Replication-Coupled PCNA Unloading by the Elg1 Complex Occurs Genome-wide and Requires Okazaki Fragment Ligation

Abstract

The sliding clamp PCNA is a crucial component of the DNA replication machinery. Timely PCNA loading and unloading are central for genome integrity and must be strictly coordinated with other DNA processing steps during replication. Here, we show that the S. cerevisiae Elg1 replication factor C-like complex (Elg1-RLC) unloads PCNA genome-wide following Okazaki fragment ligation. In the absence of Elg1, PCNA is retained on chromosomes in the wake of replication forks, rather than at specific sites. Degradation of the Okazaki fragment ligase Cdc9 leads to PCNA accumulation on chromatin, similar to the accumulation caused by lack of Elg1. We demonstrate that Okazaki fragment ligation is the critical prerequisite for PCNA unloading, since Chlorella virus DNA ligase can substitute for Cdc9 in yeast and simultaneously promotes PCNA unloading. Our results suggest that Elg1-RLC acts as a general PCNA unloader and is dependent upon DNA ligation during chromosome replication.

Graphical abstract

Figure 1

Expression of myc Tagged with Untagged PCNA Permits Normal Cell Growth (A) Cells with POL30-3myc as the only PCNA allele show sensitivity to MMS and, in an elg1Δ background, defective growth and hyper-sensitivity to MMS. Five-fold serial dilutions of cells were plated on YPD or YPD plus MMS and incubated for 2 days at 30°C. (B) Expression of myc-tagged PCNA in addition to endogenous untagged PCNA does not cause sensitivity to MMS or slow growth in the absence of Elg1. Five-fold serial dilutions of cells were plated on YPD or YPD plus MMS, and incubated for 2–3 days at 30°C. Two different isolates of ELG1⁺ and elg1Δ strains carrying POL30-3myc are shown. (C) Inferred functionality of PCNA trimers consisting of untagged and myc-tagged subunits. See also Figure S1.

Figure 2

PCNA Is Retained on Replicated DNA Genome-wide in the Absence of Elg1 (A) Outline of procedure for chromatin fractionation and ChIP-seq experiments. (B) Flow cytometry analysis. (C) PCNA accumulates on chromatin in the absence of Elg1 during DNA replication. Myc-tagged and untagged PCNA in whole-cell extracts (left) and chromatin fractions (right) detected by western blotting with anti-PCNA antibody. (D) Quantification of total PCNA on chromatin in (C), expressed as relative increase compared to alpha-factor arrested cells. (E) ChIP-seq analysis of PCNA distribution on chromatin. PCNA is unloaded behind replication forks in ELG1⁺ (black arrows) but retained in elg1Δ (white arrows). The chromosome (Chr) XI 300–600 kb region is shown; the entire chromosome XI is presented in Figure S3. (F) Median PCNA enrichment around early (n = 165) and late (n = 173) origins at 15- and 30-min time points. See also Figures S2 and S3.

Figure 3

PCNA Accumulates on Chromatin in the Absence of the Replicative DNA Ligase Cdc9 (A) Outline of procedure for cell synchronization, induction of degradation of AID-tagged proteins, and sampling for chromatin fractionation. (B) Flow cytometry analysis. (C) In the absence of Elg1 (lane 4) or the DNA ligase Cdc9 (lane 6), PCNA accumulates on chromatin during DNA replication. Histone H3 is loading control. PCNA amounts on chromatin are indicated below, relative to no degron rad9Δ G1 sample (lane 1). See also Figure S4.

Figure 4

PCNA Retention on Chromatin following Cdc9 Degradation Is Caused by Failure of Elg1-Dependent PCNA Unloading, Rather Than Re-loading of PCNA on Unligated Okazaki Fragments (A) Outline of in vitro PCNA unloading assay. Soluble cell extracts contain myc-tagged PCNA to enable monitoring of any re-loading on chromatin. Cdc9 was degraded in cells used for soluble cell extracts to prevent DNA ligation during unloading assay. (B) In vitro assay shows that PCNA is not unloaded by Elg1 in the absence of DNA ligase Cdc9, and PCNA accumulation on chromatin is not due to re-loading. PCNA retained on chromatin after treating with indicated soluble cell extracts was detected by western blotting with anti-PCNA antibody. Analysis of soluble cell extracts used (last two lanes) confirmed presence of myc-tagged PCNA. Histone H3 is loading control for chromatin samples. PCNA amounts on chromatin indicated below, relative to no treatment. (C) Outline of experiments to test PCNA re-loading on unligated Okazaki fragments in vivo. Strain is the cdc9-1 temperature-sensitive mutant with myc-tagged POL30 gene as a second copy, expressed from the GAL promoter. Cells were arrested in G1 phase at 23°C, and cultures were shifted to a restrictive temperature of 37°C for 1 hr before release into S phase. Galactose was added to the culture 26 min (i) or 86 min (ii) after release. (D) Flow cytometry analysis. (E) No re-loading of PCNA takes place on unligated Okazaki fragments in vivo, as evidenced by lack of loading of myc-tagged PCNA expressed in G2 phase in the absence of Cdc9 (right panel). Myc-tagged PCNA is loaded if expressed in S phase in the absence of Cdc9 (left panel). Loading of myc-tagged PCNA on chromatin assessed by appearance of SUMOylated forms in whole-cell extracts. WB, western blotting. (F) Quantification of the anti-PCNA blots in (E). Amounts of unmodified PCNA-3myc (gray bars) or SUMOylated PCNA-3myc (black bars, reflecting chromatin bound) shown relative to total endogenous PCNA. See also Figure S5.

