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A new MCM modification cycle regulates DNA replication initiation


The MCM DNA helicase is a central regulatory target during genome replication. MCM is kept inactive during G1, and it initiates replication after being activated in S phase. During this transition, the only known chemical change to MCM is the gain of multisite phosphorylation that promotes cofactor recruitment. Because replication initiation is intimately linked to multiple biological cues, additional changes to MCM can provide further regulatory points. Here, we describe a yeast MCM SUMOylation cycle that regulates replication. MCM subunits undergo SUMOylation upon loading at origins in G1 before MCM phosphorylation. MCM SUMOylation levels then decline as MCM phosphorylation levels rise, thus suggesting an inhibitory role of MCM SUMOylation during replication. Indeed, increasing MCM SUMOylation impairs replication initiation, partly through promoting the recruitment of a phosphatase that decreases MCM phosphorylation and activation. We propose that MCM SUMOylation counterbalances kinase-based regulation, thus ensuring accurate control of replication initiation.

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Figure 1: SUMOylation of six MCM subunits occurs on chromatin and is dependent on MCM loading at replication origins.
Figure 2: SUMOylation levels of MCM subunits oscillate during the cell cycle.
Figure 3: Loss of Mcm2–6 SUMOylation at the G1-S transition requires DDK, GINS and replication initiation.
Figure 4: Increasing SUMOylation by Mcm6-SuOn slows growth, and this defect is suppressed by a ubc9 mutant.
Figure 5: Mcm6-SuOn impairs replication initiation.
Figure 6: Low CMG levels in Mcm6-SuOn cells correlate with impaired Mcm4 phosphorylation, which is suppressed by rif1Δ.
Figure 7: rif1Δ suppresses Mcm6-SuOn growth defects, and Mcm6-SuOn leads to enhanced association between Mcm6 and the Glc7 phosphatase.

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We are very grateful to T. Zhang and J. Xiang at the Genomics Resources Core Facility, Weill Cornell Medical College for their kind assistance in genome-wide sequencing analyses. We also thank K. Labib (University of Dundee), D. Shore (Institute of Genetics and Genomics in Geneva), B. Stillman (Cold Spring Harbor Laboratory), J. Diffley (Cancer Research UK London Research Institute), D. Remus (Memorial Sloan Kettering Cancer Center), J. Torres-Rosell (Universitat de Lleida), M. Kanemaki (Japan National Institute of Genetics) and D. Koshland (University of California, Berkeley) for providing strains, plasmids and antibodies. We also thank Zhao-laboratory members B. Wan for providing reagents and P. Sarangi for discussion. This study was supported by US National Institutes of Health grant GM080670 to X.Z.

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Authors and Affiliations



L.W. and X.Z. conceived the study and designed the experiments. L.W. performed the experiments. L.W. and X.Z. analyzed the results and wrote the manuscript.

Corresponding author

Correspondence to Xiaolan Zhao.

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Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Detection of MCM-subunit SUMOylation under normal growth conditions.

a. Sumoylated forms of MCM subunits show differential shifts when SUMO is attached to differently sized tags. MCM subunits were tagged with HA and SUMO was tagged with either HF (His6-Flag) or 8His at the endogenous loci. Western blots using anti-HA antibody after Ni-PD revealed the sumoylated (arrow head) and unmodified (dot) forms of MCM proteins. The relative shift of the sumoylated forms to the unmodified forms was bigger when SUMO was tagged with the larger tag (HF) than with the smaller tag (8His). The differences were better seen in the traces of the bands generated by the image quantification function from Image J (bottom).

b. Immunoblots showing sumoylated and unmodified forms of HA-tagged Mcm2-7 subunits after the proteins were immunoprecipitated. Cells contained either HF-SUMO (+) or untagged SUMO (–). Unmodified forms of MCM subunits (dots) were detected by anti-HA antibody, and sumoylated forms (arrow heads) by anti-SUMO antibody. Sumoylated forms containing HF-SUMO (orange arrow heads) migrated more slowly than the ones containing untagged SUMO (black arrow heads). Untagged MCM (lane 3) showed no detectable bands on both blots, indicating that bands in other lanes were MCM proteins.

