Strategies for identifying new prions in yeast

Prion

Volumn 5, Issue 4, 2011, Pages 263-268

  MacLea, Kyle S ^a   Ross, Eric D ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

PSI+ ; URE3 ; Bioinformatics; Prion; Sup35; Ure2; Yeast

Indexed keywords

ASPARAGINE; GLUTAMINE; PRION PROTEIN; SUP35 PROTEIN; UNCLASSIFIED DRUG; URE2 PROTEIN;

AMINO ACID COMPOSITION; BIOINFORMATICS; GENETIC MANIPULATION; GENETIC SCREENING; GROWTH RATE; NONHUMAN; PRION; PROTEIN ANALYSIS; PROTEIN INTERACTION; REVIEW; SACCHAROMYCES CEREVISIAE; YEAST;

COMPUTATIONAL BIOLOGY; FUNGAL PROTEINS; PRIONS; YEASTS;

EID: 83755178422     PISSN: 19336896     EISSN: 1933690X     Source Type: Journal    
DOI: 10.4161/pri.5.4.17918     Document Type: Review

References (56)

1. Wickner RB. [URE3] as an altered URE2 protein: evidence for a prion analog in Saccharomyces cerevisiae. Science 1994; 264:566-9. (Pubitemid 24185861)
2. Prusiner SB. Novel proteinaceous infectious particles cause scrapie. Science 1982; 216:136-44. (Pubitemid 12089840)
3. Sipe JD, Cohen AS. Review: history of the amyloid fibril. J Struct Biol 2000; 130:88-98.
4. Kisilevsky R, Fraser PE. A beta amyloidogenesis: unique or variation on a systemic theme? Crit Rev Biochem Mol Biol 1997; 32:361-404.
5. Cox BS. PSI, a cytoplasmic suppressor of super-suppressor in yeast. Heredity 1965; 26:211-32.
6. Lacroute F. Non-Mendelian mutation allowing ureidosuccinic acid uptake in yeast. J Bacteriol 1971; 106:519-22.
7. Masison DC, Wickner RB. Prion-inducing domain of yeast Ure2p and protease resistance of Ure2p in prion-containing cells. Science 1995; 270:93-5.
8. Ter-Avanesyan MD, Kushnirov VV, Dagkesamanskaya AR, Didichenko SA, Chernoff YO, Inge-Vechtomov SG, Smirnov VN. Deletion analysis of the SUP35 gene of the yeast Saccharomyces cerevisiae reveals two non-overlapping functional regions in the encoded protein. Mol Microbiol 1993; 7:683-92. (Pubitemid 23090350)
9. DePace AH, Santoso A, Hillner P, Weissman JS. A critical role for amino-terminal glutamine/asparagine repeats in the formation and propagation of a yeast prion. Cell 1998; 93:1241-52. (Pubitemid 28307428)
10. Santoso A, Chien P, Osherovich LZ, Weissman JS. Molecular basis of a yeast prion species barrier. Cell 2000; 100:277-88. (Pubitemid 30064915)
11. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389-402. (Pubitemid 27359211)
12. Sondheimer N, Lindquist S. Rnq1: an epigenetic modifier of protein function in yeast. Mol Cell 2000; 5:163-72. (Pubitemid 30105445)
13. Baxa U, Speransky V, Steven AC, Wickner RB. Mechanism of inactivation on prion conversion of the Saccharomyces cerevisiae Ure2 protein. Proc Natl Acad Sci USA 2002; 99:5253-60. (Pubitemid 34411535)
14. Li L, Lindquist S. Creating a protein-based element of inheritance. Science 2000; 287:661-4. (Pubitemid 30070915)
15. Osherovich LZ, Cox BS, Tuite MF, Weissman JS. Dissection and design of yeast prions. PLoS Biol 2004; 2:86.
16. Osherovich LZ, Weissman JS. Multiple Gln/Asn-rich prion domains confer susceptibility to induction of the yeast [PSI(+)] prion. Cell 2001; 106:183-94. (Pubitemid 32772629)
17. Derkatch IL, Bradley ME, Hong JY, Liebman SW. Prions affect the appearance of other prions: the story of [PIN(+)]. Cell 2001; 106:171-82. (Pubitemid 32772628)
