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Miller SC, Wegrzynowicz AK, Cole SJ, Hayward RE, Ganser SJ, Hines JK. Hsp40/JDP Requirements for the Propagation of Synthetic Yeast Prions. Viruses 2022; 14:v14102160. [PMID: 36298715 PMCID: PMC9611480 DOI: 10.3390/v14102160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
Yeast prions are protein-based transmissible elements, most of which are amyloids. The chaperone protein network in yeast is inexorably linked to the spreading of prions during cell division by fragmentation of amyloid prion aggregates. Specifically, the core “prion fragmentation machinery” includes the proteins Hsp104, Hsp70 and the Hsp40/J-domain protein (JDP) Sis1. Numerous novel amyloid-forming proteins have been created and examined in the yeast system and occasionally these amyloids are also capable of continuous Hsp104-dependent propagation in cell populations, forming synthetic prions. However, additional chaperone requirements, if any, have not been determined. Here, we report the first instances of a JDP-Hsp70 system requirement for the propagation of synthetic prions. We utilized constructs from a system of engineered prions with prion-forming domains (PrDs) consisting of a polyQ stretch interrupted by a single heterologous amino acid interspersed every fifth residue. These “polyQX” PrDs are fused to the MC domains of Sup35, creating chimeric proteins of which a subset forms synthetic prions in yeast. For four of these prions, we show that SIS1 repression causes prion loss in a manner consistent with Sis1′s known role in prion fragmentation. PolyQX prions were sensitive to Sis1 expression levels to differing degrees, congruent with the variability observed among native prions. Our results expand the scope known Sis1 functionality, demonstrating that Sis1 acts on amyloids broadly, rather than through specific protein–protein interactions with individual yeast prion-forming proteins.
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2
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Kaur T, Raju M, Alshareedah I, Davis RB, Potoyan DA, Banerjee PR. Sequence-encoded and composition-dependent protein-RNA interactions control multiphasic condensate morphologies. Nat Commun 2021; 12:872. [PMID: 33558506 PMCID: PMC7870978 DOI: 10.1038/s41467-021-21089-4] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Multivalent protein-protein and protein-RNA interactions are the drivers of biological phase separation. Biomolecular condensates typically contain a dense network of multiple proteins and RNAs, and their competing molecular interactions play key roles in regulating the condensate composition and structure. Employing a ternary system comprising of a prion-like polypeptide (PLP), arginine-rich polypeptide (RRP), and RNA, we show that competition between the PLP and RNA for a single shared partner, the RRP, leads to RNA-induced demixing of PLP-RRP condensates into stable coexisting phases-homotypic PLP condensates and heterotypic RRP-RNA condensates. The morphology of these biphasic condensates (non-engulfing/ partial engulfing/ complete engulfing) is determined by the RNA-to-RRP stoichiometry and the hierarchy of intermolecular interactions, providing a glimpse of the broad range of multiphasic patterns that are accessible to these condensates. Our findings provide a minimal set of physical rules that govern the composition and spatial organization of multicomponent and multiphasic biomolecular condensates.
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Affiliation(s)
- Taranpreet Kaur
- Department of Physics, University at Buffalo, Buffalo, NY, USA
| | | | | | - Richoo B Davis
- Department of Physics, University at Buffalo, Buffalo, NY, USA
| | - Davit A Potoyan
- Department of Chemistry, Iowa State University, Ames, IA, USA.
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3
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Owen I, Rhoads S, Yee D, Wyne H, Gery K, Hannula I, Sundrum M, Shewmaker F. The prion-like domain of Fused in Sarcoma is phosphorylated by multiple kinases affecting liquid- and solid-phase transitions. Mol Biol Cell 2020; 31:2522-2536. [PMID: 32877292 PMCID: PMC7851872 DOI: 10.1091/mbc.e20-05-0290] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Fused in Sarcoma (FUS) is a ubiquitously expressed protein that can phase-separate from nucleoplasm and cytoplasm into distinct liquid-droplet structures. It is predominantly nuclear and most of its functions are related to RNA and DNA metabolism. Excessive persistence of FUS within cytoplasmic phase-separated assemblies is implicated in the diseases amyotrophic lateral sclerosis and frontotemporal dementia. Phosphorylation of FUS’s prion-like domain (PrLD) by nuclear phosphatidylinositol 3-kinase-related kinase (PIKK)-family kinases following DNA damage was previously shown to alter FUS’s liquid-phase and solid-phase transitions in cell models and in vitro. However, proteomic data suggest that FUS’s PrLD is phosphorylated at numerous additional sites, and it is unknown if other non-PIKK and nonnuclear kinases might be influencing FUS’s phase transitions. Here we evaluate disease mutations and stress conditions that increase FUS accumulation into cytoplasmic phase-separated structures. We observed that cytoplasmic liquid-phase structures contain FUS phosphorylated at novel sites, which occurred independent of PIKK-family kinases. We engineered phosphomimetic substitutions within FUS’s PrLD and observed that mimicking a few phosphorylation sites strongly inhibited FUS solid-phase aggregation, while minimally altering liquid-phase condensation. These effects occurred independent of the exact location of the phosphomimetic substitutions, suggesting that modulation of PrLD phosphorylation may offer therapeutic strategies that are specific for solid-phase aggregation observed in disease.
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Affiliation(s)
- Izzy Owen
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814
| | - Shannon Rhoads
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814
| | - Debra Yee
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814
| | - Hala Wyne
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814
| | - Kevin Gery
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814
| | - Isabelle Hannula
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814
| | - Meenakshi Sundrum
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814
| | - Frank Shewmaker
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814
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4
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Shida T, Kamatari YO, Yoda T, Yamaguchi Y, Feig M, Ohhashi Y, Sugita Y, Kuwata K, Tanaka M. Short disordered protein segment regulates cross-species transmission of a yeast prion. Nat Chem Biol 2020; 16:756-765. [PMID: 32284601 DOI: 10.1038/s41589-020-0516-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
Soluble prion proteins contingently encounter foreign prion aggregates, leading to cross-species prion transmission. However, how its efficiency is regulated by structural fluctuation of the host soluble prion protein remains unsolved. In the present study, through the use of two distantly related yeast prion Sup35 proteins, we found that a specific conformation of a short disordered segment governs interspecies prion transmissibility. Using a multidisciplinary approach including high-resolution NMR and molecular dynamics simulation, we identified critical residues within this segment that allow interspecies prion transmission in vitro and in vivo, by locally altering dynamics and conformation of soluble prion proteins. Remarkably, subtle conformational differences caused by a methylene group between asparagine and glutamine sufficed to change the short segment structure and substantially modulate the cross-seeding activity. Thus, our findings uncover how conformational dynamics of the short segment in the host prion protein impacts cross-species prion transmission. More broadly, our study provides mechanistic insights into cross-seeding between heterologous proteins.
