Recruitment of the Ulp2 protease to the inner kinetochore prevents its hyper-sumoylation to ensure accurate chromosome segregation
Autoři:
Raymond T. Suhandynata aff001; Yun Quan aff001; Yusheng Yang aff001; Wei-Tsung Yuan aff001; Claudio P. Albuquerque aff001; Huilin Zhou aff001
Působiště autorů:
Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California, United States of America
aff001; Moores Cancer Center, University of California, San Diego, La Jolla, California, United States of America
aff002
Vyšlo v časopise:
Recruitment of the Ulp2 protease to the inner kinetochore prevents its hyper-sumoylation to ensure accurate chromosome segregation. PLoS Genet 15(11): e32767. doi:10.1371/journal.pgen.1008477
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1008477
Souhrn
The kinetochore is the central molecular machine that drives chromosome segregation in all eukaryotes. Genetic studies have suggested that protein sumoylation plays a role in regulating the inner kinetochore; however, the mechanism remains elusive. Here, we show that Saccharomyces cerevisiae Ulp2, an evolutionarily conserved SUMO specific protease, contains a previously uncharacterized kinetochore-targeting motif that recruits Ulp2 to the kinetochore via the Ctf3CENP-I-Mcm16CENP-H-Mcm22CENP-K complex (CMM). Once recruited, Ulp2 selectively targets multiple subunits of the kinetochore, specifically the Constitutive Centromere-Associated Network (CCAN), via its SUMO-interacting motif (SIM). Mutations that impair the kinetochore recruitment of Ulp2 or its binding to SUMO result in an elevated rate of chromosome loss, while mutations that affect both result in a synergistic increase of chromosome loss rate, hyper-sensitivity to DNA replication stress, along with a dramatic accumulation of hyper-sumoylated CCAN. Notably, sumoylation of CCAN occurs at the kinetochore and is perturbed by DNA replication stress. These results indicate that Ulp2 utilizes its dual substrate recognition to prevent hyper-sumoylation of CCAN, ensuring accurate chromosome segregation during cell division.
Klíčová slova:
Cell cycle and cell division – Centromeres – DNA replication – Proteases – Protein expression – Saccharomyces cerevisiae – SUMOylation – Yeast
Zdroje
1. Musacchio A, Desai A. A Molecular View of Kinetochore Assembly and Function. Biology (Basel). 2017;6(1). doi: 10.3390/biology6010005 28125021.
2. Klare K, Weir JR, Basilico F, Zimniak T, Massimiliano L, Ludwigs N, et al. CENP-C is a blueprint for constitutive centromere-associated network assembly within human kinetochores. The Journal of cell biology. 2015;210(1):11–22. doi: 10.1083/jcb.201412028 26124289.
3. Hinshaw SM, Harrison SC. The structure of the Ctf19c/CCAN from budding yeast. eLife. 2019;8. doi: 10.7554/eLife.44239 30762520.
4. Cheeseman IM, Desai A. Molecular architecture of the kinetochore-microtubule interface. Nature reviews Molecular cell biology. 2008;9(1):33–46. doi: 10.1038/nrm2310 18097444.
5. De Wulf P, McAinsh AD, Sorger PK. Hierarchical assembly of the budding yeast kinetochore from multiple subcomplexes. Genes Dev. 2003;17(23):2902–21. doi: 10.1101/gad.1144403 14633972.
6. Ghosh SK, Poddar A, Hajra S, Sanyal K, Sinha P. The IML3/MCM19 gene of Saccharomyces cerevisiae is required for a kinetochore-related process during chromosome segregation. Mol Genet Genomics. 2001;265(2):249–57. doi: 10.1007/s004380000408 11361335.
7. Measday V, Hailey DW, Pot I, Givan SA, Hyland KM, Cagney G, et al. Ctf3p, the Mis6 budding yeast homolog, interacts with Mcm22p and Mcm16p at the yeast outer kinetochore. Genes Dev. 2002;16(1):101–13. doi: 10.1101/gad.949302 11782448.
8. Nishino T, Takeuchi K, Gascoigne KE, Suzuki A, Hori T, Oyama T, et al. CENP-T-W-S-X forms a unique centromeric chromatin structure with a histone-like fold. Cell. 2012;148(3):487–501. doi: 10.1016/j.cell.2011.11.061 22304917.
9. Lang J, Barber A, Biggins S. An assay for de novo kinetochore assembly reveals a key role for the CENP-T pathway in budding yeast. eLife. 2018;7. doi: 10.7554/eLife.37819 30117803.
10. Pekgoz Altunkaya G, Malvezzi F, Demianova Z, Zimniak T, Litos G, Weissmann F, et al. CCAN Assembly Configures Composite Binding Interfaces to Promote Cross-Linking of Ndc80 Complexes at the Kinetochore. Current biology: CB. 2016;26(17):2370–8. doi: 10.1016/j.cub.2016.07.005 27524485.
