1
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Buchholz HE, Dorweiler JE, Guereca S, Wisniewski BT, Shorter J, Manogaran AL. The middle domain of Hsp104 can ensure substrates are functional after processing. PLoS Genet 2024; 20:e1011424. [PMID: 39361717 DOI: 10.1371/journal.pgen.1011424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 09/10/2024] [Indexed: 10/05/2024] Open
Abstract
Molecular chaperones play a central role in protein disaggregation. However, the molecular determinants that regulate this process are poorly understood. Hsp104 is an AAA+ ATPase that disassembles stress granules and amyloids in yeast through collaboration with Hsp70 and Hsp40. In vitro studies show that Hsp104 processes different types of protein aggregates by partially translocating or threading polypeptides through the central pore of the hexamer. However, it is unclear how Hsp104 processing influences client protein function in vivo. The middle domain (MD) of Hsp104 regulates ATPase activity and interactions with Hsp70. Here, we tested how MD variants, Hsp104A503S and Hsp104A503V, process different protein aggregates. We establish that engineered MD variants fail to resolve stress granules but retain prion fragmentation activity required for prion propagation. Using the Sup35 prion protein, our in vitro and in vivo data indicate that the MD variants can disassemble Sup35 aggregates, but the disaggregated protein has reduced GTPase and translation termination activity. These results suggest that the middle domain can play a role in sensing certain substrates and plays an essential role in ensuring the processed protein is functional.
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Affiliation(s)
- Hannah E Buchholz
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
| | - Jane E Dorweiler
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
| | - Sam Guereca
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
| | - Brett T Wisniewski
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Anita L Manogaran
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
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2
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Williams FN, Travis KL, Haver HN, Umano AD, Guerra-Hernandez Y, Scaglione KM. Acute stress and multicellular development alter the solubility of the Dictyostelium Sup35 ortholog ERF3. Microbiol Spectr 2024:e0160724. [PMID: 39345220 DOI: 10.1128/spectrum.01607-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 08/26/2024] [Indexed: 10/01/2024] Open
Abstract
Among sequenced organisms, the genome of Dictyostelium discoideum is unique in that it encodes for a massive amount of repeat-rich sequences in the coding region of genes. This results in the Dictyostelium proteome encoding for thousands of repeat-rich proteins, with nearly 24% of the Dictyostelium proteome encoding Q/N-rich regions that are predicted to be prion like in nature. To begin investigating the role of prion-like proteins in Dictyostelium, we decided to investigate ERF3, the Dictyostelium ortholog of the well-characterized yeast prion protein Sup35. ERF3 lacks the Q/N-rich region required for prion formation in yeast, raising the question of whether this protein aggregates and has prion-like properties in Dictyostelium. Here, we found that ERF3 formed aggregates in response to acute cellular stress. However, unlike bona fide prions, we were unable to detect transmission of aggregates to progeny. We further found that aggregation of this protein is driven by the ordered C-terminal domain independently of the disordered N-terminal domain. Finally, we also observed aggregation of ERF3 under conditions that induce multicellular development, suggesting that this phenomenon may play a role in Dictyostelium development. Together, these findings suggest a role for regulated protein aggregation in Dictyostelium cells under stress and during development.IMPORTANCEPrion-like proteins have both beneficial and deleterious effects on cellular health, and many organisms have evolved distinct mechanisms to regulate the behaviors of these proteins. The social amoeba Dictyostelium discoideum contains the highest proportion of proteins predicted to be prion like and has mechanisms to suppress their aggregation. However, the potential roles and regulation of these proteins remain largely unknown. Here, we demonstrate that aggregation of the Dictyostelium translation termination factor ERF3 is induced by both acute cellular stress and by multicellular development. These findings imply that protein aggregation may have a regulated and functional role in the Dictyostelium stress response and during multicellular development.
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Affiliation(s)
- Felicia N Williams
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Kanesha L Travis
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Holly N Haver
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Anna D Umano
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Yaneli Guerra-Hernandez
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - K Matthew Scaglione
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
- Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, North Carolina, USA
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3
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Ruger-Herreros C, Svoboda L, Mogk A, Bukau B. Role of J-domain Proteins in Yeast Physiology and Protein Quality Control. J Mol Biol 2024; 436:168484. [PMID: 38331212 DOI: 10.1016/j.jmb.2024.168484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
The Hsp70 chaperone system is a central component of cellular protein quality control (PQC) by acting in a multitude of protein folding processes ranging from the folding of newly synthesized proteins to the disassembly and refolding of protein aggregates. This multifunctionality of Hsp70 is governed by J-domain proteins (JDPs), which act as indispensable co-chaperones that target specific substrates to Hsp70. The number of distinct JDPs present in a species always outnumbers Hsp70, documenting JDP function in functional diversification of Hsp70. In this review, we describe the physiological roles of JDPs in the Saccharomyces cerevisiae PQC system, with a focus on the abundant JDP generalists, Zuo1, Ydj1 and Sis1, which function in fundamental cellular processes. Ribosome-bound Zuo1 cooperates with the Hsp70 chaperones Ssb1/2 in folding and assembly of nascent polypeptides. Ydj1 and Sis1 cooperate with the Hsp70 members Ssa1 to Ssa4 to exert overlapping functions in protein folding and targeting of newly synthesized proteins to organelles including mitochondria and facilitating the degradation of aberrant proteins by E3 ligases. Furthermore, they act in protein disaggregation reactions, though Ydj1 and Sis1 differ in their modes of Hsp70 cooperation and substrate specificities. This results in functional specialization as seen in prion propagation and the underlying dominant role of Sis1 in targeting Hsp70 for shearing of prion amyloid fibrils.
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Affiliation(s)
- Carmen Ruger-Herreros
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot, s/n, E-41013 Sevilla, Spain
| | - Lucia Svoboda
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Axel Mogk
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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4
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Son M. A Story Between s and S: [Het-s] Prion of the Fungus Podospora anserina. MYCOBIOLOGY 2024; 52:85-91. [PMID: 38690032 PMCID: PMC11057395 DOI: 10.1080/12298093.2024.2322211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/19/2024] [Indexed: 05/02/2024]
Abstract
In filamentous fungi, vegetative cell fusion occurs within and between individuals. These fusions of growing hyphae (anastomosis) from two individuals produce binucleated cells with mixed cytoplasm known as heterokaryons. The fate of heterokaryotic cells was genetically controlled with delicacy by specific loci named het (heterokaryon) or vic (vegetative incompatibility) as a part of self-/nonself-recognition system. When het loci of two individuals are incompatible, the resulting heterokaryotic cells underwent programmed cell death or showed severely impaired fungal growth. In Podospora anserina, het-s is one of at least nine alleles that control heterokaryon incompatibility and the altered protein conformation [Het-s] prion. The present study describes the [Het-s] prion in terms of (1) the historical discovery based on early genetic and physiological studies, (2) architecture built on its common and unique nature compared with other prions, and (3) functions related to meiotic drive and programmed cell death.
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Affiliation(s)
- Moonil Son
- Department of Microbiology, Pusan National University, Busan, Korea
- Microbiological Resource Research Institute, Pusan National University, Busan, Korea
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5
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Wu J, Zhou L, Peng H, Wang Z, Wang Z, Keasling JD, Liu S, Zhou G, Ding S, Wang Q, Wang X, Chen X, Lang Y, Xia M, Guan X, Dong M, Zhou J, Chen J. A General and Convenient Peptide Self-Assembling Mechanism for Developing Supramolecular Versatile Nanomaterials Based on The Biosynthetic Hybrid Amyloid-Resilin Protein. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2304364. [PMID: 37885340 DOI: 10.1002/adma.202304364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/17/2023] [Indexed: 10/28/2023]
Abstract
Self-assembling peptides are valuable building blocks to fabricate supramolecular biomaterials, which have broad applications from biomedicine to biotechnology. However, limited choices to induce different globular proteins into hydrogels hinder these designs. Here, an easy-to-implement and tunable self-assembling strategy, which employs Ure2 amyloidogenic peptide, are described to induce any target proteins to assemble into supramolecular hydrogels alone or in combination with notable compositional control. Furthermore, the collective effect of nanoscale interactions among amyloid nanofibrils and partially disordered elastomeric polypeptides are investigated. This led to many useful macroscopic material properties simultaneously emerging from one pure protein material, i.e. strong adhesion to any substrates under wet conditions, rapidly self--assembling into robust and porous hydrogels, adaptation to remodeling processes, strongly promoting cell adhesion, proliferation and differentiation. Moreover, he demonstrated this supramolecular material's robust performance in vitro and vivo for tissue engineering, cosmetic and hemostasis applications and exhibited superior performance compared to corresponding commercial counterparts. To the best of his knowledge, few pure protein-based materials could meet such seemingly mutually exclusive properties simultaneously. Such versatility renders this novel supramolecular nanomaterial as next-generation functional protein-based materials, and he demonstrated the sequence level modulation of structural order and disorder as an untapped principle to design new proteins.
