Skip to main content
Genetics logoLink to Genetics
. 1998 Mar;148(3):1021–1029. doi: 10.1093/genetics/148.3.1021

Theme and variation among silencing proteins in Saccharomyces cerevisiae and Kluyveromyces lactis.

S U Aström 1, J Rine 1
PMCID: PMC1460018  PMID: 9539421

Abstract

The cryptic mating type loci in Saccharomyces cerevisiae act as reservoirs of mating type information used in mating type switching in homothallic yeast strains. The transcriptional silencing of these loci depends on the formation of a repressive chromatin structure that is reminiscent of heterochromatin. Silent information regulator (Sir) proteins 2-4 are absolutely required for silencing. To learn more about silencing, we investigated mating type and Sir proteins in the yeast Kluyveromyces lactis, which contains cryptic copies of the mating type genes. A functional homolog of SIR4 from K. lactis complements the silencing defect of sir4 null mutations in S. cerevisiae. K. lactis sir2 and sir4 mutant strains showed partial derepression of the silent alpha1 gene, establishing that the silencing role of these proteins is conserved. K. lactis sir2 mutants are more sensitive than the wild type to ethidium bromide, and K. lactis sir4 mutants are more resistant phenotypes that are not observed for the corresponding mutants of S. cerevisiae. Finally, the deletion of sir4 in the two yeasts leads to opposite effects on telomere length. Thus, Sir proteins from K. lactis have roles in both silencing and telomere length maintenance, reflecting conserved functional themes. The various phenotypes of sir mutants in K. lactis and S. cerevisiae, however, revealed unanticipated variation between their precise roles.