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Affiliation(s)
- Toshinobu Shida
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan.,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Japan
| | - Yuji O Kamatari
- Life Science Research Center, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Takao Yoda
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan.,Computational Biophysics Research Team, RIKEN Research Center for Computational Science, Kobe, Japan
| | - Yoshiki Yamaguchi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Japan.,RIKEN-Max Planck Joint Research Center, Wako, Japan
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yumiko Ohhashi
- Graduate School of Science, Kobe University, Kobe, Japan.,Department of Applied Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Research Center for Computational Science, Kobe, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Motomasa Tanaka
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan. .,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Japan.
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5
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Cascarina SM, Ross ED. Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes. BMC Genomics 2020; 21:23. [PMID: 31914925 PMCID: PMC6947906 DOI: 10.1186/s12864-019-6425-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Impaired proteostatic regulation of proteins with prion-like domains (PrLDs) is associated with a variety of human diseases including neurodegenerative disorders, myopathies, and certain forms of cancer. For many of these disorders, current models suggest a prion-like molecular mechanism of disease, whereby proteins aggregate and spread to neighboring cells in an infectious manner. The development of prion prediction algorithms has facilitated the large-scale identification of PrLDs among "reference" proteomes for various organisms. However, the degree to which intraspecies protein sequence diversity influences predicted prion propensity has not been systematically examined. RESULTS Here, we explore protein sequence variation introduced at genetic, post-transcriptional, and post-translational levels, and its influence on predicted aggregation propensity for human PrLDs. We find that sequence variation is relatively common among PrLDs and in some cases can result in relatively large differences in predicted prion propensity. Sequence variation introduced at the post-transcriptional level (via alternative splicing) also commonly affects predicted aggregation propensity, often by direct inclusion or exclusion of a PrLD. Finally, analysis of a database of sequence variants associated with human disease reveals a number of mutations within PrLDs that are predicted to increase prion propensity. CONCLUSIONS Our analyses expand the list of candidate human PrLDs, quantitatively estimate the effects of sequence variation on the aggregation propensity of PrLDs, and suggest the involvement of prion-like mechanisms in additional human diseases.
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Affiliation(s)
- Sean M Cascarina
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Eric D Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
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6
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Ryan VH, Fawzi NL. Physiological, Pathological, and Targetable Membraneless Organelles in Neurons. Trends Neurosci 2019; 42:693-708. [PMID: 31493925 PMCID: PMC6779520 DOI: 10.1016/j.tins.2019.08.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 07/03/2019] [Accepted: 08/05/2019] [Indexed: 12/20/2022]
Abstract
Neurons require unique subcellular compartmentalization to function efficiently. Formed from proteins and RNAs through liquid-liquid phase separation, membraneless organelles (MLOs) have emerged as one way in which cells form distinct, specialized compartments in the absence of lipid membranes. We first discuss MLOs that are common to many cell types as well as those that are specific to neurons. Interestingly, many proteins associated with neurodegenerative disease are found in MLOs, particularly in stress and transport granules. We next review possible links between neurodegeneration and MLOs, and the hypothesis that the protein and RNA inclusions formed in disease are related to the functional complexes occurring inside these MLOs. Finally, we discuss the hypothesis that protein post-translational modifications (PTMs), which can alter phase separation, can modulate MLO formation and provide potential new therapeutic strategies for currently untreatable neurodegenerative diseases.
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Affiliation(s)
- Veronica H Ryan
- Neuroscience Graduate Program, Brown University, Providence, RI 02912, USA
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA.
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7
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Prion Replication in the Mammalian Cytosol: Functional Regions within a Prion Domain Driving Induction, Propagation, and Inheritance. Mol Cell Biol 2018; 38:MCB.00111-18. [PMID: 29784771 PMCID: PMC6048315 DOI: 10.1128/mcb.00111-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/14/2018] [Indexed: 12/19/2022] Open
Abstract
Prions of lower eukaryotes are transmissible protein particles that propagate by converting homotypic soluble proteins into growing protein assemblies. Prion activity is conferred by so-called prion domains, regions of low complexity that are often enriched in glutamines and asparagines (Q/N). Prions of lower eukaryotes are transmissible protein particles that propagate by converting homotypic soluble proteins into growing protein assemblies. Prion activity is conferred by so-called prion domains, regions of low complexity that are often enriched in glutamines and asparagines (Q/N). The compositional similarity of fungal prion domains with intrinsically disordered domains found in many mammalian proteins raises the question of whether similar sequence elements can drive prion-like phenomena in mammals. Here, we define sequence features of the prototype Saccharomyces cerevisiae Sup35 prion domain that govern prion activities in mammalian cells by testing the ability of deletion mutants to assemble into self-perpetuating particles. Interestingly, the amino-terminal Q/N-rich tract crucially important for prion induction in yeast was dispensable for the prion life cycle in mammalian cells. Spontaneous and template-assisted prion induction, growth, and maintenance were preferentially driven by the carboxy-terminal region of the prion domain that contains a putative soft amyloid stretch recently proposed to act as a nucleation site for prion assembly. Our data demonstrate that preferred prion nucleation domains can differ between lower and higher eukaryotes, resulting in the formation of prions with strikingly different amyloid cores.
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8
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Cascarina SM, Paul KR, Machihara S, Ross ED. Sequence features governing aggregation or degradation of prion-like proteins. PLoS Genet 2018; 14:e1007517. [PMID: 30005071 PMCID: PMC6059496 DOI: 10.1371/journal.pgen.1007517] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/25/2018] [Accepted: 06/26/2018] [Indexed: 01/12/2023] Open
Abstract
Enhanced protein aggregation and/or impaired clearance of aggregates can lead to neurodegenerative disorders such as Alzheimer's Disease, Huntington's Disease, and prion diseases. Therefore, many protein quality control factors specialize in recognizing and degrading aggregation-prone proteins. Prions, which generally result from self-propagating protein aggregates, must therefore evade or outcompete these quality control systems in order to form and propagate in a cellular context. We developed a genetic screen in yeast that allowed us to explore the sequence features that promote degradation versus aggregation of a model glutamine/asparagine (Q/N)-rich prion domain from the yeast prion protein, Sup35, and two model glycine (G)-rich prion-like domains from the human proteins hnRNPA1 and hnRNPA2. Unexpectedly, we found that aggregation propensity and degradation propensity could be uncoupled in multiple ways. First, only a subset of classically aggregation-promoting amino acids elicited a strong degradation response in the G-rich prion-like domains. Specifically, large aliphatic residues enhanced degradation of the prion-like domains, whereas aromatic residues promoted prion aggregation without enhancing degradation. Second, the degradation-promoting effect of aliphatic residues was suppressed in the context of the Q/N-rich prion domain, and instead led to a dose-dependent increase in the frequency of spontaneous prion formation. Degradation suppression correlated with Q/N content of the surrounding prion domain, potentially indicating an underappreciated activity for these residues in yeast prion domains. Collectively, these results provide key insights into how certain aggregation-prone proteins may evade protein quality control degradation systems.