Supplementary Figure 2 Examination of protein levels or functions of Cdc6, DDK and Psf1 and chromatin-bound Mcm6.

a. Western blotting analysis of Cdc6 protein levels. Samples were the same as those in the left panel of Figure 1d. FACS profile showed proper G1 arrest.

b. Sumoylation levels of chromatin-bound Mcm6 peak in G1 and decline during S phase. Chromatin-bound Mcm6 (tagged with HA) was examined as in Figure 2a. Cells were arrested in G1 and then released into S phase. FACS profile is shown at the top. Immunoblot detection of Mcm6 is in the middle; the faster migrating band is unmodified Mcm6. The relative ratio of sumoylated to unmodified Mcm6 is plotted at the bottom, and the value of G1 cells was set to 1.

c. Western blotting analysis of phosphorylation of Mcm4, Orc6, and Rad53. Samples were the same as those of the Mcm4-HA panel in Figure 3a.

d-e. Flow cytometry and western blotting analyses of samples from Figure 3b. d. Asynchronous cultures (asyn) of Psf2-aid cells and control cells containing wild-type Psf2 were arrested in G2/M by nocodazole for 3 h. IAA was then added to the media for 1 h to degrade Psf2-aid. Subsequently, cells were released into media containing IAA and alpha-factor to arrest cells in G1 phase. Once arrest was achieved, cells were released into media containing IAA but not alpha factor. FACS analyses showed that Psf2 degradation did not affect cells entering G1 phase, but blocked G1 cells from replication when alpha-factor was washed out. The control cells showed bulk replication when released from G1. e. Western blots of cell extracts showed expected patterns of CDK-mediated Orc6 phosphorylation and DDK-mediated Mcm4 phosphorylation, and no checkpoint kinase Rad53 phosphorylation in Psf2-aid cells. In addition, degradation of Psf2-aid,tagged with a V5 tag, was validated.

f. Psf2-aid fails to support cell viability in the presence of IAA, whereas the control fully supports cell viability. Both types of cells grew well in the absence of IAA.

Supplementary Figure 3 Examination of the effects of Mcm6-SuOn on SUMOylation and MCM-complex levels.

a. Diagram depicting Mcm6 fused with SuOn or ctrl tag. The SuOn tag is part of the desumoylation domain with catalytic site mutated and exhibits strong SUMO binding34,35. The ctrl tag is the same as the SuOn, except for a single mutation disrupting SUMO binding34,35. The hexameric MCM complex, tags, and SUMO are drawn in proportion to the sizes of the proteins.

b. Examination of the modified form of the Mcm6-SuOn protein. Immunoblots showing cell extracts from the indicated strains probed by anti-Mcm6 antibody. The slow migrating bands (arrows) containing Mcm6-SuOn were sumoylated forms since HF-SUMO caused a upshift compared with untagged SUMO. The differential shift in the two situations is visualized by the trace of the bands in Image J (bottom).

c. Examination of sumoylation of Mcm6-SuOn and Mcm6-ctrl proteins. Both proteins (tagged with V5) were immunoprecipitated and probed with anti-V5 and anti-SUMO antibodies on western blots. Anti-V5 detected both unmodified and sumoylated forms, with the latter being more abundant in Mcm6-SuOn cells. Anti-SUMO antibody detection verified the sumoylated form as indicated.

d. Mcm6-SuOn increases the sumoylation of Mcm2, 4, and 7, but not Mcm3. Cells with the indicated constructs were examined by Ni-PD method. Compared with Mcm6-ctrl, Mcm6-SuOn cells had more sumoylated forms of Mcm2, 4, and 7, and less sumoylated Mcm3.

e. Mcm6-SuOn does not affect MCM complex formation. Top: Mcm6 (V5 tagged) was immunoprecipitated and Mcm4-HA was detected by immunoblotting. Note that similar levels of Mcm4 were recovered from both Mcm6-SuOn and Mcm6-ctrl strains. Bottom: Protein extracts were examined by immunoblotting to show that Mcm6 and Mcm4 protein levels were similar in Mcm6-SuOn and Mcm6-ctrl cells.

f. Mcm6-SuOn largely does not affect the sumoylation levels of several replication proteins. Samples were processed as in Fig. 1b; antibody recognizing the TAP tag was used for western blotting.

Supplementary Figure 4 Genetic examination of Mcm6-SuOn.

a. Mcm6-SuOn, but not Mcm6-ctrl, exhibits growth defects. 10-fold serial dilutions of cells were spotted on YPD plates and grown at 30˚C for 36 hours.

b. mcm4∆2-174 is synthetic lethal with Mcm6-ctrl. Spore clones of the double mutants failed to grow on dissection plates, whereas those of other genotypes grew well.

c. mcm5-bob1 showed weaker suppression of cdc7-4 growth defects than rif1∆ at 30ºC. 5-fold serial dilutions of cells were spotted.

d. Unlike rif1∆, mcm5-bob1 does not suppress the growth defects of Mcm6-SuOn. 5-fold serial dilutions of cells were spotted.

