Distinct subregions of Swi1 manifest striking differences in prion transmission and SWI/SNF function

Molecular and Cellular Biology

Volumn 30, Issue 19, 2010, Pages 4644-4655

  Du, Zhiqiang ^a   Crow, Emily T ^a   Kang, Hyun Seok ^a   Li, Liming ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID; ASPARAGINE; GLUTAMINE; PRION PROTEIN; PROTEIN SWI; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR SNF; TRANSCRIPTION FACTOR SWI1; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CHROMOSOME DELETION; NONHUMAN; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN CONFORMATION; PROTEIN EXPRESSION; PROTEIN FUNCTION;

EID: 77956654770     PISSN: 02707306     EISSN: 10985549     Source Type: Journal    
DOI: 10.1128/MCB.00225-10     Document Type: Article

References (62)

1. Alberti, S., R. Halfmann, O. King, A. Kapila, and S. Lindquist. 2009. A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell 137:146-158.
2. Bailleul, P. A., G. P. Newnam, J. N. Steenbergen, and Y. O. Chernoff. 1999. Genetic study of interactions between the cytoskeletal assembly protein SlaI and prion-forming domain of the release factor Sup35 (eRF3) in Saccharomyces cerevisiae. Genetics 153:81-94.
3. Baskakov, I. V., and L. Breydo. 2007. Converting the prion protein: what makes the protein infectious. Biochim. Biophys. Acta 1772:692-703.
4. Brachmann, A., U. Baxa, and R. B. Wickner. 2005. Prion generation in vitro: amyloid of Ure2p is infectious. EMBO J. 24:3082-3092.
5. Brown, J. C., and S. Lindquist. 2009. A heritable switch in carbon source utilization driven by an unusual yeast prion. Genes Dev. 23:2320-2332.
6. Chai, B., J. Huang, B. R. Cairns, and B. C. Laurent. 2005. Distinct roles for the RSC and Swi/Snf ATP-dependent chromatin remodelers in DNA double-strand break repair. Genes Dev. 19:1656-1661.
7. Chien, P., J. S. Weissman, and A. H. DePace. 2004. Emerging principles of conformation-based prion inheritance. Annu. Rev. Biochem. 73:617-656.
8. Côté, J., C. L. Peterson, and J. L. Workman. 1998. Perturbation of nucleosome core structure by the SWI/SNF complex persists after its detachment, enhancing subsequent transcription factor binding. Proc. Natl. Acad. Sci. U. S. A. 95:4947-4952.
9. Cox, B. 1965. [PSI], a cytoplasmic suppressor of super-suppression in yeast. Heredity 20:505-521.
10. Crow, E., Z. Du, and L. Li. 2008. New insights into prion biology from the novel [SWI+] system. Prion 2:141-144.
11. Derkatch, I. L., Y. O. Chernoff, V. V. Kushnirov, S. G. Inge-Vechtomov, and S. W. Liebman. 1996. Genesis and variability of [PSI] prion factors in Saccharomyces cerevisiae. Genetics 144:1375-1386.
12. Derkatch, I. L., S. M. Uptain, T. F. Outeiro, R. Krishnan, S. L. Lindquist, and S. W. Liebman. 2004. Effects of Q/N-rich, polyQ, and non-polyQ amyloids on the de novo formation of the [PSI+] prion in yeast and aggregation of Sup35 in vitro. Proc. Natl. Acad. Sci. U. S. A. 101:12934-12939.
13. Diaz-Avalos, R., C. Y. King, J. Wall, M. Simon, and D. L. Caspar. 2005. Strain-specific morphologies of yeast prion amyloid fibrils. Proc. Natl. Acad. Sci. U. S. A. 102:10165-10170.
14. Dror, V., and F. Winston. 2004. The Swi/Snf chromatin remodeling complex is required for ribosomal DNA and telomeric silencing in Saccharomyces cerevisiae. Mol. Cell. Biol. 24:8227-8235.
15. Du, Z., K. W. Park, H. Yu, Q. Fan, and L. Li. 2008. Newly identified prion linked to the chromatin-remodeling factor Swi1 in Saccharomyces cerevisiae. Nat. Genet. 40:460-465.
16. Fan, Q., K. W. Park, Z. Du, K. A. Morano, and L. Li. 2007. The role of Sse1 in the de novo formation and variant determination of the [PSI+] prion. Genetics 177:1583-1593. (Pubitemid 350277054)
17. Ferreira, M. E., P. Prochasson, K. D. Berndt, J. L. Workman, and A. P. Wright. 2009. Activator-binding domains of the SWI/SNF chromatin remodeling complex characterized in vitro are required for its recruitment to promoters in vivo. FEBS J. 276:2557-2565.