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Affiliation(s)
- Sean M. Cascarina
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Kacy R. Paul
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Satoshi Machihara
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Eric D. Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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9
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Affiliation(s)
- Andrea N. Killian
- Department of Chemistry, Lafayette College, Easton, Pennsylvania, United States of America
| | - Justin K. Hines
- Department of Chemistry, Lafayette College, Easton, Pennsylvania, United States of America
- * E-mail:
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10
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Monahan Z, Ryan VH, Janke AM, Burke KA, Rhoads SN, Zerze GH, O'Meally R, Dignon GL, Conicella AE, Zheng W, Best RB, Cole RN, Mittal J, Shewmaker F, Fawzi NL. Phosphorylation of the FUS low-complexity domain disrupts phase separation, aggregation, and toxicity. EMBO J 2017; 36:2951-2967. [PMID: 28790177 PMCID: PMC5641905 DOI: 10.15252/embj.201696394] [Citation(s) in RCA: 474] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 07/06/2017] [Accepted: 07/07/2017] [Indexed: 12/13/2022] Open
Abstract
Neuronal inclusions of aggregated RNA‐binding protein fused in sarcoma (FUS) are hallmarks of ALS and frontotemporal dementia subtypes. Intriguingly, FUS's nearly uncharged, aggregation‐prone, yeast prion‐like, low sequence‐complexity domain (LC) is known to be targeted for phosphorylation. Here we map in vitro and in‐cell phosphorylation sites across FUS LC. We show that both phosphorylation and phosphomimetic variants reduce its aggregation‐prone/prion‐like character, disrupting FUS phase separation in the presence of RNA or salt and reducing FUS propensity to aggregate. Nuclear magnetic resonance spectroscopy demonstrates the intrinsically disordered structure of FUS LC is preserved after phosphorylation; however, transient domain collapse and self‐interaction are reduced by phosphomimetics. Moreover, we show that phosphomimetic FUS reduces aggregation in human and yeast cell models, and can ameliorate FUS‐associated cytotoxicity. Hence, post‐translational modification may be a mechanism by which cells control physiological assembly and prevent pathological protein aggregation, suggesting a potential treatment pathway amenable to pharmacologic modulation.
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Affiliation(s)
- Zachary Monahan
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University, Bethesda, MD, USA
| | - Veronica H Ryan
- Neuroscience Graduate Program, Brown University, Providence, RI, USA
| | - Abigail M Janke
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA
| | - Kathleen A Burke
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA
| | - Shannon N Rhoads
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University, Bethesda, MD, USA
| | - Gül H Zerze
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA
| | - Robert O'Meally
- Johns Hopkins Mass Spectrometry and Proteomic Facility, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory L Dignon
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA
| | - Alexander E Conicella
- Graduate Program in Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Wenwei Zheng
- Laboratory of Chemical Physics, National Institutes of Health, Bethesda, MD, USA
| | - Robert B Best
- Laboratory of Chemical Physics, National Institutes of Health, Bethesda, MD, USA
| | - Robert N Cole
- Johns Hopkins Mass Spectrometry and Proteomic Facility, Johns Hopkins University, Baltimore, MD, USA
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA
| | - Frank Shewmaker
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University, Bethesda, MD, USA
| | - Nicolas L Fawzi
- Neuroscience Graduate Program, Brown University, Providence, RI, USA .,Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA.,Graduate Program in Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
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11
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Shattuck JE, Waechter AC, Ross ED. The effects of glutamine/asparagine content on aggregation and heterologous prion induction by yeast prion-like domains. Prion 2017; 11:249-264. [PMID: 28665753 DOI: 10.1080/19336896.2017.1344806] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Prion-like domains are low complexity, intrinsically disordered domains that compositionally resemble yeast prion domains. Many prion-like domains are involved in the formation of either functional or pathogenic protein aggregates. These aggregates range from highly dynamic liquid droplets to highly ordered detergent-insoluble amyloid-like aggregates. To better understand the amino acid sequence features that promote conversion to stable, detergent-insoluble aggregates, we used the prediction algorithm PAPA to identify predicted aggregation-prone prion-like domains with a range of compositions. While almost all of the predicted aggregation-prone domains formed foci when expressed in cells, the ability to form the detergent-insoluble aggregates was highly correlated with glutamine/asparagine (Q/N) content, suggesting that high Q/N content may specifically promote conversion to the amyloid state in vivo. We then used this data set to examine cross-seeding between prion-like proteins. The prion protein Sup35 requires the presence of a second prion, [PIN+], to efficiently form prions, but this requirement can be circumvented by the expression of various Q/N-rich protein fragments. Interestingly, almost all of the Q/N-rich domains that formed SDS-insoluble aggregates were able to promote prion formation by Sup35, highlighting the highly promiscuous nature of these interactions.
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Affiliation(s)
- Jenifer E Shattuck
- a Department of Biochemistry and Molecular Biology , Colorado State University , Fort Collins , CO , USA
| | - Aubrey C Waechter
- a Department of Biochemistry and Molecular Biology , Colorado State University , Fort Collins , CO , USA
| | - Eric D Ross
- a Department of Biochemistry and Molecular Biology , Colorado State University , Fort Collins , CO , USA
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12
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Effects of Mutations on the Aggregation Propensity of the Human Prion-Like Protein hnRNPA2B1. Mol Cell Biol 2017; 37:MCB.00652-16. [PMID: 28137911 DOI: 10.1128/mcb.00652-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 01/19/2017] [Indexed: 12/31/2022] Open
Abstract
Hundreds of human proteins contain prion-like domains, which are a subset of low-complexity domains with high amino acid compositional similarity to yeast prion domains. A recently characterized mutation in the prion-like domain of the human heterogeneous nuclear ribonucleoprotein hnRNPA2B1 increases the aggregation propensity of the protein and causes multisystem proteinopathy. The mutant protein forms cytoplasmic inclusions when expressed in Drosophila, the mutation accelerates aggregation in vitro, and the mutant prion-like domain can substitute for a portion of a yeast prion domain in supporting prion activity. To examine the relationship between amino acid sequence and aggregation propensity, we made a diverse set of point mutations in the hnRNPA2B1 prion-like domain. We found that the effects on prion formation in Saccharomyces cerevisiae and aggregation in vitro could be predicted entirely based on amino acid composition. However, composition was an imperfect predictor of inclusion formation in Drosophila; while most mutations showed similar behaviors in yeast, in vitro, and in Drosophila, a few showed anomalous behavior. Collectively, these results demonstrate the significant progress that has been made in predicting the effects of mutations on intrinsic aggregation propensity while also highlighting the challenges of predicting the effects of mutations in more complex organisms.