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Affiliation(s)
- Junjun Wu
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Lin Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Hu Peng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhaojun Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhaoshi Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jay D Keasling
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California Berkeley, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Center for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Shike Liu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Guanghong Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Shijie Ding
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Qiong Wang
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Xuejian Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xinxiu Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yifei Lang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Mo Xia
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xin Guan
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Mingsheng Dong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
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6
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Wu S, Edskes HK, Wickner RB. Human proteins curing yeast prions. Proc Natl Acad Sci U S A 2023; 120:e2314781120. [PMID: 37903258 PMCID: PMC10636303 DOI: 10.1073/pnas.2314781120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/25/2023] [Indexed: 11/01/2023] Open
Abstract
Recognition that common human amyloidoses are prion diseases makes the use of the Saccharomyces cerevisiae prion model systems to screen for possible anti-prion components of increasing importance. [PSI+] and [URE3] are amyloid-based prions of Sup35p and Ure2p, respectively. Yeast has at least six anti-prion systems that together cure nearly all [PSI+] and [URE3] prions arising in their absence. We made a GAL-promoted bank of 14,913 human open reading frames in a yeast shuttle plasmid and isolated 20 genes whose expression cures [PSI+] or [URE3]. PRPF19 is an E3 ubiquitin ligase that cures [URE3] if its U-box is intact. DNAJA1 is a J protein that cures [PSI+] unless its interaction with Hsp70s is defective. Human Bag5 efficiently cures [URE3] and [PSI+]. Bag family proteins share a 110 to 130 residue "BAG domain"; Bag 1, 2, 3, 4, and 6 each have one BAG domain while Bag5 has five BAG domains. Two BAG domains are necessary for curing [PSI+], but one can suffice to cure [URE3]. Although most Bag proteins affect autophagy in mammalian cells, mutations blocking autophagy in yeast do not affect Bag5 curing of [PSI+] or [URE3]. Curing by Bag proteins depends on their interaction with Hsp70s, impairing their role, with Hsp104 and Sis1, in the amyloid filament cleavage necessary for prion propagation. Since Bag5 curing is reduced by overproduction of Sis1, we propose that Bag5 cures prions by blocking Sis1 access to Hsp70s in its role with Hsp104 in filament cleavage.
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Affiliation(s)
- Songsong Wu
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0830
| | - Herman K. Edskes
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0830
| | - Reed B. Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0830
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7
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Jager K, Orozco-Hidalgo MT, Springstein BL, Joly-Smith E, Papazotos F, McDonough E, Fleming E, McCallum G, Yuan AH, Hilfinger A, Hochschild A, Potvin-Trottier L. Measuring prion propagation in single bacteria elucidates a mechanism of loss. Proc Natl Acad Sci U S A 2023; 120:e2221539120. [PMID: 37738299 PMCID: PMC10523482 DOI: 10.1073/pnas.2221539120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/26/2023] [Indexed: 09/24/2023] Open
Abstract
Prions are self-propagating protein aggregates formed by specific proteins that can adopt alternative folds. Prions were discovered as the cause of the fatal transmissible spongiform encephalopathies in mammals, but prions can also constitute nontoxic protein-based elements of inheritance in fungi and other species. Prion propagation has recently been shown to occur in bacteria for more than a hundred cell divisions, yet a fraction of cells in these lineages lost the prion through an unknown mechanism. Here, we investigate prion propagation in single bacterial cells as they divide using microfluidics and fluorescence microscopy. We show that the propagation occurs in two distinct modes. In a fraction of the population, cells had multiple small visible aggregates and lost the prion through random partitioning of aggregates to one of the two daughter cells at division. In the other subpopulation, cells had a stable large aggregate localized to the pole; upon division the mother cell retained this polar aggregate and a daughter cell was generated that contained small aggregates. Extending our findings to prion domains from two orthologous proteins, we observe similar propagation and loss properties. Our findings also provide support for the suggestion that bacterial prions can form more than one self-propagating state. We implement a stochastic version of the molecular model of prion propagation from yeast and mammals that recapitulates all the observed single-cell properties. This model highlights challenges for prion propagation that are unique to prokaryotes and illustrates the conservation of fundamental characteristics of prion propagation.
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Affiliation(s)
- Krista Jager
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
| | | | | | - Euan Joly-Smith
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
| | - Fotini Papazotos
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
| | | | - Eleanor Fleming
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Giselle McCallum
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
| | - Andy H. Yuan
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Andreas Hilfinger
- Department of Physics, University of Toronto, Toronto, ONM5S 1A7, Canada
- Department of Mathematics, University of Toronto, Toronto, ONM5S 2E4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ONM5S 3G5, Canada
| | - Ann Hochschild
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Laurent Potvin-Trottier
- Department of Biology, Concordia University, Montréal, QCH4B 1R6, Canada
- Department of Physics, Concordia University, Montréal, QCH4B 1R6, Canada
- Center for Applied Synthetic Biology, Concordia University, Montréal, QCH4B 1R6, Canada
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8
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La Manna S, Roviello V, Monaco V, Platts JA, Monti M, Gabano E, Ravera M, Marasco D. The inhibitory effects of platinum(II) complexes on amyloid aggregation: a theoretical and experimental approach. Dalton Trans 2023; 52:12677-12685. [PMID: 37655459 DOI: 10.1039/d3dt02187d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Platinum (Pt)(II) square planar complexes are well-known anticancer drugs whose Mechanism of Action (MOA) are finely tuned by the polar, hydrophobic and aromatic features of the ligands. In the attempt to translate this tunability to the identification of potential neurodrugs, herein, four Pt(II) complexes were investigated in their ability to modulate the self-aggregation processes of two amyloidogenic models: Sup35p7-13 and NPM1264-277 peptides. In particular, phenanthriplatin revealed the most efficient agent in the modulation of amyloid aggregation: through several biophysical assays, as Thioflavin T (ThT), electrospray ionization mass spectrometry (ESI-MS) and ultraviolet-visible (UV-vis) absorption spectroscopy, this complex revealed able to markedly suppress aggregation and to disassemble small soluble aggregates. This effect was due to a direct coordination of phenanthriplatin to the amyloid, with the loss of several ligands and different stoichiometries, by the formation of π-π and π-cation interactions as indicated from molecular dynamic simulations. Presented data support a growing and recent approach concerning the repurposing of metallodrugs as potential novel neurotherapeutics.
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Affiliation(s)
- Sara La Manna
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy.
| | - Valentina Roviello
- Department of Chemical, Materials, and Industrial Production Engineering (DICMaPI), University of Naples Federico II, 80125 Naples, Italy
| | - Vittoria Monaco
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
- CEINGE Biotecnologie Avanzate "Franco Salvatore" S.c.a r.l., 80131, Naples, Italy
| | - James A Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK
| | - Maria Monti
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
- CEINGE Biotecnologie Avanzate "Franco Salvatore" S.c.a r.l., 80131, Naples, Italy
| | - Elisabetta Gabano
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, University of Piemonte Orientale, Piazza S. Eusebio 5, 13100, Vercelli, Italy
| | - Mauro Ravera
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121 Alessandria, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy.
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9
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Xu Z, Zhang X, Dong W, lv H, Zuo L, Zhu L, Wang R, Ma X. Self-assembling and pH-responsive protein nanoparticle as potential platform for targeted tumor therapy. Front Mol Biosci 2023; 10:1172100. [PMID: 37234918 PMCID: PMC10206137 DOI: 10.3389/fmolb.2023.1172100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Frequent injections at high concentrations are often required for many therapeutic proteins due to their short in vivo half-life, which usually leads to unsatisfactory therapeutic outcomes, adverse side effects, high cost, and poor patient compliance. Herein we report a supramolecular strategy, self-assembling and pH regulated fusion protein to extend the in vivo half-life and tumor targeting ability of a therapeutically important protein trichosanthin (TCS). TCS was genetically fused to the N-terminus of a self-assembling protein, Sup35p prion domain (Sup35), to form a fusion protein of TCS-Sup35 that self-assembled into uniform spherical TCS-Sup35 nanoparticles (TCS-Sup35 NP) rather than classic nanofibrils. Importantly, due to the pH response ability, TCS-Sup35 NP well retained the bioactivity of TCS and possessed a 21.5-fold longer in vivo half-life than native TCS in a mouse model. As a result, in a tumor-bearing mouse model, TCS-Sup35 NP exhibited significantly improved tumor accumulation and antitumor activity without detectable systemic toxicity as compared with native TCS. These findings suggest that self-assembling and pH responding protein fusion may provide a new, simple, general, and effective solution to remarkably improve the pharmacological performance of therapeutic proteins with short circulation half-lives.
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10
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Narita H, Shima T, Iizuka R, Uemura S. N-terminal region of Drosophila melanogaster Argonaute2 forms amyloid-like aggregates. BMC Biol 2023; 21:78. [PMID: 37072852 PMCID: PMC10114355 DOI: 10.1186/s12915-023-01569-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/17/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Argonaute proteins play a central role in RNA silencing by forming protein-small RNA complexes responsible for the silencing process. While most Argonaute proteins have a short N-terminal region, Argonaute2 in Drosophila melanogaster (DmAgo2) harbors a long and unique N-terminal region. Previous in vitro biochemical studies have shown that the loss of this region does not impair the RNA silencing activity of the complex. However, an N-terminal mutant of Drosophila melanogaster has demonstrated abnormal RNA silencing activity. To explore the causes of this discrepancy between in vitro and in vivo studies, we investigated the biophysical properties of the region. The N-terminal region is highly rich in glutamine and glycine residues, which is a well-known property for prion-like domains, a subclass of amyloid-forming peptides. Therefore, the possibility of the N-terminal region functioning as an amyloid was tested. RESULTS Our in silico and biochemical assays demonstrated that the N-terminal region exhibits amyloid-specific properties. The region indeed formed aggregates that were not dissociated even in the presence of sodium dodecyl sulfate. Also, the aggregates enhanced the fluorescence intensity of thioflavin-T, an amyloid detection reagent. The kinetics of the aggregation followed that of typical amyloid formation exhibiting self-propagating activity. Furthermore, we directly visualized the aggregation process of the N-terminal region under fluorescence microscopy and found that the aggregations took fractal or fibril shapes. Together, the results indicate that the N-terminal region can form amyloid-like aggregates. CONCLUSIONS Many other amyloid-forming peptides have been reported to modulate the function of proteins through their aggregation. Therefore, our findings raise the possibility that aggregation of the N-terminal region regulates the RNA silencing activity of DmAgo2.
