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Monahan ZT, Rhoads SN, Yee DS, Shewmaker FP. Yeast Models of Prion-Like Proteins That Cause Amyotrophic Lateral Sclerosis Reveal Pathogenic Mechanisms. Front Mol Neurosci 2018; 11:453. [PMID: 30618605 PMCID: PMC6297178 DOI: 10.3389/fnmol.2018.00453] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/23/2018] [Indexed: 12/12/2022] Open
Abstract
Many proteins involved in the pathogenic mechanisms of amyotrophic lateral sclerosis (ALS) are remarkably similar to proteins that form prions in the yeast Saccharomyces cerevisiae. These ALS-associated proteins are not orthologs of yeast prion proteins, but are similar in having long, intrinsically disordered domains that are rich in hydrophilic amino acids. These so-called prion-like domains are particularly aggregation-prone and are hypothesized to participate in the mislocalization and misfolding processes that occur in the motor neurons of ALS patients. Methods developed for characterizing yeast prions have been adapted to studying ALS-linked proteins containing prion-like domains. These yeast models have yielded major discoveries, including identification of new ALS genetic risk factors, new ALS-causing gene mutations and insights into how disease mutations enhance protein aggregation.
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Affiliation(s)
| | | | | | - Frank P. Shewmaker
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University, Bethesda, MD, United States
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Rhoads SN, Monahan ZT, Yee DS, Leung AY, Newcombe CG, O'Meally RN, Cole RN, Shewmaker FP. The prionlike domain of FUS is multiphosphorylated following DNA damage without altering nuclear localization. Mol Biol Cell 2018; 29:1786-1797. [PMID: 29897835 PMCID: PMC6085830 DOI: 10.1091/mbc.e17-12-0735] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
FUS (fused in sarcoma) is an abundant, predominantly nuclear protein involved in RNA processing. Under various conditions, FUS functionally associates with RNA and other macromolecules to form distinct, reversible phase-separated liquid structures. Persistence of the phase-separated state and increased cytoplasmic localization are both hypothesized to predispose FUS to irreversible aggregation, which is a pathological hallmark of subtypes of amyotrophic lateral sclerosis and frontotemporal dementia. We previously showed that phosphorylation of FUS’s prionlike domain suppressed phase separation and toxic aggregation, proportionally to the number of added phosphates. However, phosphorylation of FUS’s prionlike domain was previously reported to promote its cytoplasmic localization, potentially favoring pathological behavior. Here we used mass spectrometry and human cell models to further identify phosphorylation sites within FUS’s prionlike domain, specifically following DNA-damaging stress. In total, 28 putative sites have been identified, about half of which are DNA-dependent protein kinase (DNA-PK) consensus sites. Custom antibodies were developed to confirm the phosphorylation of two of these sites (Ser-26 and Ser-30). Both sites were usually phosphorylated in a subpopulation of cellular FUS following a variety of DNA-damaging stresses but not necessarily equally or simultaneously. Importantly, we found DNA-PK–dependent multiphosphorylation of FUS’s prionlike domain does not cause cytoplasmic localization.
