Mec1 is one of multiple kinases that prime the Mcm2-7 helicase for phosphorylation by Cdc7

Abstract

Activation of the eukaryotic replicative DNA helicase, the Mcm2-7 complex, requires phosphorylation by Cdc7/Dbf4 (Dbf4-dependent kinase or DDK), which, in turn, depends on prior phosphorylation of Mcm2-7 by an unknown kinase (or kinases). We identified DDK phosphorylation sites on Mcm4 and Mcm6 and found that phosphorylation of either subunit suffices for cell proliferation. Importantly, prior phosphorylation of either S/T-P or S/T-Q motifs on these subunits is required for DDK phosphorylation of Mcm2-7 and for normal S phase passage. Phosphomimetic mutations of DDK target sites bypass both DDK function and mutation of the priming phosphorylation sites. Mrc1 facilitates Mec1 phosphorylation of the S/T-Q motifs of chromatin-bound Mcm2-7 during S phase to activate replication. Genetic interactions between priming site mutations and MRC1 or TOF1 deletion support a role for these modifications in replication fork stability. These findings identify regulatory mechanisms that modulate origin firing and replication fork assembly during cell cycle progression.

Figure 1. Identification of priming and target sites for DDK on Mcm2-7

(A) Cartoon showing locations of phosphorylation sites on Mcm2-7 either before (red) or after (blue) phosphorylation by recombinant DDK. Pre-RCs were assembled on origin DNA-bound magnetic beads using whole cell extract. Origin-bound pre-RC proteins were separated by SDS/PAGE and the bands representing Mcm2-7 were analyzed for phosphorylation using LC/MS/MS. (B) Phosphorylation sites on the Mcm4 and Mcm6 N-terminal tails. The colored residues correspond to sites mutated in this study, and are coded according to the residue at the +1 position. Blue, Pro; Red, Gln; Yellow, A/G/I/L/N; Green, Asp/Glu; Purple, Ser/Thr. Each illustration shows only unambiguously assigned sites of phosphorylation. See also Fig. S1.

Figure 2. Phenotype of putative DDK target site mutants

(A) Effect of alanine substitutions at putative DDK target sites. Strains yJCWR185, yJCWR176, yJCWR180, and yJCWR184 (see Table S2) carrying the indicated alleles of MCM4 and MCM6 in addition to a URA+ ARS/CEN MCM4+ plasmid were grown on ura+ media for 3-4 generations to allow loss of the URA+ MCM4+ plasmid. A five-fold serial dilution of cells was then spotted on plates without (left) or with (right) FOA selection against the URA+ MCM4+ plasmid. The numbers in parentheses adjacent to the allele name indicate the number of sites mutated in each allele (see also Fig. S1). (B) CDC7 bypass by phosphomimetic MCM4 alleles. The indicated MCM4 alleles were introduced into strain OAy711 (cdc7-4) by direct replacement at the chromosomal MCM4 locus. Cells were spotted on YPD at 22° and 37°.

Figure 3. Phenotype of putative priming site mutants

(A) Effect of alanine substitutions at putative priming sites. mcm4/mcm6 double-mutant strains yJCWR185, yJCWR167, yJCWR171, and yJCWR175 were analyzed as in Fig. 2A. The numbers in parentheses adjacent to the allele name indicate the number of sites mutated in each allele (see also Fig. S1). (B) S-phase progression defect of mcm4(AP+AQ) mcm6(AP+AQ) strain. DNA content was measured by FACS analysis after release from alpha factor at 25°. (C) Schematic of bypass strategy used in (D). (D) Rescue of priming site mutations by MCM4 and/or MCM6 phosphomimetic mutations at DDK target sites. Analysis of strains yJCWR185, yJCWR175, yJCWR236, and yJCWR237 was performed as in Fig. 2A.

Figure 4. S/T-P and S/T-Q sites reduces DDK targeting of Mcm2-7

(A) Elimination of S/T-P and S/T-Q sites in Mcm6 inhibits DDK phosphorylation. Pre-RCs were assembled using G1-arrested extracts from strains yJCWR128, yRH163, yJCWR129, yJCWR130, and yJCWR135 carrying the indicated sets of alanine substitutions in MCM6. All strains are wild-type for MCM4. The resulting pre-RCs were then phosphorylated by DDK using radiolabelled ATP and the labeled proteins were analyzed by immunoblotting (top panel) or autoradiography (bottom panel). (B) Mcm4-S82D83 is targeted by DDK. Pre-RCs assembly reactions were performed using G1-arrested extracts with or without Cdc6 and DDK. The resulting DNA associated proteins were analyzed by immunoblotting with anti-Mcm2-7 (UM-174, top) or phosph-S82-D83 antibodies. See also Fig. S2. (C) S/T-P and S/T-Q sites are required for DDK targeting of Mcm4 in vivo. MCM4 MCM6 or mcm4(AP+AQ) mcm6(AP+AQ) cultures (yJCWR205 or yJCWR208) were arrested in G1 phase with alpha factor. Cells were washed and released into medium lacking alpha factor for 30 minutes at 30°. Total cell protein was collected by TCA precipitation and analyzed by immunoblotting using anti-Mcm2-7 (top) and a phosphospecific antibody targeting Mcm4-S82-D83 (bottom).

