These findings are not only important for understanding yeast cells; cancer cells also need to produce ribosomes at a very high rate to sustain their rapid growth. They too might be prone to stresses that interrupt their ribosome assembly. As such, understanding more about this process could one day lead to new therapies to target cancer cells.
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Affiliation(s)
- Benjamin Albert
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | | | - Anthony K Henras
- Centre de Biologie Intégrative, Université Paul Sabatier, Toulouse, France
| | - Christophe Dez
- Centre de Biologie Intégrative, Université Paul Sabatier, Toulouse, France
| | - Maria Paula Rueda
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Xu Zhang
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Olivier Gadal
- Centre de Biologie Intégrative, Université Paul Sabatier, Toulouse, France
| | - Martin Kos
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - David Shore
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
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23
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Sethi R, Iyer SS, Das E, Roy I. Discrete roles of trehalose and Hsp104 in inhibition of protein aggregation in yeast cells. FEMS Yeast Res 2019; 18:5025658. [PMID: 29860440 DOI: 10.1093/femsyr/foy058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/29/2018] [Indexed: 01/21/2023] Open
Abstract
Heat shock response (HSR) is an important element of cellular homeostasis. In yeast, HSR comprises of the heat shock proteins (Hsps) and the osmolytes trehalose and glycerol. The respective roles of trehalose and Hsp104 in regulating protein aggregation remain ambiguous. We report that trehalose and Hsp104 are important during the early stages of protein aggregation, i.e. when the process is still reversible. This corroborates the earlier reported role of trehalose being an inhibitor of protein folding. Under in vitro conditions, trehalose is able to restore the GdHCl-induced loss of ATPase activity of recombinant Hsp104 to almost its original level. As the saturation phase of aggregation approaches, neither of the two components is able to exert any effect. Inactivation of Hsp104 at the stage when oligomers have already been formed increases the rate of formation of aggregates by inhibiting disaggregation of oligomers. In the absence of an active disaggregase, the oligomers are converted to mature irreversible aggregates, accelerating their formation. Our results suggest that the disaccharide may have a marginally stronger influence than Hsp104 in inhibiting protein aggregation in yeast cells.
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Affiliation(s)
- Ratnika Sethi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Shantanu S Iyer
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Eshita Das
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160062, India
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24
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Khan T, Kandola TS, Wu J, Venkatesan S, Ketter E, Lange JJ, Rodríguez Gama A, Box A, Unruh JR, Cook M, Halfmann R. Quantifying Nucleation In Vivo Reveals the Physical Basis of Prion-like Phase Behavior. Mol Cell 2019; 71:155-168.e7. [PMID: 29979963 PMCID: PMC6086602 DOI: 10.1016/j.molcel.2018.06.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/26/2018] [Accepted: 06/07/2018] [Indexed: 01/29/2023]
Abstract
Protein self-assemblies modulate protein activities over biological timescales that can exceed the lifetimes of the proteins or even the cells that harbor them. We hypothesized that these timescales relate to kinetic barriers inherent to the nucleation of ordered phases. To investigate nucleation barriers in living cells, we developed distributed amphifluoric FRET (DAmFRET). DAmFRET exploits a photoconvertible fluorophore, heterogeneous expression, and large cell numbers to quantify via flow cytometry the extent of a protein's self-assembly as a function of cellular concentration. We show that kinetic barriers limit the nucleation of ordered self-assemblies and that the persistence of the barriers with respect to concentration relates to structure. Supersaturation resulting from sequence-encoded nucleation barriers gave rise to prion behavior and enabled a prion-forming protein, Sup35 PrD, to partition into dynamic intracellular condensates or to form toxic aggregates. Our results suggest that nucleation barriers govern cytoplasmic inheritance, subcellular organization, and proteotoxicity.
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Affiliation(s)
- Tarique Khan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Tejbir S Kandola
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jianzheng Wu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | | | - Ellen Ketter
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Andrew Box
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Malcolm Cook
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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25
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Tuite MF. Yeast models of neurodegenerative diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 168:351-379. [DOI: 10.1016/bs.pmbts.2019.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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26
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Kumar J, Kline NL, Masison DC. Human DnaJB6 Antiamyloid Chaperone Protects Yeast from Polyglutamine Toxicity Separately from Spatial Segregation of Aggregates. Mol Cell Biol 2018; 38:e00437-18. [PMID: 30224519 PMCID: PMC6234286 DOI: 10.1128/mcb.00437-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 02/06/2023] Open
Abstract
Polyglutamine (polyQ) aggregates are associated with pathology in protein-folding diseases and with toxicity in the yeast Saccharomyces cerevisiae Protection from polyQ toxicity in yeast by human DnaJB6 coincides with sequestration of aggregates. Gathering of misfolded proteins into deposition sites by protein quality control (PQC) factors has led to the view that PQC processes protect cells by spatially segregating toxic aggregates. Whether DnaJB6 depends on this machinery to sequester polyQ aggregates, if this sequestration is needed for DnaJB6 to protect cells, and the identity of the deposition site are unknown. Here, we found DnaJB6-driven deposits share characteristics with perivacuolar insoluble protein deposition sites (IPODs). Binding of DnaJB6 to aggregates was necessary, but not enough, for detoxification. Focal formation required a DnaJB6-Hsp70 interaction and actin, polyQ could be detoxified without sequestration, and segregation of aggregates alone was not protective. Our findings suggest DnaJB6 binds to smaller polyQ aggregates to block their toxicity. Assembly and segregation of detoxified aggregates are driven by an Hsp70- and actin-dependent process. Our findings show sequestration of aggregates is not the primary mechanism by which DnaJB6 suppresses toxicity and raise questions regarding how and when misfolded proteins are detoxified during spatial segregation.