18. Ganusova, E. E., L. N. Ozolins, S. Bhagat, G. P. Newnam, R. D. Wegrzyn, M. Y. Sherman, and Y. O. Chernoff. 2006. Modulation of prion formation, aggregation, and toxicity by the actin cytoskeleton in yeast. Mol. Cell. Biol. 26:617-629.
19. +], a heritable prion-like factor of S. cerevisiae. Cell 89:811-819.
20. Holstege, F. C., E. G. Jennings, J. J. Wyrick, T. I. Lee, C. J. Hengartner, M. R. Green, T. R. Golub, E. S. Lander, and R. A. Young. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95:717-728.
21. Kadnar, M. L., G. Articov, and I. L. Derkatch. 2010. Distinct type of transmission barrier revealed by study of multiple prion determinants of Rnq1. PLoS Genet. 6:e1000824.
22. Kalastavadi, T., and H. L. True. 2008. Prion protein insertional mutations increase aggregation propensity but not fiber stability. BMC Biochem. 9:7.
23. King, C. Y., and R. Diaz-Avalos. 2004. Protein-only transmission of three yeast prion strains. Nature 428:319-323.
24. King, C. Y., P. Tittmann, H. Gross, R. Gebert, M. Aebi, and K. Wuthrich. 1997. Prion-inducing domain 2-114 of yeast Sup35 protein transforms in vitro into amyloid-like filaments. Proc. Natl. Acad. Sci. U. S. A. 94:6618-6622.
25. Lacroute, F. 1968. Regulation of pyrimidine biosynthesis in Saccharomyces cerevisiae. J. Bacteriol. 95:824-832.
26. Li, L., and S. Lindquist. 2000. Creating a protein-based element of inheritance. Science 287:661-664.
27. Liu, J. J., N. Sondheimer, and S. L. Lindquist. 2002. Changes in the middle region of Sup35 profoundly alter the nature of epigenetic inheritance for the yeast prion [PSI+]. Proc. Natl. Acad. Sci. U. S. A. 99(Suppl. 4):16446-16453.
28. Logie, C., and C. L. Peterson. 1999. Purification and biochemical properties of yeast SWI/SNF complex. Methods Enzymol. 304:726-741.
29. Michelitsch, M. D., and J. S. Weissman. 2000. A census of glutamine/asparagine-rich regions: implications for their conserved function and the prediction of novel prions. Proc. Natl. Acad. Sci. U. S. A. 97:11910-11915.
30. Mohrmann, L., and C. P. Verrijzer. 2005. Composition and functional specificity of SWI2/SNF2 class chromatin remodeling complexes. Biochim. Biophys. Acta 1681:59-73.
31. Mumberg, D., R. Muller, and M. Funk. 1995. Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. Gene 156:119-122.
32. Natarajan, K., B. M. Jackson, H. Zhou, F. Winston, and A. G. Hinnebusch. 1999. Transcriptional activation by Gcn4p involves independent interactions with the SWI/SNF complex and the SRB/mediator. Mol. Cell 4:657-664.
33. Neely, K. E., A. H. Hassan, A. E. Wallberg, D. J. Steger, B. R. Cairns, A. P. Wright, and J. L. Workman. 1999. Activation domain-mediated targeting of the SWI/SNF complex to promoters stimulates transcription from nucleosome arrays. Mol. Cell 4:649-655.
34. Neigeborn, L., and M. Carlson. 1987. Mutations causing constitutive invertase synthesis in yeast: genetic interactions with snf mutations. Genetics 115:247-253. (Pubitemid 17010181)
35. Nemecek, J., T. Nakayashiki, and R. B. Wickner. 2009. A prion of yeast metacaspase homolog (Mca1p) detected by a genetic screen. Proc. Natl. Acad. Sci. U. S. A. 106:1892-1896.
36. Park, K. W., J. S. Hahn, Q. Fan, D. J. Thiele, and L. Li. 2006. De novo appearance and "strain" formation of yeast prion [PSI+] are regulated by the heat-shock transcription factor. Genetics 173:35-47.
37. Patel, B. K., J. Gavin-Smyth, and S. W. Liebman. 2009. The yeast global transcriptional co-repressor protein Cyc8 can propagate as a prion. Nat. Cell Biol. 11:344-349.
38. Patel, B. K., and S. W. Liebman. 2007. "Prion-proof" for [PIN+]: infection with in vitro-made amyloid aggregates of Rnq1p-(132-405) induces [PIN+]. J. Mol. Biol. 365:773-782.
39. Peterson, C. L., Y. Zhao, and B. T. Chait. 1998. Subunits of the yeast SWI/SNF complex are members of the actin-related protein (ARP) family. J. Biol. Chem. 273:23641-23644.
