A Role for the Budding Yeast Separase, Esp1, in Ty1 Element Retrotransposition

English version České info

Separases are a family of cysteine proteases found in organisms ranging from yeast to humans that are required for separation of chromosomes during cell division. Separases dissolve the cohesin ring-like complex that holds sister chromatids together until chromosome separation occurs during mitosis. We used two genetic screens in the model organism budding yeast to identify additional cellular roles for separase. Surprisingly, we found that yeast separase is required for insertion of Ty1 retrotransposons into the yeast genome. Ty1 retrotransposons, or elements, are similar in their life cycle to retroviruses such as the human immunodeficiency virus type 1 (HIV-1) which is the cause of acquired immunodeficiency syndrome (AIDS). The insertion of retroviral/retrotransposon DNA into the genome requires a conserved protein encoded by the virus/retrotransposon called integrase. Until now, it was unknown which yeast host protein interacted with Ty1 integrase. We found that yeast separase interacts with Ty1 integrase, and that separase may be required for targeting Ty1 integrase into the genome via its interaction with integrase and by removing cohesin from the chromosomes. Due to the conservation of Ty1 integrase with other viral integrases, our discovery may shed light on how other viral integrases are targeted into the genome.

Vyšlo v časopise: A Role for the Budding Yeast Separase, Esp1, in Ty1 Element Retrotransposition. PLoS Genet 11(3): e32767. doi:10.1371/journal.pgen.1005109
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005109

Souhrn

Zdroje

1. Nasmyth K, Haering CH (2009) Cohesin: its roles and mechanisms. Annu Rev Genet 43: 525–558. doi: 10.1146/annurev-genet-102108-134233 19886810

2. Uhlmann F (2003) Chromosome cohesion and separation: from men and molecules. Curr Biol 13: R104–114. 12573239

3. Ciosk R, Shirayama M, Shevchenko A, Tanaka T, Toth A, et al. (2000) Cohesin's binding to chromosomes depends on a separate complex consisting of Scc2 and Scc4 proteins. Mol Cell 5: 243–254. 10882066

4. Lengronne A, Katou Y, Mori S, Yokobayashi S, Kelly GP, et al. (2004) Cohesin relocation from sites of chromosomal loading to places of convergent transcription. Nature 430: 573–578. 15229615

5. Cohen-Fix O, Peters JM, Kirschner MW, Koshland D (1996) Anaphase initiation in Saccharomyces cerevisiae is controlled by the APC-dependent degradation of the anaphase inhibitor Pds1p. Genes Dev 10: 3081–3093. 8985178

6. Farr KA, Cohen-Fix O (1999) The metaphase to anaphase transition: a case of productive destruction. Eur J Biochem 263: 14–19. 10429181

7. Hornig NC, Uhlmann F (2004) Preferential cleavage of chromatin-bound cohesin after targeted phosphorylation by Polo-like kinase. EMBO J 23: 3144–3153. 15241476

8. Uhlmann F, Lottspeich F, Nasmyth K (1999) Sister-chromatid separation at anaphase onset is promoted by cleavage of the cohesin subunit Scc1. Nature 400: 37–42. 10403247

9. Uhlmann F, Wernic D, Poupart MA, Koonin EV, Nasmyth K (2000) Cleavage of cohesin by the CD clan protease separin triggers anaphase in yeast. Cell 103: 375–386. 11081625

10. Gligoris TG, Scheinost JC, Burmann F, Petela N, Chan KL, et al. (2014) Closing the cohesin ring: structure and function of its Smc3-kleisin interface. Science 346: 963–967. doi: 10.1126/science.1256917 25414305

11. Rowland BD, Roig MB, Nishino T, Kurze A, Uluocak P, et al. (2009) Building sister chromatid cohesion: smc3 acetylation counteracts an antiestablishment activity. Mol Cell 33: 763–774. doi: 10.1016/j.molcel.2009.02.028 19328069

12. Tsou MF, Wang WJ, George KA, Uryu K, Stearns T, et al. (2009) Polo kinase and separase regulate the mitotic licensing of centriole duplication in human cells. Dev Cell 17: 344–354. doi: 10.1016/j.devcel.2009.07.015 19758559

13. Yang X, Boateng KA, Yuan L, Wu S, Baskin TI, et al. (2011) The radially swollen 4 separase mutation of Arabidopsis thaliana blocks chromosome disjunction and disrupts the radial microtubule system in meiocytes. PLoS One 6: e19459. doi: 10.1371/journal.pone.0019459 21559383