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Affiliation(s)
- Jyotsna Kumar
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Neila L Kline
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniel C Masison
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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27
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Chen JY, Parekh M, Seliman H, Bakshinskaya D, Dai W, Kwan K, Chen KY, Liu AYC. Heat shock promotes inclusion body formation of mutant huntingtin (mHtt) and alleviates mHtt-induced transcription factor dysfunction. J Biol Chem 2018; 293:15581-15593. [PMID: 30143534 PMCID: PMC6177601 DOI: 10.1074/jbc.ra118.002933] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/22/2018] [Indexed: 01/08/2023] Open
Abstract
PolyQ-expanded huntingtin (mHtt) variants form aggregates, termed inclusion bodies (IBs), in individuals with and models of Huntington's disease (HD). The role of IB versus diffusible mHtt in neurotoxicity remains unclear. Using a ponasterone (PA)-inducible cell model of HD, here we evaluated the effects of heat shock on the appearance and functional outcome of Htt103QExon1-EGFP expression. Quantitative image analysis indicated that 80-90% of this mHtt protein initially appears as "diffuse" signals in the cytosol, with IBs forming at high mHtt expression. A 2-h heat shock during the PA induction reduced the diffuse signal, but greatly increased mHtt IB formation in both cytosol and nucleus. Dose- and time-dependent mHtt expression suggested that nucleated polymerization drives IB formation. RNA-mediated knockdown of heat shock protein 70 (HSP70) and heat shock cognate 70 protein (HSC70) provided evidence for their involvement in promoting diffuse mHtt to form IBs. Reporter gene assays assessing the impacts of diffuse versus IB mHtt showed concordance of diffuse mHtt expression with the repression of heat shock factor 1, cAMP-responsive element-binding protein (CREB), and NF-κB activity. CREB repression was reversed by heat shock coinciding with mHtt IB formation. In an embryonic striatal neuron-derived HD model, the chemical chaperone sorbitol similarly promoted the structuring of diffuse mHtt into IBs and supported cell survival under stress. Our results provide evidence that mHtt IB formation is a chaperone-supported cellular coping mechanism that depletes diffusible mHtt conformers, alleviates transcription factor dysfunction, and promotes neuron survival.
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Affiliation(s)
- Justin Y Chen
- From the Department of Cell Biology and Neuroscience and
| | - Miloni Parekh
- From the Department of Cell Biology and Neuroscience and
| | - Hadear Seliman
- From the Department of Cell Biology and Neuroscience and
| | | | - Wei Dai
- From the Department of Cell Biology and Neuroscience and
| | - Kelvin Kwan
- From the Department of Cell Biology and Neuroscience and
| | - Kuang Yu Chen
- Department of Chemistry and Chemical Biology, Rutgers State University of New Jersey, Piscataway, New Jersey 08854
| | - Alice Y C Liu
- From the Department of Cell Biology and Neuroscience and
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28
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Abstract
The cellular prion protein, PrPC, is a small, cell surface glycoprotein with a function that is currently somewhat ill defined. It is also the key molecule involved in the family of neurodegenerative disorders called transmissible spongiform encephalopathies, which are also known as prion diseases. The misfolding of PrPC to a conformationally altered isoform, designated PrPTSE, is the main molecular process involved in pathogenesis and appears to precede many other pathologic and clinical manifestations of disease, including neuronal loss, astrogliosis, and cognitive loss. PrPTSE is also believed to be the major component of the infectious "prion," the agent responsible for disease transmission, and preparations of this protein can cause prion disease when inoculated into a naïve host. Thus, understanding the biochemical and biophysical properties of both PrPC and PrPTSE, and ultimately the mechanisms of their interconversion, is critical if we are to understand prion disease biology. Although entire books could be devoted to research pertaining to the protein, herein we briefly review the state of knowledge of prion biochemistry, including consideration of prion protein structure, function, misfolding, and dysfunction.
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Affiliation(s)
- Andrew C Gill
- School of Chemistry, Joseph Banks Laboratories, University of Lincoln, Lincoln, United Kingdom; Division of Neurobiology, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, United Kingdom.
| | - Andrew R Castle
- Division of Neurobiology, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, United Kingdom
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29
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Jena KK, Kolapalli SP, Mehto S, Nath P, Das B, Sahoo PK, Ahad A, Syed GH, Raghav SK, Senapati S, Chauhan S, Chauhan S. TRIM16 controls assembly and degradation of protein aggregates by modulating the p62-NRF2 axis and autophagy. EMBO J 2018; 37:embj.201798358. [PMID: 30143514 PMCID: PMC6138442 DOI: 10.15252/embj.201798358] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 07/18/2018] [Accepted: 07/26/2018] [Indexed: 12/20/2022] Open
Abstract
Sequestration of protein aggregates in inclusion bodies and their subsequent degradation prevents proteostasis imbalance, cytotoxicity, and proteinopathies. The underlying molecular mechanisms controlling the turnover of protein aggregates are mostly uncharacterized. Herein, we show that a TRIM family protein, TRIM16, governs the process of stress-induced biogenesis and degradation of protein aggregates. TRIM16 facilitates protein aggregate formation by positively regulating the p62-NRF2 axis. We show that TRIM16 is an integral part of the p62-KEAP1-NRF2 complex and utilizes multiple mechanisms for stabilizing NRF2. Under oxidative and proteotoxic stress conditions, TRIM16 activates ubiquitin pathway genes and p62 via NRF2, leading to ubiquitination of misfolded proteins and formation of protein aggregates. We further show that TRIM16 acts as a scaffold protein and, by interacting with p62, ULK1, ATG16L1, and LC3B, facilitates autophagic degradation of protein aggregates. Thus, TRIM16 streamlines the process of stress-induced aggregate clearance and protects cells against oxidative/proteotoxic stress-induced toxicity in vitro and in vivo Taken together, this work identifies a new mechanism of protein aggregate turnover, which could be relevant in protein aggregation-associated diseases such as neurodegeneration.