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Affiliation(s)
- Shannon N Rhoads
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University, Bethesda, MD 20814
| | - Zachary T Monahan
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University, Bethesda, MD 20814
| | - Debra S Yee
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University, Bethesda, MD 20814
| | - Andrew Y Leung
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University, Bethesda, MD 20814
| | - Cameron G Newcombe
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University, Bethesda, MD 20814
| | - Robert N O'Meally
- Department of Biological Chemistry, Johns Hopkins Mass Spectrometry and Proteomic Facility, Johns Hopkins University, Baltimore, MD 21205
| | - Robert N Cole
- Department of Biological Chemistry, Johns Hopkins Mass Spectrometry and Proteomic Facility, Johns Hopkins University, Baltimore, MD 21205
| | - Frank P Shewmaker
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University, Bethesda, MD 20814
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Rhoads SN, Monahan ZT, Yee DS, Shewmaker FP. The Role of Post-Translational Modifications on Prion-Like Aggregation and Liquid-Phase Separation of FUS. Int J Mol Sci 2018; 19:ijms19030886. [PMID: 29547565 PMCID: PMC5877747 DOI: 10.3390/ijms19030886] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 12/13/2022] Open
Abstract
Subcellular mislocalization and aggregation of the human FUS protein occurs in neurons of patients with subtypes of amyotrophic lateral sclerosis and frontotemporal dementia. FUS is one of several RNA-binding proteins that can functionally self-associate into distinct liquid-phase droplet structures. It is postulated that aberrant interactions within the dense phase-separated state can potentiate FUS's transition into solid prion-like aggregates that cause disease. FUS is post-translationally modified at numerous positions, which affect both its localization and aggregation propensity. These modifications may influence FUS-linked pathology and serve as therapeutic targets.
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Affiliation(s)
- Shannon N Rhoads
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| | - Zachary T Monahan
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| | - Debra S Yee
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| | - Frank P Shewmaker
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
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Abstract
The recognition that certain long-known nonchromosomal genetic elements were actually prions was based not on the specific phenotypic manifestations of those elements, but rather on their unusual genetic properties. Here, we outline methods of prion assay, methods for showing the nonchromosomal inheritance, and methods for determining whether a nonchromosomal trait has the unusual characteristics diagnostic of a prion. Finally, we discuss genetic methods often useful in the study of yeast prions.
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Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830;
| | - Herman K Edskes
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830
| | - Dmitry Kryndushkin
- Department of Pharmacology, Uniformed Services University of Health Sciences, Bethesda, Maryland 20814
| | - Frank P Shewmaker
- Department of Pharmacology, Uniformed Services University of Health Sciences, Bethesda, Maryland 20814
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Abstract
Infectious proteins (prions) are usually self-templating filamentous protein polymers (amyloids). Yeast prions are genes composed of protein and, like the multiple alleles of DNA-based genes, can have an array of "variants," each a distinct self-propagating amyloid conformation. Like the lethal mammalian prions and amyloid diseases, yeast prions may be lethal, or only mildly detrimental, and show an array of phenotypes depending on the protein involved and the prion variant. Yeast prions are models for both rare mammalian prion diseases and for several very common amyloidoses such as Alzheimer's disease, type 2 diabetes, and Parkinson's disease. Here, we describe their detection and characterization using genetic, cell biological, biochemical, and physical methods.
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Affiliation(s)
- Dmitry Kryndushkin
- Department of Pharmacology, Uniformed Services University of Health Sciences, Bethesda, Maryland 20814
| | - Herman K Edskes
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830
| | - Frank P Shewmaker
- Department of Pharmacology, Uniformed Services University of Health Sciences, Bethesda, Maryland 20814
| | - Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830
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Kryndushkin D, Pripuzova N, Shewmaker FP. Isolation and Analysis of Prion and Amyloid Aggregates from Yeast Cells. Cold Spring Harb Protoc 2017; 2017:2017/2/pdb.prot089045. [PMID: 28148850 DOI: 10.1101/pdb.prot089045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Amyloid fibers are large and extremely stable structures that can resist denaturation by strong anionic detergents, such as sodium dodecyl sulfate or sarkosyl. Here, we present two complementary analytical methods that exploit these properties, enabling the isolation and characterization of amyloid/prion aggregates. The first technique, known as semidenaturating detergent agarose gel electrophoresis, is an immunoblotting technique, conceptually similar to conventional western blotting. It enables the targeted identification of large detergent-resistant protein aggregates using antibodies specific to the protein of interest. The second method, called the technique for amyloid purification and identification, is a nontargeted approach that can isolate amyloid aggregates for analysis by tandem mass spectrometry. The latter approach requires no special genetic tools or antibodies, and can identify amyloid-forming proteins, such as prions, as well as proteins tightly associated with amyloid, from a variety of cell sources.