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Affiliation(s)
- Haruka Narita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Shima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Ryo Iizuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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11
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Jager K, Orozco-Hidalgo MT, Springstein BL, Joly-Smith E, Papazotos F, McDonough E, Fleming E, McCallum G, Hilfinger A, Hochschild A, Potvin-Trottier L. Measuring prion propagation in single bacteria elucidates mechanism of loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523042. [PMID: 36712035 PMCID: PMC9882039 DOI: 10.1101/2023.01.11.523042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Prions are self-propagating protein aggregates formed by specific proteins that can adopt alternative folds. Prions were discovered as the cause of the fatal transmissible spongiform encephalopathies in mammals, but prions can also constitute non-toxic protein-based elements of inheritance in fungi and other species. Prion propagation has recently been shown to occur in bacteria for more than a hundred cell divisions, yet a fraction of cells in these lineages lost the prion through an unknown mechanism. Here, we investigate prion propagation in single bacterial cells as they divide using microfluidics and fluorescence microscopy. We show that the propagation occurs in two distinct modes with distinct stability and inheritance characteristics. We find that the prion is lost through random partitioning of aggregates to one of the two daughter cells at division. Extending our findings to prion domains from two orthologous proteins, we observe similar propagation and loss properties. Our findings also provide support for the suggestion that bacterial prions can form more than one self-propagating state. We implement a stochastic version of the molecular model of prion propagation from yeast and mammals that recapitulates all the observed single-cell properties. This model highlights challenges for prion propagation that are unique to prokaryotes and illustrates the conservation of fundamental characteristics of prion propagation across domains of life.
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Affiliation(s)
- Krista Jager
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | | | | | - Euan Joly-Smith
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Fotini Papazotos
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - EmilyKate McDonough
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eleanor Fleming
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Giselle McCallum
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - Andreas Hilfinger
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
- Department of Mathematics, University of Toronto, Toronto, Ontario, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ann Hochschild
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Laurent Potvin-Trottier
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Department of Physics, Concordia University, Montréal, Québec, Canada
- Center for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
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12
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Flach M, Leu C, Martinisi A, Skachokova Z, Frank S, Tolnay M, Stahlberg H, Winkler DT. Trans-seeding of Alzheimer-related tau protein by a yeast prion. Alzheimers Dement 2022; 18:2481-2492. [PMID: 35142027 PMCID: PMC10078693 DOI: 10.1002/alz.12581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/01/2021] [Accepted: 12/10/2021] [Indexed: 01/31/2023]
Abstract
Abnormal tau protein aggregates constitute a hallmark of Alzheimer's disease. The mechanisms underlying the initiation of tau aggregation in sporadic neurodegeneration remain unclear. Here we investigate whether a non-human prion can seed tau aggregation. Due to their structural similarity with tau aggregates, we chose Sup35NM yeast prion domain fibrils for explorative tau seedings. Upon in vitro incubation with tau monomers, Sup35NM fibrils promoted the formation of morphologically distinct tau fibril strains. In vivo, intrahippocampal inoculation of Sup35NM fibrils accentuated tau pathology in P301S tau transgenic mice. Thus, our results provide first in vivo evidence for heterotypic cross-species seeding of a neurodegenerative human prion-like protein by a yeast prion. This opens up the conceptual perspective that non-mammalian prions present in the human microbiome could be involved in the initiation of protein misfolding in neurodegenerative disorders, a mechanism for which we propose the term "trans-seeding."
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Affiliation(s)
- Martin Flach
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,Department of Neurology, University Hospital Basel, Basel, Switzerland
| | - Cedric Leu
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Alfonso Martinisi
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,Department of Neurology, University Hospital Basel, Basel, Switzerland
| | - Zhiva Skachokova
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Stephan Frank
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Markus Tolnay
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - David T Winkler
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,Department of Neurology, University Hospital Basel, Basel, Switzerland.,Neurology, Medical University Clinic, Kantonsspital Baselland, Liestal, Switzerland
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13
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Kodera N, Ando T. Guide to studying intrinsically disordered proteins by high-speed atomic force microscopy. Methods 2022; 207:44-56. [PMID: 36055623 DOI: 10.1016/j.ymeth.2022.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/16/2022] [Indexed: 12/29/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are partially or entirely disordered. Their intrinsically disordered regions (IDRs) dynamically explore a wide range of structural space by their highly flexible nature. Due to this distinct feature largely different from structured proteins, conventional structural analyses relying on ensemble averaging is unsuitable for characterizing the dynamic structure of IDPs. Therefore, single-molecule measurement tools have been desired in IDP studies. High-speed atomic force microscopy (HS-AFM) is a unique tool that allows us to directly visualize single biomolecules at 2-3 nm lateral and ∼ 0.1 nm vertical spatial resolution, and at sub-100 ms temporal resolution under near physiological conditions, without any chemical labeling. HS-AFM has been successfully used not only to characterize the shape and motion of IDP molecules but also to visualize their function-related dynamics. In this article, after reviewing the principle and current performances of HS-AFM, we describe experimental considerations in the HS-AFM imaging of IDPs and methods to quantify molecular features from captured images. Finally, we outline recent HS-AFM imaging studies of IDPs.
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Affiliation(s)
- Noriyuki Kodera
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
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14
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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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15
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Hromadkova L, Siddiqi MK, Liu H, Safar JG. Populations of Tau Conformers Drive Prion-like Strain Effects in Alzheimer's Disease and Related Dementias. Cells 2022; 11:2997. [PMID: 36230957 PMCID: PMC9562632 DOI: 10.3390/cells11192997] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Recent findings of diverse populations of prion-like conformers of misfolded tau protein expand the prion concept to Alzheimer's disease (AD) and monogenic frontotemporal lobar degeneration (FTLD)-MAPT P301L, and suggest that distinct strains of misfolded proteins drive the phenotypes and progression rates in many neurodegenerative diseases. Notable progress in the previous decades has generated many lines of proof arguing that yeast, fungal, and mammalian prions determine heritable as well as infectious traits. The extraordinary phenotypic diversity of human prion diseases arises from structurally distinct prion strains that target, at different progression speeds, variable brain structures and cells. Although human prion research presents beneficial lessons and methods to study the mechanism of strain diversity of protein-only pathogens, the fundamental molecular mechanism by which tau conformers are formed and replicate in diverse tauopathies is still poorly understood. In this review, we summarize up to date advances in identification of diverse tau conformers through biophysical and cellular experimental paradigms, and the impact of heterogeneity of pathological tau strains on personalized structure- and strain-specific therapeutic approaches in major tauopathies.
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Affiliation(s)
- Lenka Hromadkova
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | | | - He Liu
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jiri G. Safar
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Neuroscience, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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16
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Anti-Prion Systems in Saccharomyces cerevisiae Turn an Avalanche of Prions into a Flurry. Viruses 2022; 14:v14091945. [PMID: 36146752 PMCID: PMC9503967 DOI: 10.3390/v14091945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/01/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022] Open
Abstract
Prions are infectious proteins, mostly having a self-propagating amyloid (filamentous protein polymer) structure consisting of an abnormal form of a normally soluble protein. These prions arise spontaneously in the cell without known reason, and their effects were generally considered to be fatal based on prion diseases in humans or mammals. However, the wide array of prion studies in yeast including filamentous fungi revealed that their effects can range widely, from lethal to very mild (even cryptic) or functional, depending on the nature of the prion protein and the specific prion variant (or strain) made by the same prion protein but with a different conformation. This prion biology is affected by an array of molecular chaperone systems, such as Hsp40, Hsp70, Hsp104, and combinations of them. In parallel with the systems required for prion propagation, yeast has multiple anti-prion systems, constantly working in the normal cell without overproduction of or a deficiency in any protein, which have negative effects on prions by blocking their formation, curing many prions after they arise, preventing prion infections, and reducing the cytotoxicity produced by prions. From the protectors of nascent polypeptides (Ssb1/2p, Zuo1p, and Ssz1p) to the protein sequesterase (Btn2p), the disaggregator (Hsp104), and the mysterious Cur1p, normal levels of each can cure the prion variants arising in its absence. The controllers of mRNA quality, nonsense-mediated mRNA decay proteins (Upf1, 2, 3), can cure newly formed prion variants by association with a prion-forming protein. The regulator of the inositol pyrophosphate metabolic pathway (Siw14p) cures certain prion variants by lowering the levels of certain organic compounds. Some of these proteins have other cellular functions (e.g., Btn2), while others produce an anti-prion effect through their primary role in the normal cell (e.g., ribosomal chaperones). Thus, these anti-prion actions are the innate defense strategy against prions. Here, we outline the anti-prion systems in yeast that produce innate immunity to prions by a multi-layered operation targeting each step of prion development.
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17
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Meisl G, Xu CK, Taylor JD, Michaels TCT, Levin A, Otzen D, Klenerman D, Matthews S, Linse S, Andreasen M, Knowles TPJ. Uncovering the universality of self-replication in protein aggregation and its link to disease. SCIENCE ADVANCES 2022; 8:eabn6831. [PMID: 35960802 PMCID: PMC9374340 DOI: 10.1126/sciadv.abn6831] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Fibrillar protein aggregates are a hallmark of a range of human disorders, from prion diseases to dementias, but are also encountered in several functional contexts. Yet, the fundamental links between protein assembly mechanisms and their functional or pathological roles have remained elusive. Here, we analyze the aggregation kinetics of a large set of proteins that self-assemble by a nucleated-growth mechanism, from those associated with disease, over those whose aggregates fulfill functional roles in biology, to those that aggregate only under artificial conditions. We find that, essentially, all such systems, regardless of their biological role, are capable of self-replication. However, for aggregates that have evolved to fulfill a structural role, the rate of self-replication is too low to be significant on the biologically relevant time scale. By contrast, all disease-related proteins are able to self-replicate quickly compared to the time scale of the associated disease. Our findings establish the ubiquity of self-replication and point to its potential importance across aggregation-related disorders.
