In 1994 we discovered that yeast can have prions, infectious proteins analogous to the transmissible spongiform encephalopathies of mammals. We showed that the non-Mendelian genetic element, URE3, is a prion of the Ure2 protein, and that PSI+ is a prion of Sup35p (1,2), each prion an amyloid of the respective protein (3). Our discovery showed that proteins can be genes. Unexpectedly, shuffling the prion domain amino acid sequence of Ure2p or Sup35p did not alter the ability of these domains to support prion formation, suggesting that the amyloid structure is parallel in-register (4). We showed by solid-state NMR (with Rob Tycko of NIDDK) that the amyloids of Ure2p, Sup35p and Rnq1p are indeed folded in-register parallel beta sheets (5-8). From this architecture we explained how a given protein sequence can template its structure, and thus how a protein can act as a gene (9). This is the first and only explanation that has been offered for the templating of protein conformation that is central to the prion phenomenon and amyloid diseases. Prion-forming ability of Ure2p and Sup35p are not conserved among yeast and fungal species (10, 11), and the prion (amyloid)-forming parts of Ure2p and Sup35p have normal non-prion functions. We found that PSI+ and URE3 are rare in wild strains, though they would be common if they were advantageous (12,13). We showed that PSI+ and URE3 variants are most often toxic or even lethal, again showing that these are diseases of yeast (14). Understanding their mechanisms of pathogenesis may be useful in understanding human amyloidoses. We found that overproduction of Btn2p or Cur1p could cure the URE3 prion (15), and that in the process of curing URE3, Btn1p collects Ure2p aggregates at a single locus (15). The large majority of URE3 variants isolated in a btn2 cur1 mutant are cured by restoring just the normal level of Btn2p and Cur1p (16). Moreover, we find that it is specifically URE3 variants of low seed number that are cured by normal levels of these proteins (16). We propose that Btn2p collects prion aggregates, increasing the likelihood that one of the progeny cells will not get any prion seeds and so be cured. We showed that overproduced Hsp42, a small heat shock protein, also cures URE3, and Hsp42 is necessary for curing of URE3 by overproduced Btn2p (16). Btn2p, Cur1p and Hsp42 work together at normal levels to cure URE3 prions that arise. They comprise an anti-prion system. Btn2p has low level homology with mammalian HOOK proteins which are involved in transporting aggregates and organelles around the cell, including formation of the mammalian 'aggresome'. The disaggregating chaperone Hsp104 is necessary for the propagation of nearly all amyloid-based yeast prions, but Hsp104 can cure the PSI+ prion if overexpressed. Mutants in the Hsp104 N-terminal domain, such as T160M can propagate PSI+ normally, but cannot cure it even if overexpressed. We found that most PSI+ variants isolated in the Hsp104 T160M mutant are cured by restoration of normal levels of w.t. Hsp104, showing that this activity is an antiprion system that works under normal circumstances to diminish the risk of prion pathology (17). Screening for proteins which, at normal expression levels, cure PSI+ prion variants arising in their absence, we found Siw14p, a pyrophosphatase specific for 5-diphosphoinositol pentakisphosphate (5PP-IP5)(18). This study showed that essentially all PSI+ variants require 5PP-IP5 or related inositol polyphosphates for their propagation. Further, 1PP-IP5 has a prion-inhibiting action in the absence of the inositol-5 pyrophosphates (18). The same screen showed that components of the nonsense-mediated mRNA decay pathway, Upf1, Upf2 and Upf3, at normal expression levels, cure most PSI+ prion variants arising in their absence (19). The Upf proteins normally are in a complex with Sup35p, and it is this normal binding to Sup35p that blocks most PSI+ prion formation and cures most of those PSI+ prions arising in their absence (19). Upf1p blocks amyloid formation by Sup35p in vitro, and co-localizes with Sup35p aggregates in vivo in PSI+ cells. We infer that normal protein-protein interactions prevent the abnormal protein-protein interactions that produce prions. This array of anti-prion systems shows that the real frequency of prions arising in normal cells is much higher than had been appreciated, but that most variants arising are cured by these systems before they can be detected in the usual type of test. We used transposon mutagenesis and next-generation sequencing to find proteins that prevent growth defects that would otherwise be produced by the URE3 prion (20). We found that Lug1p/Yrl353wp prevents a growth defect on non-fermentable carbon sources (e.g. glycerol) that is produced by the URE3 prion in