18. Alberti S, Halfmann R, King O, Kapila A, Lindquist S. A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell 2009; 137:146-58.
19. Kabani M, Cosnier B, Bousset L, Rousset JP, Melki R, Fabret C. A mutation within the C-terminal domain of Sup35p that affects [PSI(+)] prion propagation. Mol Microbiol 2011; 81: 640-58.
20. Kochneva-Pervukhova NV, Poznyakovski AI, Smirnov VN, Ter-Avanesyan MD. C-terminal truncation of the Sup35 protein increases the frequency of de novo generation of a prion-based [PSI+] determinant in Saccharomyces cerevisiae. Curr Genet 1998; 34:146-51. (Pubitemid 28431878)
21. Noree C, Sato BK, Broyer RM, Wilhelm JE. Identification of novel filament-forming proteins in Saccharomyces cerevisiae and Drosophila melanogaster. J Cell Biol 2010; 190:541-51.
22. Gonzalez Nelson AC, Ross ED. Interactions between non-identical prion proteins. Semin Cell Dev Biol 2011; In press.
23. Derkatch IL, Bradley ME, Zhou P, Chernoff YO, Liebman SW. Genetic and environmental factors Aafecting the de novo appearance of the [PSI(+)] prion in Saccharomyces cerevisiae. Genetics 1997; 147:507-19. (Pubitemid 27418562)
24. Derkatch IL, Bradley ME, Masse SV, Zadorsky SP, Polozkov GV, Inge-Vechtomov SG, Liebman SW. Dependence and independence of [PSI(+)] and [PIN(+)]: a two-prion system in yeast? EMBO J 2000; 19:1942-52. (Pubitemid 30237570)
25. Du Z, Park KW, Yu H, Fan Q, Li L. Newly identified prion linked to the chromatin-remodeling factor Swi1 in Saccharomyces cerevisiae. Nat Genet 2008; 40:460-5. (Pubitemid 351450881)
26. Patel BK, Gavin-Smyth J, Liebman SW. The yeast global transcriptional co-repressor protein Cyc8 can propagate as a prion. Nat Cell Biol 2009; 11:344-9.
27. Ross CD, McCarty BM, Hamilton M, Ben-Hur A, Ross ED. A promiscuous prion: Efficient induction of [URE3] prion formation by heterologous prion domains. Genetics 2009; 183:929-40.
28. Michelitsch MD, Weissman JS. A census of glutamine/asparagine-rich regions: implications for their conserved function and the prediction of novel prions. Proc Natl Acad Sci USA 2000; 97:11910-5.
29. +] in yeast is a nuclear-residing prion form of the global transcriptional regulator Sfp1. Proc Natl Acad Sci USA 2010; 107:10573-7.
30. Harrison PM, Gerstein M. A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes. Genome Biol 2003; 4:40.
31. Toombs JA, McCarty BR, Ross ED. Compositional determinants of prion formation in yeast. Mol Cell Biol 2010; 30:319-32.
32. Ross ED, Baxa U, Wickner RB. Scrambled prion domains form prions and amyloid. Mol Cell Biol 2004; 24:7206-13. (Pubitemid 39014446)
33. Ross ED, Edskes HK, Terry MJ, Wickner RB. Primary sequence independence for prion formation. Proc Natl Acad Sci USA 2005; 102:12825-30. (Pubitemid 41279450)
34. Halfmann R, Alberti S, Krishnan R, Lyle N, O'Donnell CW, King OD, et al. Opposing effects of glutamine and asparagine govern prion formation by intrinsically disordered proteins. Mol Cell 2011; 43:72-84.
35. Ross ED, Toombs JA. The effects of amino acid composition on yeast prion formation and prion domain interactions. Prion 2010; 4:60-5.
36. True HL, Lindquist SL. A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature 2000; 407:477-83.