14. Pandey R, Heidmann S, Lehner CF (2005) Epithelial re-organization and dynamics of progression through mitosis in Drosophila separase complex mutants. J Cell Sci 118: 733–742. 15671062

15. Sullivan M, Lehane C, Uhlmann F (2001) Orchestrating anaphase and mitotic exit: separase cleavage and localization of Slk19. Nat Cell Biol 3: 771–777. 11533655

16. D'Amours D, Amon A (2004) At the interface between signaling and executing anaphase—Cdc14 and the FEAR network. Genes Dev 18: 2581–2595. 15520278

17. Bardin AJ, Amon A (2001) Men and sin: what's the difference? Nat Rev Mol Cell Biol 2: 815–826. 11715048

18. Stegmeier F, Visintin R, Amon A (2002) Separase, polo kinase, the kinetochore protein Slk19, and Spo12 function in a network that controls Cdc14 localization during early anaphase. Cell 108: 207–220. 11832211

19. Sullivan M, Uhlmann F (2003) A non-proteolytic function of separase links the onset of anaphase to mitotic exit. Nat Cell Biol 5: 249–254. 12598903

20. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364–2368. 11743205

21. Beauregard A, Curcio MJ, Belfort M (2008) The take and give between retrotransposable elements and their hosts. Annu Rev Genet 42: 587–617. doi: 10.1146/annurev.genet.42.110807.091549 18680436

22. Lesage P, Todeschini AL (2005) Happy together: the life and times of Ty retrotransposons and their hosts. Cytogenet Genome Res 110: 70–90. 16093660

23. Qi X, Sandmeyer S (2012) In vitro targeting of strand transfer by the Ty3 retroelement integrase. J Biol Chem 287: 18589–18595. doi: 10.1074/jbc.M111.326025 22493285

24. Xie W, Gai X, Zhu Y, Zappulla DC, Sternglanz R, et al. (2001) Targeting of the yeast Ty5 retrotransposon to silent chromatin is mediated by interactions between integrase and Sir4p. Mol Cell Biol 21: 6606–6614. 11533248

25. Baum P, Yip C, Goetsch L, Byers B (1988) A yeast gene essential for regulation of spindle pole duplication. Mol Cell Biol 8: 5386–5397. 3072479

26. Baskerville C, Segal M, Reed SI (2008) The protease activity of yeast separase (esp1) is required for anaphase spindle elongation independently of its role in cleavage of cohesin. Genetics 178: 2361–2372. doi: 10.1534/genetics.107.085308 18430955

27. Tong AH, Lesage G, Bader GD, Ding H, Xu H, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303: 808–813. 14764870

28. Giaever G, Chu AM, Ni L, Connelly C, Riles L, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387–391. 12140549

29. Sopko R, Huang D, Preston N, Chua G, Papp B, et al. (2006) Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell 21: 319–330. 16455487

30. Young BP, Loewen CJ (2013) Balony: a software package for analysis of data generated by synthetic genetic array experiments. BMC Bioinformatics 14: 354. doi: 10.1186/1471-2105-14-354 24305553

31. Sarin S, Ross KE, Boucher L, Green Y, Tyers M, et al. (2004) Uncovering novel cell cycle players through the inactivation of securin in budding yeast. Genetics 168: 1763–1771. 15579722

32. Measday V, Hieter P (2002) Synthetic dosage lethality. Methods Enzymol 350: 316–326. 12073321

33. Baetz K, Measday V, Andrews B (2006) Revealing hidden relationships among yeast genes involved in chromosome segregation using systematic synthetic lethal and synthetic dosage lethal screens. Cell Cycle 5: 592–595. 16582600

34. Measday V, Baetz K, Guzzo J, Yuen K, Kwok T, et al. (2005) Systematic yeast synthetic lethal and synthetic dosage lethal screens identify genes required for chromosome segregation. Proc Natl Acad Sci U S A 102: 13956–13961. 16172405

35. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498–2504. 14597658

36. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, et al. (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25: 1091–1093. doi: 10.1093/bioinformatics/btp101 19237447

37. McAleenan A, Clemente-Blanco A, Cordon-Preciado V, Sen N, Esteras M, et al. (2013) Post-replicative repair involves separase-dependent removal of the kleisin subunit of cohesin. Nature 493: 250–254. doi: 10.1038/nature11630 23178808

38. Jensen S, Segal M, Clarke DJ, Reed SI (2001) A novel role of the budding yeast separin Esp1 in anaphase spindle elongation: evidence that proper spindle association of Esp1 is regulated by Pds1. J Cell Biol 152: 27–40. 11149918

