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The Mutability of Yeast Prions. Viruses 2022; 14:v14112337. [PMID: 36366434 PMCID: PMC9696419 DOI: 10.3390/v14112337] [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: 08/01/2022] [Revised: 10/10/2022] [Accepted: 10/23/2022] [Indexed: 02/01/2023] Open
Abstract
Prions replicate by a self-templating mechanism. Infidelity in the process can lead to the emergence of new infectious structures, referred to as variants or strains. The question of whether prions are prone to mis-templating is not completely answered. Our previous experiments with 23 variants of the yeast [PSI+] prion do not support broad mutability. However, it became clear recently that the heat shock protein Hsp104 can restrict [PSI+] strain variation. This raises the possibility that many transmutable variants of the prion may have been mistaken as faithful-propagating simply because the mutant structure was too sturdy or too frail to take root in the wild-type cell. Here, I alter the strength of Hsp104 in yeast, overexpressing wild-type Hsp104 or expressing the hypo-active Hsp104T160M mutant, and check if the new environments enable the variants to mutate. Two variants hitherto thought of as faithful-propagating are discovered to generate different structures, which are stabilized with the hypo-active chaperone. In contrast, most transmutable variants discovered in cells overexpressing Hsp104 have been correctly identified as such previously in wild-type cells without the overexpression. The majority of transmutable variants only mis-template the structure of VH, VK, or VL, which are the most frequently observed variants and do not spontaneously mutate. There are four additional variants that never give rise to different structures in all cell conditions tested. Therefore, quite a few [PSI+] variants are faithful-propagating, and even the transmutable ones do not freely evolve but can only change to limited structural types.
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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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Huang YW, King CY. A complete catalog of wild-type Sup35 prion variants and their protein-only propagation. Curr Genet 2019; 66:97-122. [DOI: 10.1007/s00294-019-01003-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/28/2019] [Accepted: 06/01/2019] [Indexed: 10/26/2022]
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Yeast Sup35 Prion Structure: Two Types, Four Parts, Many Variants. Int J Mol Sci 2019; 20:ijms20112633. [PMID: 31146333 PMCID: PMC6600473 DOI: 10.3390/ijms20112633] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 12/14/2022] Open
Abstract
The yeast [PSI+] prion, formed by the Sup35 (eRF3) protein, has multiple structural variants differing in the strength of nonsense suppressor phenotype. Structure of [PSI+] and its variation are characterized poorly. Here, we mapped Sup35 amyloid cores of 26 [PSI+] ex vivo prions of different origin using proteinase K digestion and mass spectrometric identification of resistant peptides. In all [PSI+] variants the Sup35 amino acid residues 2-32 were fully resistant and the region up to residue 72 was partially resistant. Proteinase K-resistant structures were also found within regions 73-124, 125-153, and 154-221, but their presence differed between [PSI+] isolates. Two distinct digestion patterns were observed for region 2-72, which always correlated with the "strong" and "weak" [PSI+] nonsense suppressor phenotypes. Also, all [PSI+] with a weak pattern were eliminated by multicopy HSP104 gene and were not toxic when combined with multicopy SUP35. [PSI+] with a strong pattern showed opposite properties, being resistant to multicopy HSP104 and lethal with multicopy SUP35. Thus, Sup35 prion cores can be composed of up to four elements. [PSI+] variants can be divided into two classes reliably distinguishable basing on structure of the first element and the described assays.
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Yu CI, King CY. Forms and abundance of chaperone proteins influence yeast prion variant competition. Mol Microbiol 2019; 111:798-810. [PMID: 30582872 DOI: 10.1111/mmi.14192] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2018] [Indexed: 02/01/2023]
Abstract
[PSI+ ] variants are different infectious conformations of the same Sup35 protein. We show that when [PSI+ ] variants VK and VL co-infect a dividing host, only one prevails in the end and the host genetic background is involved in winner selection. In the 5V-H19 background, the VK variant dominates over the VL variant. The order of dominance is reversed in the 74-D694 background, where VL can coexists with VK for a short period, but will eventually take over. Differential interaction of chaperone proteins with distinct prion variant conformations can influence the outcome of competition. Expanding the Glycine/Methionine-rich domain of Sis1, an Hsp40 protein, helps the propagation of VL. Over-expression of the Hsp70 protein Ssa2 lowers the number of prion particles (propagons) in the cell. There is more reduction for VK than VL, causing the latter to dominate in some of the 5V-H19 and all of the 74-D694 cells tested. Consistently, depleting Ssa1 in 74-D694 strengthens VK. Swapping chromosomal alleles of SSA1/2 and SIS1 between 5V-H19 and 74-D694, including cognate promoters, is not sufficient to change the native dominance order of each background, suggesting there exist additional polymorphic factors that modulate [PSI+ ] competition.
