Small ubiquitin-like modifier (SUMO) E3 ligases are known to have a major role in preventing gross chromosomal rearrangements (GCRs); however, relatively little is known about the role of SUMO isopeptidases in genome maintenance and their role in controlling intracellular sumoylation homeostasis. Here we show the SUMO isopeptidase Ulp2 in Saccharomyces cerevisiae does not prevent the accumulation of GCRs, and interestingly, its loss causes subunit-specific changes of sumoylated minichromosome maintenance (MCM) helicase in addition to drastic accumulation of sumoylated nucleolar RENT and inner kinetochore complexes. In contrast, loss of Ulp1 or its mis-localization from the nuclear periphery causes substantial accumulations of GCRs and elevated sumoylation of most proteins except for Ulp2 targets. Interestingly, the E3 ligase Mms21, which has a major role in genome maintenance, preferentially controls the sumoylation of Mcm3 during DNA replication. These findings reveal distinct roles for Ulp1 and Ulp2 in controlling homeostasis of intracellular sumoylation and show that sumoylation of MCM is controlled in a subunit-specific and cell cycle dependent manner.Protein sumoylation is an essential post-translational modification in eukaryotes (1, 2). Two families of enzymes control reversible sumoylation of specific substrates, including SUMO 3 (small ubiquitin-like modifier) E3 ligases and SUMO isopeptidases. Three SUMO E3 ligases Siz1, Siz2, and Mms21 have been identified in Saccharomyces cerevisiae and are shown to have distinct, but partially overlapping roles in catalyzing substratespecific sumoylation (3-6). Siz1 and Siz2 are paralogs, and they redundantly catalyze the bulk of sumoylation in cells (5, 6). Mms21 catalyzes sumoylation of fewer substrates but plays a more important role in genome maintenance than Siz1 and Siz2 (6, 7). Deletion of SIZ1 and SIZ2 is lethal in cells lacking Mms21 E3 ligase activity (4, 5). Moreover, deletion of either SIZ1 or SIZ2 causes further accumulation of gross chromosome rearrangements (GCRs) in cells lacking Mms21 E3 ligase activity (6). These findings suggest that the functions of these E3 ligases are partially redundant, which correlates with their partially overlapping roles in catalyzing intracellular sumoylation (5, 6).Besides SUMO E3 ligases, homeostasis of intracellular sumoylation is also regulated by SUMO isopeptidases, which catalyze the removal of SUMO from its targets. Two SUMO isopeptidases Ulp1 and Ulp2 have been identified in S. cerevisiae (8 -10). Ulp2 is not required for cell viability; however, its loss causes accumulation of poly-SUMO chains, resulting in pleiotropic effects including slow growth and sensitivity to higher temperature (9, 11). Moreover, overexpression of ULP2