40. Prochasson, P., K. E. Neely, A. H. Hassan, B. Li, and J. L. Workman. 2003. Targeting activity is required for SWI/SNF function in vivo and is accomplished through two partially redundant activator-interaction domains. Mol. Cell 12:983-990.
41. Quinn, J., A. M. Fyrberg, R. W. Ganster, M. C. Schmidt, and C. L. Peterson. 1996. DNA-binding properties of the yeast SWI/SNF complex. Nature 379:844-847.
42. Rogoza, T., A. Goginashvili, S. Rodionova, M. Ivanov, O. Viktorovskaya, A. Rubel, K. Volkov, and L. Mironova. 2010. Non-Mendelian determinant [ISP+] in yeast is a nuclear-residing prion form of the global transcriptional regulator Sfp1. Proc. Natl. Acad. Sci. U. S. A. 107:10573-10577.
43. Sabaté, R., U. Baxa, L. Benkemoun, N. Sanchez de Groot, B. Coulary-Salin, M. L. Maddelein, L. Malato, S. Ventura, A. C. Steven, and S. J. Saupe. 2007. Prion and non-prion amyloids of the HET-s prion forming domain. J. Mol. Biol. 370:768-783.
44. Salnikova, A. B., D. S. Kryndushkin, V. N. Smirnov, V. V. Kushnirov, and M. D. Ter-Avanesyan. 2005. Nonsense suppression in yeast cells overproducing Sup35 (eRF3) is caused by its non-heritable amyloids. J. Biol. Chem. 280:8808-8812.
45. Santoso, A., P. Chien, L. Z. Osherovich, and J. S. Weissman. 2000. Molecular basis of a yeast prion species barrier. Cell 100:277-288.
46. Sinha, M., S. Watanabe, A. Johnson, D. Moazed, and C. L. Peterson. 2009. Recombinational repair within heterochromatin requires ATP-dependent chromatin remodeling. Cell 138:1109-1121.
47. Smith, C. L., R. Horowitz-Scherer, J. F. Flanagan, C. L. Woodcock, and C. L. Peterson. 2003. Structural analysis of the yeast SWI/SNF chromatin remodeling complex. Nat. Struct. Biol. 10:141-145.
48. Sondheimer, N., and S. Lindquist. 2000. Rnq1: an epigenetic modifier of protein function in yeast. Mol. Cell 5:163-172. (Pubitemid 30105445)
49. Stern, M., R. Jensen, and I. Herskowitz. 1984. Five SWI genes are required for expression of the HO gene in yeast. J. Mol. Biol. 178:853-868.
50. Sudarsanam, P., V. R. Iyer, P. O. Brown, and F. Winston. 2000. Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 97:3364-3369.
51. Tanaka, M., P. Chien, N. Naber, R. Cooke, and J. S. Weissman. 2004. Conformational variations in an infectious protein determine prion strain differences. Nature 428:323-328.
52. Tanaka, M., and J. S. Weissman. 2006. An efficient protein transformation protocol for introducing prions into yeast. Methods Enzymol. 412:185-200.
53. Taylor, K. L., N. Cheng, R. W. Williams, A. C. Steven, and R. B. Wickner. 1999. Prion domain initiation of amyloid formation in vitro from native Ure2p. Science 283:1339-1343.
54. Toombs, J. A., B. R. McCarty, and E. D. Ross. 2010. Compositional determinants of prion formation in yeast. Mol. Cell. Biol. 30:319-332.
55. Tuite, M. F. 2000. Yeast prions and their prion-forming domain. Science 287:562-563.
56. Tuite, M. F., and B. S. Cox. 2009. Prions remodel gene expression in yeast. Nat. Cell Biol. 11:241-243.
57. Tuite, M. F., and B. S. Cox. 2003. Propagation of yeast prions. Nat. Rev. Mol. Cell Biol. 4:878-890.
58. Uptain, S. M., and S. Lindquist. 2002. Prions as protein-based genetic elements. Annu. Rev. Microbiol. 56:703-741.
59. Vishveshwara, N., M. E. Bradley, and S. W. Liebman. 2009. Sequestration of essential proteins causes prion associated toxicity in yeast. Mol. Microbiol. 73:1101-1114.
60. Wickner, R. B. 1994. [URE3] as an altered Ure2 protein: evidence for a prion analog in Saccharomyces cerevisiae. Science 264:566-569.
61. Wilsker, D., A. Patsialou, S. D. Zumbrun, S. Kim, Y. Chen, P. B. Dallas, and E. Moran. 2004. The DNA-binding properties of the ARID-containing subunits of yeast and mammalian SWI/SNF complexes. Nucleic Acids Res. 32:1345-1353. (Pubitemid 38864679)
62. Yudkovsky, N., C. Logie, S. Hahn, and C. L. Peterson. 1999. Recruitment of the SWI/SNF chromatin remodeling complex by transcriptional activators. Genes Dev. 13:2369-2374.