Mitotic Disassembly of Nuclear Pore Complexes Involves CDK1- and PLK1-Mediated Phosphorylation of Key Interconnecting Nucleoporins

Abstract

During interphase, the nuclear envelope (NE) serves as a selective barrier between cytosol and nucleoplasm. When vertebrate cells enter mitosis, the NE is dismantled in the process of nuclear envelope breakdown (NEBD). Disassembly of nuclear pore complexes (NPCs) is a key aspect of NEBD, required for NE permeabilization and formation of a cytoplasmic mitotic spindle. Here, we show that both CDK1 and polo-like kinase 1 (PLK1) support mitotic NPC disintegration by hyperphosphorylation of Nup98, the gatekeeper nucleoporin, and Nup53, a central nucleoporin linking the inner NPC scaffold to the pore membrane. Multisite phosphorylation of Nup53 critically contributes to its liberation from its partner nucleoporins, including the pore membrane protein NDC1. Initial steps of NPC disassembly in semi-permeabilized cells can be reconstituted by a cocktail of mitotic kinases including cyclinB-CDK1, NIMA, and PLK1, suggesting that the unzipping of nucleoporin interactions by protein phosphorylation is an important principle underlying mitotic NE permeabilization.

Keywords: CDK1; NDC1; NPC; NPC disassembly; Nup53; Nup98; PLK1; mitosis; nucleoporin; phosphorylation.

Graphical abstract

Figure 1

Immunodepletion of PLK1 from Mitotic Extracts Delays NEBD In Vitro (A) Schematic representation of the in vitro NPC disassembly assay. (B) Mitotic cell extract (ME) was either mock-treated (control depletion with protein A/G sepharose) or depleted with anti-PLK1 antibodies. Extracts were supplemented with a 155 kDa fluorescent dextran and added to semi-permeabilized HeLa cells expressing 2GFP-Nup58. NPC disassembly was monitored by confocal time-lapse microscopy. Scale bar, 10 m. (C) Quantification of dextran-positive nuclei over time. N = 3, n > 100 cells. Error bars, SEM. (D) Quantification of 2GFP-Nup58 intensity at the NE. Error bars, SEM. (E) Quantification of the average time point at which 50% of nuclei were dextran-positive (t₅₀). Error bars, SD; ^∗p < 0.05, unpaired t test, two-tailed. (F) Immunoblot analysis of PLK1 immunodepletion. (G) In vitro kinase assays with mock and PLK1-depleted extracts using histone H1 and zz-Nup98(678–714) as readouts for CDK1 and PLK1 activity, respectively. Incorporation of ³²P was analyzed by autoradiography.

Figure 2

PLK1 Activity Is Required for Timely NPC Disassembly In Vitro (A) Mitotic extracts used for NPC disassembly were supplemented with either DMSO, 500 nM of the PLK inhibitor BI2536, or BI2536 plus 750 nM purified PLK1. NPC disassembly was monitored by time-lapse microscopy. Scale bar, 10 μm. (B) Quantification of dextran-positive nuclei over time. N = 3, n > 100 cells. Error bars, SEM. (C) Quantification of 2GFP-Nup58 intensity at the NE. Error bars, SEM. (D) Quantification of t₅₀. Error bars, SD; ^∗∗p < 0.005, unpaired t test, two-tailed. (E) In vitro kinase assays monitoring PLK1 and CDK1 activities in the indicated mitotic extracts, as in Figure 1G.