11. Poddar A, Roy N, Sinha P. MCM21 and MCM22, two novel genes of the yeast Saccharomyces cerevisiae are required for chromosome transmission. Mol Microbiol. 1999;31(1):349–60. doi: 10.1046/j.1365-2958.1999.01179.x 9987135.
12. Hyland KM, Kingsbury J, Koshland D, Hieter P. Ctf19p: A novel kinetochore protein in Saccharomyces cerevisiae and a potential link between the kinetochore and mitotic spindle. The Journal of cell biology. 1999;145(1):15–28. doi: 10.1083/jcb.145.1.15 10189365.
13. Sanyal K, Ghosh SK, Sinha P. The MCM16 gene of the yeast Saccharomyces cerevisiae is required for chromosome segregation. Molecular & general genetics: MGG. 1998;260(2–3):242–50. doi: 10.1007/s004380050892 9862478.
14. Pot I, Measday V, Snydsman B, Cagney G, Fields S, Davis TN, et al. Chl4p and iml3p are two new members of the budding yeast outer kinetochore. Molecular biology of the cell. 2003;14(2):460–76. doi: 10.1091/mbc.E02-08-0517 12589047.
15. Nagpal H, Fukagawa T. Kinetochore assembly and function through the cell cycle. Chromosoma. 2016;125(4):645–59. doi: 10.1007/s00412-016-0608-3 27376724.
16. Cheeseman IM, Anderson S, Jwa M, Green EM, Kang J, Yates JR 3rd, et al. Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p. Cell. 2002;111(2):163–72. doi: 10.1016/s0092-8674(02)00973-x 12408861.
17. Kotwaliwale CV, Biggins S. Post-Translational Modifications that Regulate Kinetochore Activity. In: De Wulf P, Earnshaw WC, editors. The Kinetochore: From Molecular Discoveries to Cancer Therapy. New York, NY: Springer New York; 2009. p. 1–51.
18. Meluh PB, Koshland D. Evidence that the MIF2 gene of Saccharomyces cerevisiae encodes a centromere protein with homology to the mammalian centromere protein CENP-C. Molecular biology of the cell. 1995;6(7):793–807. doi: 10.1091/mbc.6.7.793 7579695.
19. Fukagawa T, Regnier V, Ikemura T. Creation and characterization of temperature-sensitive CENP-C mutants in vertebrate cells. Nucleic acids research. 2001;29(18):3796–803. doi: 10.1093/nar/29.18.3796 11557811.
20. Wilson NR, Hochstrasser M. The Regulation of Chromatin by Dynamic SUMO Modifications. Methods Mol Biol. 2016;1475:23–38. doi: 10.1007/978-1-4939-6358-4_2 27631795.
21. Johnson ES. Protein modification by SUMO. Annual review of biochemistry. 2004;73:355–82. doi: 10.1146/annurev.biochem.73.011303.074118 15189146.
22. Li SJ, Hochstrasser M. A new protease required for cell-cycle progression in yeast. Nature. 1999;398(6724):246–51. doi: 10.1038/18457 10094048.
23. Li SJ, Hochstrasser M. The yeast ULP2 (SMT4) gene encodes a novel protease specific for the ubiquitin-like Smt3 protein. Mol Cell Biol. 2000;20(7):2367–77. doi: 10.1128/mcb.20.7.2367-2377.2000 10713161.
24. Kunz K, Piller T, Muller S. SUMO-specific proteases and isopeptidases of the SENP family at a glance. Journal of cell science. 2018;131(6). doi: 10.1242/jcs.211904 29559551.
25. Strunnikov AV, Aravind L, Koonin EV. Saccharomyces cerevisiae SMT4 encodes an evolutionarily conserved protease with a role in chromosome condensation regulation. Genetics. 2001;158(1):95–107. 11333221.
26. Stephens AD, Snider CE, Bloom K. The SUMO deconjugating peptidase Smt4 contributes to the mechanism required for transition from sister chromatid arm cohesion to sister chromatid pericentromere separation. Cell Cycle. 2015;14(14):2206–18. doi: 10.1080/15384101.2015.1046656 25946564.
27. Ryu HY, Wilson NR, Mehta S, Hwang SS, Hochstrasser M. Loss of the SUMO protease Ulp2 triggers a specific multichromosome aneuploidy. Genes Dev. 2016;30(16):1881–94. doi: 10.1101/gad.282194.116 27585592.
28. Pelisch F, Sonneville R, Pourkarimi E, Agostinho A, Blow JJ, Gartner A, et al. Dynamic SUMO modification regulates mitotic chromosome assembly and cell cycle progression in Caenorhabditis elegans. Nature communications. 2014;5:5485. doi: 10.1038/ncomms6485 25475837.
29. Mukhopadhyay D, Arnaoutov A, Dasso M. The SUMO protease SENP6 is essential for inner kinetochore assembly. The Journal of cell biology. 2010;188(5):681–92. doi: 10.1083/jcb.200909008 20212317.