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Affiliation(s)
- Dmitry Kryndushkin
- Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
| | - Natalia Pripuzova
- Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
| | - Frank P Shewmaker
- Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
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Wear MP, Kryndushkin D, O’Meally R, Sonnenberg JL, Cole RN, Shewmaker FP. Proteins with Intrinsically Disordered Domains Are Preferentially Recruited to Polyglutamine Aggregates. PLoS One 2015; 10:e0136362. [PMID: 26317359 PMCID: PMC4552826 DOI: 10.1371/journal.pone.0136362] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/31/2015] [Indexed: 12/12/2022] Open
Abstract
Intracellular protein aggregation is the hallmark of several neurodegenerative diseases. Aggregates formed by polyglutamine (polyQ)-expanded proteins, such as Huntingtin, adopt amyloid-like structures that are resistant to denaturation. We used a novel purification strategy to isolate aggregates formed by human Huntingtin N-terminal fragments with expanded polyQ tracts from both yeast and mammalian (PC-12) cells. Using mass spectrometry we identified the protein species that are trapped within these polyQ aggregates. We found that proteins with very long intrinsically-disordered (ID) domains (≥100 amino acids) and RNA-binding proteins were disproportionately recruited into aggregates. The removal of the ID domains from selected proteins was sufficient to eliminate their recruitment into polyQ aggregates. We also observed that several neurodegenerative disease-linked proteins were reproducibly trapped within the polyQ aggregates purified from mammalian cells. Many of these proteins have large ID domains and are found in neuronal inclusions in their respective diseases. Our study indicates that neurodegenerative disease-associated proteins are particularly vulnerable to recruitment into polyQ aggregates via their ID domains. Also, the high frequency of ID domains in RNA-binding proteins may explain why RNA-binding proteins are frequently found in pathological inclusions in various neurodegenerative diseases.
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Affiliation(s)
- Maggie P. Wear
- Department of Pharmacology, Uniformed Services University of the Heath Sciences, Bethesda, Maryland, 20814, United States of America
| | - Dmitry Kryndushkin
- Department of Pharmacology, Uniformed Services University of the Heath Sciences, Bethesda, Maryland, 20814, United States of America
| | - Robert O’Meally
- Johns Hopkins Mass Spectrometry and Proteomic Facility, Johns Hopkins University, Baltimore, Maryland, 21218, United States of America
| | - Jason L. Sonnenberg
- Chemistry department, School of Sciences, Stevenson University, Stevenson, Maryland, 21153, United States of America
| | - Robert N. Cole
- Johns Hopkins Mass Spectrometry and Proteomic Facility, Johns Hopkins University, Baltimore, Maryland, 21218, United States of America
| | - Frank P. Shewmaker
- Department of Pharmacology, Uniformed Services University of the Heath Sciences, Bethesda, Maryland, 20814, United States of America
- * E-mail:
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Wickner RB, Edskes HK, Shewmaker FP, Kryndushkin D, Nemecek J, McGlinchey R, Bateman D. The relationship of prions and translation. Wiley Interdiscip Rev RNA 2012; 1:81-9. [PMID: 21339834 DOI: 10.1002/wrna.8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Prions are infectious proteins, without the need for an accompanying nucleic acid. Nonetheless, there are connections of prions with translation and RNA, which we explore here. Most prions are based on self-propagating amyloids. The yeast [PSI+] prion is an amyloid of Sup35p, a subunit of the translation termination factor. The normal function of the Sup35p prion domain is in shortening the 3 polyA of mRNAs and thus in mRNA turnover. The [ISP+] prion is so named because it produces antisuppression, the opposite of the effect of [PSI+]. Another connection of prions with translation is the influence on prion propagation and generation of ribosome-associated chaperones, the Ssbs, and a chaperone activity intrinsic to the 60S ribosomal subunits.
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Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA.
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