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Affiliation(s)
- Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Catherine K. Xu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Jonathan D. Taylor
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Thomas C. T. Michaels
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Aviad Levin
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus DK-8000, Denmark
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- U.K. Dementia Research Institute, University of Cambridge, Cambridge CB2 0XY, UK
| | - Steve Matthews
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
- Corresponding author. (S.L.); (M.A.); (T.P.J.K.)
| | - Maria Andreasen
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Aarhus DK-8000, Denmark
- Corresponding author. (S.L.); (M.A.); (T.P.J.K.)
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, UK
- Corresponding author. (S.L.); (M.A.); (T.P.J.K.)
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18
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Naeimi WR, Serio TR. Beyond Amyloid Fibers: Accumulation, Biological Relevance, and Regulation of Higher-Order Prion Architectures. Viruses 2022; 14:v14081635. [PMID: 35893700 PMCID: PMC9332770 DOI: 10.3390/v14081635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/14/2022] [Accepted: 07/23/2022] [Indexed: 12/19/2022] Open
Abstract
The formation of amyloid fibers is associated with a diverse range of disease and phenotypic states. These amyloid fibers often assemble into multi-protofibril, high-order architectures in vivo and in vitro. Prion propagation in yeast, an amyloid-based process, represents an attractive model to explore the link between these aggregation states and the biological consequences of amyloid dynamics. Here, we integrate the current state of knowledge, highlight opportunities for further insight, and draw parallels to more complex systems in vitro. Evidence suggests that high-order fibril architectures are present ex vivo from disease relevant environments and under permissive conditions in vivo in yeast, including but not limited to those leading to prion formation or instability. The biological significance of these latter amyloid architectures or how they may be regulated is, however, complicated by inconsistent experimental conditions and analytical methods, although the Hsp70 chaperone Ssa1/2 is likely involved. Transition between assembly states could form a mechanistic basis to explain some confounding observations surrounding prion regulation but is limited by a lack of unified methodology to biophysically compare these assembly states. Future exciting experimental entryways may offer opportunities for further insight.
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19
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Mahapatra S, Sarbahi A, Madhu P, Swasthi HM, Sharma A, Singh P, Mukhopadhyay S. Sub-stoichiometric Hsp104 regulates the genesis and persistence of self-replicable amyloid seeds of Sup35 prion domain. J Biol Chem 2022; 298:102143. [PMID: 35714774 PMCID: PMC9304785 DOI: 10.1016/j.jbc.2022.102143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 11/21/2022] Open
Abstract
Prion-like self-perpetuating conformational conversion of proteins is involved in both transmissible neurodegenerative diseases in mammals and non-Mendelian inheritance in yeast. The transmissibility of amyloid-like aggregates is dependent on the stoichiometry of chaperones such as heat shock proteins (Hsps), including disaggregases. To provide the mechanistic underpinnings of the formation and persistence of prefibrillar amyloid seeds, we investigated the role of substoichiometric Hsp104 on the in vitro amyloid aggregation of the prion domain (NM-domain) of Saccharomyces cerevisiae Sup35. At low substoichiometric concentrations, we show Hsp104 exhibits a dual role: it considerably accelerates the formation of prefibrillar species by shortening the lag phase but also prolongs their persistence by introducing unusual kinetic halts and delaying their conversion into mature amyloid fibers. Additionally, Hsp104-modulated amyloid species displayed a better seeding capability compared to NM-only amyloids. Using biochemical and biophysical tools coupled with site-specific dynamic readouts, we characterized the distinct structural and dynamical signatures of these amyloids. We reveal that Hsp104-remodeled amyloidogenic species are compositionally diverse in prefibrillar aggregates and are packed in a more ordered fashion compared to NM-only amyloids. Finally, we show these Hsp104-remodeled, conformationally distinct NM aggregates display an enhanced autocatalytic self-templating ability that might be crucial for phenotypic outcomes. Taken together, our results demonstrate that substoichiometric Hsp104 promotes compositional diversity and conformational modulations during amyloid formation, yielding effective prefibrillar seeds that are capable of driving prion-like Sup35 propagation. Our findings underscore the key functional and pathological roles of substoichiometric chaperones in prion-like propagation.
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Affiliation(s)
- Sayanta Mahapatra
- Centre for Protein Science, Design and Engineering; Department of Biological Sciences
| | - Anusha Sarbahi
- Centre for Protein Science, Design and Engineering; Department of Biological Sciences
| | - Priyanka Madhu
- Centre for Protein Science, Design and Engineering; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Hema M Swasthi
- Centre for Protein Science, Design and Engineering; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Abhishek Sharma
- CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Priyanka Singh
- CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering; Department of Biological Sciences; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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20
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Han ZZ, Kang SG, Arce L, Westaway D. Prion-like strain effects in tauopathies. Cell Tissue Res 2022; 392:179-199. [PMID: 35460367 PMCID: PMC9034081 DOI: 10.1007/s00441-022-03620-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/25/2022] [Indexed: 12/30/2022]
Abstract
Tau is a microtubule-associated protein that plays crucial roles in physiology and pathophysiology. In the realm of dementia, tau protein misfolding is associated with a wide spectrum of clinicopathologically diverse neurodegenerative diseases, collectively known as tauopathies. As proposed by the tau strain hypothesis, the intrinsic heterogeneity of tauopathies may be explained by the existence of structurally distinct tau conformers, “strains”. Tau strains can differ in their associated clinical features, neuropathological profiles, and biochemical signatures. Although prior research into infectious prion proteins offers valuable lessons for studying how a protein-only pathogen can encompass strain diversity, the underlying mechanism by which tau subtypes are generated remains poorly understood. Here we summarize recent advances in understanding different tau conformers through in vivo and in vitro experimental paradigms, and the implications of heterogeneity of pathological tau species for drug development.
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Affiliation(s)
- Zhuang Zhuang Han
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada.,Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Sang-Gyun Kang
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada.,Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Luis Arce
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada.,Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - David Westaway
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada. .,Department of Medicine, University of Alberta, Edmonton, AB, Canada. .,Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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21
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Zhouravleva GA, Bondarev SA, Zemlyanko OM, Moskalenko SE. Role of Proteins Interacting with the eRF1 and eRF3 Release Factors in the Regulation of Translation and Prionization. Mol Biol 2022. [DOI: 10.1134/s0026893322010101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Nakagawa Y, Shen HCH, Komi Y, Sugiyama S, Kurinomaru T, Tomabechi Y, Krayukhina E, Okamoto K, Yokoyama T, Shirouzu M, Uchiyama S, Inaba M, Niwa T, Sako Y, Taguchi H, Tanaka M. Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system. Nat Chem Biol 2022; 18:321-331. [PMID: 35177839 DOI: 10.1038/s41589-021-00951-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 11/23/2021] [Indexed: 01/17/2023]
Abstract
Disaggregation of amyloid fibrils is a fundamental biological process required for amyloid propagation. However, due to the lack of experimental systems, the molecular mechanism of how amyloid is disaggregated by cellular factors remains poorly understood. Here, we established a robust in vitro reconstituted system of yeast prion propagation and found that heat-shock protein 104 (Hsp104), Ssa1 and Sis1 chaperones are essential for efficient disaggregation of Sup35 amyloid. Real-time imaging of single-molecule fluorescence coupled with the reconstitution system revealed that amyloid disaggregation is achieved by ordered, timely binding of the chaperones to amyloid. Remarkably, we uncovered two distinct prion strain conformation-dependent modes of disaggregation, fragmentation and dissolution. We characterized distinct chaperone dynamics in each mode and found that transient, repeated binding of Hsp104 to the same site of amyloid results in fragmentation. These findings provide a physical foundation for otherwise puzzling in vivo observations and for therapeutic development for amyloid-associated neurodegenerative diseases.
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Affiliation(s)
- Yoshiko Nakagawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan
| | - Howard C-H Shen
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yusuke Komi
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan
| | - Shinju Sugiyama
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan
| | | | - Yuri Tomabechi
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | | | - Kenji Okamoto
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Susumu Uchiyama
- Research Department, U-Medico Inc., Suita, Japan.,Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan.,Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Japan
| | - Megumi Inaba
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tatsuya Niwa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan. .,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
| | - Motomasa Tanaka
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan. .,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
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23
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Dennis EM, Garcia DM. Biochemical Principles in Prion-Based Inheritance. EPIGENOMES 2022; 6:4. [PMID: 35225957 PMCID: PMC8883993 DOI: 10.3390/epigenomes6010004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/13/2022] [Accepted: 01/20/2022] [Indexed: 12/14/2022] Open
Abstract
Prions are proteins that can stably fold into alternative structures that frequently alter their activities. They can self-template their alternate structures and are inherited across cell divisions and generations. While they have been studied for more than four decades, their enigmatic nature has limited their discovery. In the last decade, we have learned just how widespread they are in nature, the many beneficial phenotypes that they confer, while also learning more about their structures and modes of inheritance. Here, we provide a brief review of the biochemical principles of prion proteins, including their sequences, characteristics and structures, and what is known about how they self-template, citing examples from multiple organisms. Prion-based inheritance is the most understudied segment of epigenetics. Here, we lay a biochemical foundation and share a framework for how to define these molecules, as new examples are unearthed throughout nature.
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Affiliation(s)
- Emily M. Dennis
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA;
| | - David M. Garcia
- Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
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24
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Kodera N, Ando T. Visualization of intrinsically disordered proteins by high-speed atomic force microscopy. Curr Opin Struct Biol 2022; 72:260-266. [PMID: 34998124 DOI: 10.1016/j.sbi.2021.11.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 12/30/2022]
Abstract
High-speed atomic force microscopy (HS-AFM) is a powerful tool established 13 years ago. This methodology can capture individual protein molecules carrying out functional activities under near-physiological conditions, without chemical labeling, at 2-3 nm lateral and ∼0.1 nm vertical spatial resolution, and at sub-100 ms temporal resolution. Although most biological HS-AFM studies thus far target structured proteins, HS-AFM is also ideally suited to study the dynamics of intrinsically disordered proteins. Here we review some of the dynamic structures and processes of intrinsically disordered proteins that have been unveiled by HS-AFM imaging.