37. Eaglestone SS, Cox BS, Tuite MF. Translation termination efficiency can be regulated in Saccharomyces cerevisiae by environmental stress through a prion-mediated mechanism. EMBO J 1999; 18:1974-81. (Pubitemid 29158540)
38. +] are diseases. Proc Natl Acad Sci USA 2005; 102:10575-80.
39. +]. Genetics 2009; 181:1057-63.
40. Prilusky J, Felder CE, Zeev-Ben-Mordehai T, Rydberg EH, Man O, Beckmann JS, et al. FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 2005; 21:3435-8. (Pubitemid 41222454)
41. +] maintenance is dependent on the composition, not primary sequence, of the oligopeptide repeat domain. PLoS One 2011; 6:21953.
42. Alexandrov IM, Vishnevskaya AB, Ter-Avanesyan MD, Kushnirov VV. Appearance and propagation of polyglutamine-based amyloids in yeast: tyrosine residues enable polymer fragmentation. J Biol Chem 2008; 283:15185-92.
43. Coustou V, Deleu C, Saupe S, Begueret J. The protein product of the het-s heterokaryon incompatibility gene of the fungus Podospora anserina behaves as a prion analog. Proc Natl Acad Sci USA 1997; 94:9773-8. (Pubitemid 27408139)
44. Taneja V, Maddelein ML, Talarek N, Saupe SJ, Liebman SW. A non-Q/N-rich prion domain of a foreign prion, [Het-s], can propagate as a prion in yeast. Mol Cell 2007; 27:67-77. (Pubitemid 46991382)
45. Fernandez-Escamilla AM, Rousseau F, Schymkowitz J, Serrano L. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 2004; 22:1302-6. (Pubitemid 39336784)
46. Tartaglia GG, Pawar AP, Campioni S, Dobson CM, Chiti F, Vendruscolo M. Prediction of aggregation-prone regions in structured proteins. J Mol Biol 2008; 380:425-36.
47. Bryan AW Jr, Menke M, Cowen LJ, Lindquist SL, Berger B. BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis. PLoS Comput Biol 2009; 5:1000333.
48. Maurer-Stroh S, Debulpaep M, Kuemmerer N, Lopez de la Paz M, Martins IC, Reumers J, et al. Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat Methods 2010; 7:237-42.
49. Goldschmidt L, Teng PK, Riek R, Eisenberg D. Identifying the amylome, proteins capable of forming amyloid-like fibrils. Proc Natl Acad Sci USA 2010; 107:3487-92.
50. Linding R, Schymkowitz J, Rousseau F, Diella F, Serrano L. A comparative study of the relationship between protein structure and [beta]-aggregation in globular and intrinsically disordered proteins. J Mol Biol 2004; 342:345-53. (Pubitemid 39094525)
51. Esteras-Chopo A, Serrano L, de la Paz ML. The amyloid stretch hypothesis: Recruiting proteins toward the dark side. Proc Natl Acad Sci USA 2005; 102:16672-7. (Pubitemid 41688835)
52. Berryman JT, Radford SE, Harris SA. Systematic examination of polymorphism in amyloid fibrils by molecular- dynamics simulation. Biophys 2011; 100:2234-42.
53. Gendoo DM, Harrison PM. Discordant and chameleon sequences: their distribution and implications for amyloidogenicity. Protein Sci 2011; 20:567-79.
54. Ross ED, Wickner RB. Prions of yeast fail to elicit a transcriptional response. Yeast 2004; 21:963-72. (Pubitemid 39213907)
55. Si K, Lindquist S, Kandel ER. A neuronal isoform of the aplysia CPEB has prion-like properties. Cell 2003; 115:879-91. (Pubitemid 38058499)
56. Volkov KV, Aksenova AY, Soom MJ, Osipov KV, Svitin AV, Kurischko C, et al. Novel non-Mendelian determinant involved in the control of translation accuracy in Saccharomyces cerevisiae. Genetics 2002; 160:25-36. (Pubitemid 34118268)