Prions of Yeast and Anti-Prion Systems

National Institute Of Diabetes And Digestive And Kidney Diseases

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Abstract

In 1994 we discovered prions (infectious proteins) infecting yeast (1) analogous to the transmissible spongiform encephalopathies of mammals. URE3 is a prion of Ure2p, and PSI+ is a prion of Sup35p (1,2), each an amyloid of the respective protein (reviewed in ref. 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 (5,6). From this architecture we explained how a given protein sequence can template its conformation, and thus how a protein can act as a gene (7). 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 (8, 9), and the prion (amyloid)-forming parts of Ure2p and Sup35p have normal non-prion functions. PSI+ and URE3 are rare in wild strains (10,11) and most variants are toxic or even lethal, showing that these are diseases of yeast (12). Overproducing Btn2p or Cur1p, acting with Hsp42, cures all variants of the URE3 prion, but normal levels of each cure nearly all URE3 prions except those with the highest seed number (13, 14). Btn2p cures by collecting Ure2p aggregates at a single locus (sequestration), increasing the likelihood that one of the progeny cells will not get any prion seeds and so be cured (13). These are antiprion systems. Btn2p has homology with mammalian HOOK proteins which are involved in transporting aggregates and organelles around the cell, including formation of the mammalian 'aggresome'. We find that overactive proteasomes prevent prion curing by Btn2 or Cur1 (15) and partially inactive proteasomes result in URE3 curing as a result of the dramatically elevated levels of Btn2 and Cur1 (16). Partial inactivation of proteasomes by a pre9 mutation elevates Btn2 and Cur1 levels >200 fold, the most of any of >4600 yeast proteins surveyed by SILAC (16). We propose that proteasomes overwhelmed by denatured proteins in stress conditions automatically turn on the Btn2 and Cur1 systems to help in the clean-up. The disaggregase Hsp104 is necessary for the propagation of all amyloid-based yeast prions, but cures PSI+ if overexpressed. Hsp104 N-terminal domain mutants, e.g. T160M 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+ prions arising in their absence, we found Siw14p, a pyrophosphatase specific for 5-diphosphoinositol pentakisphosphate (5PP-IP5)(18). We showed that most PSI+ prions require 5PP-IP5 or related inositol polyphosphates for their propagation, and 1PP-IP5 has a prion-inhibiting action in the absence of the inositol-5 pyrophosphates (18). We found that nonsense-mediated mRNA decay pathway components Upf1, Upf2 and Upf3, at normal expression levels, cure most PSI+ prions arising in their absence (19). The Upf proteins normally 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. We also find that ribosome-associated chaperones Ssb, Ssz1 and Zuo1, that insure proper folding of nascent proteins, cure most of the PSI+ prions arising in their absence (20). Mutation of any results in 15-fold elevated prion generation frequency. Triple mutant ssz1 upf1 hsp104T160M cells produce PSI+ up to 5000-fold more often than wild type, but most prions arising are cured by replacing any one of the defective genes (21). Thus these antiprion systems act independently, and the real frequency of prions arising in normal cells is much higher than had been appreciated, but 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 (22). We found that Lug1p/Ylr352wp prevents a growth defect on non-fermentable carbon sources (e.g. glycerol) that is produced by the URE3 prion in the absence of Lug1p (22). This effect is suppressed by overproduction of Hap4p, a transcription factor promoting expression of mitochondrial-bound proteins. A 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 an 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. Multiple systems prevent prion formation, cure most of the prions that do manage to arise, and limit the pathology from the few prions that evade the other systems. There are probably analogous or even homologous systems in mammals, and our discovery and characterization of these yeast systems will doubtless facilitate searches for the human systems. Just as we utilize humoral, cellular and innate immune systems to treat or cure or limit the damage from viral and bacterial infections, 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) PNAS 103: 19754 - 19759. 6. Gorkovskiy A, Thurber KR, Tycko R, Wickner RB (2014) PNAS 111:E4615-22. 7. Wickner RB, Edskes HK, Shewmaker F, Nakayashiki T 2007 Nat. Rev. Microbiol. 5: 611-618. 8. Edskes HK, Engel A, McCann LM, Brachmann A, Tsai H-F, Wickner RB (2011) Genetics 188:81 90. 9. Edskes HE, Khamar HJ, Winchester C-L, Greenler AJ, Zhou A, McGlinchey RP, Gorkovskiy A, Wickner RB (2014) Genetics, 198: 605-616. 10. Nakayashiki T, Kurtzman CP, Edskes HK, Wickner RB (2005) PNAS 102:10575-80. 11. Kelly AC, Shewmaker FP, Kryndushkin D, Wickner RB (2012) PNAS 109: E2683 - E2690. 12. McGlinchey R, Kryndushkin D, Wickner RB (2011) PNAS 108:5337 - 41. 13. Kryndushkin D, Shewmaker FP, Wickner RB (2008) EMBO J. 27: 2725 - 2735. 14. Wickner RB, Bezsonov E Bateman DA (2014) PNAS 111: E2711-20. 15. Bezsonov EE, Edskes HK, Wickner RB (2021) Genetics 217: doi: 10.1093/genetics/iyab013. 16. Edskes HK, Stroobant EE, DeWilde M, Bezsonov EE, Wickner RB (2021) Genetics 218: doi: 10.1093/genetics/iyab037 17. Gorkovskiy A, Reidy M, Masison DC, Wickner RB (2017) PNAS 114: E4193-E4202. 18. Wickner RB, Kelly AC, Bezsonov EE, Edskes HE (2017) 114: E8402-E8410. 19. Son M, Wickner RB (2018) PNAS 115: E1184-E1193. 20. Son M, Wickner RB (2020) PNAS 117: 26298-26306. 21. Son M, Wickner RB (2022) PNAS 119: e2205500119. 22. Edskes HK, Mukhamedova M, Edskes BK, Wickner RB (2018)