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Affiliation(s)
- Noriyuki Kodera
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
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25
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Kim C, Haldiman T, Kang SG, Hromadkova L, Han ZZ, Chen W, Lissemore F, Lerner A, de Silva R, Cohen ML, Westaway D, Safar JG. Distinct populations of highly potent TAU seed conformers in rapidly progressing Alzheimer's disease. Sci Transl Med 2022; 14:eabg0253. [PMID: 34985969 DOI: 10.1126/scitranslmed.abg0253] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Chae Kim
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Tracy Haldiman
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Sang-Gyun Kang
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton T6G 2M8, Canada
| | - Lenka Hromadkova
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Zhuang Zhuang Han
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton T6G 2M8, Canada
| | - Wei Chen
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Frances Lissemore
- Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Alan Lerner
- Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Rohan de Silva
- Reta Lila Weston Institute of Neurological Studies and Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 1PJ, UK
| | - Mark L Cohen
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - David Westaway
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton T6G 2M8, Canada
| | - Jiri G Safar
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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26
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Aggregation-induced emission active luminescent polymeric nanofibers: From design, synthesis, fluorescent mechanism to applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2021.116502] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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27
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Khan AN, Qureshi IA, Khan UK, Uversky VN, Khan RH. Inhibition and disruption of amyloid formation by the antibiotic levofloxacin: A new direction for antibiotics in an era of multi-drug resistance. Arch Biochem Biophys 2021; 714:109077. [PMID: 34728171 DOI: 10.1016/j.abb.2021.109077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/16/2021] [Accepted: 10/29/2021] [Indexed: 12/24/2022]
Abstract
Neurodegenerative diseases are a group of debilitating maladies involving protein aggregation. To this day, all advances in neurodegenerative disease therapeutics have helped symptomatically but have not prevented the root cause of the disease, i.e., the aggregation of involved proteins. Antibiotics are becoming increasingly obsolete due to the rising multidrug resistance strains of bacteria. Thus, antibiotics, if put to different use as therapeutics against other diseases, could pave a new direction to the world of antibiotics. Hence, we studied the antibiotic levofloxacin for its potential anti-amyloidogenic behavior using human lysozyme, a protein involved in non-systemic amyloidosis, as a model system. At the sub-stoichiometric level, levofloxacin was able to inhibit amyloid formation in human lysozyme as observed by various spectroscopic and microscopic methods, with IC50 values as low as 8.8 ± 0.1 μM. Levofloxacin also displayed a retarding effect on seeding phenomena by elongating the lag-phase (from 0 to 88 h) at lower concentration, and arresting lysozyme fibrillation at the lag stage in sub-stoichiometric concentrations. Structural and computational analyses provided mechanistic insight showing that levofloxacin stabilizes the lysozyme in the native state by binding to the aggregation-prone residues, and thereby inhibiting amyloid fibrillation. Levofloxacin also showed the property of disrupting amyloid fibrils into a smaller polymeric form of proteins which were less cytotoxic as confirmed by hemolytic assay. Therefore, we throw new light on levofloxacin as an amyloid inhibitor and disruptor which could pave way to utilization of levofloxacin as a potential therapeutic against non-systemic amyloidosis and neurodegenerative diseases.
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Affiliation(s)
- Asra Nasir Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Umar Khalid Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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28
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Amyloid Fragmentation and Disaggregation in Yeast and Animals. Biomolecules 2021; 11:biom11121884. [PMID: 34944528 PMCID: PMC8699242 DOI: 10.3390/biom11121884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 12/29/2022] Open
Abstract
Amyloids are filamentous protein aggregates that are associated with a number of incurable diseases, termed amyloidoses. Amyloids can also manifest as infectious or heritable particles, known as prions. While just one prion is known in humans and animals, more than ten prion amyloids have been discovered in fungi. The propagation of fungal prion amyloids requires the chaperone Hsp104, though in excess it can eliminate some prions. Even though Hsp104 acts to disassemble prion fibrils, at normal levels it fragments them into multiple smaller pieces, which ensures prion propagation and accelerates prion conversion. Animals lack Hsp104, but disaggregation is performed by the same complement of chaperones that assist Hsp104 in yeast—Hsp40, Hsp70, and Hsp110. Exogenous Hsp104 can efficiently cooperate with these chaperones in animals and promotes disaggregation, especially of large amyloid aggregates, which indicates its potential as a treatment for amyloid diseases. However, despite the significant effects, Hsp104 and its potentiated variants may be insufficient to fully dissolve amyloid. In this review, we consider chaperone mechanisms acting to disassemble heritable protein aggregates in yeast and animals, and their potential use in the therapy of human amyloid diseases.
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29
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Wang Y, Fang S, Chen G, Ganti R, Chernova TA, Zhou L, Duong D, Kiyokawa H, Li M, Zhao B, Shcherbik N, Chernoff YO, Yin J. Regulation of the endocytosis and prion-chaperoning machineries by yeast E3 ubiquitin ligase Rsp5 as revealed by orthogonal ubiquitin transfer. Cell Chem Biol 2021; 28:1283-1297.e8. [PMID: 33667410 PMCID: PMC8380759 DOI: 10.1016/j.chembiol.2021.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/22/2020] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Attachment of the ubiquitin (UB) peptide to proteins via the E1-E2-E3 enzymatic machinery regulates diverse biological pathways, yet identification of the substrates of E3 UB ligases remains a challenge. We overcame this challenge by constructing an "orthogonal UB transfer" (OUT) cascade with yeast E3 Rsp5 to enable the exclusive delivery of an engineered UB (xUB) to Rsp5 and its substrate proteins. The OUT screen uncovered new Rsp5 substrates in yeast, such as Pal1 and Pal2, which are partners of endocytic protein Ede1, and chaperones Hsp70-Ssb, Hsp82, and Hsp104 that counteract protein misfolding and control self-perpetuating amyloid aggregates (prions), resembling those involved in human amyloid diseases. We showed that prion formation and effect of Hsp104 on prion propagation are modulated by Rsp5. Overall, our work demonstrates the capacity of OUT to deconvolute the complex E3-substrate relationships in crucial biological processes such as endocytosis and protein assembly disorders through protein ubiquitination.
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Affiliation(s)
- Yiyang Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou 510632, Guangdong, China
| | - Shuai Fang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Geng Chen
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, Guangdong, China
| | - Rakhee Ganti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Li Zhou
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Duc Duong
- Integrated Proteomics Core, Emory University, Atlanta, GA 30322, USA
| | - Hiroaki Kiyokawa
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Ming Li
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48019, USA
| | - Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
| | - Natalia Shcherbik
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA.
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia.
| | - Jun Yin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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30
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Innate immunity to prions: anti-prion systems turn a tsunami of prions into a slow drip. Curr Genet 2021; 67:833-847. [PMID: 34319422 DOI: 10.1007/s00294-021-01203-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/17/2022]
Abstract
The yeast prions (infectious proteins) [URE3] and [PSI+] are essentially non-functional (or even toxic) amyloid forms of Ure2p and Sup35p, whose normal function is in nitrogen catabolite repression and translation termination, respectively. Yeast has an array of systems working in normal cells that largely block infection with prions, block most prion formation, cure most nascent prions and mitigate the toxic effects of those prions that escape the first three types of systems. Here we review recent progress in defining these anti-prion systems, how they work and how they are regulated. Polymorphisms of the prion domains partially block infection with prions. Ribosome-associated chaperones ensure proper folding of nascent proteins, thus reducing [PSI+] prion formation and curing many [PSI+] variants that do form. Btn2p is a sequestering protein which gathers [URE3] amyloid filaments to one place in the cells so that the prion is often lost by progeny cells. Proteasome impairment produces massive overexpression of Btn2p and paralog Cur1p, resulting in [URE3] curing. Inversely, increased proteasome activity, by derepression of proteasome component gene transcription or by 60S ribosomal subunit gene mutation, prevents prion curing by Btn2p or Cur1p. The nonsense-mediated decay proteins (Upf1,2,3) cure many nascent [PSI+] variants by associating with Sup35p directly. Normal levels of the disaggregating chaperone Hsp104 can also cure many [PSI+] prion variants. By keeping the cellular levels of certain inositol polyphosphates / pyrophosphates low, Siw14p cures certain [PSI+] variants. It is hoped that exploration of the yeast innate immunity to prions will lead to discovery of similar systems in humans.
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31
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Kharkov BB, Podkorytov IS, Bondarev SA, Belousov MV, Salikov VA, Zhouravleva GA, Skrynnikov NR. The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils. Angew Chem Int Ed Engl 2021; 60:15445-15451. [PMID: 33891789 DOI: 10.1002/anie.202102408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/19/2021] [Indexed: 11/08/2022]
Abstract
Pulsed-field gradient (PFG) NMR is an important tool for characterization of biomolecules and supramolecular assemblies. However, for micrometer-sized objects, such as amyloid fibrils, these experiments become difficult to interpret because in addition to translational diffusion they are also sensitive to rotational diffusion. We have constructed a mathematical theory describing the outcome of PFG NMR experiments on rod-like fibrils. To test its validity, we have studied the fibrils formed by Sup35NM segment of the prion protein Sup35. The interpretation of the PFG NMR data in this system is fully consistent with the evidence from electron microscopy. Contrary to some previously expressed views, the signals originating from disordered regions in the fibrils can be readily differentiated from the similar signals representing small soluble species (e.g. proteolytic fragments). This paves the way for diffusion-sorted NMR experiments on complex amyloidogenic samples.