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13
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Batlle C, Iglesias V, Navarro S, Ventura S. Prion-like proteins and their computational identification in proteomes. Expert Rev Proteomics 2017; 14:335-350. [DOI: 10.1080/14789450.2017.1304214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Cristina Batlle
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Valentin Iglesias
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
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14
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MacLea KS. What Makes a Prion: Infectious Proteins From Animals to Yeast. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:227-276. [PMID: 28109329 DOI: 10.1016/bs.ircmb.2016.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
While philosophers in ancient times had many ideas for the cause of contagion, the modern study of infective agents began with Fracastoro's 1546 proposal that invisible "spores" spread infectious disease. However, firm categorization of the pathogens of the natural world would need to await a mature germ theory that would not arise for 300 years. In the 19th century, the earliest pathogens described were bacteria and other cellular microbes. By the close of that century, the work of Ivanovsky and Beijerinck introduced the concept of a virus, an infective particle smaller than any known cell. Extending into the early-mid-20th century there was an explosive growth in pathogenic microbiology, with a cellular or viral cause identified for nearly every transmissible disease. A few occult pathogens remained to be discovered, including the infectious proteins (prions) proposed by Prusiner in 1982. This review discusses the prions identified in mammals, yeasts, and other organisms, focusing on the amyloid-based prions. I discuss the essential biochemical properties of these agents and the application of this knowledge to diseases of protein misfolding and aggregation, as well as the utility of yeast as a model organism to study prion and amyloid proteins that affect human and animal health. Further, I summarize the ideas emerging out of these studies that the prion concept may go beyond proteinaceous infectious particles and that prions may be a subset of proteins having general nucleating or seeding functions involved in noninfectious as well as infectious pathogenic protein aggregation.
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Affiliation(s)
- K S MacLea
- University of New Hampshire, Manchester, NH, United States.
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15
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Abstract
Despite major efforts devoted to understanding the phenomenon of prion transmissibility, it is still poorly understood how this property is encoded in the amino acid sequence. In recent years, experimental data on yeast prion domains allow to start at least partially decrypting the sequence requirements of prion formation. These experiments illustrate the need for intrinsically disordered sequence regions enriched with a particularly high proportion of glutamine and asparagine. Bioinformatic analysis suggests that these regions strike a balance between sufficient amyloid nucleation propensity on the one hand and disorder on the other, which ensures availability of the amyloid prone regions but entropically prevents unwanted nucleation and facilitates brittleness required for propagation.
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Affiliation(s)
- Raimon Sabate
- a Departament de Fisicoquímica ; Facultat de Farmàcia; and Institut de Nanociència i Nanotecnologia (IN2UB); Universitat de Barcelona ; Barcelona , Spain
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16
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Espargaró A, Busquets MA, Estelrich J, Sabate R. Predicting the aggregation propensity of prion sequences. Virus Res 2015; 207:127-35. [PMID: 25747492 DOI: 10.1016/j.virusres.2015.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 02/19/2015] [Accepted: 03/02/2015] [Indexed: 11/19/2022]
Abstract
The presence of prions can result in debilitating and neurodegenerative diseases in mammals and protein-based genetic elements in fungi. Prions are defined as a subclass of amyloids in which the self-aggregation process becomes self-perpetuating and infectious. Like all amyloids, prions polymerize into fibres with a common core formed of β-sheet structures oriented perpendicular to the fibril axes which form a structure known as a cross-β structure. The intermolecular β-sheet propensity, a characteristic of the amyloid pattern, as well as other key parameters of amyloid fibril formation can be predicted. Mathematical algorithms have been proposed to predict both amyloid and prion propensities. However, it has been shown that the presence of amyloid-prone regions in a polypeptide sequence could be insufficient for amyloid formation. It has also often been stated that the formation of amyloid fibrils does not imply that these are prions. Despite these limitations, in silico prediction of amyloid and prion propensities should help detect potential new prion sequences in mammals. In addition, the determination of amyloid-prone regions in prion sequences could be very useful in understanding the effect of sporadic mutations and polymorphisms as well as in the search for therapeutic targets.
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Affiliation(s)
- Alba Espargaró
- Department of Physical Chemistry, Faculty of Pharmacy, University of Barcelona, Avda. Joan XXIII 27-31, E-08028 Barcelona, Spain; Institute of Nanoscience and Nanotechnology of the University of Barcelona (IN(2)UB), Spain
| | - Maria Antònia Busquets
- Department of Physical Chemistry, Faculty of Pharmacy, University of Barcelona, Avda. Joan XXIII 27-31, E-08028 Barcelona, Spain; Institute of Nanoscience and Nanotechnology of the University of Barcelona (IN(2)UB), Spain
| | - Joan Estelrich
- Department of Physical Chemistry, Faculty of Pharmacy, University of Barcelona, Avda. Joan XXIII 27-31, E-08028 Barcelona, Spain; Institute of Nanoscience and Nanotechnology of the University of Barcelona (IN(2)UB), Spain
| | - Raimon Sabate
- Department of Physical Chemistry, Faculty of Pharmacy, University of Barcelona, Avda. Joan XXIII 27-31, E-08028 Barcelona, Spain; Institute of Nanoscience and Nanotechnology of the University of Barcelona (IN(2)UB), Spain.