Figure 5

PCNA Accumulation on Chromatin Is Caused by Failure of DNA Ligation Rather Than Lack of Cdc9 Interaction with PCNA (A) Schematic structure of Cdc9 protein (left) and defective PCNA interaction of an N-terminally truncated Cdc9 mutant (cdc9-NΔ60) that lacks the PCNA interaction motif (right). HA-tagged versions of wild-type CDC9 or its NΔ60, K419A, K598A mutants were overexpressed under the GAL promoter and immunoprecipitated with anti-HA antibody. PCNA was then detected by western blot with anti-PCNA antibody. Asterisk indicates a heavy chain of antibody used for immunoprecipitation. (B) cdc9-NΔ60 complements the growth defect of cells with endogenous Cdc9 degraded. Serial dilutions (1:5) of cells grown on SC-His-Ura containing 2% glucose, 2% galactose + 2% raffinose, or 2% galactose + 2% raffinose + 0.5 mM auxin (IAA) for 2 days at 30°C. (C) Outline of cell synchronization, induction of degradation of endogenous Cdc9, and sampling for chromatin fraction. Plasmid-borne CDC9 alleles being tested were expressed under the natural CDC9 promoter from the HIS3 marker plasmid pRS313. (D) Flow cytometry analysis. (E) PCNA accumulates on chromatin in cdc9 ligase-null mutants (cdc9-K419A and cdc9-K598A), but not in a cdc9 mutant defective for PCNA interaction (cdc9-NΔ60). PCNA in whole-cell extracts (top) and chromatin fractions (bottom) detected by western blotting with anti-PCNA antibody. PCNA amounts on chromatin shown below, relative to cdc9-fullAID with empty vector (vector). Histone H3 is the loading control.

Figure 6

Okazaki Fragment Ligation by Chlorella Virus DNA Ligase Facilitates PCNA Unloading (A) Chlorella virus DNA ligase (ChVLig) does not physically interact with PCNA. HA-tagged ChVLig and Cdc9 overexpressed from the GAL promoter were immunoprecipitated with anti-HA antibody. PCNA was detected by western blot with anti-PCNA antibody. Asterisk indicates a heavy chain of the antibody used for immunoprecipitation. (B) Chlorella virus DNA ligase (ChVLig) complements the growth defect of cells in which yeast DNA ligase Cdc9 is degraded. Serial dilution (1:5) of cells grown on SC-His-Ura containing 2% glucose, 2% galactose + 2% raffinose, or 2% galactose + 2% raffinose + 0.5 mM auxin (IAA) for 2–3 days at 30°C. ChVLig is expressed under the GAL promoter. (C) Experimental outline for Okazaki fragment detection and chromatin fractionation. Galactose was added before cell-cycle synchronization to maximize expression of ChVLig. (D) Flow cytometry analysis. (E) Okazaki fragments can be ligated by ChVLig. Each lane contains genomic DNA prepared from same number of cells, with Okazaki fragments visualized by ³²P end-labeling. nt, nucleotides. (F) Quantification of Okazaki fragments prepared from cdc9-fullAID carrying empty vector (vec) or expressing ChVLig (ChVLig) in (D). Values plotted are the increase over 0 min in intensity of fragments shorter than 1,500 nt. (G) PCNA retention on chromatin caused by Cdc9 degradation is partially relieved by expression of ChVLig. PCNA in whole-cell extracts (top) and chromatin fractions (bottom) detected by western blotting with anti-PCNA antibody. HA-tagged ChVLig expression was confirmed by anti-HA antibody. Histone H3 is the loading control. (H) Quantification of chromatin-bound PCNA in (F), expressed relative to vector 0-min sample. See also Figure S6.

Figure 7

Elg1 Is Required for Efficient PCNA Unloading following Okazaki Fragment Ligation by Chlorella Virus DNA Ligase (A) Chromatin-enriched fractions prepared from the indicated strains with/without Chlorella virus DNA ligase (ChVLig: +/−). Expression of ChVLig, cell-cycle synchronization, and Cdc9 degradation were performed as for Figure 6C. Cells were collected in S phase (40 min after release). Chromatin-bound proteins were detected by western blotting. (B) Quantification of chromatin-bound PCNA in (A), expressed relative to wild-type (WT) carrying empty vector i.e., lane 1 in (A). Expression of ChVLig reduced chromatin-bound PCNA to 40% in cdc9-fullAID cells, but only to 87% in cdc9-fullAID elg1Δ cells. (C) Model of PCNA unloading by the Elg1-RLC. (i) In an ELG1⁺ strain, PCNA and SUMO-PCNA are unloaded by the Elg1-RLC from the lagging strand following Okazaki fragment ligation. (ii) In an elg1Δ mutant, PCNA is retained on chromatin. (iii) Removal of the DNA ligase Cdc9 causes PCNA retention on chromatin, as Elg1-RLC does not unload PCNA prior to DNA ligation. This failure of PCNA unloading could potentially be caused by continuing presence of other PCNA interacting partners (such as DNA polymerase δ or FEN-1), which might interfere with access to PCNA by Elg1. See also Figure S7.