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Affiliation(s)
- Kautilya Kumar Jena
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, India.,School of Biotechnology, KIIT University, Bhubaneswar, India
| | | | - Subhash Mehto
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Parej Nath
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, India.,School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Biswajit Das
- Tumor Microenvironment and Animal Models, Institute of Life Sciences, Bhubaneswar, India.,Manipal University, Manipal, India
| | - Pradyumna Kumar Sahoo
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Abdul Ahad
- Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Gulam Hussain Syed
- Molecular Virology and Infectious Diseases, Institute of Life Sciences, Bhubaneswar, India
| | - Sunil K Raghav
- Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Shantibhusan Senapati
- Tumor Microenvironment and Animal Models, Institute of Life Sciences, Bhubaneswar, India
| | - Swati Chauhan
- Translational Research, Institute of Life Sciences, Bhubaneswar, India
| | - Santosh Chauhan
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar, India
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30
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Wisniewski BT, Sharma J, Legan ER, Paulson E, Merrill SJ, Manogaran AL. Toxicity and infectivity: insights from de novo prion formation. Curr Genet 2018; 64:117-123. [PMID: 28856415 PMCID: PMC5777878 DOI: 10.1007/s00294-017-0736-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 08/15/2017] [Accepted: 08/17/2017] [Indexed: 02/07/2023]
Abstract
Prions are infectious misfolded proteins that assemble into oligomers and large aggregates, and are associated with neurodegeneration. It is believed that the oligomers contribute to cytotoxicity, although genetic and environmental factors have also been shown to have additional roles. The study of the yeast prion [PSI +] has provided valuable insights into how prions form and why they are toxic. Our recent work suggests that SDS-resistant oligomers arise and remodel early during the prion formation process, and lysates containing these newly formed oligomers are infectious. Previous work shows that toxicity is associated with prion formation and this toxicity is exacerbated by deletion of the VPS5 gene. Here, we show that newly made oligomer formation and infectivity of vps5∆ lysates are similar to wild-type strains. However using green fluorescent protein fusions, we observe that the assembly of fluorescent cytoplasmic aggregates during prion formation is different in vps5∆ strains. Instead of large immobile aggregates, vps5∆ strains have an additional population of small mobile foci. We speculate that changes in the cellular milieu in vps5∆ strains may reduce the cell's ability to efficiently recruit and sequester newly formed prion particles into central deposition sites, resulting in toxicity.
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Affiliation(s)
- Brett T Wisniewski
- Department of Biological Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201-1881, USA
| | - Jaya Sharma
- Department of Biological Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201-1881, USA
| | - Emily R Legan
- Department of Biological Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201-1881, USA
| | - Emily Paulson
- Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53201, USA
| | - Stephen J Merrill
- Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53201, USA
| | - Anita L Manogaran
- Department of Biological Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201-1881, USA.
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31
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Wickner RB, Kryndushkin D, Shewmaker F, McGlinchey R, Edskes HK. Study of Amyloids Using Yeast. Methods Mol Biol 2018; 1779:313-339. [PMID: 29886541 PMCID: PMC7337124 DOI: 10.1007/978-1-4939-7816-8_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We detail some of the genetic, biochemical, and physical methods useful in studying amyloids in yeast, particularly the yeast prions. These methods include cytoduction (cytoplasmic mixing), infection of cells with prion amyloids, use of green fluorescent protein fusions with amyloid-forming proteins for cytology, protein purification and amyloid formation, and electron microscopy of filaments.
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Affiliation(s)
- Reed B. Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Insititutes of Health, Bethesda, MD 20892-0830
| | - Dmitry Kryndushkin
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Insititutes of Health, Bethesda, MD 20892-0830,Dept. of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Frank Shewmaker
- Dept. of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Ryan McGlinchey
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Insititutes of Health, Bethesda, MD 20892-0830
| | - Herman K. Edskes
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Insititutes of Health, Bethesda, MD 20892-0830
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32
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Klaips CL, Jayaraj GG, Hartl FU. Pathways of cellular proteostasis in aging and disease. J Cell Biol 2017; 217:51-63. [PMID: 29127110 PMCID: PMC5748993 DOI: 10.1083/jcb.201709072] [Citation(s) in RCA: 461] [Impact Index Per Article: 65.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/17/2017] [Accepted: 10/18/2017] [Indexed: 12/19/2022] Open
Abstract
Ensuring cellular protein homeostasis, or proteostasis, requires precise control of protein synthesis, folding, conformational maintenance, and degradation. A complex and adaptive proteostasis network coordinates these processes with molecular chaperones of different classes and their regulators functioning as major players. This network serves to ensure that cells have the proteins they need while minimizing misfolding or aggregation events that are hallmarks of age-associated proteinopathies, including neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. It is now clear that the capacity of cells to maintain proteostasis undergoes a decline during aging, rendering the organism susceptible to these pathologies. Here we discuss the major proteostasis pathways in light of recent research suggesting that their age-dependent failure can both contribute to and result from disease. We consider different strategies to modulate proteostasis capacity, which may help develop urgently needed therapies for neurodegeneration and other age-dependent pathologies.