Figure 3

PLK1 Co-localizes with NPCs in Prophase, and Its C-Terminal PBD Exerts a Dominant-Negative Effect on NPC Disassembly Kinetics In Vitro (A) Confocal images of immunostaining of PLK1 and NPCs (mAb414) in combination with Hoechst (DNA) staining in HeLa cells. Note that PLK1 localizes to the nuclear rim specifically in prophase cells, as evident by the onset of chromatin condensation, but not in interphase cells (top row). Scale bar, 10 μm. (B) Lysates of cells treated with control or PLK1 siRNAs were analyzed by immunoblotting with the indicated antibodies. (C) Immunostaining of PLK1 in GFP-Nup58 expressing HeLa cells. DNA was visualized with Hoechst and prophase cells identified by the onset of chromatin condensation. Scale bar, 10 μm; inset 5 μm. (D) Confocal images of HeLa cells expressing GFP-PLK, GFP-PBD^WT, or GFP-PBD^AA. Cells were immunostained with antibodies against Nup88 or mAb414, as indicated. Scale bar, 10 μm. (E) Mitotic HeLa cell extracts were supplemented with either buffer, 2.5 μM recombinant PBD^WT or a PBD^AA mutant of reduced affinity for phospho-peptides, and used for in vitro NPC disassembly on semi-permeabilized, 2GFP-Nup58-expressing HeLa cells. Quantification of dextran-positive nuclei over time. Error bars, SEM. (F) Quantification of 2GFP-Nup58 intensity at the NE. N = 3, n > 100 cells. Error bars, SEM. (G) Quantification of t₅₀. Error bars, SD; ^∗p < 0.05, unpaired t test, two-tailed. (H) In vitro kinase assay monitoring CDK1 activity in the supplemented mitotic extracts, as in Figure 1G.

Figure 4

Nup98 Is a PLK1 Substrate, and Its Phosphorylation by Multiple Kinases Including PLK1 Promotes NPC Disassembly In Vitro (A) Schematic representation of human Nup98 indicating the position of CDK1 and PLK1 consensus sites (referring to isoform P52948-2). GLFG, Gly-Leu-Phe-Gly repeat domain; GLEBS, Gle2-binding sequence motif; APD, autoproteolytic domain. (B) The purified C-terminal domain (amino acids: 506–863) of Nup98 (WT) or a mutant derivative containing Ala substitutions at 5 PLK1 sites (5A) (Coomassie) were incubated with PLK1 in the presence of [γ-³²P]ATP. Protein phosphorylation was analyzed by autoradiography. (C) GFP-Nup98^WT and the indicated phosphomimetic mutants were transiently expressed in HeLa cells and analyzed by confocal microscopy. Scale bar, 10 μm. (D) Quantification of GFP intensity across the NE of the experiment in (C) by averaging line scans. n ≥ 50 cells per condition. (E) Quantification of dextran-positive nuclei over time during NPC disassembly in semi-permeabilized cells expressing the indicated Nup98 derivatives. N = 3, n > 100 cells. Error bars, SEM. (F) Quantification of t₅₀. Error bars, SD; ^∗p < 0.05, unpaired t test, two-tailed. (G) Comparison of dextran influx during in vitro NPC disassembly in semi-permeabilized GFP-Nup98 and GFP-Nup58 expressing cells, in the absence or presence of BI2536. N = 4, n > 100 cells. Error bars, SEM. (H) Comparison of GFP-Nup98 and GFP-Nup58 release in the absence or presence of BI2536. N = 4, n > 100 cells. Error bars, SEM. (I) Quantification of t₅₀. Error bars, SD; ^∗∗p < 0.005, unpaired t test, two-tailed. (J) In vitro kinase assay monitoring PLK1 activity in the mitotic extracts.

Figure 5

Nup53 Is Phosphorylated by CDK1 and PLK1 in Mitosis (A) GST pull-down experiment from mitotic HeLa cell extract using the indicated baits. Of the input and the eluates, 4% and 20%, respectively, were analyzed by immunoblotting with the indicated antibodies. (B) Scheme of human Nup53 indicating its binding domains for partner Nups and mitotic phosphorylation sites. Sixteen sites matching the CDK1 consensus ([pS/pT]-[P]) are shown in black, and a site matching the PLK1 phosphorylation motif [E/D]X[pS/pT][I/L/V/M]X[E] is highlighted in red. Residues in green squares were confirmed by our mass spectrometric analysis of mitotic Nup53 (see Table S1). RRM, RNA recognition motif. (C) Interphase or mitotic cell lysates from HeLa cell lines expressing GFP-Nup53^WT or the indicated mutant variants were treated without or with alkaline phosphatase (CIP) and processed for immunoblotting with the indicated antibodies. Phosphorylation of histone H3 at S10 served as control for both the cell-cycle state of the extracts and phosphatase treatment. Actin served as control for equal loading. Note that we mutated S314 to a phosphodeficient cysteine as a change of S314 to alanine slightly affected NE localization of Nup53 (Figure S6), suggesting that the chemical features of this residue are critical for integration of Nup53 into NPCs. (D) In vitro phosphorylation of GST-Nup53^WT and GST-Nup53^16A by cyclinB1-CDK1 using [γ-³²P]ATP. Protein phosphorylation was analyzed by autoradiography. (E) In vitro phosphorylation of GST-Nup53^WT by cyclinB1-CDK1 or PLK1 using [γ-³²P]ATP. Phosphorylated GST-Nup53^WT was detected by autoradiography. (F) Far-western analysis of the interaction between the PBD of PLK1 (bait) and GST-Nup53^WT or GST-Nup53^16A(CDK1) (preys), both pre-treated with cyclinB1-CDK1 in the presence of ATP before separation by SDS-PAGE and blotting onto a membrane. (G) Sequential in vitro kinase assay. The indicated GST-Nup53 derivatives were first incubated with or without cyclinB1-CDK1 in the presence of unlabeled ATP. After heat inactivation of CDK1, samples were further incubated with [γ-³²P]ATP in the absence or presence of PLK1. Phosphorylation of GST-Nup53 variants was analyzed by autoradiography.