Supplementary Figure 5 Genome-wide profiles of copy-number changes in Mcm6-SuOn and Mcm6-ctrl cells.

Results for all 16 chromosomes from samples in Figure 5e are shown. Cells collected from 0 min and 30 min post cdc7-4 release were subjected to whole-genome sequencing, and relative copy number changes were plotted. Open circles on the x-axis represent confirmed replication origins.

Supplementary Figure 6 Examination of Mcm6-SUMO fusion and Glc7-Mcm6 association.

a. Lower levels of Cdc45 and Psf1 are associated with Mcm6-SUMO fusion. Cells were arrested in G1 using alpha factor (0’) and released into S phase. Co-immunoprecipitation of Cdc45 and Psf1 with Mcm6-HA or Mcm6-HA-SUMO was examined. Relative ratios of Psf1/Mcm6 in the IP fraction are indicated and a two- to three- fold reduction is seen for Mcm6-HA-SUMO strain compared to the control Mcm6-HA strain.

b. Mcm6-SUMO fusion yields a slow replication profile. Both Mcm6-HA-SUMO fusion and Mcm6-HA control strains were arrested in G1 phase using alpha factor and released into S phase. Samples at indicated time points were examined by FACS.

c. Cells containing Mcm6-SUMO fusion grow slowly compared to control cells. 10-fold serial dilutions of cells were spotted.

d. Examination of Mcm4 phosphorylation in Mcm6-ctrl strains (related to Figure 6b). Mcm4 phosphorylation in Mcm6-ctrl was similar to wild-type cells (e.g. Fig. 2b), and rif1∆ increased this modification as expected.

e. Increased amounts of Glc7 are associated with Mcm6-SuOn than Mcm6-ctrl in both G1 and S phase samples. Similar to Figure 7b, except both G1-arrested and S phase (30 min after G1 release) cells were examined.

f. Increased Glc7-Mcm6 association in rif1∆ cells. G1-arrested cells were examined for Glc7 association with Mcm6-SuOn as in e.

Supplementary Figure 7 Examination of SUMOylated Mcm2, 4 and 6 proteins and deSUMOylation enzyme mutants, and verification of Mcm3 protein levels.

a. rif1∆ decreases sumoylation of Mcm2 and Mcm6 in G1 cells. Experiments were done as in Figure 2a.

b. Lambda phosphatase treatment does not affect the mobility of the sumoylated form of Mcm4 on western blots. Left, in the control, phosphatase treatment reduced the mobility of phosphorylated Mcm4. Right, phosphatase treatment did not reduce the mobility of sumoylated Mcm4.

c. Ulp2 loss leads to increased levels of sumoylated Mcm4 and 6. Sumoylation changes in Mcm4 and 6 were examined by HA-IP in the presence or absence of Ulp2. Ulp2 depletion was achieved by the use Ulp2-aid degron tagged with V5 upon the addition of 1 mM IAA for 1 hr (+IAA), and verified by western blotting (bottom). For Mcm4 and 6, Ulp2 depletion increased the levels of poly-sumoylated forms (-Sn) of the proteins, such that the total sumoylated Mcm4 or 6 increased 2-4 fold. Increase of poly-sumoylated form of the proteins upon Ulp2 depletion is consistent with the previous finding of the enzyme’s preferences in desumoylating poly-sumoylated proteins.

d. Sumoylation of Mcm6 does not change upon Ulp1 depletion. Experiments were similar as in (c), except that Ulp1-aid was used.

e. Mcm4 and 6 sumoylation is detected in the chromatin fraction when Ulp2 is depleted. As in panel (c), except chromatin-bound (Ch) and soluble (Su) fractions were examined as in Figure 1c.

f. Examination of the protein levels of Mcm3 tagged with HA. N-terminal HA-tagged Mcm3 was used in the study due to toxicity of C-terminal tagging. This construct was expressed at the endogenous MCM3 locus from the ADH1 promoter. It is known that endogenous Mcm3 protein levels are about half that of Mcm740. This ratio was maintained in our strains wherein Mcm7-HA was driven by its own promoter and Mcm3-HA from the ADH1 promoter.

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Wei, L., Zhao, X. A new MCM modification cycle regulates DNA replication initiation. Nat Struct Mol Biol 23, 209–216 (2016).

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