39. Aye M, Irwin B, Beliakova-Bethell N, Chen E, Garrus J, et al. (2004) Host factors that affect Ty3 retrotransposition in Saccharomyces cerevisiae. Genetics 168: 1159–1176. 15579677

40. Griffith JL, Coleman LE, Raymond AS, Goodson SG, Pittard WS, et al. (2003) Functional genomics reveals relationships between the retrovirus-like Ty1 element and its host Saccharomyces cerevisiae. Genetics 164: 867–879. 12871900

41. Irwin B, Aye M, Baldi P, Beliakova-Bethell N, Cheng H, et al. (2005) Retroviruses and yeast retrotransposons use overlapping sets of host genes. Genome Res 15: 641–654. 15837808

42. Nyswaner KM, Checkley MA, Yi M, Stephens RM, Garfinkel DJ (2008) Chromatin-associated genes protect the yeast genome from Ty1 insertional mutagenesis. Genetics 178: 197–214. doi: 10.1534/genetics.107.082602 18202368

43. Scholes DT, Banerjee M, Bowen B, Curcio MJ (2001) Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance. Genetics 159: 1449–1465. 11779788

44. Checkley MA, Nagashima K, Lockett SJ, Nyswaner KM, Garfinkel DJ (2010) P-body components are required for Ty1 retrotransposition during assembly of retrotransposition-competent virus-like particles. Mol Cell Biol 30: 382–398. doi: 10.1128/MCB.00251-09 19901074

45. Risler JK, Kenny AE, Palumbo RJ, Gamache ER, Curcio MJ (2012) Host co-factors of the retrovirus-like transposon Ty1. Mob DNA 3: 12. doi: 10.1186/1759-8753-3-12 22856544

46. Bryk M, Banerjee M, Conte D Jr., Curcio MJ (2001) The Sgs1 helicase of Saccharomyces cerevisiae inhibits retrotransposition of Ty1 multimeric arrays. Mol Cell Biol 21: 5374–5388. 11463820

47. Sundararajan A, Lee BS, Garfinkel DJ (2003) The Rad27 (Fen-1) nuclease inhibits Ty1 mobility in Saccharomyces cerevisiae. Genetics 163: 55–67. 12586696

48. Burkett TJ, Garfinkel DJ (1994) Molecular characterization of the SPT23 gene: a dosage-dependent suppressor of Ty-induced promoter mutations from Saccharomyces cerevisiae. Yeast 10: 81–92. 8203154

49. Fassler JS, Winston F (1988) Isolation and analysis of a novel class of suppressor of Ty insertion mutations in Saccharomyces cerevisiae. Genetics 118: 203–212. 2834263

50. Clark-Adams CD, Norris D, Osley MA, Fassler JS, Winston F (1988) Changes in histone gene dosage alter transcription in yeast. Genes Dev 2: 150–159. 2834270

51. Malone EA, Clark CD, Chiang A, Winston F (1991) Mutations in SPT16/CDC68 suppress cis- and trans-acting mutations that affect promoter function in Saccharomyces cerevisiae. Mol Cell Biol 11: 5710–5717. 1922073

52. Winston F, Chaleff DT, Valent B, Fink GR (1984) Mutations affecting Ty-mediated expression of the HIS4 gene of Saccharomyces cerevisiae. Genetics 107: 179–197. 6329902

53. Curcio MJ, Garfinkel DJ (1992) Posttranslational control of Ty1 retrotransposition occurs at the level of protein processing. Mol Cell Biol 12: 2813–2825. 1317008

54. Yamamoto A, Guacci V, Koshland D (1996) Pds1p is required for faithful execution of anaphase in the yeast, Saccharomyces cerevisiae. J Cell Biol 133: 85–97. 8601616

55. Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng WT, et al. (2004) Exploration of essential gene functions via titratable promoter alleles. Cell 118: 31–44. 15242642

56. Curcio MJ, Garfinkel DJ (1991) Single-step selection for Ty1 element retrotransposition. Proc Natl Acad Sci U S A 88: 936–940. 1846969

57. Winston F, Durbin KJ, Fink GR (1984) The SPT3 gene is required for normal transcription of Ty elements in S. cerevisiae. Cell 39: 675–682. 6096019

58. Rattray AJ, Shafer BK, Garfinkel DJ (2000) The Saccharomyces cerevisiae DNA recombination and repair functions of the RAD52 epistasis group inhibit Ty1 transposition. Genetics 154: 543–556. 10655210