Figure 6

CDK1- and PLK1-Mediated Phosphorylation of Nup53 Is Required for Its Efficient Release from the NPC (A) Confocal images of HeLa cells depleted of endogenous Nup53 by RNAi and expressing siRNA-resistant GFP-Nup53^WT and the indicated GFP-Nup53 variants. Scale bar, 10 μm. (B) Quantification of GFP intensity across the NE of experiment in (A) by averaging line scans. n ≥ 50 cells per condition. (C) Quantification of dextran influx in the course of in vitro NEBD reactions performed with semi-permeabilized HeLa cells depleted of endogenous Nup53 and expressing siRNA-resistant GFP-Nup53^WT or GFP-Nup53 variants. WT(-TET); GFP-Nup53^WT cells in the absence of tetracycline and RNAi. N = 4, n > 100 cells. Error bars, SEM. (D) Quantification of release of GFP-Nup53^WT or the indicated GFP-Nup53 variants from the NE in the course of NPC disassembly in vitro monitored by confocal microscopy. Error bars, SEM. (E) Quantification of t₅₀. Error bars, SD; ^∗p < 0.05, ^∗∗p < 0.005, unpaired t test, two-tailed. (F) GST pull-down experiment from interphase HeLa cell extracts with either GST or the indicated Nup53 phosphomimetic mutants. Of the input and the eluates, 4% and 20%, respectively, were analyzed by immunoblotting with the indicated antibodies. Ponceau-stained membrane serves as loading control. (G) GST, GST-Nup53^WT or the indicated phosphomimetic GST-Nup53 variants (all with mutations F179E and W210E to decrease direct membrane binding), were incubated with lysates derived from E. coli overexpressing either the C-terminal membrane-embedded nucleoplasmic domain of Xenopus GP210 or mouse full-length NDC1. 25% of the eluates and 3% of the input were analyzed by immunoblotting using an anti-His₆ antibody. (H) Quantification of GP210 or NDC1 binding to the GST-Nup53 variants normalized to GST. Average of four independent experiments. Individual data points are shown.

Figure 7

The Combined Activities of Recombinant Kinases Are Sufficient to Induce NPC Disassembly In Vitro (A) In vitro kinase assays were used to adjust the activity of purified recombinant cyclinB1-CDK1, PLK1^T210D, and NIMA to the respective activities in the mitotic extract (ME) used for in vitro NPC disassembly. Phosphorylation reactions were performed in buffer, ME, or in buffer supplemented with the indicated recombinant protein kinases using histone H1, zz-Nup98(678–714) and casein as readouts for CDK1, PLK1, and NIMA activity, respectively. Incorporation of ³²P was analyzed by autoradiography. Coomassie-stained gel serves as loading control. (B) Quantification of dextran influx into the nuclei of semi-permeabilized HeLa cells expressing 2GFP-Nup58 induced by the addition of the indicated recombinant mitotic protein kinases in buffer supplemented with an energy-regenerating system. N = 4, n > 100 cells. Error bars, SEM. (C) Quantification of 2GFP-Nup58 intensity at the NE. Error bars, SEM. Note that upper and lower panels in (B) and (C) are derived from the same set of experiments. (D) Representative confocal images derived form in vitro NPC disassembly experiments shown in (B) and (C), comparing buffer, the mixture of cyclinB1-CDK1, PLK1^T210D, and NIMA, and ME.