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Affiliation(s)
- Courtney L Klaips
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
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33
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Tardiff DF, Brown LE, Yan X, Trilles R, Jui NT, Barrasa MI, Caldwell KA, Caldwell GA, Schaus SE, Lindquist S. Dihydropyrimidine-Thiones and Clioquinol Synergize To Target β-Amyloid Cellular Pathologies through a Metal-Dependent Mechanism. ACS Chem Neurosci 2017; 8:2039-2055. [PMID: 28628299 PMCID: PMC5705239 DOI: 10.1021/acschemneuro.7b00187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The lack of therapies for neurodegenerative diseases arises from our incomplete understanding of their underlying cellular toxicities and the limited number of predictive model systems. It is critical that we develop approaches to identify novel targets and lead compounds. Here, a phenotypic screen of yeast proteinopathy models identified dihydropyrimidine-thiones (DHPM-thiones) that selectively rescued the toxicity caused by β-amyloid (Aβ), the peptide implicated in Alzheimer's disease. Rescue of Aβ toxicity by DHPM-thiones occurred through a metal-dependent mechanism of action. The bioactivity was distinct, however, from that of the 8-hydroxyquinoline clioquinol (CQ). These structurally dissimilar compounds strongly synergized at concentrations otherwise not competent to reduce toxicity. Cotreatment ameliorated Aβ toxicity by reducing Aβ levels and restoring functional vesicle trafficking. Notably, these low doses significantly reduced deleterious off-target effects caused by CQ on mitochondria at higher concentrations. Both single and combinatorial treatments also reduced death of neurons expressing Aβ in a nematode, indicating that DHPM-thiones target a conserved protective mechanism. Furthermore, this conserved activity suggests that expression of the Aβ peptide causes similar cellular pathologies from yeast to neurons. Our identification of a new cytoprotective scaffold that requires metal-binding underscores the critical role of metal phenomenology in mediating Aβ toxicity. Additionally, our findings demonstrate the valuable potential of synergistic compounds to enhance on-target activities, while mitigating deleterious off-target effects. The identification and prosecution of synergistic compounds could prove useful for developing AD therapeutics where combination therapies may be required to antagonize diverse pathologies.
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Affiliation(s)
- Daniel F. Tardiff
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, United States
| | - Lauren E. Brown
- Department of Chemistry, Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts 02215, United States
| | - Xiaohui Yan
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Richard Trilles
- Department of Chemistry, Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts 02215, United States
| | - Nathan T. Jui
- Department of Chemistry, MIT, Cambridge, Massachusetts 02139, United States
| | - M. Inmaculada Barrasa
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, United States
| | - Kim A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Guy A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Scott E. Schaus
- Department of Chemistry, Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts 02215, United States
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, United States
- Department of Biology, MIT, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02139, United States
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34
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Wang M, Huang M, Zhang J, Ma Y, Li S, Wang J. A novel secretion and online-cleavage strategy for production of cecropin A in Escherichia coli. Sci Rep 2017; 7:7368. [PMID: 28779147 PMCID: PMC5544755 DOI: 10.1038/s41598-017-07411-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/23/2017] [Indexed: 01/08/2023] Open
Abstract
Antimicrobial peptides, promising antibiotic candidates, are attracting increasing research attention. Current methods for production of antimicrobial peptides are chemical synthesis, intracellular fusion expression, or direct separation and purification from natural sources. However, all these methods are costly, operation-complicated and low efficiency. Here, we report a new strategy for extracellular secretion and online-cleavage of antimicrobial peptides on the surface of Escherichia coli, which is cost-effective, simple and does not require complex procedures like cell disruption and protein purification. Analysis by transmission electron microscopy and semi-denaturing detergent agarose gel electrophoresis indicated that fusion proteins contain cecropin A peptides can successfully be secreted and form extracellular amyloid aggregates at the surface of Escherichia coli on the basis of E. coli curli secretion system and amyloid characteristics of sup35NM. These amyloid aggregates can be easily collected by simple centrifugation and high-purity cecropin A peptide with the same antimicrobial activity as commercial peptide by chemical synthesis was released by efficient self-cleavage of Mxe GyrA intein. Here, we established a novel expression strategy for the production of antimicrobial peptides, which dramatically reduces the cost and simplifies purification procedures and gives new insights into producing antimicrobial and other commercially-viable peptides.
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Affiliation(s)
- Meng Wang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
| | - Minhua Huang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
| | - Junjie Zhang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
| | - Yi Ma
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
| | - Shan Li
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
| | - Jufang Wang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China.
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China.
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35
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Abstract
Prions are infectious protein polymers that have been found to cause fatal diseases in mammals. Prions have also been identified in fungi (yeast and filamentous fungi), where they behave as cytoplasmic non-Mendelian genetic elements. Fungal prions correspond in most cases to fibrillary β-sheet-rich protein aggregates termed amyloids. Fungal prion models and, in particular, yeast prions were instrumental in the description of fundamental aspects of prion structure and propagation. These models established the "protein-only" nature of prions, the physical basis of strain variation, and the role of a variety of chaperones in prion propagation and amyloid aggregate handling. Yeast and fungal prions do not necessarily correspond to harmful entities but can have adaptive roles in these organisms.
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36
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Gottschling DE, Nyström T. The Upsides and Downsides of Organelle Interconnectivity. Cell 2017; 169:24-34. [PMID: 28340346 DOI: 10.1016/j.cell.2017.02.030] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/13/2017] [Accepted: 02/21/2017] [Indexed: 12/31/2022]
Abstract
Interconnectivity and feedback control are hallmarks of biological systems. This includes communication between organelles, which allows them to function and adapt to changing cellular environments. While the specific mechanisms for all communications remain opaque, unraveling the wiring of organelle networks is critical to understand how biological systems are built and why they might collapse, as occurs in aging. A comprehensive understanding of all the routes involved in inter-organelle communication is still lacking, but important themes are beginning to emerge, primarily in budding yeast. These routes are reviewed here in the context of sub-system proteostasis and complex adaptive systems theory.