Full Text

The Full Text of this article is available as a PDF (319.2 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Aparicio O. M., Billington B. L., Gottschling D. E. Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell. 1991 Sep 20;66(6):1279–1287. doi: 10.1016/0092-8674(91)90049-5. [DOI] [PubMed] [Google Scholar]
  3. Barns S. M., Lane D. J., Sogin M. L., Bibeau C., Weisburg W. G. Evolutionary relationships among pathogenic Candida species and relatives. J Bacteriol. 1991 Apr;173(7):2250–2255. doi: 10.1128/jb.173.7.2250-2255.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brachmann C. B., Sherman J. M., Devine S. E., Cameron E. E., Pillus L., Boeke J. D. The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression, and chromosome stability. Genes Dev. 1995 Dec 1;9(23):2888–2902. doi: 10.1101/gad.9.23.2888. [DOI] [PubMed] [Google Scholar]
  5. Bryk M., Banerjee M., Murphy M., Knudsen K. E., Garfinkel D. J., Curcio M. J. Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev. 1997 Jan 15;11(2):255–269. doi: 10.1101/gad.11.2.255. [DOI] [PubMed] [Google Scholar]
  6. Chen X. J., Clark-Walker G. D. sir2 mutants of Kluyveromyces lactis are hypersensitive to DNA-targeting drugs. Mol Cell Biol. 1994 Jul;14(7):4501–4508. doi: 10.1128/mcb.14.7.4501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chen X. J. Low- and high-copy-number shuttle vectors for replication in the budding yeast Kluyveromyces lactis. Gene. 1996 Jun 12;172(1):131–136. doi: 10.1016/0378-1119(96)00125-4. [DOI] [PubMed] [Google Scholar]
  8. Chien C. T., Buck S., Sternglanz R., Shore D. Targeting of SIR1 protein establishes transcriptional silencing at HM loci and telomeres in yeast. Cell. 1993 Nov 5;75(3):531–541. doi: 10.1016/0092-8674(93)90387-6. [DOI] [PubMed] [Google Scholar]
  9. Christianson T. W., Sikorski R. S., Dante M., Shero J. H., Hieter P. Multifunctional yeast high-copy-number shuttle vectors. Gene. 1992 Jan 2;110(1):119–122. doi: 10.1016/0378-1119(92)90454-w. [DOI] [PubMed] [Google Scholar]
  10. Emr S. D., Vassarotti A., Garrett J., Geller B. L., Takeda M., Douglas M. G. The amino terminus of the yeast F1-ATPase beta-subunit precursor functions as a mitochondrial import signal. J Cell Biol. 1986 Feb;102(2):523–533. doi: 10.1083/jcb.102.2.523. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Foss M., McNally F. J., Laurenson P., Rine J. Origin recognition complex (ORC) in transcriptional silencing and DNA replication in S. cerevisiae. Science. 1993 Dec 17;262(5141):1838–1844. doi: 10.1126/science.8266071. [DOI] [PubMed] [Google Scholar]
  12. Gottschling D. E., Aparicio O. M., Billington B. L., Zakian V. A. Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell. 1990 Nov 16;63(4):751–762. doi: 10.1016/0092-8674(90)90141-z. [DOI] [PubMed] [Google Scholar]
  13. Grigliatti T. Position-effect variegation--an assay for nonhistone chromosomal proteins and chromatin assembly and modifying factors. Methods Cell Biol. 1991;35:587–627. [PubMed] [Google Scholar]
  14. Ivy J. M., Klar A. J., Hicks J. B. Cloning and characterization of four SIR genes of Saccharomyces cerevisiae. Mol Cell Biol. 1986 Feb;6(2):688–702. doi: 10.1128/mcb.6.2.688. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kayne P. S., Kim U. J., Han M., Mullen J. R., Yoshizaki F., Grunstein M. Extremely conserved histone H4 N terminus is dispensable for growth but essential for repressing the silent mating loci in yeast. Cell. 1988 Oct 7;55(1):27–39. doi: 10.1016/0092-8674(88)90006-2. [DOI] [PubMed] [Google Scholar]
  16. Kennedy B. K., Austriaco N. R., Jr, Zhang J., Guarente L. Mutation in the silencing gene SIR4 can delay aging in S. cerevisiae. Cell. 1995 Feb 10;80(3):485–496. doi: 10.1016/0092-8674(95)90499-9. [DOI] [PubMed] [Google Scholar]
  17. Krauskopf A., Blackburn E. H. Control of telomere growth by interactions of RAP1 with the most distal telomeric repeats. Nature. 1996 Sep 26;383(6598):354–357. doi: 10.1038/383354a0. [DOI] [PubMed] [Google Scholar]
  18. Laurenson P., Rine J. Silencers, silencing, and heritable transcriptional states. Microbiol Rev. 1992 Dec;56(4):543–560. doi: 10.1128/mr.56.4.543-560.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Longtine M. S., Wilson N. M., Petracek M. E., Berman J. A yeast telomere binding activity binds to two related telomere sequence motifs and is indistinguishable from RAP1. Curr Genet. 1989 Oct;16(4):225–239. doi: 10.1007/BF00422108. [DOI] [PubMed] [Google Scholar]
