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A complete catalog of wild-type Sup35 prion variants and their protein-only propagation

Abstract

Twenty-three prion variants of the wild-type Sup35 protein are obtained, including 19 novel ones and 4 previously documented, namely, VH, VK, VL, and W8. Their uniqueness and non-composite nature are demonstrated. Specific infectivity is generated de novo for most variants by adding prion particles to solutions of a purified Sup35 N-terminal fragment, thereby supporting the protein-only composition. Sup35 prions isolated by other laboratories are identified within the collection and found to fall into a narrow set of five variant types that are readily inducible in vivo by Sup35 overexpression. The work establishes an unambiguous and extensive collection of prion variants, demonstrating that a protein, by itself, in the absence of genetic and conformational co-factors, could adopt a great number of structures. In light of recent high-resolution structures of other amyloids, we discuss how the diverse folding is achieved in spite of apparent contradiction to the classical paradigm that a protein’s structure is uniquely determined by its sequence.

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References

  1. Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223–230

  2. Astbury WT, Dickinson S, Bailey K (1935) The X-ray interpretation of denaturation and the structure of the seed globulins. Biochem J 29(2351–2360):1. https://doi.org/10.1042/bj0292351

  3. Bateman DA, Wickner RB (2013) The [PSI+] prion exists as a dynamic cloud of variants. PLoS Genet 9:e1003257. https://doi.org/10.1371/journal.pgen.1003257

  4. Bradley ME, Edskes HK, Hong JY et al (2002) Interactions among prions and prion “strains” in yeast. Proc Natl Acad Sci USA 99(Suppl 4):16392–16399. https://doi.org/10.1073/pnas.152330699

  5. Bruce ME (1993) Scrapie strain variation and mutation. Br Med Bull 49:822–838

  6. Bruce ME, Boyle A, Cousens S et al (2002) Strain characterization of natural sheep scrapie and comparison with BSE. J Gen Virol 83:695–704. https://doi.org/10.1099/0022-1317-83-3-695

  7. Carp RI, Callahan SM (1991) Variation in the characteristics of 10 mouse-passaged scrapie lines derived from five scrapie-positive sheep. J Gen Virol 72:293–298. https://doi.org/10.1099/0022-1317-72-2-293

  8. Castilla J, Gonzalez-Romero D, Saá P et al (2008) Crossing the species barrier by PrPSc replication in vitro generates unique infectious prions. Cell 134:757–768. https://doi.org/10.1016/j.cell.2008.07.030

  9. Chang H-Y, Lin J-Y, Lee H-C et al (2008) Strain-specific sequences required for yeast [PSI+] prion propagation. Proc Natl Acad Sci USA 105:13345–13350. https://doi.org/10.1073/pnas.0802215105

  10. Chen B, Bruce KL, Newnam GP et al (2010) Genetic and epigenetic control of the efficiency and fidelity of cross-species prion transmission. Mol Microbiol 76:1483–1499. https://doi.org/10.1111/j.1365-2958.2010.07177.x

  11. Chernoff YO, Lindquist SL, Ono B et al (1995) Role of the chaperone protein Hsp104 in propagation of the yeast prion-like factor [psi+]. Science 268:880–884

  12. Chiti F, Dobson CM (2006) Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 75:333–366. https://doi.org/10.1146/annurev.biochem.75.101304.123901

  13. Clavaguera F, Bolmont T, Crowther RA et al (2009) Transmission and spreading of tauopathy in transgenic mouse brain. Nat Cell Biol 11:909–913. https://doi.org/10.1038/ncb1901

  14. Colby DW, Prusiner SB (2011) Prions. Cold Spring Harb Perspect Biol 3:a006833. https://doi.org/10.1101/cshperspect.a006833

  15. Colvin MT, Silvers R, Ni QZ et al (2016) Atomic resolution structure of monomorphic Aβ42 amyloid fibrils. J Am Chem Soc 138:9663–9674. https://doi.org/10.1021/jacs.6b05129

  16. Cox BS (1965) Ψ, A cytoplasmic suppressor of super-suppressor in yeast. Heredity 20:505

  17. Cox B, Tuite M (2018) The life of [PSI]. Curr Genet 64:1–8. https://doi.org/10.1007/s00294-017-0714-7

  18. DeArmond SJ, Qiu Y, Sànchez H et al (1999) PrPC glycoform heterogeneity as a function of brain region: implications for selective targeting of neurons by prion strains. J Neuropathol Exp Neurol 58:1000–1009

  19. Deleault NR, Walsh DJ, Piro JR et al (2012) Cofactor molecules maintain infectious conformation and restrict strain properties in purified prions. Proc Natl Acad Sci USA 109:E1938–E1946. https://doi.org/10.1073/pnas.1206999109

  20. Dergalev AA, Alexandrov AI, Ivannikov RI, et al (2019) Yeast Sup35 Prion Structure: Two Types, Four Parts, Many Variants. Int J Mol Sci 20:604660. https://doi.org/10.3390/ijms20112633

  21. Derkatch IL, Chernoff YO, Kushnirov VV et al (1996) Genesis and variability of [PSI] prion factors in Saccharomyces cerevisiae. Genetics 144:1375–1386

  22. Derkatch IL, Bradley ME, Hong JY, Liebman SW (2001) Prions affect the appearance of other prions: the Story of [PIN+]. Cell 106:171–182

  23. Diaz-Avalos R, King C-Y, Wall J et al (2005) Strain-specific morphologies of yeast prion amyloid fibrils. Proc Natl Acad Sci USA 102:10165–10170. https://doi.org/10.1073/pnas.0504599102

  24. Falcon B, Zhang W, Murzin AG et al (2018) Structures of filaments from Pick’s disease reveal a novel tau protein fold. Nature 561:137–140. https://doi.org/10.1038/s41586-018-0454-y

  25. Fitzpatrick AWP, Falcon B, He S et al (2017) Cryo-EM structures of tau filaments from Alzheimer’s disease. Nature 547:185–190. https://doi.org/10.1038/nature23002

  26. Gietz RD, Sugino A (1988) New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74:527–534

  27. Goldstein AL, McCusker JH (1999) Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 15:1541–1553. https://doi.org/10.1002/(SICI)1097-0061(199910)15:14%3c1541:AID-YEA476%3e3.0.CO;2-K

  28. Gorkovskiy A, Reidy M, Masison DC, Wickner RB (2017) Hsp104 disaggregase at normal levels cures many [PSI+] prion variants in a process promoted by Sti1p, Hsp90, and Sis1p. Proc Natl Acad Sci USA 114:E4193–E4202. https://doi.org/10.1073/pnas.1704016114

  29. Gremer L, Schölzel D, Schenk C et al (2017) Fibril structure of amyloid-β(1-42) by cryo-electron microscopy. Science 358:116–119. https://doi.org/10.1126/science.aao2825

  30. Guerrero-Ferreira R, Taylor NM, Mona D et al (2018) Cryo-EM structure of alpha-synuclein fibrils. Elife. https://doi.org/10.7554/elife.36402

  31. Güldener U, Heck S, Fielder T et al (1996) A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res 24:2519–2524

  32. Halfmann R, Jarosz DF, Jones SK et al (2012) Prions are a common mechanism for phenotypic inheritance in wild yeasts. Nature 482:363–368. https://doi.org/10.1038/nature10875

  33. Hennetin J, Jullian B, Steven AC, Kajava AV (2006) Standard conformations of β-arches in β-solenoid proteins. J Mol Biol 358:1094–1105. https://doi.org/10.1016/j.jmb.2006.02.039

  34. Huang VJ, Stein KC, True HL (2013) Spontaneous variants of the [RNQ+] prion in yeast demonstrate the extensive conformational diversity possible with prion proteins. PLoS One 8:e79582. https://doi.org/10.1371/journal.pone.0079582

  35. Huang Y-W, Chang Y-C, Diaz-Avalos R, King C-Y (2015) W8, a new Sup35 prion strain, transmits distinctive information with a conserved assembly scheme. Prion 9:207–227. https://doi.org/10.1080/19336896.2015.1039217

  36. Kajava AV, Baxa U, Steven AC (2010) β arcades: recurring motifs in naturally occurring and disease-related amyloid fibrils. FASEB J 24:1311–1319. https://doi.org/10.1096/fj.09-145979

  37. Kaufman SK, Sanders DW, Thomas TL et al (2016) Tau prion strains dictate patterns of cell pathology, progression rate, and regional vulnerability in vivo. Neuron 92:796–812. https://doi.org/10.1016/j.neuron.2016.09.055

  38. Kimberlin RH, Walker CA, Fraser H (1989) The genomic identity of different strains of mouse scrapie is expressed in hamsters and preserved on reisolation in mice. J Gen Virol 70:2017–2025. https://doi.org/10.1099/0022-1317-70-8-2017

  39. King C-Y (2001) Supporting the structural basis of prion strains: induction and identification of [PSI] variants. J Mol Biol 307:1247–1260. https://doi.org/10.1006/jmbi.2001.4542

  40. King C-Y, Diaz-Avalos R (2004) Protein-only transmission of three yeast prion strains. Nature 428:319–323. https://doi.org/10.1038/nature02391

  41. Kochneva-Pervukhova NV, Chechenova MB, Valouev IA et al (2001) [PSI+] prion generation in yeast: characterization of the “strain” difference. Yeast 18:489–497. https://doi.org/10.1002/yea.700

  42. Kryndushkin DS, Alexandrov IM, Ter-Avanesyan MD, Kushnirov VV (2003) Yeast [PSI+] prion aggregates are formed by small Sup35 polymers fragmented by Hsp104. J Biol Chem 278:49636–49643. https://doi.org/10.1074/jbc.M307996200

  43. Kryndushkin D, Pripuzova N, Burnett BG, Shewmaker F (2013) Non-targeted identification of prions and amyloid-forming proteins from yeast and mammalian cells. J Biol Chem 288:27100–27111. https://doi.org/10.1074/jbc.M113.485359

  44. Legname G, Baskakov IV, Nguyen H-OB et al (2004) Synthetic mammalian prions. Science 305:673–676. https://doi.org/10.1126/science.1100195

  45. Li J, Browning S, Mahal SP, Oelschlegal AM, Weissmann C (2010) Darwinian evolution of prions in cell culture. Science 327:869–873

  46. Li B, Ge P, Murray KA et al (2018) Cryo-EM of full-length α-synuclein reveals fibril polymorphs with a common structural kernel. Nat Commun 9:3609. https://doi.org/10.1038/s41467-018-05971-2

  47. Liberta F, Loerch S, Rennegarbe M et al (2018) Cryo-EM structure of an amyloid fibril from systemic amyloidosis. bioRxiv. https://doi.org/10.1101/357129

  48. Liebman SW, All-Robyn JA (1984) A non-Mendelian factor, [eta+], causes lethality of yeast omnipotent-suppressor strains. Curr Genet 8:567–573. https://doi.org/10.1007/BF00395701

  49. Lu J-X, Qiang W, Yau W-M et al (2013) Molecular structure of β-amyloid fibrils in Alzheimer’s disease brain tissue. Cell 154:1257–1268. https://doi.org/10.1016/j.cell.2013.08.035

  50. Ma J (2012) The role of cofactors in prion propagation and infectivity. PLoS Pathog 8:e1002589. https://doi.org/10.1371/journal.ppat.1002589

  51. Marczynski GT, Jaehning JA (1985) A transcription map of a yeast centromere plasmid: unexpected transcripts and altered gene expression. Nucleic Acids Res 13:8487–8506. https://doi.org/10.1093/nar/13.23.8487

  52. Mathur V, Hong JY, Liebman SW (2009) Ssa1 Overexpression and [PIN+] variants cure [PSI+] by dilution of aggregates. J Mol Biol 390:155–167. https://doi.org/10.1016/j.jmb.2009.04.063

  53. McGlinchey RP, Kryndushkin D, Wickner RB (2011) Suicidal [PSI+] is a lethal yeast prion. Proc Natl Acad Sci USA 108:5337–5341. https://doi.org/10.1073/pnas.1102762108

  54. Meier BH, Böckmann A (2015) The structure of fibrils from “misfolded” proteins. Curr Opin Struct Biol 30:43–49. https://doi.org/10.1016/j.sbi.2014.12.001

  55. Meinhardt J, Sachse C, Hortschansky P et al (2009) Aβ(1-40) fibril polymorphism implies diverse interaction patterns in amyloid fibrils. J Mol Biol 386:869–877. https://doi.org/10.1016/j.jmb.2008.11.005

  56. Miyazawa K, Masujin K, Matsuura Y et al (2018) Interspecies transmission to bovinized transgenic mice uncovers new features of a CH1641-like scrapie isolate. Vet Res 49:116. https://doi.org/10.1186/s13567-018-0611-1

  57. Nishina KA, Deleault NR, Mahal SP et al (2006) The stoichiometry of host PrPC glycoforms modulates the efficiency of PrPSc formation in vitro. Biochemistry 45:14129–14139. https://doi.org/10.1021/bi061526k

  58. Ohhashi Y, Ito K, Toyama BH et al (2010) Differences in prion strain conformations result from non-native interactions in a nucleus. Nat Chem Biol 6:225–230. https://doi.org/10.1038/nchembio.306

  59. Ohhashi Y, Yamaguchi Y, Kurahashi H et al (2018) Molecular basis for diversification of yeast prion strain conformation. Proc Natl Acad Sci USA 115:2389–2394. https://doi.org/10.1073/pnas.1715483115

  60. Resende C, Parham SN, Tinsley C et al (2002) The Candida albicans Sup35p protein (CaSup35p): function, prion-like behaviour and an associated polyglutamine length polymorphism. Microbiology 148:1049–1060. https://doi.org/10.1099/00221287-148-4-1049

  61. Saá P, Sferrazza GF, Ottenberg G et al (2012) Strain-specific role of RNAs in prion replication. J Virol 86:10494–10504. https://doi.org/10.1128/JVI.01286-12

  62. Sawaya MR, Sambashivan S, Nelson R et al (2007) Atomic structures of amyloid cross-β spines reveal varied steric zippers. Nature 447:453–457. https://doi.org/10.1038/nature05695

  63. Schmidt M, Rohou A, Lasker K et al (2015) Peptide dimer structure in an Aβ(1-42) fibril visualized with cryo-EM. Proc Natl Acad Sci USA 112:11858–11863. https://doi.org/10.1073/pnas.1503455112

  64. Sharma J, Liebman SW (2012) [PSI+] prion variant establishment in yeast. Mol Microbiol 86:866–881. https://doi.org/10.1111/mmi.12024

  65. Sharma J, Liebman SW (2013) Exploring the basis of [PIN+] variant differences in [PSI+] induction. J Mol Biol 425:3046–3059. https://doi.org/10.1016/j.jmb.2013.06.006

  66. Sherman F (1991) Getting started with yeast. Methods Enzymol 194:3–21

  67. Shewmaker F, Wickner RB, Tycko R (2006) Amyloid of the prion domain of Sup35p has an in-register parallel β-sheet structure. Proc Natl Acad Sci USA 103:19754–19759. https://doi.org/10.1073/pnas.0609638103

  68. Skerra A, Schmidt TG (2000) Use of the Strep-Tag and streptavidin for detection and purification of recombinant proteins. Methods Enzymol 326:271–304

  69. Supattapone S (2014) Elucidating the role of cofactors in mammalian prion propagation. Prion 8:100–105

  70. Tanaka M, Chien P, Naber N et al (2004) Conformational variations in an infectious protein determine prion strain differences. Nature 428:323–328. https://doi.org/10.1038/nature02392

  71. Tanaka M, Chien P, Yonekura K, Weissman JS (2005) Mechanism of cross-species prion transmission: an infectious conformation compatible with two highly divergent yeast prion proteins. Cell 121:49–62. https://doi.org/10.1016/j.cell.2005.03.008

  72. Ter-Avanesyan MD, Dagkesamanskaya AR, Kushnirov VV, Smirnov VN (1994) The SUP35 omnipotent suppressor gene is involved in the maintenance of the non-Mendelian determinant [psi+] in the yeast Saccharomyces cerevisiae. Genetics 137:671–676

  73. Tuite MF, Staniforth GL, Cox BS (2015) [PSI+] turns 50. Prion 9:318–332. https://doi.org/10.1080/19336896.2015.1111508