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Affiliation(s)
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden.
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37
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Overexpression of the essential Sis1 chaperone reduces TDP-43 effects on toxicity and proteolysis. PLoS Genet 2017; 13:e1006805. [PMID: 28531192 PMCID: PMC5460882 DOI: 10.1371/journal.pgen.1006805] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 06/06/2017] [Accepted: 05/05/2017] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by selective loss of motor neurons with inclusions frequently containing the RNA/DNA binding protein TDP-43. Using a yeast model of ALS exhibiting TDP-43 dependent toxicity, we now show that TDP-43 overexpression dramatically alters cell shape and reduces ubiquitin dependent proteolysis of a reporter construct. Furthermore, we show that an excess of the Hsp40 chaperone, Sis1, reduced TDP-43’s effect on toxicity, cell shape and proteolysis. The strength of these effects was influenced by the presence of the endogenous yeast prion, [PIN+]. Although overexpression of Sis1 altered the TDP-43 aggregation pattern, we did not detect physical association of Sis1 with TDP-43, suggesting the possibility of indirect effects on TDP-43 aggregation. Furthermore, overexpression of the mammalian Sis1 homologue, DNAJB1, relieves TDP-43 mediated toxicity in primary rodent cortical neurons, suggesting that Sis1 and its homologues may have neuroprotective effects in ALS. Many neurodegenerative diseases are associated with aggregation of specific proteins. Thus we are interested in factors that influence the aggregation and how the aggregated proteins are associated with pathology. Here, we study a protein called TDP-43 that is frequently aggregated in the neurons of patients with amyotrophic lateral sclerosis (ALS). TDP-43 aggregates and is toxic when expressed in yeast, providing a useful model for ALS. Remarkably, a protein that modified TDP-43 toxicity in yeast successfully predicted a new ALS susceptibility gene in humans. We now report a new modifier of TDP-43 toxicity, Sis1. We show that expression of TDP-43 in yeast inhibits degradation of damaged protein, while overexpression of Sis1 restores degradation. Thus suggests a link between protein degradation and TDP-43 toxicity. Furthermore we show that a mammalian protein similar to Sis1 reduces TDP-43 toxicity in primary rodent neurons. This identifies the mammalian Sis1-like gene as a new ALS therapeutic target and possible susceptibility gene.
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38
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Barbitoff YA, Matveenko AG, Moskalenko SE, Zemlyanko OM, Newnam GP, Patel A, Chernova TA, Chernoff YO, Zhouravleva GA. To CURe or not to CURe? Differential effects of the chaperone sorting factor Cur1 on yeast prions are mediated by the chaperone Sis1. Mol Microbiol 2017; 105:242-257. [PMID: 28431189 DOI: 10.1111/mmi.13697] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2017] [Indexed: 02/06/2023]
Abstract
Yeast self-perpetuating protein aggregates (prions) provide a convenient model for studying various components of the cellular protein quality control system. Molecular chaperones and chaperone-sorting factors, such as yeast Cur1 protein, play key role in proteostasis via tight control of partitioning and recycling of misfolded proteins. In this study, we show that, despite the previously described ability of Cur1 to antagonize the yeast prion [URE3], it enhances propagation and phenotypic manifestation of another prion, [PSI+ ]. We demonstrate that both curing of [URE3] and enhancement of [PSI+ ] in the presence of excess Cur1 are counteracted by the cochaperone Hsp40-Sis1 in a dosage-dependent manner, and show that the effect of Cur1 on prions parallels effects of the attachment of nuclear localization signal to Sis1, indicating that Cur1 acts on prions via its previously reported ability to relocalize Sis1 from the cytoplasm to nucleus. This shows that the direction in which Cur1 influences a prion depends on how this specific prion responds to relocalization of Sis1.
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Affiliation(s)
- Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Svetlana E Moskalenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Olga M Zemlyanko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Gary P Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA
| | - Ayesha Patel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yury O Chernoff
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA.,Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
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39
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Hill SM, Hanzén S, Nyström T. Restricted access: spatial sequestration of damaged proteins during stress and aging. EMBO Rep 2017; 18:377-391. [PMID: 28193623 PMCID: PMC5331209 DOI: 10.15252/embr.201643458] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/19/2016] [Accepted: 01/24/2017] [Indexed: 01/08/2023] Open
Abstract
The accumulation of damaged and aggregated proteins is a hallmark of aging and increased proteotoxic stress. To limit the toxicity of damaged and aggregated proteins and to ensure that the damage is not inherited by succeeding cell generations, a system of spatial quality control operates to sequester damaged/aggregated proteins into inclusions at specific protective sites. Such spatial sequestration and asymmetric segregation of damaged proteins have emerged as key processes required for cellular rejuvenation. In this review, we summarize findings on the nature of the different quality control sites identified in yeast, on genetic determinants required for spatial quality control, and on how aggregates are recognized depending on the stress generating them. We also briefly compare the yeast system to spatial quality control in other organisms. The data accumulated demonstrate that spatial quality control involves factors beyond the canonical quality control factors, such as chaperones and proteases, and opens up new venues in approaching how proteotoxicity might be mitigated, or delayed, upon aging.