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Affiliation(s)
- Boris B Kharkov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Ivan S Podkorytov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia.,Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St. Petersburg, Russia
| | - Vladislav A Salikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia.,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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32
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Kharkov BB, Podkorytov IS, Bondarev SA, Belousov MV, Salikov VA, Zhouravleva GA, Skrynnikov NR. The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Boris B. Kharkov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Ivan S. Podkorytov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
| | - Mikhail V. Belousov
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
- Laboratory for Proteomics of Supra-Organismal Systems All-Russia Research Institute for Agricultural Microbiology (ARRIAM) 196608 St. Petersburg Russia
| | - Vladislav A. Salikov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
| | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
- Department of Chemistry Purdue University West Lafayette IN 47907 USA
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33
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Russell MJ. The "Water Problem"( sic), the Illusory Pond and Life's Submarine Emergence-A Review. Life (Basel) 2021; 11:429. [PMID: 34068713 PMCID: PMC8151828 DOI: 10.3390/life11050429] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/30/2021] [Accepted: 05/01/2021] [Indexed: 01/10/2023] Open
Abstract
The assumption that there was a "water problem" at the emergence of life-that the Hadean Ocean was simply too wet and salty for life to have emerged in it-is here subjected to geological and experimental reality checks. The "warm little pond" that would take the place of the submarine alkaline vent theory (AVT), as recently extolled in the journal Nature, flies in the face of decades of geological, microbiological and evolutionary research and reasoning. To the present author, the evidence refuting the warm little pond scheme is overwhelming given the facts that (i) the early Earth was a water world, (ii) its all-enveloping ocean was never less than 4 km deep, (iii) there were no figurative "Icelands" or "Hawaiis", nor even an "Ontong Java" then because (iv) the solidifying magma ocean beneath was still too mushy to support such salient loadings on the oceanic crust. In place of the supposed warm little pond, we offer a well-protected mineral mound precipitated at a submarine alkaline vent as life's womb: in place of lipid membranes, we suggest peptides; we replace poisonous cyanide with ammonium and hydrazine; instead of deleterious radiation we have the appropriate life-giving redox and pH disequilibria; and in place of messy chemistry we offer the potential for life's emergence from the simplest of geochemically available molecules and ions focused at a submarine alkaline vent in the Hadean-specifically within the nano-confined flexible and redox active interlayer walls of the mixed-valent double layer oxyhydroxide mineral, fougerite/green rust comprising much of that mound.
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Affiliation(s)
- Michael J Russell
- Dipartimento di Chimica, Università degli Studi di Torino, via P. Giuria 7, 10125 Turin, Italy
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34
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Bandyopadhyay A, Sannigrahi A, Chattopadhyay K. Membrane composition and lipid to protein ratio modulate amyloid kinetics of yeast prion protein. RSC Chem Biol 2021; 2:592-605. [PMID: 34458802 PMCID: PMC8341755 DOI: 10.1039/d0cb00203h] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/15/2021] [Indexed: 12/22/2022] Open
Abstract
Understanding of prion aggregation in a membrane environment may help to ameliorate neurodegenerative complications caused by the amyloid forms of prions. Here, we investigated the membrane binding-induced aggregation of yeast prion protein Sup35. Using the combination of fluorescence correlation spectroscopy (FCS) at single molecule resolution and other biophysical studies, we establish that lipid composition and lipid/protein ratio are key modulators of the aggregation kinetics of Sup35. In the presence of a zwitterionic membrane (DMPC), Sup35 exhibited novel biphasic aggregation kinetics at lipid/protein ratios ranging between 20 : 1 and 70 : 1 (termed here as the optimum lipid concentration, OLC). In ratios below (low lipid concentration, LLC) and above (ELC, excess lipid concentration) that range, the aggregation was found to be monophasic. In contrast, in the presence of negatively charged membranes, we did not observe any bi-phasic aggregation kinetics in the entire range of protein to lipid ratios. Our results provide a mechanistic description of the role that membrane concentration/composition-modulated aggregation may play in neurodegenerative diseases.
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Affiliation(s)
- Arnab Bandyopadhyay
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road Kolkata 700032 India
| | - Achinta Sannigrahi
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road Kolkata 700032 India
| | - Krishnananda Chattopadhyay
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road Kolkata 700032 India
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35
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Michiels E, Liu S, Gallardo R, Louros N, Mathelié-Guinlet M, Dufrêne Y, Schymkowitz J, Vorberg I, Rousseau F. Entropic Bristles Tune the Seeding Efficiency of Prion-Nucleating Fragments. Cell Rep 2021; 30:2834-2845.e3. [PMID: 32101755 PMCID: PMC7043027 DOI: 10.1016/j.celrep.2020.01.098] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/07/2020] [Accepted: 01/28/2020] [Indexed: 01/04/2023] Open
Abstract
Prions of lower eukaryotes are self-templating protein aggregates with cores formed by parallel in-register beta strands. Short aggregation-prone glutamine (Q)- and asparagine (N)-rich regions embedded in longer disordered domains have been proposed to act as nucleation sites that initiate refolding of soluble prion proteins into highly ordered fibrils, termed amyloid. We demonstrate that a short Q/N-rich peptide corresponding to a proposed nucleation site in the prototype Saccharomyces cerevisiae prion protein Sup35 is sufficient to induce infectious cytosolic prions in mouse neuroblastoma cells ectopically expressing the soluble Sup35 NM prion domain. Embedding this nucleating core in a non-native N-rich sequence that does not form amyloid but acts as an entropic bristle quadruples seeding efficiency. Our data suggest that large disordered sequences flanking an aggregation core in prion proteins act as not only solubilizers of the monomeric protein but also breakers of the formed amyloid fibrils, enhancing infectivity of the prion seeds. A short peptide derived from Sup35 (p103–113) forms rigid amyloid fibrils p103–113 fibrils can induce infectious Sup35 NM prions in mammalian cells Embedding p103–113 in an N-rich sequence increases fibril brittleness Increased fibril brittleness enhances prion-inducing capacity
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Affiliation(s)
- Emiel Michiels
- VIB Center for Brain and Disease Research, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, 3000 Leuven, Belgium
| | - Shu Liu
- German Center for Neurodegenerative Diseases Bonn (DZNE e.V.), Venusberg-Campus 1, Building 99, 53127 Bonn, Germany
| | - Rodrigo Gallardo
- VIB Center for Brain and Disease Research, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, 3000 Leuven, Belgium
| | - Nikolaos Louros
- VIB Center for Brain and Disease Research, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, 3000 Leuven, Belgium
| | - Marion Mathelié-Guinlet
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.06, 1348 Louvain-la-Neuve, Belgium
| | - Yves Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.06, 1348 Louvain-la-Neuve, Belgium; Walloon Excellence in Life Sciences and Biotechnology (WELBIO), 1300 Wavre, Belgium
| | - Joost Schymkowitz
- VIB Center for Brain and Disease Research, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, 3000 Leuven, Belgium.
| | - Ina Vorberg
- German Center for Neurodegenerative Diseases Bonn (DZNE e.V.), Venusberg-Campus 1, Building 99, 53127 Bonn, Germany; Rheinische Friedrich-Wilhelms-Universität Bonn, Siegmund-Freud-Str. 25, 53127 Bonn, Germany.
| | - Frederic Rousseau
- VIB Center for Brain and Disease Research, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, 3000 Leuven, Belgium.
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36
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Preparation, Functionalization, Modification, and Applications of Nanostructured Gold: A Critical Review. ENERGIES 2021. [DOI: 10.3390/en14051278] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Gold nanoparticles (Au NPs) play a significant role in science and technology because of their unique size, shape, properties and broad range of potential applications. This review focuses on the various approaches employed for the synthesis, modification and functionalization of nanostructured Au. The potential catalytic applications and their enhancement upon modification of Au nanostructures have also been discussed in detail. The present analysis also offers brief summaries of the major Au nanomaterials synthetic procedures, such as hydrothermal, solvothermal, sol-gel, direct oxidation, chemical vapor deposition, sonochemical deposition, electrochemical deposition, microwave and laser pyrolysis. Among the various strategies used for improving the catalytic performance of nanostructured Au, the modification and functionalization of nanostructured Au produced better results. Therefore, various synthesis, modification and functionalization methods employed for better catalytic outcomes of nanostructured Au have been summarized in this review.
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37
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Bezsonov EE, Edskes HK, Wickner RB. Innate immunity to yeast prions: Btn2p and Cur1p curing of the [URE3] prion is prevented by 60S ribosomal protein deficiency or ubiquitin/proteasome system overactivity. Genetics 2021; 217:6127178. [PMID: 33857305 DOI: 10.1093/genetics/iyab013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/09/2021] [Indexed: 12/13/2022] Open
Abstract
[URE3] is an amyloid-based prion of Ure2p, a negative regulator of poor nitrogen source catabolism in Saccharomyces cerevisiae. Overproduced Btn2p or its paralog Cur1p, in processes requiring Hsp42, cure the [URE3] prion. Btn2p cures by collecting Ure2p amyloid filaments at one place in the cell. We find that rpl4aΔ, rpl21aΔ, rpl21bΔ, rpl11bΔ, and rpl16bΔ (large ribosomal subunit proteins) or ubr2Δ (ubiquitin ligase targeting Rpn4p, an activator of proteasome genes) reduce curing by overproduced Btn2p or Cur1p. Impaired curing in ubr2Δ or rpl21bΔ is restored by an rpn4Δ mutation. No effect of rps14aΔ or rps30bΔ on curing was observed, indicating that 60S subunit deficiency specifically impairs curing. Levels of Hsp42p, Sis1p, or Btn3p are unchanged in rpl4aΔ, rpl21bΔ, or ubr2Δ mutants. Overproduction of Cur1p or Btn2p was enhanced in rpn4Δ and hsp42Δ mutants, lower in ubr2Δ strains, and restored to above wild-type levels in rpn4Δ ubr2Δ strains. As in the wild-type, Ure2N-GFP colocalizes with Btn2-RFP in rpl4aΔ, rpl21bΔ, or ubr2Δ strains, but not in hsp42Δ. Btn2p/Cur1p overproduction cures [URE3] variants with low seed number, but seed number is not increased in rpl4aΔ, rpl21bΔ or ubr2Δ mutants. Knockouts of genes required for the protein sorting function of Btn2p did not affect curing of [URE3], nor did inactivation of the Hsp104 prion-curing activity. Overactivity of the ubiquitin/proteasome system, resulting from 60S subunit deficiency or ubr2Δ, may impair Cur1p and Btn2p curing of [URE3] by degrading Cur1p, Btn2p or another component of these curing systems.
