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PLOS Genetics  2013 

Distinct SUMO Ligases Cooperate with Esc2 and Slx5 to Suppress Duplication-Mediated Genome Rearrangements

DOI: 10.1371/journal.pgen.1003670

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Abstract:

Suppression of duplication-mediated gross chromosomal rearrangements (GCRs) is essential to maintain genome integrity in eukaryotes. Here we report that SUMO ligase Mms21 has a strong role in suppressing GCRs in Saccharomyces cerevisiae, while Siz1 and Siz2 have weaker and partially redundant roles. Understanding the functions of these enzymes has been hampered by a paucity of knowledge of their substrate specificity in vivo. Using a new quantitative SUMO-proteomics technology, we found that Siz1 and Siz2 redundantly control the abundances of most sumoylated substrates, while Mms21 more specifically regulates sumoylation of RNA polymerase-I and the SMC-family proteins. Interestingly, Esc2, a SUMO-like domain-containing protein, specifically promotes the accumulation of sumoylated Mms21-specific substrates and functions with Mms21 to suppress GCRs. On the other hand, the Slx5-Slx8 complex, a SUMO-targeted ubiquitin ligase, suppresses the accumulation of sumoylated Mms21-specific substrates. Thus, distinct SUMO ligases work in concert with Esc2 and Slx5-Slx8 to control substrate specificity and sumoylation homeostasis to prevent GCRs.