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Affiliation(s)
- Sandra Malmgren Hill
- Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Sarah Hanzén
- Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Thomas Nyström
- Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
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40
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Chernova TA, Wilkinson KD, Chernoff YO. Prions, Chaperones, and Proteostasis in Yeast. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a023663. [PMID: 27815300 DOI: 10.1101/cshperspect.a023663] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Prions are alternatively folded, self-perpetuating protein isoforms involved in a variety of biological and pathological processes. Yeast prions are protein-based heritable elements that serve as an excellent experimental system for studying prion biology. The propagation of yeast prions is controlled by the same Hsp104/70/40 chaperone machinery that is involved in the protection of yeast cells against proteotoxic stress. Ribosome-associated chaperones, proteolytic pathways, cellular quality-control compartments, and cytoskeletal networks influence prion formation, maintenance, and toxicity. Environmental stresses lead to asymmetric prion distribution in cell divisions. Chaperones and cytoskeletal proteins mediate this effect. Overall, this is an intimate relationship with the protein quality-control machinery of the cell, which enables prions to be maintained and reproduced. The presence of many of these same mechanisms in higher eukaryotes has implications for the diagnosis and treatment of mammalian amyloid diseases.
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Affiliation(s)
- Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Keith D Wilkinson
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332-2000.,Laboratory of Amyloid Biology and Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
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41
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Sideri T, Yashiroda Y, Ellis DA, Rodríguez-López M, Yoshida M, Tuite MF, Bähler J. The copper transport-associated protein Ctr4 can form prion-like epigenetic determinants in Schizosaccharomyces pombe. MICROBIAL CELL 2017; 4:16-28. [PMID: 28191457 PMCID: PMC5302157 DOI: 10.15698/mic2017.01.552] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Prions are protein-based infectious entities associated with fatal brain diseases
in animals, but also modify a range of host-cell phenotypes in the budding
yeast, Saccharomyces cerevisiae. Many questions remain about
the evolution and biology of prions. Although several functionally distinct
prion-forming proteins exist in S. cerevisiae, [HET-s] of
Podospora anserina is the only other known fungal prion.
Here we investigated prion-like, protein-based epigenetic transmission in the
fission yeast Schizosaccharomyces pombe. We show that
S. pombe cells can support the formation and maintenance of
the prion form of the S. cerevisiae Sup35 translation factor
[PSI+], and that the formation and propagation
of these Sup35 aggregates is inhibited by guanidine hydrochloride, indicating
commonalities in prion propagation machineries in these evolutionary diverged
yeasts. A proteome-wide screen identified the Ctr4 copper transporter subunit as
a putative prion with a predicted prion-like domain. Overexpression of
the ctr4 gene resulted in large Ctr4 protein aggregates
that were both detergent and proteinase-K resistant. Cells carrying such
[CTR+] aggregates showed increased sensitivity
to oxidative stress, and this phenotype could be transmitted to aggregate-free
[ctr-] cells by transformation with
[CTR+] cell extracts. Moreover, this
[CTR+] phenotype was inherited in a
non-Mendelian manner following mating with naïve
[ctr-] cells, but intriguingly the
[CTR+] phenotype was not eliminated by
guanidine-hydrochloride treatment. Thus, Ctr4 exhibits multiple features
diagnostic of other fungal prions and is the first example of a prion in fission
yeast. These findings suggest that transmissible protein-based determinants of
traits may be more widespread among fungi.
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Affiliation(s)
- Theodora Sideri
- University College London, Research Department of Genetics, Evolution & Environment and Institute of Healthy Ageing, London, U.K
| | - Yoko Yashiroda
- Chemical Genetics Laboratory, RIKEN and Chemical Genomics Research Group, RIKEN CSRS, Saitama, Japan
| | - David A Ellis
- University College London, Research Department of Genetics, Evolution & Environment and Institute of Healthy Ageing, London, U.K
| | - María Rodríguez-López
- University College London, Research Department of Genetics, Evolution & Environment and Institute of Healthy Ageing, London, U.K
| | - Minoru Yoshida
- Chemical Genetics Laboratory, RIKEN and Chemical Genomics Research Group, RIKEN CSRS, Saitama, Japan
| | - Mick F Tuite
- Kent Fungal Group, University of Kent, School of Biosciences, Canterbury, Kent, U.K
| | - Jürg Bähler
- University College London, Research Department of Genetics, Evolution & Environment and Institute of Healthy Ageing, London, U.K
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42
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Tikhodeyev ON, Tarasov OV, Bondarev SA. Allelic variants of hereditary prions: The bimodularity principle. Prion 2017; 11:4-24. [PMID: 28281926 PMCID: PMC5360123 DOI: 10.1080/19336896.2017.1283463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 01/04/2017] [Accepted: 01/10/2017] [Indexed: 12/26/2022] Open
Abstract
Modern biology requires modern genetic concepts equally valid for all discovered mechanisms of inheritance, either "canonical" (mediated by DNA sequences) or epigenetic. Applying basic genetic terms such as "gene" and "allele" to protein hereditary factors is one of the necessary steps toward these concepts. The basic idea that different variants of the same prion protein can be considered as alleles has been previously proposed by Chernoff and Tuite. In this paper, the notion of prion allele is further developed. We propose the idea that any prion allele is a bimodular hereditary system that depends on a certain DNA sequence (DNA determinant) and a certain epigenetic mark (epigenetic determinant). Alteration of any of these 2 determinants may lead to establishment of a new prion allele. The bimodularity principle is valid not only for hereditary prions; it seems to be universal for any epigenetic hereditary factor.