Figure 5. Mcm2-7 SQ sites are phosphorylated on chromatin in S phase

(A) S/T-P and S/T-Q phosphorylation in G1 and S phase. Extracts of MCM4 MCM6 or mcm4(AP+AQ) mcm6(AP+AQ) cells were prepared as described in 4C and analyzed by immunoblotting using anti-Mcm2-7 and the indicated phosphospecific antisera. Arrows indicate the phosphospecific bands. (B) SQ phosphorylation in cells arrested at the G1/S transition. Wild-type, cdc4-1 or cdc7-4 cells were grown to mid-log phase at 25°, arrested in G1 using α-factor, then released at 37°. TCA-precipitated protein was analyzed by immunoblotting using anti-Mcm2-7 or anti-Mcm4-phospho-S87-Q88 sera. (C) S/T-Q phosphorylation is specific for chromatin-associated Mcm2-7. W303BLa cells were arrested in α-factor (αF) or nocodazole (noc) with or without 30 min release at 30°. Total cell protein was separated by a chromatin fractionation procedure into input (I), supernatant (S), and pelleted chromatin (P) fractions and analyzed by immunoblotting with sera detecting Mcm2-7, Mcm6-phospho-S19-P20, Mcm4-phospho-S87-Q88, or Orc2.

Figure 6. Mec1 targets Mcm4 in vivo independent of checkpoint activation

(A) Effect of deletion of MEC1, TEL1 and MRC1 on Mcm4 SQ phosphorylation. Extracts were prepared from cells after arrest in α-factor (αF), hydroxyurea (HU), nocodazol (noc) or 30 minutes after α-factor release (S-phase, S) as indicated and analyzed by immunoblotting using anti-Mcm2-7 and the indicated phosphospecific antisera. Upper panel: yCC29, yRH109, yRH110, yJCWR79, yJCWR78; lower panel: yJCWR200, yJCWR220, yCC98, yCC100. (B) Deletion of MEC1 reduces viability of mcm4-AP mcm6-AP cells. Strains yJCWR214, yJCWR216, yJCWR217, yJCWR218 yJCWR214, yJCWR216, and yJCWR221 were analyzed as in Fig. 2A. The relevant genotype is indicated to the left of each strain. (C) Eliminating Mec1 target sites on Mcm4 and Mcm6 does not render cells sensitive to hydroxyurea. Strains yJCWR205, yJCWR206, yJCWR207, and yJCWR208 carrying the indicated WT or mutant alleles of MCM4 and MCM6 as the only copy of those genes were plated on YPD in the absence or presence of 50 mM hydroxyurea (HU), as indicated. (D) Deletion of checkpoint genes reduces viability of mcm4-AP mcm6-AP cells. Strains yJCWR214, yJCWR216, yJCWR219, yCC48, yCC55, yJCWR167, and yJCWR175 were analyzed as in Fig. 2A. All of these strains include a deletion of SML1. See also Fig. S3. (E) Phosphomimetic mutations at DDK target sites rescue the deletion of MEC1 andRAD53 but not MRC1 in the mcm4(AP+AQ) mcm6(AP+AQ) strain background. Strains yJCWR175, yJCWR236, yJCWR237, yCC90, yCC94, yCC95, yCC114, yCC116, yCC117, yCC73, yCC75, and yCC77 were analyzed as in Fig. 2A.

Figure 7. A model for phospho-regulation of Mcm2-7

(A) Prior to replication we propose that SP sites in Mcm4 and Mcm6 are phosphorylated either by G1-CDKs or Pho85. It is also possible that this phosphorylation occurs earlier (e.g. by S-CDKs) and is not readily removed during G1. Upon entry into S phase we envision two possible mechanisms of DDK targeting: (i) DDK targets S-S^Pi-P and S-D/E sites to trigger helicase/origin activation; or (ii) Mec1 targets S-S-Q sites followed by DDK targeting of S-S^Pi-P, S-S^Pi-Q and S-D/E sites to trigger initiation. Based on our cell cycle studies, we propose that Mec1 is activated initially as a consequence of initiation events mediated by type (i) DDK targeting. Additional activation of Mec1 could be mediated by replication intermediates derived from type (ii) DDK driven initiation or checkpoint signaling. (B) Mec1 coordinates multiple events in both unperturbed and perturbed cell cycles. In a normal S phase, Mec1 activates both dNTP synthesis and DDK targeting to Mcm2-7. Under conditions of DNA damage or stalled replication forks, Mec1 activates a checkpoint pathway that stabilizes stalled forks and inhibits further origin firing. We propose that Mec1 activation could also facilitate firing of additional origins upon checkpoint recovery.