  74. Tuttle MD, Comellas G, Nieuwkoop AJ et al (2016) Solid-state NMR structure of a pathogenic fibril of full-length human α-synuclein. Nat Struct Mol Biol 23:409–415. https://doi.org/10.1038/nsmb.3194

  75. Tycko R (2014) Physical and structural basis for polymorphism in amyloid fibrils. Protein Sci 23:1528–1539. https://doi.org/10.1002/pro.2544

  76. von der Haar T (2007) Optimized protein extraction for quantitative proteomics of yeasts. PLoS One 2:e1078. https://doi.org/10.1371/journal.pone.0001078

  77. Wälti MA, Ravotti F, Arai H et al (2016) Atomic-resolution structure of a disease-relevant Aβ(1-42) amyloid fibril. Proc Natl Acad Sci USA 113:E4976–E4984. https://doi.org/10.1073/pnas.1600749113

  78. Wang F, Wang X, Yuan C-G, Ma J (2010) Generating a prion with bacterially expressed recombinant prion protein. Science 327:1132–1135. https://doi.org/10.1126/science.1183748

  79. Wang F, Zhang Z, Wang X et al (2012) Genetic informational RNA is not required for recombinant prion infectivity. J Virol 86:1874–1876. https://doi.org/10.1128/JVI.06216-11

  80. Wasmer C, Lange A, Van Melckebeke H et al (2008) Amyloid fibrils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic core. Science 319:1523–1526. https://doi.org/10.1126/science.1151839

  81. Westergard L, True HL (2014) Wild yeast harbour a variety of distinct amyloid structures with strong prion-inducing capabilities. Mol Microbiol 92:183–193. https://doi.org/10.1111/mmi.12543

  82. Wickner RB (2016) Yeast and fungal prions. Cold Spring Harb Perspect Biol 8:1–16. https://doi.org/10.1101/cshperspect.a023531

  83. Wickner RB, Kelly AC, Bezsonov EE, Edskes HK (2017) [PSI+] prion propagation is controlled by inositol polyphosphates. Proc Natl Acad Sci USA. https://doi.org/10.1073/pnas.1714361114

  84. Wickner RB, Edskes HK, Bezsonov EE et al (2018) Prion propagation and inositol polyphosphates. Curr Genet 64:571–574. https://doi.org/10.1007/s00294-017-0788-2

  85. Yu C-I, King C-Y (2018) Forms and abundance of chaperone proteins influence yeast prion variant competition. Mol Microbiol. https://doi.org/10.1111/mmi.14192

  86. Zhang R, Hu X, Khant H et al (2009) Interprotofilament interactions between Alzheimer’s Aβ1-42 peptides in amyloid fibrils revealed by cryoEM. Proc Natl Acad Sci USA 106:4653–4658. https://doi.org/10.1073/pnas.0901085106

  87. Zhang W, Falcon B, Murzin AG et al (2019) Heparin-induced tau filaments are polymorphic and differ from those in Alzheimer’s and Pick’s diseases. Elife. https://doi.org/10.7554/elife.43584

  88. Zhou P, Derkatch IL, Uptain SM et al (1999) The yeast non-Mendelian factor [ETA+] is a variant of [PSI+], a prion-like form of release factor eRF3. EMBO J 18:1182–1191. https://doi.org/10.1093/emboj/18.5.1182

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Acknowledgements

We thank Drs. S. W. Liebman, M. Tanaka, and R. B. Wickner for yeast strains; Drs. V. V. Kushnirov, M. Tanaka, and R. B. Wickner for discussion; S.-P.Lee, S.-P. Tsai, and W.-L. Pong for help with imaging; T. T. Le, Y. Chen, H.-C. Lee, and C.-I. Yu for technical assistance. This work was supported by Grant 105-2311-B-001-056 from Ministry of Science and Technology, Taiwan, Republic of China.

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Both authors designed the study, performed experiments, and wrote the manuscript.

Correspondence to Chih-Yen King.

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Huang, Y., King, C. A complete catalog of wild-type Sup35 prion variants and their protein-only propagation. Curr Genet 66, 97–122 (2020). https://doi.org/10.1007/s00294-019-01003-8

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Keywords

  • [PSI+]
  • Prion
  • Variants
  • Amyloid
  • Saccharomyces cerevisiae