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Affiliation(s)
- Oleg N. Tikhodeyev
- Department of Genetics & Biotechnology, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Oleg V. Tarasov
- Department of Genetics & Biotechnology, Saint-Petersburg State University, Saint-Petersburg, Russia
- Saint-Petersburg Scientific Center of RAS, Saint-Petersburg, Russia
| | - Stanislav A. Bondarev
- Department of Genetics & Biotechnology, Saint-Petersburg State University, Saint-Petersburg, Russia
- The Laboratory of Amyloid Biology, Saint-Petersburg State University, Saint-Petersburg, Russia
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43
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Ungelenk S, Moayed F, Ho CT, Grousl T, Scharf A, Mashaghi A, Tans S, Mayer MP, Mogk A, Bukau B. Small heat shock proteins sequester misfolding proteins in near-native conformation for cellular protection and efficient refolding. Nat Commun 2016; 7:13673. [PMID: 27901028 PMCID: PMC5141385 DOI: 10.1038/ncomms13673] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 10/24/2016] [Indexed: 12/30/2022] Open
Abstract
Small heat shock proteins (sHsp) constitute an evolutionary conserved yet diverse family of chaperones acting as first line of defence against proteotoxic stress. sHsps coaggregate with misfolded proteins but the molecular basis and functional implications of these interactions, as well as potential sHsp specific differences, are poorly explored. In a comparative analysis of the two yeast sHsps, Hsp26 and Hsp42, we show in vitro that model substrates retain near-native state and are kept physically separated when complexed with either sHsp, while being completely unfolded when aggregated without sHsps. Hsp42 acts as aggregase to promote protein aggregation and specifically ensures cellular fitness during heat stress. Hsp26 in contrast lacks aggregase function but is superior in facilitating Hsp70/Hsp100-dependent post-stress refolding. Our findings indicate the sHsps of a cell functionally diversify in stress defence, but share the working principle to promote sequestration of misfolding proteins for storage in native-like conformation.
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Affiliation(s)
- Sophia Ungelenk
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg D-69120, Germany
| | - Fatemeh Moayed
- FOM Institute for Atomic and Molecular Physics (AMOLF), Science Park 104, Amsterdam 1098 XG, The Netherlands
| | - Chi-Ting Ho
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg D-69120, Germany
| | - Tomas Grousl
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg D-69120, Germany
| | - Annette Scharf
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Alireza Mashaghi
- FOM Institute for Atomic and Molecular Physics (AMOLF), Science Park 104, Amsterdam 1098 XG, The Netherlands
| | - Sander Tans
- FOM Institute for Atomic and Molecular Physics (AMOLF), Science Park 104, Amsterdam 1098 XG, The Netherlands
| | - Matthias P Mayer
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Axel Mogk
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg D-69120, Germany
| | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg D-69120, Germany
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44
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Use ofade1andade2mutations for development of a versatile red/white colour assay of amyloid-induced oxidative stress insaccharomyces cerevisiae. Yeast 2016; 33:607-620. [DOI: 10.1002/yea.3209] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 09/14/2016] [Accepted: 09/14/2016] [Indexed: 12/20/2022] Open
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45
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Matveenko AG, Drozdova PB, Belousov MV, Moskalenko SE, Bondarev SA, Barbitoff YA, Nizhnikov AA, Zhouravleva GA. SFP1-mediated prion-dependent lethality is caused by increased Sup35 aggregation and alleviated by Sis1. Genes Cells 2016; 21:1290-1308. [DOI: 10.1111/gtc.12444] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 09/14/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew G. Matveenko
- St Petersburg Branch; Vavilov Institute of General Genetics of the Russian Academy of Sciences; St Petersburg Russia
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| | - Polina B. Drozdova
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| | - Mikhail V. Belousov
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
| | - Svetlana E. Moskalenko
- St Petersburg Branch; Vavilov Institute of General Genetics of the Russian Academy of Sciences; St Petersburg Russia
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| | - Yury A. Barbitoff
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
| | - Anton A. Nizhnikov
- St Petersburg Branch; Vavilov Institute of General Genetics of the Russian Academy of Sciences; St Petersburg Russia
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- All-Russia Research Institute for Agricultural Microbiology; Pushkin St Petersburg Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
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46
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Sethi R, Patel V, Saleh AA, Roy I. Cellular toxicity of yeast prion protein Rnq1 can be modulated by N-terminal wild type huntingtin. Arch Biochem Biophys 2016; 590:82-89. [DOI: 10.1016/j.abb.2015.11.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 11/20/2015] [Accepted: 11/21/2015] [Indexed: 01/07/2023]
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47
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Reidy M, Sharma R, Roberts BL, Masison DC. Human J-protein DnaJB6b Cures a Subset of Saccharomyces cerevisiae Prions and Selectively Blocks Assembly of Structurally Related Amyloids. J Biol Chem 2015; 291:4035-47. [PMID: 26702057 DOI: 10.1074/jbc.m115.700393] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Indexed: 11/06/2022] Open
Abstract
Human chaperone DnaJB6, an Hsp70 co-chaperone whose defects cause myopathies, protects cells from polyglutamine toxicity and prevents purified polyglutamine and Aβ peptides from forming amyloid. Yeast prions [URE3] and [PSI(+)] propagate as amyloid forms of Ure2 and Sup35 proteins, respectively. Here we find DnaJB6-protected yeast cells from polyglutamine toxicity and cured yeast of both [URE3] prions and weak variants of [PSI(+)] prions but not strong [PSI(+)] prions. Weak and strong variants of [PSI(+)] differ only in the structural conformation of their amyloid cores. In line with its anti-prion effects, DnaJB6 prevented purified Sup35NM from forming amyloids at 37 °C, which produce predominantly weak [PSI(+)] variants when used to infect yeast, but not at 4 °C, which produces mostly strong [PSI(+)] variants. Thus, structurally distinct amyloids composed of the same protein were differentially sensitive to the anti-amyloid activity of DnaJB6 both in vitro and in vivo. These findings have important implications for strategies using DnaJB6 as a target for therapy in amyloid disorders.
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Affiliation(s)
- Michael Reidy
- From the Laboratory of Biochemistry and Genetics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Ruchika Sharma
- From the Laboratory of Biochemistry and Genetics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Brittany-Lee Roberts
- From the Laboratory of Biochemistry and Genetics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Daniel C Masison
- From the Laboratory of Biochemistry and Genetics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
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48
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Moosavi B, Mousavi B, Yang GF. Actin, Membrane Trafficking and the Control of Prion Induction, Propagation and Transmission in Yeast. Traffic 2015; 17:5-20. [PMID: 26503767 DOI: 10.1111/tra.12344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/23/2015] [Accepted: 10/23/2015] [Indexed: 12/16/2022]
Abstract
The model eukaryotic yeast Saccharomyces cerevisiae has proven a useful model system in which prion biogenesis and elimination are studied. Several yeast prions exist in budding yeast and a number of studies now suggest that these alternate protein conformations may play important roles in the cell. During the last few years cellular factors affecting prion induction, propagation and elimination have been identified. Amongst these, proteins involved in the regulation of the actin cytoskeleton and dynamic membrane processes such as endocytosis have been found to play a critical role not only in facilitating de novo prion formation but also in prion propagation. Here we briefly review prion formation and maintenance with special attention given to the cellular processes that require the functionality of the actin cytoskeleton.
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Affiliation(s)
- Behrooz Moosavi
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, P.R. China
| | - Bibimaryam Mousavi
- Laboratory of Organometallics, Catalysis and Ordered Materials, State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan, P.R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, P.R. China
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49
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Kumar N, Gaur D, Gupta A, Puri A, Sharma D. Hsp90-Associated Immunophilin Homolog Cpr7 Is Required for the Mitotic Stability of [URE3] Prion in Saccharomyces cerevisiae. PLoS Genet 2015; 11:e1005567. [PMID: 26473735 PMCID: PMC4608684 DOI: 10.1371/journal.pgen.1005567] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/14/2015] [Indexed: 11/18/2022] Open
Abstract
The role of Hsp70 chaperones in yeast prion propagation is well established. Highly conserved Hsp90 chaperones participate in a number of cellular processes, such as client protein maturation, protein degradation, cellular signalling and apoptosis, but little is known about their role in propagation of infectious prion like aggregates. Here, we examine the influence of Hsp90 in the maintenance of yeast prion [URE3] which is a prion form of native protein Ure2, and reveal a previously unknown role of Hsp90 as an important regulator of [URE3] stability. We show that the C-terminal MEEVD pentapeptide motif, but not the client maturation activity of Hsp90, is essential for [URE3] prion stability. In testing deletions of various Hsp90 co-chaperones known to bind this motif, we find the immunophilin homolog Cpr7 is essential for [URE3] propagation. We show that Cpr7 interacts with Ure2 and enhances its fibrillation. The requirement of Cpr7 is specific for [URE3] as its deletion does not antagonize both strong and weak variant of another yeast prion [PSI+], suggesting a distinct role of the Hsp90 co-chaperone with different yeast prions. Our data show that, similar to the Hsp70 family, the Hsp90 chaperones also influence yeast prion maintenance, and that immunophilins could regulate protein multimerization independently of their activity as peptidyl-prolyl isomerases.
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Affiliation(s)
- Navinder Kumar
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Deepika Gaur
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Arpit Gupta
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Anuradhika Puri
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Deepak Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
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50
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Walters RW, Muhlrad D, Garcia J, Parker R. Differential effects of Ydj1 and Sis1 on Hsp70-mediated clearance of stress granules in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2015; 21:1660-1671. [PMID: 26199455 PMCID: PMC4536325 DOI: 10.1261/rna.053116.115] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 06/05/2015] [Indexed: 05/27/2023]
Abstract
Stress granules and P-bodies are conserved assemblies of nontranslating mRNAs in eukaryotic cells that can be related to RNA-protein aggregates found in some neurodegenerative diseases. Herein, we examine how the Hsp70/Hsp40 protein chaperones affected the assembly and disassembly of stress granules and P-bodies in yeast. We observed that Hsp70 and the Ydj1 and Sis1 Hsp40 proteins accumulated in stress granules and defects in these proteins led to decreases in the disassembly and/or clearance of stress granules. We observed that individual Hsp40 proteins have different effects on stress granules with defects in Ydj1 leading to accumulation of stress granules in the vacuole and limited recovery of translation following stress, which suggests that Ydj1 promotes disassembly of stress granules to promote translation. In contrast, defects in Sis1 did not affect recovery of translation, accumulated cytoplasmic stress granules, and showed reductions in the targeting of stress granules to the vacuole. This demonstrates a new principle whereby alternative disassembly machineries lead to different fates of components within stress granules, thereby providing additional avenues for regulation of their assembly, composition, and function. Moreover, a role for Hsp70 and Hsp40 proteins in stress granule disassembly couples the assembly of these stress responsive structures to the proteostatic state of the cell.
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Affiliation(s)
- Robert W Walters
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80303, USA
| | - Denise Muhlrad
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80303, USA Howard Hughes Medical Institute, Boulder, Colorado 80303, USA
| | - Jennifer Garcia
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80303, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80303, USA Howard Hughes Medical Institute, Boulder, Colorado 80303, USA
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