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Affiliation(s)
- Evgeny E Bezsonov
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
| | - Herman K Edskes
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
| | - Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
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Fomicheva A, Ross ED. From Prions to Stress Granules: Defining the Compositional Features of Prion-Like Domains That Promote Different Types of Assemblies. Int J Mol Sci 2021; 22:ijms22031251. [PMID: 33513942 PMCID: PMC7865556 DOI: 10.3390/ijms22031251] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Stress granules are ribonucleoprotein assemblies that form in response to cellular stress. Many of the RNA-binding proteins found in stress granule proteomes contain prion-like domains (PrLDs), which are low-complexity sequences that compositionally resemble yeast prion domains. Mutations in some of these PrLDs have been implicated in neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia, and are associated with persistent stress granule accumulation. While both stress granules and prions are macromolecular assemblies, they differ in both their physical properties and complexity. Prion aggregates are highly stable homopolymeric solids, while stress granules are complex dynamic biomolecular condensates driven by multivalent homotypic and heterotypic interactions. Here, we use stress granules and yeast prions as a paradigm to examine how distinct sequence and compositional features of PrLDs contribute to different types of PrLD-containing assemblies.
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Levkovich SA, Rencus-Lazar S, Gazit E, Laor Bar-Yosef D. Microbial Prions: Dawn of a New Era. Trends Biochem Sci 2021; 46:391-405. [PMID: 33423939 DOI: 10.1016/j.tibs.2020.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/22/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022]
Abstract
Protein misfolding and aggregation are associated with human diseases and aging. However, microorganisms widely exploit the self-propagating properties of misfolded infectious protein particles, prions, as epigenetic information carriers that drive various phenotypic adaptations and encode molecular information. Microbial prion research has faced a paradigm shift in recent years, with breakthroughs that demonstrate the great functional and structural diversity of these agents. Here, we outline unorthodox examples of microbial prions in yeast and other microorganisms, focusing on their noncanonical functions. We discuss novel molecular mechanisms for the inheritance of conformationally-encoded epigenetic information and the evolutionary advantages they confer. Lastly, in light of recent advancements in the field of molecular self-assembly, we present a hypothesis regarding the existence of non-proteinaceous prion-like entities.
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Affiliation(s)
- Shon A Levkovich
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sigal Rencus-Lazar
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ehud Gazit
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel; Sagol Interdisciplinary School of Neurosciences, Tel Aviv University, Tel Aviv, Israel.
| | - Dana Laor Bar-Yosef
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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Kabani M. Extracellular Vesicles and the Propagation of Yeast Prions. Curr Top Microbiol Immunol 2021; 432:57-66. [DOI: 10.1007/978-3-030-83391-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Ishikawa T. Saccharomyces cerevisiae in neuroscience: how unicellular organism helps to better understand prion protein? Neural Regen Res 2021; 16:489-495. [PMID: 32985470 PMCID: PMC7996030 DOI: 10.4103/1673-5374.293137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The baker’s yeast Saccharomyces (S.) cerevisiae is a single-celled eukaryotic model organism widely used in research on life sciences. Being a unicellular organism, S. cerevisiae has some evident limitations in application to neuroscience. However, yeast prions are extensively studied and they are known to share some hallmarks with mammalian prion protein or other amyloidogenic proteins found in the pathogenesis of Alzheimer’s, Parkinson’s, or Huntington’s diseases. Therefore, the yeast S. cerevisiae has been widely used for basic research on aggregation properties of proteins in cellulo and on their propagation. Recently, a yeast-based study revealed that some regions of mammalian prion protein and amyloid β1–42 are capable of induction and propagation of yeast prions. It is one of the examples showing that evolutionarily distant organisms share common mechanisms underlying the structural conversion of prion proteins making yeast cells a useful system for studying mammalian prion protein. S. cerevisiae has also been used to design novel screening systems for anti-prion compounds from chemical libraries. Yeast-based assays are cheap in maintenance and safe for the researcher, making them a very good choice to perform preliminary screening before further characterization in systems engaging mammalian cells infected with prions. In this review, not only classical red/white colony assay but also yeast-based screening assays developed during last year are discussed. Computational analysis and research carried out using yeast prions force us to expect that prions are widely present in nature. Indeed, the last few years brought us several examples indicating that the mammalian prion protein is no more peculiar protein – it seems that a better understanding of prion proteins nature-wide may aid us with the treatment of prion diseases and other amyloid-related medical conditions.
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Affiliation(s)
- Takao Ishikawa
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Extracellular Vesicles-Encapsulated Yeast Prions and What They Can Tell Us about the Physical Nature of Propagons. Int J Mol Sci 2020; 22:ijms22010090. [PMID: 33374854 PMCID: PMC7794690 DOI: 10.3390/ijms22010090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/14/2020] [Accepted: 12/20/2020] [Indexed: 12/25/2022] Open
Abstract
The yeast Saccharomyces cerevisiae hosts an ensemble of protein-based heritable traits, most of which result from the conversion of structurally and functionally diverse cytoplasmic proteins into prion forms. Among these, [PSI+], [URE3] and [PIN+] are the most well-documented prions and arise from the assembly of Sup35p, Ure2p and Rnq1p, respectively, into insoluble fibrillar assemblies. Yeast prions propagate by molecular chaperone-mediated fragmentation of these aggregates, which generates small self-templating seeds, or propagons. The exact molecular nature of propagons and how they are faithfully transmitted from mother to daughter cells despite spatial protein quality control are not fully understood. In [PSI+] cells, Sup35p forms detergent-resistant assemblies detectable on agarose gels under semi-denaturant conditions and cytosolic fluorescent puncta when the protein is fused to green fluorescent protein (GFP); yet, these macroscopic manifestations of [PSI+] do not fully correlate with the infectivity measured during growth by the mean of protein infection assays. We also discovered that significant amounts of infectious Sup35p particles are exported via extracellular (EV) and periplasmic (PV) vesicles in a growth phase and glucose-dependent manner. In the present review, I discuss how these vesicles may be a source of actual propagons and a suitable vehicle for their transmission to the bud.
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Wang W, Ventura S. Prion domains as a driving force for the assembly of functional nanomaterials. Prion 2020; 14:170-179. [PMID: 32597308 PMCID: PMC7518758 DOI: 10.1080/19336896.2020.1785659] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 01/06/2023] Open
Abstract
Amyloids display a highly ordered fibrillar structure. Many of these assemblies appear associated with human disease. However, the controllable, stable, tunable, and robust nature of amyloid fibrils can be exploited to build up remarkable nanomaterials with a wide range of applications in biomedicine and biotechnology. Functional prions constitute a particular class of amyloids. These transmissible proteins exhibit a modular architecture, with a disordered prion domain responsible for the assembly and one or more globular domains that account for the activity. Importantly, the original globular protein can be replaced with any protein of interest, without compromising the fibrillation potential. These genetic fusions form fibrils in which the globular domain remains folded, rendering functional nanostructures. However, in some cases, steric hindrance restricts the activity of these fibrils. This limitation can be solved by dissecting prion domains into shorter sequences that keep their self-assembling properties while allowing better access to the active protein in the fibrillar state. In this review, we will discuss the properties of prion-like functional nanomaterials and the amazing applications of these biocompatible fibrillar arrangements.
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Affiliation(s)
- Weiqiang Wang
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
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Mukhopadhyay S. The Dynamism of Intrinsically Disordered Proteins: Binding-Induced Folding, Amyloid Formation, and Phase Separation. J Phys Chem B 2020; 124:11541-11560. [PMID: 33108190 DOI: 10.1021/acs.jpcb.0c07598] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Intrinsically disordered proteins (IDPs) or natively unfolded proteins do not undergo autonomous folding into a well-defined 3-D structure and challenge the conventional structure-function paradigm. They are involved in a multitude of critical physiological functions by adopting various structural states via order-to-disorder transitions or by maintaining their disordered characteristics in functional complexes. In recent times, there has been a burgeoning interest in the investigation of intriguing behavior of IDPs using highly multidisciplinary and complementary approaches due to the pivotal role of this unique class of protein chameleons in physiology and disease. Over the past decade or so, our laboratory has been actively investigating the unique physicochemical properties of this class of highly dynamic, flexible, rapidly interconverting proteins. We have utilized a diverse array of existing and emerging tools involving steady-state and time-resolved fluorescence, Raman spectroscopy, circular dichroism, light scattering, fluorescence microscopy, and atomic force microscopy coupled with site-directed mutagenesis and other biochemical and biophysical tools to study a variety of interesting and important aspects of IDPs. In this Feature Article, I describe our work on the conformational characteristics, solvation dynamics, binding-induced folding, amyloid formation, and liquid-liquid phase separation of a number of amyloidogenic IDPs. A series of these studies described here captures the role of conformational plasticity and dynamics in directing binding, folding, assembly, aggregation, and phase transitions implicated in physiology and pathology.
