Concerted loading of Mcm2-7 double hexamers around DNA during DNA replication origin licensing

Abstract

The licensing of eukaryotic DNA replication origins, which ensures once-per-cell-cycle replication, involves the loading of six related minichromosome maintenance proteins (Mcm2-7) into prereplicative complexes (pre-RCs). Mcm2-7 forms the core of the replicative DNA helicase, which is inactive in the pre-RC. The loading of Mcm2-7 onto DNA requires the origin recognition complex (ORC), Cdc6, and Cdt1, and depends on ATP. We have reconstituted Mcm2-7 loading with purified budding yeast proteins. Using biochemical approaches and electron microscopy, we show that single heptamers of Cdt1*Mcm2-7 are loaded cooperatively and result in association of stable, head-to-head Mcm2-7 double hexamers connected via their N-terminal rings. DNA runs through a central channel in the double hexamer, and, once loaded, Mcm2-7 can slide passively along double-stranded DNA. Our work has significant implications for understanding how eukaryotic DNA replication origins are chosen and licensed, how replisomes assemble during initiation, and how unwinding occurs during DNA replication.

Figure 1. Purification of pre-RC proteins

(A and B) Purified ORC and Cdc6, respectively, analyzed by SDS-PAGE and Coomassie staining of the gel. Molecular mass markers (kDa) are indicated on the left, positions of ORC and Cdc6 are indicated on the right, respectively. (C) Purified Cdc6-wt (lanes 1-2) and Cdc6-8A (lanes 3-4) were analyzed by SDS-PAGE and Coomassie staining before (lanes 1 and 3) and after (lanes 2 and 4) λ-phosphatase treatment. (D) Gel-filtration analysis of Mcm4-FLAG immuno-affinity purified from whole-cell extract. Fractions were analyzed by SDS-PAGE and silver staining. Elution positions of molecular size markers (thyroglobulin, 670 kDa; bovine γ-globulin, 158 kDa) and the void position are indicated on the top. Gel-positions of identified proteins are indicated on the right. (E) Western blot analysis of purified Cdt1·Mcm2-7 complex using specific antibodies indicated on the top of each lane. (F) Transmission electron microscopy of negatively stained purified Cdt1·Mcm2-7. A representative micrograph is shown on the left. Examples of side-views and top-views are encircled in black and white, respectively. Panels on the right show representative reference-free class averages of top/bottom (upper two panels) or side views (lower two panels). The class averages, resulting from 4 rounds of SPIDER alignment and IMAGIC classification, corresponds to 65, 47, 58 and 55 aligned images, respectively (top to bottom). Arrowheads indicate an asymmetric protein appendage. Arrows indicate the two stacked protein layers in the side view.

Figure 2. Reconstitution of Mcm2-7 loading in vitro

(A) Western blot analysis of DNA-bead-bound fractions of loading reactions performed at a constant concentration of ORC (25 nM) and Cdc6 (50 nM) and indicated concentrations of Cdt1·Mcm2-7. Reactions were performed in presence of 5 mM ATP (lanes 1-6) or 5 mM ATPγS (lanes 7-12). Beads were washed twice with low-salt buffer (0.3 M K-glutamate; lanes 1-3 and 7-9) or once with low-salt and once with high-salt (0.5 M NaCl) buffer (lanes 4-6 and 10-12). Proteins analyzed are indicated on the right. (B) DNA bead association of all six MCM subunits (Mcm2-7) and indicated proteins following loading reactions in the presence of ATP (lanes 1-2) or ATPγS (lanes 3-4) without (lanes 1 and 3) and with (lanes 2 and 4) high-salt extraction. (C) Loading was performed in the presence of ATP and DNA-bead association of the indicated proteins after low-salt (lane 1) or high-salt wash (lane 2) was analyzed by Western blotting. High-salt-washed beads of a loading reaction in ATP were subjected to EcoR1 cleavage and proteins present in the bead-containing (lane 3) or supernatant DNA-containing (lane 4) fraction were analyzed. DNA was analyzed by 0.8% agarose gel electrophoresis and ethidium bromide staining (bottom panel). (D) Time course analysis of Mcm2-7 loading. ORC and Mcm2-7 binding to DNA-beads was monitored at the indicated time points after low-salt (lanes 1-5) or high-salt (lanes 6-10) wash. Quantified Western blot signals for Mcm2, -7, and -5 at the indicated time points after low-salt (closed squares) or high-salt (open triangles) wash are plotted in the bottom graph relative to loading at 40 min after low-salt wash. (E) Silver-stained SDS-PAGE gel analysis of loading reactions performed in the presence of 50 nM Cdc6, 50 nM Cdt1·Mcm2-7, and increasing amounts of ORC as indicated. Visible bands are annotated on the right.

