Slx5/Slx8 Promotes Replication Stress Tolerance by Facilitating Mitotic Progression

Abstract

Loss of minichromosome maintenance protein 10 (Mcm10) causes replication stress. We uncovered that S. cerevisiae mcm10-1 mutants rely on the E3 SUMO ligase Mms21 and the SUMO-targeted ubiquitin ligase complex Slx5/8 for survival. Using quantitative mass spectrometry, we identified changes in the SUMO proteome of mcm10-1 mutants and revealed candidates regulated by Slx5/8. Such candidates included subunits of the chromosome passenger complex (CPC), Bir1 and Sli15, known to facilitate spindle assembly checkpoint (SAC) activation. We show here that Slx5 counteracts SAC activation in mcm10-1 mutants under conditions of moderate replication stress. This coincides with the proteasomal degradation of sumoylated Bir1. Importantly, Slx5-dependent mitotic relief was triggered not only by Mcm10 deficiency but also by treatment with low doses of the alkylating drug methyl methanesulfonate. Based on these findings, we propose a model in which Slx5/8 allows for passage through mitosis when replication stress is tolerable.

Figure 1. mcm10-1 mutants are synthetically sick with slx5Δ

(A, B) Successive 10-fold serial dilutions of indicated strains carrying an empty vector (EV), SLX5, CC561/564SS (RING mutant of SLX5) or MCM10 were grown on synthetic complete medium lacking uracil. See also Figures S1.

Figure 2. Cobalt affinity purification of SUMO conjugates

(A) Top: The cartoon illustrates the His₈-tagged SUMO gene (SMT3) and the 3′ UTR integrated at the endogenous SMT3 locus. TRP1 (TRP) is a selection marker. Bottom: Indicated strains were grown on YPD plates in successive 10-fold serial dilutions. (B) SUMO patterns of whole cell extracts (WCEs) are shown for indicated strains. The red line indicates differences between WT and mcm10-1 mutants at 37°C. Tubulin was a loading control. (C) Sumoylated PCNA isolated by nickel or cobalt affinity purification from mcm10-1 mutants expressing SMT3 or HIS₈SMT3 at 37°C. (D–F) Indicated strains were grown at 37°C. Eluates from cobalt affinity purification were analyzed with an anti-PCNA (D), -Rfa1 (E) or -Rfa2 (F) antibody. Free SUMO was used as a loading control. See also Figure S2.

Figure 3. Directed RIPPER (DRIPPER) reveals SUMO conjugates enriched or depleted in mcm10-1 cells

(A) DRIPPER separates peptide quantification (MS1) from identification (MS2). (B) The scatter plot illustrates the relative abundance of SUMO conjugates from the inclusion list. Relative intensities were determined by the ratios of peptide intensities from mcm10-1 to WT samples. Blue or red shaded areas represent arbitrary units (>8 = peptide intensities of 0 in WT, <−8 = peptide intensities of 0 in mcm10-1). Proteins from the same macromolecular complex or of similar function were depicted with matching symbols. Not all proteins are marked. See also Figure S3 and Table S1.

Figure 4. SUMO conjugates down-regulated in mcm10-1 mutants are potential substrates of the Slx5/8 complex

(A) The bar graph displays SUMO conjugates commonly identified by two independent DRIPPER analyses. (B) Gene ontology (GO) analysis was performed on SUMO targets identified by experiment 2. Top ten enriched GO terms are shown. (C) The Venn diagram presents overlap between SUMO targets identified in experiment 2 and potential Slx5/8 targets revealed in a study by Albuquerque et al. (Albuquerque et al., 2013). Listed proteins represent SUMO conjugates that were depleted (black) or enriched (red) in mcm10-1 cells. See also Figure S4, Tables S2 and S3.

Figure 5. Slx5 destabilizes sumoylated Bir1 and Sli15 in mcm10-1 cells

Bir1 (A) and Sli15 (B) were purified from indicated strains grown at 35°C for 3 h. Eluates were immunoblotted with a SUMO- or HA-specific antibody. Equal amounts of total protein were loaded. The asterisk indicates a non-specific band. (C–E) Successive 10-fold serial dilutions of indicated strains were spotted on YPD plates and grown at different temperatures. See also Figure S5.

Figure 6. Slx5 allows for mitotic progression when replication stress is moderate

(A, B) Asynchronous cultures of mcm10-1 and mcm10-1 slx5Δ mutants were grown at 33°C or 35°C. Samples were collected at indicated times and DNA content was analyzed by flow cytometry analysis (FACS). (C, D) Rad53 activation was monitored in samples shown in A and B. Tubulin was a loading control. Numbers represent the ratios of hyper-phosphorylated to unmodified Rad53. Red circles indicate unmodified Rad53. (E) Bir1 was purified from indicated strains grown at 33°C for 3 h treated with DMSO or MG132. Eluates were immunoblotted with a SUMO- or HA-specific antibody. Equal amounts of total Bir1 protein were loaded. (F) The experiment was performed as described in (E) and WCEs were immunoblotted with a HA-specific antibody. Tubulin was a loading control. See also Figures S6 and S7.

Figure 7. Slx5/8 promotes replication stress tolerance

(A, B) Asynchronous cultures of WT and slx5Δ mutants were treated with 0.003% MMS. Samples were collected at indicated times for FACS analysis (A) or Rad53-specific immunoblots (B). Tubulin was a loading control. Numbers represent the ratios of hyper-phosphorylated to unmodified Rad53. Red circles indicate unmodified Rad53. (C) Model for a role of Slx5/8 in mitotic progression under conditions of high or moderate replication stress. Replication stress causes exposure of RPA-coated ssDNA. Moderate stress triggers low-level Rad53 activation, allowing cells to progress through S phase. Checkpoint activation may also promote the activity of Mms21 (not shown), resulting in sumoylation of chromatin-associated proteins. Under these circumstances, Slx5/8 regulation of CPC, composed of Bir1, Sli15, Ipl1 (increase in ploidy 1) kinase, Nbl1 (N-terminal-Borealin like protein 1), promotes escape from mitotic arrest. When stress levels are high, robust hyperactivation of Rad53 inhibits S phase progression. In this case, Slx5/8 dependent regulation of CPC has no effect.