30. de Albuquerque CP, Liang J, Gaut NJ, Zhou H. Molecular Circuitry of the SUMO (Small Ubiquitin-like Modifier) Pathway in Controlling Sumoylation Homeostasis and Suppressing Genome Rearrangements. The Journal of biological chemistry. 2016;291(16):8825–35. doi: 10.1074/jbc.M116.716399 26921322.
31. de Albuquerque CP, Suhandynata RT, Carlson CR, Yuan WT, Zhou H. Binding to small ubiquitin-like modifier and the nucleolar protein Csm1 regulates substrate specificity of the Ulp2 protease. The Journal of biological chemistry. 2018;293(31):12105–19. doi: 10.1074/jbc.RA118.003022 29903909.
32. Liang J, Singh N, Carlson CR, Albuquerque CP, Corbett KD, Zhou H. Recruitment of a SUMO isopeptidase to rDNA stabilizes silencing complexes by opposing SUMO targeted ubiquitin ligase activity. Genes Dev. 2017;31(8):802–15. doi: 10.1101/gad.296145.117 28487408.
33. Albuquerque CP, Wang G, Lee NS, Kolodner RD, Putnam CD, Zhou H. Distinct SUMO ligases cooperate with Esc2 and Slx5 to suppress duplication-mediated genome rearrangements. PLoS genetics. 2013;9(8):e1003670. doi: 10.1371/journal.pgen.1003670 23935535.
34. Elmore ZC, Donaher M, Matson BC, Murphy H, Westerbeck JW, Kerscher O. Sumo-dependent substrate targeting of the SUMO protease Ulp1. BMC biology. 2011;9:74. doi: 10.1186/1741-7007-9-74 22034919.
35. Mossessova E, Lima CD. Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Molecular cell. 2000;5(5):865–76. doi: 10.1016/s1097-2765(00)80326-3 10882122.
36. Schleiffer A, Maier M, Litos G, Lampert F, Hornung P, Mechtler K, et al. CENP-T proteins are conserved centromere receptors of the Ndc80 complex. Nature cell biology. 2012;14(6):604–13. doi: 10.1038/ncb2493 22561346.
37. Li R, Murray AW. Feedback control of mitosis in budding yeast. Cell. 1991;66(3):519–31. doi: 10.1016/0092-8674(81)90015-5 1651172.
38. Srikumar T, Lewicki MC, Costanzo M, Tkach JM, van Bakel H, Tsui K, et al. Global analysis of SUMO chain function reveals multiple roles in chromatin regulation. The Journal of cell biology. 2013;201(1):145–63. doi: 10.1083/jcb.201210019 23547032.
39. Ryu HY, Lopez-Giraldez F, Knight J, Hwang SS, Renner C, Kreft SG, et al. Distinct adaptive mechanisms drive recovery from aneuploidy caused by loss of the Ulp2 SUMO protease. Nature communications. 2018;9(1):5417. doi: 10.1038/s41467-018-07836-0 30575729.
40. Pearson CG, Maddox PS, Zarzar TR, Salmon ED, Bloom K. Yeast kinetochores do not stabilize Stu2p-dependent spindle microtubule dynamics. Molecular biology of the cell. 2003;14(10):4181–95. doi: 10.1091/mbc.E03-03-0180 14517328.
41. Dasso M. Emerging roles of the SUMO pathway in mitosis. Cell division. 2008;3:5. doi: 10.1186/1747-1028-3-5 18218095.
42. Hay RT. SUMO: a history of modification. Molecular cell. 2005;18(1):1–12. doi: 10.1016/j.molcel.2005.03.012 15808504.
43. Bylebyl GR, Belichenko I, Johnson ES. The SUMO isopeptidase Ulp2 prevents accumulation of SUMO chains in yeast. The Journal of biological chemistry. 2003;278(45):44113–20. doi: 10.1074/jbc.M308357200 12941945.
44. Denison C, Rudner AD, Gerber SA, Bakalarski CE, Moazed D, Gygi SP. A proteomic strategy for gaining insights into protein sumoylation in yeast. Molecular & cellular proteomics: MCP. 2005;4(3):246–54. doi: 10.1074/mcp.M400154-MCP200 15542864.
45. Panse VG, Hardeland U, Werner T, Kuster B, Hurt E. A proteome-wide approach identifies sumoylated substrate proteins in yeast. The Journal of biological chemistry. 2004;279(40):41346–51. doi: 10.1074/jbc.M407950200 15292183.
46. Wohlschlegel JA, Johnson ES, Reed SI, Yates JR 3rd. Global analysis of protein sumoylation in Saccharomyces cerevisiae. The Journal of biological chemistry. 2004;279(44):45662–8. doi: 10.1074/jbc.M409203200 15326169.
47. Meluh PB, Koshland D. Budding yeast centromere composition and assembly as revealed by in vivo cross-linking. Genes Dev. 1997;11(24):3401–12. doi: 10.1101/gad.11.24.3401 9407032.
Štítky
Genetika Reprodukční medicínaČlánek vyšel v časopise
PLOS Genetics
2019 Číslo 11
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