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Affiliation(s)
- Chang-I Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chih-Yen King
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
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Bondarev SA, Bondareva OV, Zhouravleva GA, Kajava AV. BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures. Bioinformatics 2018; 34:599-608. [PMID: 29444233 DOI: 10.1093/bioinformatics/btx629] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/03/2017] [Indexed: 11/12/2022] Open
Abstract
Motivation Numerous experimental studies have suggested that polypeptide chains of large amyloidogenic regions zig-zag in β-serpentine arrangements. These β-serpentines are stacked axially and form the superpleated β-structure. Despite this progress in the understanding of amyloid folds, the determination of their 3D structure at the atomic level is still a problem due to the polymorphism of these fibrils and incompleteness of experimental structural data. Today, the way to get insight into the atomic structure of amyloids is a combination of experimental studies with bioinformatics. Results We developed a computer program BetaSerpentine that reconstructs β-serpentine arrangements from individual β-arches predicted by ArchCandy program and ranks them in order of preference. It was shown that the BetaSerpentine program in combination with the experimental data can be used to gain insight into the detailed 3D structure of amyloids. It opens avenues to the structure-based interpretation and design of the experiments. Availability and implementation BetaSerpentine webserver can be accessed through website: http://bioinfo.montp.cnrs.fr/b-serpentine. Source code is available in git.hub repository (github.com/stanislavspbgu/BetaSerpentine). Contact stanislavspbgu@gmail.com or andrey.kajava@crbm.cnrs.fr. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stanislav A Bondarev
- Laboratory of Amyloid Biology and Department of Genetics and Biotechnology, St. Petersburg State University, Saint Petersburg 199034, Russia
| | - Olga V Bondareva
- Laboratory of Molecular Systematics, Zoological Institute RAS, Saint Petersburg 199034, Russia
| | - Galina A Zhouravleva
- Laboratory of Amyloid Biology and Department of Genetics and Biotechnology, St. Petersburg State University, Saint Petersburg 199034, Russia
| | - Andrey V Kajava
- Structural Bioinformatics and Molecular Modeling, Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France.,Institut de Biologie Computationnelle, Montpellier 34095, France.,Bioengineering Department, University ITMO, Saint Petersburg, 197101, Russia
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Grizel AV, Rubel AA, Chernoff YO. Strain conformation controls the specificity of cross-species prion transmission in the yeast model. Prion 2017; 10:269-82. [PMID: 27565563 DOI: 10.1080/19336896.2016.1204060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transmissible self-assembled fibrous cross-β polymer infectious proteins (prions) cause neurodegenerative diseases in mammals and control non-Mendelian heritable traits in yeast. Cross-species prion transmission is frequently impaired, due to sequence differences in prion-forming proteins. Recent studies of prion species barrier on the model of closely related yeast species show that colocalization of divergent proteins is not sufficient for the cross-species prion transmission, and that an identity of specific amino acid sequences and a type of prion conformational variant (strain) play a major role in the control of transmission specificity. In contrast, chemical compounds primarily influence transmission specificity via favoring certain strain conformations, while the species origin of the host cell has only a relatively minor input. Strain alterations may occur during cross-species prion conversion in some combinations. The model is discussed which suggests that different recipient proteins can acquire different spectra of prion strain conformations, which could be either compatible or incompatible with a particular donor strain.