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Affiliation(s)
- Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, India
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45
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Normal levels of ribosome-associated chaperones cure two groups of [PSI+] prion variants. Proc Natl Acad Sci U S A 2020; 117:26298-26306. [PMID: 33020283 DOI: 10.1073/pnas.2016954117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The yeast prion [PSI+] is a self-propagating amyloid of the translation termination factor, Sup35p. For known pathogenic prions, such as [PSI+], a single protein can form an array of different amyloid structures (prion variants) each stably inherited and with differing biological properties. The ribosome-associated chaperones, Ssb1/2p (Hsp70s), and RAC (Zuo1p (Hsp40) and Ssz1p (Hsp70)), enhance de novo protein folding by protecting nascent polypeptide chains from misfolding and maintain translational fidelity by involvement in translation termination. Ssb1/2p and RAC chaperones were previously found to inhibit [PSI+] prion generation. We find that most [PSI+] variants arising in the absence of each chaperone were cured by restoring normal levels of that protein. [PSI+] variants hypersensitive to Ssb1/2p have distinguishable biological properties from those hypersensitive to Zuo1p or Ssz1p. The elevated [PSI+] generation frequency in each deletion strain is not due to an altered [PIN+], another prion that primes [PSI+] generation. [PSI+] prion generation/propagation may be inhibited by Ssb1/2/RAC chaperones by ensuring proper folding of nascent Sup35p, thus preventing its joining amyloid fibers. Alternatively, the effect of RAC/Ssb mutations on translation termination and the absence of an effect on the [URE3] prion suggest an effect on the mature Sup35p such that it does not readily join amyloid filaments. Ssz1p is degraded in zuo1Δ [psi-] cells, but not if the cells carry any of several [PSI+] variants. Our results imply that prions arise more frequently than had been thought but the cell has evolved exquisite antiprion systems that rapidly eliminate most variants.
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Sulatskaya AI, Bondarev SA, Sulatsky MI, Trubitsina NP, Belousov MV, Zhouravleva GA, Llanos MA, Kajava AV, Kuznetsova IM, Turoverov KK. Point mutations affecting yeast prion propagation change the structure of its amyloid fibrils. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bousset L, Luckgei N, Kabani M, Gardiennet C, Schütz AK, Melki R, Meier BH, Böckmann A. Prion Amyloid Polymorphs - The Tag Might Change It All. Front Mol Biosci 2020; 7:190. [PMID: 32850974 PMCID: PMC7423878 DOI: 10.3389/fmolb.2020.00190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/20/2020] [Indexed: 11/13/2022] Open
Abstract
Sup35p is a protein from Saccharomyces cerevisiae. It can propagate using a prion-like mechanism, which means that it can recruit non-prion soluble Sup35p into insoluble fibrils. Sup35p is a large protein showing three distinct domains, N, M and an extended globular domain. We have previously studied the conformations of the full-length and truncated NM versions carrying poly-histidine tags on the N-terminus. Comparison with structural data from C-terminally poly-histidine tagged NM from the literature surprisingly revealed discrepancies. Here we investigated fibrils from the untagged, as well as a C-terminally poly-histidine tagged NM construct, using solid-state NMR. We find that the conformation of untagged NM is very close to the N-terminally tagged NM and confirms our previous findings. The C-terminal poly-histidine tag, in contrast, drastically changes the NM fibril structure, and yields data consistent with results obtained previously on this construct. We conclude that the C-terminally located Sup35p globular domain influences the structure of the fibrillar core at the N domain, as previously shown. We further conclude, based on the present data, that small tags on NM C-terminus have a substantial, despite different, impact. Modifications at this remote localization thus shows an unexpected influence on the fibril structure, and importantly also its propensity to induce [PSI+].
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Affiliation(s)
- Luc Bousset
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-aux-Roses, France
| | - Nina Luckgei
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Universite de Lyon, Lyon, France
| | - Mehdi Kabani
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-aux-Roses, France
| | - Carole Gardiennet
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Universite de Lyon, Lyon, France
| | - Anne K Schütz
- ETH Zürich, Laboratory of Physical Chemistry, Zurich, Switzerland
| | - Ronald Melki
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-aux-Roses, France
| | - Beat H Meier
- ETH Zürich, Laboratory of Physical Chemistry, Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Universite de Lyon, Lyon, France
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Kabani M, Melki R. The Yarrowia lipolytica orthologs of Sup35p assemble into thioflavin T-negative amyloid fibrils. Biochem Biophys Res Commun 2020; 529:533-539. [PMID: 32736670 DOI: 10.1016/j.bbrc.2020.06.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 11/26/2022]
Abstract
The translation terminator Sup35p assembles into self-replicating fibrillar aggregates that are responsible for the [PSI+] prion state. The Q/N-rich N-terminal domain together with the highly charged middle-domain (NM domain) drive the assembly of Sup35p into amyloid fibrils in vitro. NM domains are highly divergent among yeasts. The ability to convert to a prion form is however conserved among Sup35 orthologs. In particular, the Yarrowia lipolytica Sup35p stands out with an exceptionally high prion conversion rate. In the present work, we show that different Yarrowia lipolytica strains contain one of two Sup35p orthologs that differ by the number of repeats within their NM domain. The Y. lipolytica Sup35 proteins are able to assemble into amyloid fibrils. Contrary to S. cerevisiae Sup35p, fibrils made of full-length or NM domains of Y. lipolytica Sup35 proteins did not bind Thioflavin-T, a well-known marker of amyloid aggregates.
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Affiliation(s)
- Mehdi Kabani
- Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale (DRF), Laboratoire des Maladies Neurodégénératives, Centre National de la Recherche Scientifique (CNRS), F-92265, Fontenay-aux-Roses, France.
| | - Ronald Melki
- Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale (DRF), Laboratoire des Maladies Neurodégénératives, Centre National de la Recherche Scientifique (CNRS), F-92265, Fontenay-aux-Roses, France
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Wickner RB, Edskes HK, Son M, Wu S, Niznikiewicz M. How Do Yeast Cells Contend with Prions? Int J Mol Sci 2020; 21:ijms21134742. [PMID: 32635197 PMCID: PMC7369894 DOI: 10.3390/ijms21134742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 06/26/2020] [Accepted: 06/30/2020] [Indexed: 12/11/2022] Open
Abstract
Infectious proteins (prions) include an array of human (mammalian) and yeast amyloid diseases in which a protein or peptide forms a linear β-sheet-rich filament, at least one functional amyloid prion, and two functional infectious proteins unrelated to amyloid. In Saccharomyces cerevisiae, at least eight anti-prion systems deal with pathogenic amyloid yeast prions by (1) blocking their generation (Ssb1,2, Ssz1, Zuo1), (2) curing most variants as they arise (Btn2, Cur1, Hsp104, Upf1,2,3, Siw14), and (3) limiting the pathogenicity of variants that do arise and propagate (Sis1, Lug1). Known mechanisms include facilitating proper folding of the prion protein (Ssb1,2, Ssz1, Zuo1), producing highly asymmetric segregation of prion filaments in mitosis (Btn2, Hsp104), competing with the amyloid filaments for prion protein monomers (Upf1,2,3), and regulation of levels of inositol polyphosphates (Siw14). It is hoped that the discovery of yeast anti-prion systems and elucidation of their mechanisms will facilitate finding analogous or homologous systems in humans, whose manipulation may be useful in treatment.
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50
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Daude N, Kim C, Kang SG, Eskandari-Sedighi G, Haldiman T, Yang J, Fleck SC, Gomez-Cardona E, Han ZZ, Borrego-Ecija S, Wohlgemuth S, Julien O, Wille H, Molina-Porcel L, Gelpi E, Safar JG, Westaway D. Diverse, evolving conformer populations drive distinct phenotypes in frontotemporal lobar degeneration caused by the same MAPT-P301L mutation. Acta Neuropathol 2020; 139:1045-1070. [PMID: 32219515 PMCID: PMC7244472 DOI: 10.1007/s00401-020-02148-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/18/2020] [Accepted: 03/09/2020] [Indexed: 01/29/2023]
Abstract
Tau protein accumulation is a common denominator of major dementias, but this process is inhomogeneous, even when triggered by the same germline mutation. We considered stochastic misfolding of human tau conformers followed by templated conversion of native monomers as an underlying mechanism and derived sensitive conformational assays to test this concept. Assessments of brains from aged TgTauP301L transgenic mice revealed a prodromal state and three distinct signatures for misfolded tau. Frontotemporal lobar degeneration (FTLD)-MAPT-P301L patients with different clinical phenotypes also displayed three signatures, two resembling those found in TgTauP301L mice. As physicochemical and cell bioassays confirmed diverse tau strains in the mouse and human brain series, we conclude that evolution of diverse tau conformers is intrinsic to the pathogenesis of this uni-allelic form of tauopathy. In turn, effective therapeutic interventions in FTLD will need to address evolving repertoires of misfolded tau species rather than singular, static molecular targets.
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Affiliation(s)
- Nathalie Daude
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, T6G 2M8, Canada
| | - Chae Kim
- Department of Pathology, Case Western Reserve University, Institute of Pathology Building, Rm 406, 2085 Adelbert Road, Cleveland, OH, 44106-4907, USA
| | - Sang-Gyun Kang
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, T6G 2M8, Canada
| | - Ghazaleh Eskandari-Sedighi
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, T6G 2M8, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Tracy Haldiman
- Department of Pathology, Case Western Reserve University, Institute of Pathology Building, Rm 406, 2085 Adelbert Road, Cleveland, OH, 44106-4907, USA
| | - Jing Yang
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, T6G 2M8, Canada
| | - Shelaine C Fleck
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, T6G 2M8, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | | | - Zhuang Zhuang Han
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, T6G 2M8, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Sergi Borrego-Ecija
- Neurological Tissue Bank of the Biobanc, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Serene Wohlgemuth
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, T6G 2M8, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Holger Wille
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, T6G 2M8, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | | | - Ellen Gelpi
- Neurological Tissue Bank of the Biobanc, Hospital Clinic, IDIBAPS, Barcelona, Spain
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Jiri G Safar
- Department of Pathology, Case Western Reserve University, Institute of Pathology Building, Rm 406, 2085 Adelbert Road, Cleveland, OH, 44106-4907, USA.
- Department of Neurology, Case Western Reserve University, Institute of Pathology Building, Rm 406, 2085 Adelbert Road, Cleveland, OH, 44106-4907, USA.
| | - David Westaway
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, T6G 2M8, Canada.
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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