Figure 3. Protein and DNA sequence dependencies of Mcm2-7 loading in vitro

(A) Loading reactions performed in the absence (lanes 1, 5, 9, and 13) or presence of indicated amounts of Cdc6 (lanes 2-4, 6-8, 10-12, 14-16. All reactions contained ORC (25 nM) and Cdt1·Mcm2-7 (50 nM) and either 5 mM ATP (lanes 1-8) or 5 mM ATPγS (lanes 9-16). (B) Loading reactions carried out in the absence or presence of indicated amounts of ORC. All reactions contained Cdc6 (50 nM) and Cdt1·Mcm2-7 (50 nM) and either 5 mM ATP (lanes 1-8) or 5 mM ATPγS (lanes 9-16). (C) Comparison of the loading efficiencies of wild-type Cdc6 (lanes 1-6) and Cdc6-8A (lanes 7-12). Reactions were performed in the presence of 5 mM ATP, 25 nM ORC, and 50 nM Cdt1·Mcm2-7, and Cdc6 protein as indicated. (D) DNA sequence specificity of Mcm2-7 loading in vitro. Reactions contained 50 nM Cdc6, 50 nM Cdt1·Mcm2-7, 5 mM ATP, and either 25 nM or 50 nM ORC as indicated. Binding to wild-type ARS1 DNA (lanes 1-4 and 9-12) or A^-B2^- mutant ARS1 (lanes 5-8 and 13-16) was monitored either in the absence (lanes 1-8) or presence (lanes 9-16) of 0.8 mg/ml poly(dIdC)·poly(dIdC) and 10 mg/ml BSA.

Figure 4. Transmission electron microscopy of negatively stained Mcm2-7 double hexamers

(A) Representative micrograph of DNA-bound Mcm2-7 complexes eluted from bDNA beads after high-salt-wash fraction by EcoR1 cleavage. Rectangular, four-tiered Mcm2-7 double hexamers are encircled. (B) Micrograph showing proteins of complete loading reaction performed in solution. Mcm2-7 double hexamers (encircled) are distinguishable among other particles corresponding to free Cdt1·Mcm2-7, ORC and Cdc6. (C) Representative class averages (i-iv) of Mcm2-7 double hexamers containing ~100 particles each. Averages in the top row were obtained from purified particles as in (A), averages in the bottom row were obtained from particles observed in whole loading reactions as in (B). Horizontal arrows mark the four tiers of the Mcm2-7 double hexamer side view; thicker arrows mark the AAA+ containing outer tiers, thinner arrows mark the inner N-terminal tiers. Vertical arrows indicate the path of the central channel. (D) Class average of ~100 particles of Mcm2-7 double hexamers bound to α-FLAG IgG directed against the Mcm4 C-terminus. Brackets mark extra density due to bound IgG.

Figure 5. 3D reconstruction of the Mcm2-7 double hexamer

(A-E) Surface representations of a 3D reconstruction of the Mcm2-7 double hexamer filtered to 30 Å at the predicted molecular weight for the Mcm2-7 double hexamer. (F) Cut-open side view. Channel dimensions at various positions are indicated.

Figure 6. Mcm2-7 double hexamers can slide on DNA

(A) Mcm2-7 double hexamers bound to linear 1kb ARS305-containing DNA visualized after tungsten rotary shadowcasting. (B) Time course analysis of Mcm2-7 retention on linear DNA after loading. Following the final high-salt wash of a loading reaction DNA beads were resuspended in 25 mM Hepes-KOH pH 7.6/0.5 M NaCl/5 mM Mg(OAc)₂/0.02% NP-40/10% glycerol/1 mM DTT. The suspension was incubated at 30°C and at the indicated time points an aliquot was removed from the suspension and DNA-bead-associated fractions (lanes 1-5) and supernatant fractions (lanes 6-10) analyzed by Western blotting. Quantified Western blot signals are plotted in the graph below (squares: supernatant; triangles: DNA-bead-associated). (C) Time-dependent Mcm2-7 double hexamer retention on linear (lanes 1-5) or circular (lanes 6-10) 1 kb ARS305 DNA. DNA beads after a loading reaction were resuspended in buffer as in (B) either in the absence (upper panels) or presence of 5 mM ATP (lower panels). MCM2, -7, and -5 Western blot signals in each time course experiment were quantified, normalized in each series to the earliest time point, and plotted in the graph below (closed triangles, circular DNA (-) ATP; open triangles, circular DNA (+) ATP; closed squares, linear DNA (-) ATP; open squares, linear DNA (+) ATP). (D) As (C), except that Mcm2-7 retention on DNA was monitored in buffer containing 0.1 M NaCl instead of 0.5 M NaCl. (E) Mcm2-7 double hexamers bound to circular 1kb ARS305-containing DNA visualized as in (A).