59. Lee BS, Bi L, Garfinkel DJ, Bailis AM (2000) Nucleotide excision repair/TFIIH helicases RAD3 and SSL2 inhibit short-sequence recombination and Ty1 retrotransposition by similar mechanisms. Mol Cell Biol 20: 2436–2445. 10713167

60. Ji H, Moore DP, Blomberg MA, Braiterman LT, Voytas DF, et al. (1993) Hotspots for unselected Ty1 transposition events on yeast chromosome III are near tRNA genes and LTR sequences. Cell 73: 1007–1018. 8388781

61. Baller JA, Gao J, Stamenova R, Curcio MJ, Voytas DF (2012) A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon. Genome Res 22: 704–713. doi: 10.1101/gr.129585.111 22219511

62. Mularoni L, Zhou Y, Bowen T, Gangadharan S, Wheelan SJ, et al. (2012) Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots. Genome Res 22: 693–703. doi: 10.1101/gr.129460.111 22219510

63. Jager H, Herzig B, Herzig A, Sticht H, Lehner CF, et al. (2004) Structure predictions and interaction studies indicate homology of separase N-terminal regulatory domains and Drosophila THR. Cell Cycle 3: 182–188. 14712087

64. Viadiu H, Stemmann O, Kirschner MW, Walz T (2005) Domain structure of separase and its binding to securin as determined by EM. Nat Struct Mol Biol 12: 552–553. 15880121

65. Lu Y, Cross F (2009) Mitotic exit in the absence of separase activity. Mol Biol Cell 20: 1576–1591. doi: 10.1091/mbc.E08-10-1042 19144818

66. Stegmeier F, Amon A (2004) Closing mitosis: the functions of the Cdc14 phosphatase and its regulation. Annu Rev Genet 38: 203–232. 15568976

67. Bachman N, Gelbart ME, Tsukiyama T, Boeke JD (2005) TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs. Genes Dev 19: 955–964. 15833918

68. Gelbart ME, Bachman N, Delrow J, Boeke JD, Tsukiyama T (2005) Genome-wide identification of Isw2 chromatin-remodeling targets by localization of a catalytically inactive mutant. Genes Dev 19: 942–954. 15833917

69. Kenna MA, Brachmann CB, Devine SE, Boeke JD (1998) Invading the yeast nucleus: a nuclear localization signal at the C terminus of Ty1 integrase is required for transposition in vivo. Mol Cell Biol 18: 1115–1124. 9448009

70. McLane LM, Pulliam KF, Devine SE, Corbett AH (2008) The Ty1 integrase protein can exploit the classical nuclear protein import machinery for entry into the nucleus. Nucleic Acids Res 36: 4317–4326. doi: 10.1093/nar/gkn383 18586821

71. Moore SP, Rinckel LA, Garfinkel DJ (1998) A Ty1 integrase nuclear localization signal required for retrotransposition. Mol Cell Biol 18: 1105–1114. 9448008

72. Michaelis C, Ciosk R, Nasmyth K (1997) Cohesins: chromosomal proteins that prevent premature separation of sister chromatids. Cell 91: 35–45. 9335333

73. Toth A, Ciosk R, Uhlmann F, Galova M, Schleiffer A, et al. (1999) Yeast cohesin complex requires a conserved protein, Eco1p(Ctf7), to establish cohesion between sister chromatids during DNA replication. Genes Dev 13: 320–333. 9990856

74. Kulemzina I, Schumacher MR, Verma V, Reiter J, Metzler J, et al. (2012) Cohesin rings devoid of Scc3 and Pds5 maintain their stable association with the DNA. PLoS Genet 8: e1002856. doi: 10.1371/journal.pgen.1002856 22912589

75. D'Ambrosio C, Schmidt CK, Katou Y, Kelly G, Itoh T, et al. (2008) Identification of cis-acting sites for condensin loading onto budding yeast chromosomes. Genes Dev 22: 2215–2227. doi: 10.1101/gad.1675708 18708580

76. Lopez-Serra L, Kelly G, Patel H, Stewart A, Uhlmann F (2014) The Scc2-Scc4 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions. Nat Genet 46: 1147–1151. doi: 10.1038/ng.3080 25173104

77. Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, et al. (2014) Total synthesis of a functional designer eukaryotic chromosome. Science 344: 55–58. doi: 10.1126/science.1249252 24674868

78. Devine SE, Boeke JD (1996) Integration of the yeast retrotransposon Ty1 is targeted to regions upstream of genes transcribed by RNA polymerase III. Genes Dev 10: 620–633. 8598291