  20. Loo S., Fox C. A., Rine J., Kobayashi R., Stillman B., Bell S. The origin recognition complex in silencing, cell cycle progression, and DNA replication. Mol Biol Cell. 1995 Jun;6(6):741–756. doi: 10.1091/mbc.6.6.741. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Loo S., Laurenson P., Foss M., Dillin A., Rine J. Roles of ABF1, NPL3, and YCL54 in silencing in Saccharomyces cerevisiae. Genetics. 1995 Nov;141(3):889–902. doi: 10.1093/genetics/141.3.889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Loo S., Rine J. Silencers and domains of generalized repression. Science. 1994 Jun 17;264(5166):1768–1771. doi: 10.1126/science.8209257. [DOI] [PubMed] [Google Scholar]
  23. Lupas A., Van Dyke M., Stock J. Predicting coiled coils from protein sequences. Science. 1991 May 24;252(5009):1162–1164. doi: 10.1126/science.252.5009.1162. [DOI] [PubMed] [Google Scholar]
  24. Lustig A. J., Kurtz S., Shore D. Involvement of the silencer and UAS binding protein RAP1 in regulation of telomere length. Science. 1990 Oct 26;250(4980):549–553. doi: 10.1126/science.2237406. [DOI] [PubMed] [Google Scholar]
  25. Marcand S., Buck S. W., Moretti P., Gilson E., Shore D. Silencing of genes at nontelomeric sites in yeast is controlled by sequestration of silencing factors at telomeres by Rap 1 protein. Genes Dev. 1996 Jun 1;10(11):1297–1309. doi: 10.1101/gad.10.11.1297. [DOI] [PubMed] [Google Scholar]
  26. Marcand S., Gilson E., Shore D. A protein-counting mechanism for telomere length regulation in yeast. Science. 1997 Feb 14;275(5302):986–990. doi: 10.1126/science.275.5302.986. [DOI] [PubMed] [Google Scholar]
  27. Marshall M., Mahoney D., Rose A., Hicks J. B., Broach J. R. Functional domains of SIR4, a gene required for position effect regulation in Saccharomyces cerevisiae. Mol Cell Biol. 1987 Dec;7(12):4441–4452. doi: 10.1128/mcb.7.12.4441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Micklem G., Rowley A., Harwood J., Nasmyth K., Diffley J. F. Yeast origin recognition complex is involved in DNA replication and transcriptional silencing. Nature. 1993 Nov 4;366(6450):87–89. doi: 10.1038/366087a0. [DOI] [PubMed] [Google Scholar]
  29. Moazed D., Johnson D. A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae. Cell. 1996 Aug 23;86(4):667–677. doi: 10.1016/s0092-8674(00)80139-7. [DOI] [PubMed] [Google Scholar]
  30. Moretti P., Freeman K., Coodly L., Shore D. Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1. Genes Dev. 1994 Oct 1;8(19):2257–2269. doi: 10.1101/gad.8.19.2257. [DOI] [PubMed] [Google Scholar]
  31. Palladino F., Laroche T., Gilson E., Axelrod A., Pillus L., Gasser S. M. SIR3 and SIR4 proteins are required for the positioning and integrity of yeast telomeres. Cell. 1993 Nov 5;75(3):543–555. doi: 10.1016/0092-8674(93)90388-7. [DOI] [PubMed] [Google Scholar]
  32. Scherer S., Davis R. W. Replacement of chromosome segments with altered DNA sequences constructed in vitro. Proc Natl Acad Sci U S A. 1979 Oct;76(10):4951–4955. doi: 10.1073/pnas.76.10.4951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Sikorski R. S., Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 1989 May;122(1):19–27. doi: 10.1093/genetics/122.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Singh J., Klar A. J. Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast. Genes Dev. 1992 Feb;6(2):186–196. doi: 10.1101/gad.6.2.186. [DOI] [PubMed] [Google Scholar]
  35. Smith J. S., Boeke J. D. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 1997 Jan 15;11(2):241–254. doi: 10.1101/gad.11.2.241. [DOI] [PubMed] [Google Scholar]
  36. Strahl-Bolsinger S., Hecht A., Luo K., Grunstein M. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 1997 Jan 1;11(1):83–93. doi: 10.1101/gad.11.1.83. [DOI] [PubMed] [Google Scholar]
  37. Sussel L., Shore D. Separation of transcriptional activation and silencing functions of the RAP1-encoded repressor/activator protein 1: isolation of viable mutants affecting both silencing and telomere length. Proc Natl Acad Sci U S A. 1991 Sep 1;88(17):7749–7753. doi: 10.1073/pnas.88.17.7749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Susskind M. M., Botstein D. Molecular genetics of bacteriophage P22. Microbiol Rev. 1978 Jun;42(2):385–413. doi: 10.1128/mr.42.2.385-413.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Thompson J. S., Ling X., Grunstein M. Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast. Nature. 1994 May 19;369(6477):245–247. doi: 10.1038/369245a0. [DOI] [PubMed] [Google Scholar]
  40. Yuan Y. O., Stroke I. L., Fields S. Coupling of cell identity to signal response in yeast: interaction between the alpha 1 and STE12 proteins. Genes Dev. 1993 Aug;7(8):1584–1597. doi: 10.1101/gad.7.8.1584. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES