The dynamics of eukaryotic replication initiation: origin specificity, licensing, and firing at the single-molecule level

Abstract

Eukaryotic replication initiation is highly regulated and dynamic. It begins with the origin recognition complex (ORC) binding DNA sites called origins of replication. ORC, together with Cdc6 and Cdt1, mediate pre-replicative complex (pre-RC) assembly by loading a double hexamer of Mcm2-7: the core of the replicative helicase. Here, we use single-molecule imaging to directly visualize Saccharomyces cerevisiae pre-RC assembly and replisome firing in real time. We show that ORC can locate and stably bind origins within large tracts of non-origin DNA and that Cdc6 drives ordered pre-RC assembly. We further show that the dynamics of the ORC-Cdc6 interaction dictate Mcm2-7 loading specificity and that Mcm2-7 double hexamers form preferentially at a native origin sequence. Finally, we demonstrate that single Mcm2-7 hexamers propagate bidirectionally, monotonically, and processively as constituents of active replisomes.

Figure 1. DNA Curtain Assay for Visualizing pre-RC Assembly

(A) Schematic of the DNA curtain setup. The left panel shows single-tethered DNA and the right panel shows a double-tethered variation. (B) AT content and ACS-like sequences of the λ_ARS1 DNA substrate. The magenta arrow indicates the cloned ARS1 sequence. (C–D) (C) Wide-field image of a DNA curtain following incubation with 0.5 nM ORC and (D) 1.0 nM ORC. (E) Kymogram of a single-tethered DNA molecule with bound ORC, showing flow on/off events. See also Figure S1.

Figure 2. ORC Binding Distributions

(A) 1 nM ORC binding distribution histogram on λ_ARS1. Binding positions were scored at a single time point following a 2 minute incubation and the removal of excess protein. For all position distribution histograms, error bars indicate an 85% confidence interval based on 300 bootstrapping samples. N = number of ORC molecules. See also Figure S2. (B) 1 nM ORC binding distribution histogram on native λ. (C–D) Kymograms showing examples of (C) ORC binding to ARS1 directly from solution and (D) 1D sliding of ORC along λ_ARS1 to its target.

Figure 3. Cdc6 and the ORC Binding Distribution

(A) 1 nM ORC binding distribution histogram on λ_ARS1 in the presence of 4 nM Cdc6. The higher specificity is reduced (inset), even in the presence of 40 nM Cdc6, by allowing a longer incubation time of 8 minutes. (B) 2 nM ORC in the presence of 8 nM unlabeled Cdc6 binds across the AT-rich region of λ_ARS1. (C) In the absence of Cdc6, 2 nM ORC results in ORC aggregation across the DNA (top panel). Many of the DNA molecules have been ripped from their tethers by the compacting effect of excessive ORC binding. Subsequent addition of 4 nM Cdc6 does not reverse ORC binding (bottom panel). (D) The initial 0.5 nM ORC distribution (cyan) does not change 7 minutes after excess protein is flushed out (magenta), nor after an additional 7 minutes after Cdc6 is introduced (yellow). (The dead volume of the microfluidics requires 1.5 minutes for the controlled introduction of Cdc6.)

Figure 4. Cdc6 Binding Dynamics

(A) Cdc6 labeled with fluorescent streptavidin binds transiently to DNA-ORC (unlabeled). See also Figure S3. (B) Cdc6 interacts preferentially with ARS1-ORC. (C) The magenta survival probability plot of Cdc6 interacting with ARS1-ORC (every 5^th 85% CI bootstrapped data point shown, for clarity), and the blue survival probability plot of Cdc6 interacting with non-ARS1-ORC (every 6^th 85% CI bootstrapped data point shown) are fit with single exponential decay functions. The existence of two lifetimes was ascertained by a statistical F-test (F = 5024, P < .0001; see Supplemental Experimental Procedures). (D) Kymogram showing sequential binding of ORC (magenta) and Cdc6 (cyan) to DNA.

Figure 5. Cdc6 Dynamics Control Mcm2-7 Specificity

(A) Mcm2-7 binding distribution histogram on λ_ARS1. See also Figure S4. (B) Mcm2-7 loading efficiency under various conditions. Mcm2-7 molecules per DNA was quantified by labeling the DNA with the intercalating dye YOYO-1 after the completion of Mcm2-7 loading. N = number of DNA molecules. (C) Order-of-addition experiment showing that Cdc6 must be present in solution for Mcm2-7 loading. (D) Kymogram showing direct binding of Mcm2-7/Cdt1 to DNA-ORC-Cdc6. All Mcm2-7/Cdt1 molecules bind DNA-ORC-Cdc6 directly out of solution (right panel). (E) Wide-field image of Mcm2-7^Mcm4-DY549 bound to a double-tethered λ_ARS1 curtain. Proteins nonspecifically associate with the chromium barriers at the top and bottom of the double-tethered curtain, and these regions are excluded from all analyses. (F) Examples of one-step and two-step photobleaching curves of ARS1-localized Mcm2-7^Mcm4-DY549. Pie charts show the proportions of 1-step, 2-step, and 3-step photobleaching at ARS1 (top) and non-ARS1 sites (bottom). (G) An order-of-addition experiment shows that ORC is not required in solution to load Mcm2-7 double hexamers.

Figure 6. Replication Initiation and Replisome Progression

(A) A cartoon of replisome assembly around loaded Mcm2-7 double hexamers and subsequent bidirectional replication. See also Figure S5. (B) A kymogram of bidirectional Mcm2-7^Mcm4-DY549 progression during replication. (C) Mcm2-7 double hexamer firing is highly efficient. (D) Replication initiation begins 54.3 ± 1.4 min. after the introduction of S-phase extract (± S.E.M.; σ = 9.9 min.). (E) The replisome progression rate is 8 ± 0.4 bp/s (± S.E.M.; σ = 3.1 bp/s). (F) The median apparent processivity is 7.4 kbp. (G) Cdc45 binds loaded Mcm2-7 and progresses with the replisome. Poor labeling efficiency prevents visualization of the second Cdc45, presumed to progress in the opposite direction (dotted line). (H) Efficient Cdc45 binding requires prior DDK phosphorylation of Mcm2-7 (DDK₁) and supplemented DDK in the S-phase extract (DDK₂). The bar graph shows Cdc45 binding efficiency (as number of Cdc45 binding events per Region of Interest, which amounts to four DNA curtains) under different DDK conditions.

Figure 7. Schematic of Replication Initiation Dynamics

(A) ORC has a moderate to high preference for ACS-like sequences and a high preference for ARS1. (B) Cdc6 is likelier to bind ARS1-ORC, and once there, bind for longer. (C) Mcm2-7 interacts only with the DNA-ORC-Cdc6 species. (D) Mcm2-7 double hexamers form preferentially at ARS1. For clarity, the figure depicts only the Mcm2-7 double hexamer. However, our data do not address the presence or absence of other pre-RC components at this stage. (E) DDK phosphorylation of Mcm2-7 followed by incubation with S-phase extract leads to replisome assembly, but firing of any individual replisome is prevented until both sisters are properly assembled. (F) Once fully assembled, sister forks fire simultaneously, initiating processive, bidirectional replication.