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Affiliation(s)
- Anastasia V Grizel
- a Laboratory of Amyloid Biology, St. Petersburg State University , St. Petersburg , Russia.,b Institute of Translational Biomedicine, St. Petersburg State University , St. Petersburg , Russia.,c Department of Genetics and Biotechnology , St. Petersburg State University , St. Petersburg , Russia
| | - Aleksandr A Rubel
- a Laboratory of Amyloid Biology, St. Petersburg State University , St. Petersburg , Russia.,b Institute of Translational Biomedicine, St. Petersburg State University , St. Petersburg , Russia.,c Department of Genetics and Biotechnology , St. Petersburg State University , St. Petersburg , Russia
| | - Yury O Chernoff
- a Laboratory of Amyloid Biology, St. Petersburg State University , St. Petersburg , Russia.,b Institute of Translational Biomedicine, St. Petersburg State University , St. Petersburg , Russia.,d School of Biological Sciences, Georgia Institute of Technology , Atlanta , GA , USA
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Sharma A, Bruce KL, Chen B, Gyoneva S, Behrens SH, Bommarius AS, Chernoff YO. Contributions of the Prion Protein Sequence, Strain, and Environment to the Species Barrier. J Biol Chem 2015; 291:1277-88. [PMID: 26565023 DOI: 10.1074/jbc.m115.684100] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Indexed: 11/06/2022] Open
Abstract
Amyloid propagation requires high levels of sequence specificity so that only molecules with very high sequence identity can form cross-β-sheet structures of sufficient stringency for incorporation into the amyloid fibril. This sequence specificity presents a barrier to the transmission of prions between two species with divergent sequences, termed a species barrier. Here we study the relative effects of protein sequence, seed conformation, and environment on the species barrier strength and specificity for the yeast prion protein Sup35p from three closely related species of the Saccharomyces sensu stricto group; namely, Saccharomyces cerevisiae, Saccharomyces bayanus, and Saccharomyces paradoxus. Through in vivo plasmid shuffle experiments, we show that the major characteristics of the transmission barrier and conformational fidelity are determined by the protein sequence rather than by the cellular environment. In vitro data confirm that the kinetics and structural preferences of aggregation of the S. paradoxus and S. bayanus proteins are influenced by anions in accordance with their positions in the Hofmeister series, as observed previously for S. cerevisiae. However, the specificity of the species barrier is primarily affected by the sequence and the type of anion present during the formation of the initial seed, whereas anions present during the seeded aggregation process typically influence kinetics rather than the specificity of prion conversion. Therefore, our work shows that the protein sequence and the conformation variant (strain) of the prion seed are the primary determinants of cross-species prion specificity both in vivo and in vitro.
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Affiliation(s)
- Aditi Sharma
- From the Schools of Chemical & Biomolecular Engineering and
| | - Kathryn L Bruce
- Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 and
| | - Buxin Chen
- Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 and
| | - Stefka Gyoneva
- Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 and
| | - Sven H Behrens
- From the Schools of Chemical & Biomolecular Engineering and
| | | | - Yury O Chernoff
- Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 and the Laboratory of Amyloid Biology and Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
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Wong SH, King CY. Amino Acid Proximities in Two Sup35 Prion Strains Revealed by Chemical Cross-linking. J Biol Chem 2015; 290:25062-71. [PMID: 26265470 DOI: 10.1074/jbc.m115.676379] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Indexed: 12/26/2022] Open
Abstract
Strains of the yeast prion [PSI] are different folding patterns of the same Sup35 protein, which stacks up periodically to form a prion fiber. Chemical cross-linking is employed here to probe different fiber structures assembled with a mutant Sup35 fragment. The photo-reactive cross-linker, p-benzoyl-l-phenylalanine (pBpa), was biosynthetically incorporated into bacterially prepared recombinant Sup(1-61)-GFP, containing the first 61 residues of Sup35, followed by the green fluorescent protein. Four methionine substitutions and two alanine substitutions were introduced at fixed positions in Sup(1-61) to allow cyanogen bromide cleavage to facilitate subsequent mass spectrometry analysis. Amyloid fibers of pBpa and Met/Ala-substituted Sup(1-61)-GFP were nucleated from purified yeast prion particles of two different strains, namely VK and VL, and shown to faithfully transmit specific strain characteristics to yeast expressing the wild type Sup35 protein. Intra- and intermolecular cross-linking were distinguished by tandem mass spectrometry analysis on fibers seeded from solutions containing equal amounts of (14)N- and (15)N-labeled protein. Fibers propagating the VL strain type exhibited intra- and intermolecular cross-linking between amino acid residues 3 and 28, as well as intra- and intermolecular linking between 32 and 55. Inter- and intramolecular cross-linking between residues 32 and 55 were detected in fibers propagating the VK strain type. Adjacencies of amino acid residues in space revealed by cross-linking were used to constrain possible chain folds of different [PSI] strains.
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Affiliation(s)
- Shenq-Huey Wong
- From the Molecular Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan and the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Yen King
- the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
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