References

[1]  Gordenin DA, Resnick MA (1998) Yeast ARMs (DNA at-risk motifs) can reveal sources of genome instability. Mutat Res 400: 45–58. doi: 10.1016/s0027-5107(98)00047-5
[2]  Deininger PL, Batzer MA (1999) Alu repeats and human disease. Mol Genet Metab 67: 183–193 doi:10.1006/mgme.1999.2864.
[3]  Ji Y, Eichler EE, Schwartz S, Nicholls RD (2000) Structure of chromosomal duplicons and their role in mediating human genomic disorders. Genome Res 10: 597–610. doi: 10.1101/gr.10.5.597
[4]  Kolodner RD, Putnam CD, Myung K (2002) Maintenance of genome stability in Saccharomyces cerevisiae. Science 297: 552–557 doi:10.1126/science.1075277.
[5]  Putnam CD, Hayes TK, Kolodner RD (2009) Specific pathways prevent duplication-mediated genome rearrangements. Nature 460: 984–989 doi:10.1038/nature08217.
[6]  Ohya T, Arai H, Kubota Y, Shinagawa H, Hishida T (2008) A SUMO-like domain protein, Esc2, is required for genome integrity and sister chromatid cohesion in Saccharomyces cerevisiae. Genetics 180: 41–50 doi:10.1534/genetics.107.086249.
[7]  Sollier J, Driscoll R, Castellucci F, Foiani M, Jackson SP, et al. (2009) The Saccharomyces cerevisiae Esc2 and Smc5-6 proteins promote sister chromatid junction-mediated intra-S repair. Mol Biol Cell 20: 1671–1682 doi:10.1091/mbc.E08-08-0875.
[8]  Novatchkova M, Bachmair A, Eisenhaber B, Eisenhaber F (2005) Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family. BMC Bioinformatics 6: 22 doi:10.1186/1471-2105-6-22.
[9]  Xie Y, Kerscher O, Kroetz MB, McConchie HF, Sung P, et al. (2007) The yeast Hex3.Slx8 heterodimer is a ubiquitin ligase stimulated by substrate sumoylation. J Biol Chem 282: 34176–34184 doi:10.1074/jbc.M706025200.
[10]  Prudden J, Pebernard S, Raffa G, Slavin DA, Perry JJP, et al. (2007) SUMO-targeted ubiquitin ligases in genome stability. EMBO J 26: 4089–4101 doi:10.1038/sj.emboj.7601838.
[11]  Johnson ES, Gupta AA (2001) An E3-like factor that promotes SUMO conjugation to the yeast septins. Cell 106: 735–744. doi: 10.1016/s0092-8674(01)00491-3
[12]  Putnam CD, Hayes TK, Kolodner RD (2010) Post-replication repair suppresses duplication-mediated genome instability. PLoS Genet 6: e1000933 doi:10.1371/journal.pgen.1000933.
[13]  Kats ES, Enserink JM, Martinez S, Kolodner RD (2009) The Saccharomyces cerevisiae Rad6 postreplication repair and Siz1/Srs2 homologous recombination-inhibiting pathways process DNA damage that arises in asf1 mutants. Mol Cell Biol 29: 5226–5237 doi:10.1128/MCB.00894-09.
[14]  Hochstrasser M (2001) SP-RING for SUMO: new functions bloom for a ubiquitin-like protein. Cell 107: 5–8. doi: 10.1016/s0092-8674(01)00519-0
[15]  Johnson ES, Schwienhorst I, Dohmen RJ, Blobel G (1997) The ubiquitin-like protein Smt3p is activated for conjugation to other proteins by an Aos1p/Uba2p heterodimer. EMBO J 16: 5509–5519 doi:10.1093/emboj/16.18.5509.
[16]  Johnson ES, Blobel G (1997) Ubc9p is the conjugating enzyme for the ubiquitin-like protein Smt3p. J Biol Chem 272: 26799–26802. doi: 10.1074/jbc.272.43.26799
[17]  Zhao X, Blobel G (2005) A SUMO ligase is part of a nuclear multiprotein complex that affects DNA repair and chromosomal organization. Proc Natl Acad Sci USA 102: 4777–4782 doi:10.1073/pnas.0500537102.
[18]  Li SJ, Hochstrasser M (1999) A new protease required for cell-cycle progression in yeast. Nature 398: 246–251 doi:10.1038/18457.
[19]  Li SJ, Hochstrasser M (2000) The yeast ULP2 (SMT4) gene encodes a novel protease specific for the ubiquitin-like Smt3 protein. Mol Cell Biol 20: 2367–2377. doi: 10.1128/mcb.20.7.2367-2377.2000
[20]  Mossessova E, Lima CD (2000) Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Mol Cell 5: 865–876. doi: 10.1016/s1097-2765(00)80326-3
[21]  Strunnikov AV, Hogan E, Koshland D (1995) SMC2, a Saccharomyces cerevisiae gene essential for chromosome segregation and condensation, defines a subgroup within the SMC family. Genes Dev 9: 587–599. doi: 10.1101/gad.9.5.587
[22]  Li S-J, Hochstrasser M (2003) The Ulp1 SUMO isopeptidase: distinct domains required for viability, nuclear envelope localization, and substrate specificity. J Cell Biol 160: 1069–1081 doi:10.1083/jcb.200212052.
[23]  Reindle A, Belichenko I, Bylebyl GR, Chen XL, Gandhi N, et al. (2006) Multiple domains in Siz SUMO ligases contribute to substrate selectivity. J Cell Sci 119: 4749–4757 doi:10.1242/jcs.03243.
[24]  Matunis MJ, Pickart CM (2005) Beginning at the end with SUMO. Nat Struct Mol Biol 12: 565–566 doi:10.1038/nsmb0705-565.
[25]  Bergink S, Jentsch S (2009) Principles of ubiquitin and SUMO modifications in DNA repair. Nature 458: 461–467 doi:10.1038/nature07963.
[26]  Cremona CA, Sarangi P, Yang Y, Hang LE, Rahman S, et al. (2012) Extensive DNA damage-induced sumoylation contributes to replication and repair and acts in addition to the mec1 checkpoint. Mol Cell 45: 422–432 doi:10.1016/j.molcel.2011.11.028.
[27]  Takahashi Y, Yong-Gonzalez V, Kikuchi Y, Strunnikov A (2006) SIZ1/SIZ2 control of chromosome transmission fidelity is mediated by the sumoylation of topoisomerase II. Genetics 172: 783–794 doi:10.1534/genetics.105.047167.
[28]  McAleenan A, Cordón-Preciado V, Clemente-Blanco A, Liu I-C, Sen N, et al. (2012) SUMOylation of the α-Kleisin Subunit of Cohesin Is Required for DNA Damage-Induced Cohesion. Curr Biol 22: 1564–1575 doi:10.1016/j.cub.2012.06.045.
[29]  Burgess RC, Rahman S, Lisby M, Rothstein R, Zhao X (2007) The Slx5-Slx8 complex affects sumoylation of DNA repair proteins and negatively regulates recombination. Mol Cell Biol 27: 6153–6162 doi:10.1128/MCB.00787-07.
[30]  Montpetit B, Hazbun TR, Fields S, Hieter P (2006) Sumoylation of the budding yeast kinetochore protein Ndc10 is required for Ndc10 spindle localization and regulation of anaphase spindle elongation. J Cell Biol 174: 653–663 doi:10.1083/jcb.200605019.
[31]  Zhou W, Ryan JJ, Zhou H (2004) Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses. J Biol Chem 279: 32262–32268 doi:10.1074/jbc.M404173200.
[32]  Denison C, Rudner AD, Gerber SA, Bakalarski CE, Moazed D, et al. (2005) A proteomic strategy for gaining insights into protein sumoylation in yeast. Mol Cell Proteomics 4: 246–254 doi:10.1074/mcp.M400154-MCP200.
[33]  Panse VG, Hardeland U, Werner T, Kuster B, Hurt E (2004) A proteome-wide approach identifies sumoylated substrate proteins in yeast. J Biol Chem 279: 41346–41351 doi:10.1074/jbc.M407950200.
[34]  Hannich JT, Lewis A, Kroetz MB, Li S-J, Heide H, et al. (2005) Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J Biol Chem 280: 4102–4110 doi:10.1074/jbc.M413209200.
[35]  Wohlschlegel JA, Johnson ES, Reed SI, Yates JR (2004) Global analysis of protein sumoylation in Saccharomyces cerevisiae. J Biol Chem 279: 45662–45668 doi:10.1074/jbc.M409203200.
[36]  Chen XL, Silver HR, Xiong L, Belichenko I, Adegite C, et al. (2007) Topoisomerase I-dependent viability loss in saccharomyces cerevisiae mutants defective in both SUMO conjugation and DNA repair. Genetics 177: 17–30 doi:10.1534/genetics.107.074708.
[37]  Hwang J-Y, Smith S, Ceschia A, Torres-Rosell J, Aragón L, et al. (2008) Smc5-Smc6 complex suppresses gross chromosomal rearrangements mediated by break-induced replications. DNA Repair (Amst) 7: 1426–1436 doi:10.1016/j.dnarep.2008.05.006.
[38]  Duan X, Sarangi P, Liu X, Rangi GK, Zhao X, et al. (2009) Structural and functional insights into the roles of the Mms21 subunit of the Smc5/6 complex. Mol Cell 35: 657–668 doi:10.1016/j.molcel.2009.06.032.
[39]  Mankouri HW, Ngo H-P, Hickson ID (2009) Esc2 and Sgs1 act in functionally distinct branches of the homologous recombination repair pathway in Saccharomyces cerevisiae. Mol Biol Cell 20: 1683–1694 doi:10.1091/mbc.E08-08-0877.
[40]  Choi K, Szakal B, Chen Y-H, Branzei D, Zhao X (2010) The Smc5/6 complex and Esc2 influence multiple replication-associated recombination processes in Saccharomyces cerevisiae. Mol Biol Cell 21: 2306–2314 doi:10.1091/mbc.E10-01-0050.
[41]  Ong S-E, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, et al. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1: 376–386. doi: 10.1074/mcp.m200025-mcp200
[42]  Chen S-H, Albuquerque CP, Liang J, Suhandynata RT, Zhou H (2010) A proteome-wide analysis of kinase-substrate network in the DNA damage response. J Biol Chem 285: 12803–12812 doi:10.1074/jbc.M110.106989.
[43]  Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, et al. (2008) A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics 7: 1389–1396 doi:10.1074/mcp.M700468-MCP200.
[44]  Johnson ES, Blobel G (1999) Cell cycle-regulated attachment of the ubiquitin-related protein SUMO to the yeast septins. J Cell Biol 147: 981–994. doi: 10.1083/jcb.147.5.981
[45]  Hoege C, Pfander B, Moldovan G-L, Pyrowolakis G, Jentsch S (2002) RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 419: 135–141 doi:10.1038/nature00991.
[46]  Silver HR, Nissley JA, Reed SH, Hou Y-M, Johnson ES (2011) A role for SUMO in nucleotide excision repair. DNA Repair (Amst) 10: 1243–1251 doi:10.1016/j.dnarep.2011.09.013.