the absence of Lug1p (20). This effect is suppressed by overproduction of Hap4p, a transcription factor promoting expression of mitochondrial-bound proteins. Defect in Gln1p (glutamine synthase) also suppress the growth defect of lug1 URE3 strains. This also identifies a new function for Ure2p. Lug1p is an F-box protein, a substrate-directing subunit of a E3 ubiquitin ligase. We also found that mutation of any of a wide array of chaperones results in a selective disadvantage for URE3 - carrying cells. Thus, cells act to limit the pathology produced on prion infection. Thus, cells have multiple systems that prevent prion formation, cure most of the prions that do manage to arise, and limit the pathology that is produced by the few prions that evade the other systems. It is likely that there are analogous or even homologous systems in mammals, and our discovery and characterization of these yeast systems will doubtless facility searches for the human systems. Just as we utilize humoral, cellular and inate immune systems to treat or cure or limit the damage from viral and bacterial systems, we suggest that these anti-prion systems will prove to be useful in treatment or prevention of prion/amyloid diseases of humans. 1. Wickner RB (1994) Science 264: 566 - 569. 2. Masison DC & Wickner RB (1995) Science 270: 93 - 95. 3. Wickner RB, Edskes HK, Ross ED, Pierce MM, Baxa U, Brachmann A & Shewmaker F (2004) Ann. Rev. Genetics 38: 681-707. 4. Ross ED, Minton AP & Wickner RB (2005) Nature Cell Biol. 7: 1039-1044. 5. Shewmaker F, Wickner RB & Tycko R (2006) Proc. Natl. Acad. Sci. USA 103: 19754 - 19759. 6. Baxa U, Wickner RB, Steven AC, Anderson D, Marekov L, Yau W-M & Tycko R (2007) Biochemistry 46: 13149 - 13162. 7. Wickner RB, Dyda F & Tycko R (2008) Proc Natl Acad Sci U S A 105: 2403 - 2408. 8. Gorkovskiy A, Thurber KR, Tycko R, Wickner RB (2014) Proc. Natl. Acad. Sci. USA, 111:E4615-22. 9. Wickner RB, Edskes HK, Shewmaker F, Nakayashiki T 2007 Nat. Rev. Microbiol. 5: 611-618. 10. Edskes HK, Engel A, McCann LM, Brachmann A, Tsai H-F, Wickner RB (2011) Genetics 188:81 90. 11. Edskes HE, Khamar HJ, Winchester C-L, Greenler AJ, Zhou A, McGlinchey RP, Gorkovskiy A, Wickner RB (2014) Genetics, 198: 605-616. 12. Nakayashiki T, Kurtzman CP, Edskes HK, Wickner RB (2005) Proc Natl Acad Sci U S A 102:10575-80. 13. Kelly, A. C., Busby, B. and Wickner, R. B. (2014) Genetics, 197: 1007 - 1024. 14. McGlinchey R, Kryndushkin D, Wickner RB (2011) Proc Natl Acad Sci USA 108:5337 - 41. 15. Kryndushkin D, Shewmaker FP, Wickner RB (2008) EMBO J. 27: 2725 - 2735. 16. Wickner RB, Bezsonov E Bateman DA (2014) Proc. Natl. Acad. Sci. USA, 111: E2711-20. 17. Gorkovskiy A, Reidy M, Masison DC, Wickner RB (2017) Proc. Natl. Acad. Sci. USA, 114: E4193-E4202. 18. Wickner RB, Kelly AC, Bezsonov EE, Edskes HE (2017) Proc. Natl. Acad. Sci. USA 114, E8402-E8410. 19. Son M, Wickner RB (2018) Proc. Natl. Acad. Sci. USA, E1184-E1193. 20. Edskes HK, Mukhamedova M, Edskes BK, Wickner RB (2018) Genetics 20

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Wickner, Reed B; Edskes, Herman K; Son, Moonil et al. (2018) Yeast Prions Compared to Functional Prions and Amyloids. J Mol Biol :
Wickner, Reed B; Edskes, Herman K; Bezsonov, Evgeny E et al. (2018) Prion propagation and inositol polyphosphates. Curr Genet 64:571-574
Wickner, Reed B; Bezsonov, Evgeny E; Son, Moonil et al. (2018) Anti-Prion Systems in Yeast and Inositol Polyphosphates. Biochemistry 57:1285-1292
Wickner, Reed B; Kryndushkin, Dmitry; Shewmaker, Frank et al. (2018) Study of Amyloids Using Yeast. Methods Mol Biol 1779:313-339
Son, Moonil; Wickner, Reed B (2018) Nonsense-mediated mRNA decay factors cure most [PSI+] prion variants. Proc Natl Acad Sci U S A 115:E1184-E1193
Edskes, Herman K; Mukhamedova, Maryam; Edskes, Bouke K et al. (2018) Hermes Transposon Mutagenesis Shows [URE3] Prion Pathology Prevented by a Ubiquitin-Targeting Protein: Evidence for Carbon/Nitrogen Assimilation Cross Talk and a Second Function for Ure2p in Saccharomyces cerevisiae. Genetics 209:789-800
Edskes, Herman K; Kryndushkin, Dmitry; Shewmaker, Frank et al. (2017) Prion Transfection of Yeast. Cold Spring Harb Protoc 2017:pdb.prot089037
Wickner, Reed B; Kelly, Amy C; Bezsonov, Evgeny E et al. (2017) [PSI+] prion propagation is controlled by inositol polyphosphates. Proc Natl Acad Sci U S A 114:E8402-E8410
Gorkovskiy, Anton; Reidy, Michael; Masison, Daniel C et al. (2017) Hsp104 disaggregase at normal levels cures many [PSI(+)] prion variants in a process promoted by Sti1p, Hsp90, and Sis1p. Proc Natl Acad Sci U S A 114:E4193-E4202
Wickner, Reed B; Edskes, Herman K; Kryndushkin, Dmitry et al. (2017) Genetic Methods for Studying Yeast Prions. Cold Spring Harb Protoc 2017:pdb.prot089029

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