79. Hani J, Feldmann H (1998) tRNA genes and retroelements in the yeast genome. Nucleic Acids Res 26: 689–696. 9443958

80. Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF (1998) Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 8: 464–478. 9582191

81. Nagao K, Adachi Y, Yanagida M (2004) Separase-mediated cleavage of cohesin at interphase is required for DNA repair. Nature 430: 1044–1048. 15329725

82. Blat Y, Kleckner N (1999) Cohesins bind to preferential sites along yeast chromosome III, with differential regulation along arms versus the centric region. Cell 98: 249–259. 10428036

83. Megee PC, Mistrot C, Guacci V, Koshland D (1999) The centromeric sister chromatid cohesion site directs Mcd1p binding to adjacent sequences. Mol Cell 4: 445–450. 10518226

84. Snider CE, Stephens AD, Kirkland JG, Hamdani O, Kamakaka RT, et al. (2014) Dyskerin, tRNA genes, and condensin tether pericentric chromatin to the spindle axis in mitosis. J Cell Biol 207: 189–199. doi: 10.1083/jcb.201405028 25332162

85. Hoang C, Ferre-D'Amare AR (2001) Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme. Cell 107: 929–939. 11779468

86. Alexandru G, Uhlmann F, Mechtler K, Poupart MA, Nasmyth K (2001) Phosphorylation of the cohesin subunit Scc1 by Polo/Cdc5 kinase regulates sister chromatid separation in yeast. Cell 105: 459–472. 11371343

87. Thompson M, Haeusler RA, Good PD, Engelke DR (2003) Nucleolar clustering of dispersed tRNA genes. Science 302: 1399–1401. 14631041

88. Wang BD, Yong-Gonzalez V, Strunnikov AV (2004) Cdc14p/FEAR pathway controls segregation of nucleolus in S. cerevisiae by facilitating condensin targeting to rDNA chromatin in anaphase. Cell Cycle 3: 960–967. 15190202

89. Cherepanov P, Ambrosio AL, Rahman S, Ellenberger T, Engelman A (2005) Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75. Proc Natl Acad Sci U S A 102: 17308–17313. 16260736

90. Goldstein AL, McCusker JH (1999) Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 15: 1541–1553. 10514571

91. Tong AH, Boone C (2006) Synthetic genetic array analysis in Saccharomyces cerevisiae. Methods Mol Biol 313: 171–192. 16118434

92. Field J, Nikawa J, Broek D, MacDonald B, Rodgers L, et al. (1988) Purification of a RAS-responsive adenylyl cyclase complex from Saccharomyces cerevisiae by use of an epitope addition method. Mol Cell Biol 8: 2159–2165. 2455217

93. Shevchenko A, Chernushevich I, Wilm M, Mann M (2000) De Novo peptide sequencing by nanoelectrospray tandem mass spectrometry using triple quadrupole and quadrupole/time-of-flight instruments. Methods Mol Biol 146: 1–16. 10948493

94. Ishihama Y, Rappsilber J, Mann M (2006) Modular stop and go extraction tips with stacked disks for parallel and multidimensional Peptide fractionation in proteomics. J Proteome Res 5: 988–994. 16602707

95. Rappsilber J, Ishihama Y, Mann M (2003) Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem 75: 663–670. 12585499

96. Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2: 1896–1906. 17703201

97. Olsen JV, de Godoy LM, Li G, Macek B, Mortensen P, et al. (2005) Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics 4: 2010–2021. 16249172

98. Eichinger DJ, Boeke JD (1988) The DNA intermediate in yeast Ty1 element transposition copurifies with virus-like particles: cell-free Ty1 transposition. Cell 54: 955–966. 2843295

99. Teste MA, Duquenne M, Francois JM, Parrou JL (2009) Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae. BMC Mol Biol 10: 99. doi: 10.1186/1471-2199-10-99 19874630

100. Lee BS, Lichtenstein CP, Faiola B, Rinckel LA, Wysock W, et al. (1998) Posttranslational inhibition of Ty1 retrotransposition by nucleotide excision repair/transcription factor TFIIH subunits Ssl2p and Rad3p. Genetics 148: 1743–1761. 9560391

101. Mou Z, Kenny AE, Curcio MJ (2006) Hos2 and Set3 promote integration of Ty1 retrotransposons at tRNA genes in Saccharomyces cerevisiae. Genetics 172: 2157–2167. 16415356

102. Conte D Jr., Barber E, Banerjee M, Garfinkel DJ, Curcio MJ (1998) Posttranslational regulation of Ty1 retrotransposition by mitogen-activated protein kinase Fus3. Mol Cell Biol 18: 2502–2513. 9566871