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17
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Sabate R, Rousseau F, Schymkowitz J, Ventura S. What makes a protein sequence a prion? PLoS Comput Biol 2015; 11:e1004013. [PMID: 25569335 PMCID: PMC4288708 DOI: 10.1371/journal.pcbi.1004013] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 10/29/2014] [Indexed: 11/18/2022] Open
Abstract
Typical amyloid diseases such as Alzheimer's and Parkinson's were thought to exclusively result from de novo aggregation, but recently it was shown that amyloids formed in one cell can cross-seed aggregation in other cells, following a prion-like mechanism. Despite the large experimental effort devoted to understanding the phenomenon of prion transmissibility, it is still poorly understood how this property is encoded in the primary sequence. In many cases, prion structural conversion is driven by the presence of relatively large glutamine/asparagine (Q/N) enriched segments. Several studies suggest that it is the amino acid composition of these regions rather than their specific sequence that accounts for their priogenicity. However, our analysis indicates that it is instead the presence and potency of specific short amyloid-prone sequences that occur within intrinsically disordered Q/N-rich regions that determine their prion behaviour, modulated by the structural and compositional context. This provides a basis for the accurate identification and evaluation of prion candidate sequences in proteomes in the context of a unified framework for amyloid formation and prion propagation.
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Affiliation(s)
- Raimon Sabate
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, Barcelona, Spain
- * E-mail: (RS); (SV)
| | - Frederic Rousseau
- VIB Switch Laboratory, VIB, Leuven, Belgium
- Departement for Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- VIB Switch Laboratory, VIB, Leuven, Belgium
- Departement for Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
- * E-mail: (RS); (SV)
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18
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Abstract
Prions (infectious proteins) cause fatal neurodegenerative diseases in mammals. In the yeast Saccharomyces cerevisiae, many toxic and lethal variants of the [PSI+] and [URE3] prions have been identified in laboratory strains, although some commonly studied variants do not seem to impair cell growth. Phylogenetic analysis has revealed four major clades of S. cerevisiae that share histories of two prion proteins and largely correspond to different ecological niches of yeast. The [PIN+] prion was most prevalent in commercialized niches, infrequent among wine/vineyard strains, and not observed in ancestral isolates. As previously reported, the [PSI+] and [URE3] prions are not found in any of these strains. Patterns of heterozygosity revealed genetic mosaicism and indicated extensive outcrossing among divergent strains in commercialized environments. In contrast, ancestral isolates were all homozygous and wine/vineyard strains were closely related to each other and largely homozygous. Cellular growth patterns were highly variable within and among clades, although ancestral isolates were the most efficient sporulators and domesticated strains showed greater tendencies for flocculation. [PIN+]-infected strains had a significantly higher likelihood of polyploidy, showed a higher propensity for flocculation compared to uninfected strains, and had higher sporulation efficiencies compared to domesticated, uninfected strains. Extensive phenotypic variability among strains from different environments suggests that S. cerevisiae is a niche generalist and that most wild strains are able to switch from asexual to sexual and from unicellular to multicellular growth in response to environmental conditions. Our data suggest that outbreeding and multicellular growth patterns adapted for domesticated environments are ecological risk factors for the [PIN+] prion in wild yeast.
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19
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Abstract
Prion formation involves the conversion of proteins from a soluble form into an infectious amyloid form. Most yeast prion proteins contain glutamine/asparagine-rich regions that are responsible for prion aggregation. Prion formation by these domains is driven primarily by amino acid composition, not primary sequence, yet there is a surprising disconnect between the amino acids thought to have the highest aggregation propensity and those that are actually found in yeast prion domains. Specifically, a recent mutagenic screen suggested that both aromatic and non-aromatic hydrophobic residues strongly promote prion formation. However, while aromatic residues are common in yeast prion domains, non-aromatic hydrophobic residues are strongly under-represented. Here, we directly test the effects of hydrophobic and aromatic residues on prion formation. Remarkably, we found that insertion of as few as two hydrophobic residues resulted in a multiple orders-of-magnitude increase in prion formation, and significant acceleration of in vitro amyloid formation. Thus, insertion or deletion of hydrophobic residues provides a simple tool to control the prion activity of a protein. These data, combined with bioinformatics analysis, suggest a limit on the number of strongly prion-promoting residues tolerated in glutamine/asparagine-rich domains. This limit may explain the under-representation of non-aromatic hydrophobic residues in yeast prion domains. Prion activity requires not only that a protein be able to form prion fibers, but also that these fibers be cleaved to generate new independently-segregating aggregates to offset dilution by cell division. Recent studies suggest that aromatic residues, but not non-aromatic hydrophobic residues, support the fiber cleavage step. Therefore, we propose that while both aromatic and non-aromatic hydrophobic residues promote prion formation, aromatic residues are favored in yeast prion domains because they serve a dual function, promoting both prion formation and chaperone-dependent prion propagation.
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20
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Rubin J, Khosravi H, Bruce KL, Lydon ME, Behrens SH, Chernoff YO, Bommarius AS. Ion-specific effects on prion nucleation and strain formation. J Biol Chem 2013; 288:30300-30308. [PMID: 23990463 DOI: 10.1074/jbc.m113.467829] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ordered, fibrous, self-seeding aggregates of misfolded proteins known as amyloids are associated with important diseases in mammals and control phenotypic traits in fungi. A given protein may adopt multiple amyloid conformations, known as variants or strains, each of which leads to a distinct disease pattern or phenotype. Here, we study the effect of Hofmeister ions on amyloid nucleation and strain generation by the prion domain-containing fragment (Sup35NM) of a yeast protein Sup35p. Strongly hydrated anions (kosmotropes) initiate nucleation quickly and cause rapid fiber elongation, whereas poorly hydrated anions (chaotropes) delay nucleation and mildly affect the elongation rate. For the first time, we demonstrate that kosmotropes favor formation of amyloid strains that are characterized by lower thermostability and higher frangibility in vitro and stronger phenotypic and proliferation patterns effectively in vivo as compared with amyloids formed in chaotropes. These phenomena point to inherent differences in the biochemistry of Hofmeister ions. Our work shows that the ionic composition of a solution not only influences the kinetics of amyloid nucleation but also determines the amyloid strain that is preferentially formed.
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Affiliation(s)
- Jonathan Rubin
- From the School of Chemical and Biomolecular Engineering,; Parker H. Petit Institute of Bioengineering and Bioscience
| | - Hasan Khosravi
- Parker H. Petit Institute of Bioengineering and Bioscience,; School of Chemistry and Biochemistry, and
| | - Kathryn L Bruce
- Parker H. Petit Institute of Bioengineering and Bioscience,; School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332
| | | | - Sven H Behrens
- From the School of Chemical and Biomolecular Engineering,; Parker H. Petit Institute of Bioengineering and Bioscience
| | - Yury O Chernoff
- Parker H. Petit Institute of Bioengineering and Bioscience,; School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332.
| | - Andreas S Bommarius
- From the School of Chemical and Biomolecular Engineering,; Parker H. Petit Institute of Bioengineering and Bioscience,; School of Chemistry and Biochemistry, and.
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21
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Derkatch IL, Liebman SW. The story of stolen chaperones: how overexpression of Q/N proteins cures yeast prions. Prion 2013; 7:294-300. [PMID: 23924684 PMCID: PMC3904315 DOI: 10.4161/pri.26021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Prions are self-seeding alternate protein conformations. Most yeast prions contain glutamine/asparagine (Q/N)-rich domains that promote the formation of amyloid-like prion aggregates. Chaperones, including Hsp104 and Sis1, are required to continually break these aggregates into smaller “seeds.” Decreasing aggregate size and increasing the number of growing aggregate ends facilitates both aggregate transmission and growth. Our previous work showed that overexpression of 11 proteins with Q/N-rich domains facilitates the de novo aggregation of Sup35 into the [PSI+] prion, presumably by a cross-seeding mechanism. We now discuss our recent paper, in which we showed that overexpression of most of these same 11 Q/N-rich proteins, including Pin4C and Cyc8, destabilized pre-existing Q/N rich prions. Overexpression of both Pin4C and Cyc8 caused [PSI+] aggregates to enlarge. This is incompatible with a previously proposed “capping” model where the overexpressed Q/N-rich protein poisons, or “caps,” the growing aggregate ends. Rather the data match what is expected of a reduction in prion severing by chaperones. Indeed, while Pin4C overexpression does not alter chaperone levels, Pin4C aggregates sequester chaperones away from the prion aggregates. Cyc8 overexpression cures [PSI+] by inducing an increase in Hsp104 levels, as excess Hsp104 binds to [PSI+] aggregates in a way that blocks their shearing.
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Affiliation(s)
- Irina L Derkatch
- Department of Neuroscience; Columbia University; New York, NY USA
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22
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Yang Z, Hong JY, Derkatch IL, Liebman SW. Heterologous gln/asn-rich proteins impede the propagation of yeast prions by altering chaperone availability. PLoS Genet 2013; 9:e1003236. [PMID: 23358669 PMCID: PMC3554615 DOI: 10.1371/journal.pgen.1003236] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 11/26/2012] [Indexed: 12/16/2022] Open
Abstract
Prions are self-propagating conformations of proteins that can cause heritable phenotypic traits. Most yeast prions contain glutamine (Q)/asparagine (N)-rich domains that facilitate the accumulation of the protein into amyloid-like aggregates. Efficient transmission of these infectious aggregates to daughter cells requires that chaperones, including Hsp104 and Sis1, continually sever the aggregates into smaller “seeds.” We previously identified 11 proteins with Q/N-rich domains that, when overproduced, facilitate the de novo aggregation of the Sup35 protein into the [PSI+] prion state. Here, we show that overexpression of many of the same 11 Q/N-rich proteins can also destabilize pre-existing [PSI+] or [URE3] prions. We explore in detail the events leading to the loss (curing) of [PSI+] by the overexpression of one of these proteins, the Q/N-rich domain of Pin4, which causes Sup35 aggregates to increase in size and decrease in transmissibility to daughter cells. We show that the Pin4 Q/N-rich domain sequesters Hsp104 and Sis1 chaperones away from the diffuse cytoplasmic pool. Thus, a mechanism by which heterologous Q/N-rich proteins impair prion propagation appears to be the loss of cytoplasmic Hsp104 and Sis1 available to sever [PSI+]. Certain proteins can occasionally misfold into infectious aggregates called prions. Once formed, these aggregates grow by attracting the soluble form of that protein to join them. The presence of these aggregates can cause profound effects on cells and, in humans, can cause diseases such as transmissible spongiform encephalopathies (TSEs). In yeast, the aggregates are efficiently transmitted to daughter cells because they are cut into small pieces by molecular scissors (chaperones). Here we show that heritable prion aggregates are frequently lost when we overproduce certain other proteins with curing activity. We analyzed one such protein in detail and found that when it is overproduced it forms aggregates that sequester chaperones. This sequestration appears to block the ability of the chaperones to cut the prion aggregates. The result is that the prions get too large to be transmitted to daughter cells. Such sequestration of molecular scissors provides a potential approach to thwart the propagation of disease-causing infectious protein aggregates.
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Affiliation(s)
- Zi Yang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Joo Y. Hong
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, United States of America
| | - Irina L. Derkatch
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Neuroscience, Columbia University, New York, New York, United States of America
| | - Susan W. Liebman
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, United States of America
- * E-mail:
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23
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Ross ED, Maclea KS, Anderson C, Ben-Hur A. A bioinformatics method for identifying Q/N-rich prion-like domains in proteins. Methods Mol Biol 2013; 1017:219-28. [PMID: 23719919 DOI: 10.1007/978-1-62703-438-8_16] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Numerous proteins contain domains that are enriched in glutamine and asparagine residues, and aggregation of some of these proteins has been linked to both prion formation in yeast and a number of human diseases. Unfortunately, predicting whether a given glutamine/asparagine-rich protein will aggregate has proven difficult. Here we describe a recently developed algorithm designed to predict the aggregation propensity of glutamine/asparagine-rich proteins. We discuss the basis for the algorithm, its limitations, and usage of recently developed online and downloadable versions of the algorithm.
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Affiliation(s)
- Eric D Ross
- Department of Biochemistry, Colorado State University, Fort Collins, CO, USA
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24
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Abstract
Prions are important disease agents and epigenetic regulatory elements. Prion formation involves the structural conversion of proteins from a soluble form into an insoluble amyloid form. In many cases, this structural conversion is driven by a glutamine/asparagine (Q/N)-rich prion-forming domain. However, our understanding of the sequence requirements for prion formation and propagation by Q/N-rich domains has been insufficient for accurate prion propensity prediction or prion domain design. By focusing exclusively on amino acid composition, we have developed a prion aggregation prediction algorithm (PAPA), specifically designed to predict prion propensity of Q/N-rich proteins. Here, we show not only that this algorithm is far more effective than traditional amyloid prediction algorithms at predicting prion propensity of Q/N-rich proteins, but remarkably, also that PAPA is capable of rationally designing protein domains that function as prions in vivo.
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25
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Abstract
Prions are infectious proteins with altered conformations converted from otherwise normal host proteins. While there is only one known mammalian prion protein, PrP, a handful of prion proteins have been identified in the yeast Saccharomyces cerevisiae. Yeast prion proteins usually have a defined region called prion domain (PrD) essential for prion properties, which are typically rich in glutamine (Q) and asparagine (N). Despite sharing several common features, individual yeast PrDs are generally intricate and divergent in their compositional characteristics, which potentially implicates their prion phenotypes, such as prion-mediated transcriptional regulations.
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Affiliation(s)
- Zhiqiang Du
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, IL, USA.
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26
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Kryndushkin D, Shewmaker F. Modeling ALS and FTLD proteinopathies in yeast: an efficient approach for studying protein aggregation and toxicity. Prion 2011; 5:250-7. [PMID: 22052354 DOI: 10.4161/pri.17229] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In recent years there have been several reports of human neurodegenerative diseases that involve protein misfolding being modeled in the yeast Saccharomyces cerevisiae. This review summarizes recent advances in understanding the specific mechanisms underlying intracellular neuronal pathology during Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Lobar Degeneration (FTLD), including SOD1, TDP-43 and FUS protein inclusions and the potential of these proteins to be involved in pathogenic prion-like mechanisms. More specifically, we focus on findings from yeast systems that offer tremendous possibilities for screening for genetic and chemical modifiers of disease-related proteotoxicity.
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Affiliation(s)
- Dmitry Kryndushkin
- Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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27
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Abstract
The unexpected discovery of two prions, [URE3] and [PSI+], in Saccharomyces cerevisiae led to questions about how many other proteins could undergo similar prion-based structural conversions. However, [URE3] and [PSI+] were discovered by serendipity in genetic screens. Cataloging the full range of prions in yeast or in other organisms will therefore require more systematic search methods. Taking advantage of some of the unique features of prions, various researchers have developed bioinformatic and experimental methods for identifying novel prion proteins. These methods have generated long lists of prion candidates. The systematic testing of some of these prion candidates has led to notable successes; however, even in yeast, where rapid growth rate and ease of genetic manipulation aid in testing for prion activity, such candidate testing is laborious. Development of better methods to winnow the field of prion candidates will greatly aid in the discovery of new prions, both in yeast and in other organisms, and help us to better understand the role of prions in biology.
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Affiliation(s)
- Kyle S MacLea
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
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28
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Toombs JA, Liss NM, Cobble KR, Ben-Musa Z, Ross ED. [PSI+] maintenance is dependent on the composition, not primary sequence, of the oligopeptide repeat domain. PLoS One 2011; 6:e21953. [PMID: 21760933 PMCID: PMC3132755 DOI: 10.1371/journal.pone.0021953] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 06/14/2011] [Indexed: 01/29/2023] Open
Abstract
[PSI+], the prion form of the yeast Sup35 protein, results from the structural conversion of Sup35 from a soluble form into an infectious amyloid form. The infectivity of prions is thought to result from chaperone-dependent fiber cleavage that breaks large prion fibers into smaller, inheritable propagons. Like the mammalian prion protein PrP, Sup35 contains an oligopeptide repeat domain. Deletion analysis indicates that the oligopeptide repeat domain is critical for [PSI+] propagation, while a distinct region of the prion domain is responsible for prion nucleation. The PrP oligopeptide repeat domain can substitute for the Sup35 oligopeptide repeat domain in supporting [PSI+] propagation, suggesting a common role for repeats in supporting prion maintenance. However, randomizing the order of the amino acids in the Sup35 prion domain does not block prion formation or propagation, suggesting that amino acid composition is the primary determinant of Sup35's prion propensity. Thus, it is unclear what role the oligopeptide repeats play in [PSI+] propagation: the repeats could simply act as a non-specific spacer separating the prion nucleation domain from the rest of the protein; the repeats could contain specific compositional elements that promote prion propagation; or the repeats, while not essential for prion propagation, might explain some unique features of [PSI+]. Here, we test these three hypotheses and show that the ability of the Sup35 and PrP repeats to support [PSI+] propagation stems from their amino acid composition, not their primary sequences. Furthermore, we demonstrate that compositional requirements for the repeat domain are distinct from those of the nucleation domain, indicating that prion nucleation and propagation are driven by distinct compositional features.
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Affiliation(s)
- James A. Toombs
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Nathan M. Liss
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Kacy R. Cobble
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Zobaida Ben-Musa
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Eric D. Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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29
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Hines JK, Craig EA. The sensitive [SWI (+)] prion: new perspectives on yeast prion diversity. Prion 2011; 5:164-8. [PMID: 21811098 DOI: 10.4161/pri.5.3.16895] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Yeast prions are heritable protein-based genetic elements which rely on molecular chaperone proteins for stable transmission to cell progeny. Within the past few years, five new prions have been validated and 18 additional putative prions identified in Saccharomyces cerevisiae. The exploration of the physical and biological properties of these "nouveau prions" has begun to reveal the extent of prion diversity in yeast. We recently reported that one such prion, [SWI(+)], differs from the best studied, archetypal prion [PSI(+)] in several significant ways. ( 1) Notably, [SWI(+)] is highly sensitive to alterations in Hsp70 system chaperone activity and is lost upon growth at elevated temperatures. In that report we briefly noted a correlation amongst prions regarding amino acid composition, seed number and sensitivity to the activity of the Hsp70 chaperone system. Here we extend that analysis and put forth the idea that [SWI(+)] may be representative of a class of asparagine-rich yeast prions which also includes [URE3], [MOT3(+)] and [ISP(+)], distinct from the glutamine-rich prions such as [PSI(+)] and [RNQ(+)]. While much work remains, it is apparent that our understanding of the extent of the diversity of prion characteristics is in its infancy.
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Affiliation(s)
- Justin K Hines
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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30
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A small, glutamine-free domain propagates the [SWI(+)] prion in budding yeast. Mol Cell Biol 2011; 31:3436-44. [PMID: 21670156 DOI: 10.1128/mcb.05338-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeast prions are self-propagating protein conformations that transmit heritable phenotypes in an epigenetic manner. The recently identified yeast prion [SWI(+)] is an alternative conformation of Swi1, a component of the evolutionarily conserved SWI/SNF chromatin-remodeling complex. Formation of the [SWI(+)] prion results in a partial loss-of-function phenotype for Swi1. The amino-terminal region of Swi1 is dispensable for its normal function but is required for [SWI(+)] formation and propagation; however, the precise prion domain (PrD) of Swi1 has not been elucidated. Here, we define the minimal Swi1 PrD as the first 37 amino acids of the protein. This region is extremely asparagine rich but, unexpectedly, contains no glutamine residues. This unusually small prion domain is sufficient for aggregation, propagation, and transmission of the [SWI(+)] prion. Because of its unusual size and composition, the Swi1 prion domain defined here has important implications for describing and identifying novel prions.