[47]  Takahashi Y, Dulev S, Liu X, Hiller NJ, Zhao X, et al. (2008) Cooperation of sumoylated chromosomal proteins in rDNA maintenance. PLoS Genet 4: e1000215 doi:10.1371/journal.pgen.1000215.
[48]  Psakhye I, Jentsch S (2012) Protein Group Modification and Synergy in the SUMO Pathway as Exemplified in DNA Repair. Cell 151: 807–820 doi:10.1016/j.cell.2012.10.021.
[49]  Song J, Durrin LK, Wilkinson TA, Krontiris TG, Chen Y (2004) Identification of a SUMO-binding motif that recognizes SUMO-modified proteins. Proc Natl Acad Sci USA 101: 14373–14378 doi:10.1073/pnas.0403498101.
[50]  Armstrong AA, Mohideen F, Lima CD (2012) Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2. Nature 483: 59–63 doi:10.1038/nature10883.
[51]  Koren A, Soifer I, Barkai N (2010) MRC1-dependent scaling of the budding yeast DNA replication timing program. Genome Res 20: 781–790 doi:10.1101/gr.102764.109.
[52]  Parker JL, Bucceri A, Davies AA, Heidrich K, Windecker H, et al. (2008) SUMO modification of PCNA is controlled by DNA. EMBO J 27: 2422–2431 doi:10.1038/emboj.2008.162.
[53]  Xie Y, Rubenstein EM, Matt T, Hochstrasser M (2010) SUMO-independent in vivo activity of a SUMO-targeted ubiquitin ligase toward a short-lived transcription factor. Genes Dev 24: 893–903 doi:10.1101/gad.1906510.
[54]  Galanty Y, Belotserkovskaya R, Coates J, Jackson SP (2012) RNF4, a SUMO-targeted ubiquitin E3 ligase, promotes DNA double-strand break repair. Genes Dev 26: 1179–1195 doi:10.1101/gad.188284.112.
[55]  Johnson ES (2004) Protein modification by SUMO. Annu Rev Biochem 73: 355–382 doi:10.1146/annurev.biochem.73.011303.074118.
[56]  Chen XL, Reindle A, Johnson ES (2005) Misregulation of 2 microm circle copy number in a SUMO pathway mutant. Mol Cell Biol 25: 4311–4320 doi:10.1128/MCB.25.10.4311-4320.2005.
[57]  Branzei D, Sollier J, Liberi G, Zhao X, Maeda D, et al. (2006) Ubc9- and mms21-mediated sumoylation counteracts recombinogenic events at damaged replication forks. Cell 127: 509–522 doi:10.1016/j.cell.2006.08.050.
[58]  Byrne KP, Wolfe KH (2005) The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 15: 1456–1461 doi:10.1101/gr.3672305.
[59]  Prudden J, Perry JJP, Nie M, Vashisht AA, Arvai AS, et al. (2011) DNA repair and global sumoylation are regulated by distinct Ubc9 noncovalent complexes. Mol Cell Biol 31: 2299–2310 doi:10.1128/MCB.05188-11.
[60]  Boddy MN, Shanahan P, McDonald WH, Lopez-Girona A, Noguchi E, et al. (2003) Replication checkpoint kinase Cds1 regulates recombinational repair protein Rad60. Mol Cell Biol 23: 5939–5946. doi: 10.1128/mcb.23.16.5939-5946.2003
[61]  Mullen JR, Das M, Brill SJ (2011) Genetic evidence that polysumoylation bypasses the need for a SUMO-targeted Ub ligase. Genetics 187: 73–87 doi:10.1534/genetics.110.124347.
[62]  Chan JE, Kolodner RD (2011) A genetic and structural study of genome rearrangements mediated by high copy repeat Ty1 elements. PLoS Genet 7: e1002089 doi:10.1371/journal.pgen.1002089.
[63]  Str?m L, Karlsson C, Lindroos HB, Wedahl S, Katou Y, et al. (2007) Postreplicative formation of cohesion is required for repair and induced by a single DNA break. Science 317: 242–245 doi:10.1126/science.1140649.
[64]  Unal E, Heidinger-Pauli JM, Koshland D (2007) DNA double-strand breaks trigger genome-wide sister-chromatid cohesion through Eco1 (Ctf7). Science 317: 245–248 doi:10.1126/science.1140637.
[65]  Sj?gren C, Nasmyth K (2001) Sister chromatid cohesion is required for postreplicative double-strand break repair in Saccharomyces cerevisiae. Curr Biol 11: 991–995. doi: 10.1016/s0960-9822(01)00271-8
[66]  Yamamoto A, Guacci V, Koshland D (1996) Pds1p, an inhibitor of anaphase in budding yeast, plays a critical role in the APC and checkpoint pathway(s). J Cell Biol 133: 99–110. doi: 10.1083/jcb.133.1.99
[67]  Cohen-Fix O, Koshland D (1997) The anaphase inhibitor of Saccharomyces cerevisiae Pds1p is a target of the DNA damage checkpoint pathway. Proc Natl Acad Sci USA 94: 14361–14366. doi: 10.1073/pnas.94.26.14361
[68]  Gardner R, Putnam CW, Weinert T (1999) RAD53, DUN1 and PDS1 define two parallel G2/M checkpoint pathways in budding yeast. EMBO J 18: 3173–3185 doi:10.1093/emboj/18.11.3173.
[69]  Sanchez Y, Bachant J, Wang H, Hu F, Liu D, et al. (1999) Control of the DNA damage checkpoint by chk1 and rad53 protein kinases through distinct mechanisms. Science 286: 1166–1171. doi: 10.1126/science.286.5442.1166
[70]  Putnam CD, Kolodner RD (2010) Determination of gross chromosomal rearrangement rates. Cold Spring Harb Protoc 2010: pdb.prot5492. doi: 10.1101/pdb.prot5492

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