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31
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Gonzalez Nelson AC, Ross ED. Interactions between non-identical prion proteins. Semin Cell Dev Biol 2011; 22:437-43. [PMID: 21354317 DOI: 10.1016/j.semcdb.2011.02.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Revised: 02/16/2011] [Accepted: 02/17/2011] [Indexed: 11/24/2022]
Abstract
Prion formation involves the conversion of soluble proteins into an infectious amyloid form. This process is highly specific, with prion aggregates templating the conversion of identical proteins. However, in some cases non-identical prion proteins can interact to promote or inhibit prion formation or propagation. These interactions affect both the efficiency with which prion diseases are transmitted across species and the normal physiology of yeast prion formation and propagation. Here we examine two types of heterologous prion interactions: interactions between related proteins from different species (the species barrier) and interactions between unrelated prion proteins within a single species. Interestingly, although very subtle changes in protein sequence can significantly reduce or eliminate cross-species prion transmission, in Saccharomyces cerevisiae completely unrelated prion proteins can interact to affect prion formation and propagation.
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Affiliation(s)
- Aaron C Gonzalez Nelson
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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32
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Hines JK, Li X, Du Z, Higurashi T, Li L, Craig EA. [SWI], the prion formed by the chromatin remodeling factor Swi1, is highly sensitive to alterations in Hsp70 chaperone system activity. PLoS Genet 2011; 7:e1001309. [PMID: 21379326 PMCID: PMC3040656 DOI: 10.1371/journal.pgen.1001309] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 01/12/2011] [Indexed: 11/24/2022] Open
Abstract
The yeast prion [SWI+], formed of heritable amyloid aggregates of the Swi1 protein, results in a partial loss of function of the SWI/SNF chromatin-remodeling complex, required for the regulation of a diverse set of genes. Our genetic analysis revealed that [SWI+] propagation is highly dependent upon the action of members of the Hsp70 molecular chaperone system, specifically the Hsp70 Ssa, two of its J-protein co-chaperones, Sis1 and Ydj1, and the nucleotide exchange factors of the Hsp110 family (Sse1/2). Notably, while all yeast prions tested thus far require Sis1, [SWI+] is the only one known to require the activity of Ydj1, the most abundant J-protein in yeast. The C-terminal region of Ydj1, which contains the client protein interaction domain, is required for [SWI+] propagation. However, Ydj1 is not unique in this regard, as another, closely related J-protein, Apj1, can substitute for it when expressed at a level approaching that of Ydj1. While dependent upon Ydj1 and Sis1 for propagation, [SWI+] is also highly sensitive to overexpression of both J-proteins. However, this increased prion-loss requires only the highly conserved 70 amino acid J-domain, which serves to stimulate the ATPase activity of Hsp70 and thus to stabilize its interaction with client protein. Overexpression of the J-domain from Sis1, Ydj1, or Apj1 is sufficient to destabilize [SWI+]. In addition, [SWI+] is lost upon overexpression of Sse nucleotide exchange factors, which act to destabilize Hsp70's interaction with client proteins. Given the plethora of genes affected by the activity of the SWI/SNF chromatin-remodeling complex, it is possible that this sensitivity of [SWI+] to the activity of Hsp70 chaperone machinery may serve a regulatory role, keeping this prion in an easily-lost, meta-stable state. Such sensitivity may provide a means to reach an optimal balance of phenotypic diversity within a cell population to better adapt to stressful environments. Yeast prions are heritable genetic elements, formed spontaneously by aggregation of a single protein. Prions can thus generate diverse phenotypes in a dominant, non-Mendelian fashion, without a corresponding change in chromosomal gene structure. Since the phenotypes caused by the presence of a prion are thought to affect the ability of cells to survive under different environmental conditions, those that have global effects on cell physiology are of particular interest. Here we report the results of a study of one such prion, [SWI+], formed by a component of the SWI/SNF chromatin-remodeling complex, which is required for the regulation of a diverse set of genes. We found that, compared to previously well-studied prions, [SWI+] is highly sensitive to changes in the activities of molecular chaperones, particularly components of the Hsp70 machinery. Both under- and over-expression of components of this system initiated rapid loss of the prion from the cell population. Since expression of molecular chaperones, often known as heat shock proteins, are known to vary under diverse environmental conditions, such “chaperone sensitivity” may allow alteration of traits that under particular environmental conditions convey a selective advantage and may be a common characteristic of prions formed from proteins involved in global gene regulation.
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Affiliation(s)
- Justin K. Hines
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Xiaomo Li
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Zhiqiang Du
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Takashi Higurashi
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Liming Li
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- * E-mail: (EAC); (LL)
| | - Elizabeth A. Craig
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail: (EAC); (LL)
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Abstract
The unexpected discovery of two prions, [URE3] and [PSI+], in Saccharomyces cerevisiae led to questions about how many other proteins could undergo similar prion-based structural conversions. However, [URE3] and [PSI+] were discovered by serendipity in genetic screens. Cataloging the full range of prions in yeast or in other organisms will therefore require more systematic search methods. Taking advantage of some of the unique features of prions, various researchers have developed bioinformatic and experimental methods for identifying novel prion proteins. These methods have generated long lists of prion candidates. The systematic testing of some of these prion candidates has led to notable successes; however, even in yeast, where rapid growth rate and ease of genetic manipulation aid in testing for prion activity, such candidate testing is laborious. Development of better methods to winnow the field of prion candidates will greatly aid in the discovery of new prions, both in yeast and in other organisms, and help us to better understand the role of prions in biology.
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Kryndushkin D, Shewmaker F. Modeling ALS and FTLD proteinopathies in yeast: an efficient approach for studying protein aggregation and toxicity. Prion 2011; 5. [PMID: 22052354 PMCID: PMC4012400 DOI: 10.4161/pri.5.4.17229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
In recent years there have been several reports of human neurodegenerative diseases that involve protein misfolding being modeled in the yeast Saccharomyces cerevisiae. This review summarizes recent advances in understanding the specific mechanisms underlying intracellular neuronal pathology during Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Lobar Degeneration (FTLD), including SOD1, TDP-43 and FUS protein inclusions and the potential of these proteins to be involved in pathogenic prion-like mechanisms. More specifically, we focus on findings from yeast systems that offer tremendous possibilities for screening for genetic and chemical modifiers of disease-related proteotoxicity.
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35
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Abstract
Prions are infectious proteins with altered conformations converted from otherwise normal host proteins. While there is only one known mammalian prion protein, PrP, a handful of prion proteins have been identified in the yeast Saccharomyces cerevisiae. Yeast prion proteins usually have a defined region called prion domain (PrD) essential for prion properties, which are typically rich in glutamine (Q) and asparagine (N). Despite sharing several common features, individual yeast PrDs are generally intricate and divergent in their compositional characteristics, which potentially implicates their prion phenotypes, such as prion-mediated transcriptional regulations.
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