Research ArticleMitosis

Aurora B opposes PP1 function in mitosis by phosphorylating the conserved PP1-binding RVxF motif in PP1 regulatory proteins

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Sci. Signal.  15 May 2018:
Vol. 11, Issue 530, eaai8669
DOI: 10.1126/scisignal.aai8669

Yin and yang of mitotic phosphorylation

Mitotic kinases promote cell cycle progression by targeting a large set of proteins that collectively drive mitosis. Phosphatases, such as protein phosphatase 1 (PP1), reverse these phosphorylation events to enable cells to exit mitosis. The subcellular localization and activity of PP1 are controlled by regulatory proteins that bind to PP1 through conserved RVxF motifs. Nasa et al. found that RVxF motifs in a subset of PP1 regulatory proteins in which the “x” residue is a serine or threonine (RV[S/T]F) were phosphorylated during mitosis. Phosphorylation of these motifs, which was mediated primarily by the mitotic kinase Aurora B, prevented proteins that harbored these motifs from interacting with PP1 and was required for maintaining the high amount of overall protein phosphorylation in mitotic cells. These findings identify a mechanism that coordinates the activities of Aurora B and PP1 to control cell cycle progression.

Abstract

Protein phosphatase 1 (PP1) is a highly conserved protein phosphatase that performs most of the serine- and threonine-dephosphorylation reactions in eukaryotes and opposes the actions of a diverse set of serine and threonine (Ser-Thr) protein kinases. PP1 gains substrate specificity through binding to a large number (>200) of regulatory proteins that control PP1 localization, activity, and interactions with substrates. PP1 recognizes the well-characterized RVxF binding motif that is present in many of these regulatory proteins, thus generating a multitude of distinct PP1 holoenzymes. We showed that a subset of the RVxF binding motifs, in which x is a phosphorylatable amino acid (RV[S/T]F), was phosphorylated specifically during mitosis and that this phosphorylation event abrogated the interaction of PP1 with the regulatory protein. We determined that this phosphorylation was primarily governed by the mitotic protein kinase Aurora B and that high phosphorylation site stoichiometry of these sites maintained the phosphorylation of PP1 substrates during mitosis by disrupting the assembly of PP1 holoenzymes. We generated an antibody that recognizes the phosphorylated form of the RV[S/T]F motif (RVp[S/T]F) and used it to identify known PP1 regulatory proteins (KNL1, CDCA2, and RIF1) and multiple proteins that could potentially act as PP1 binding partners (UBR5, ASPM, SEH1, and ELYS) governed by this mechanism. Together, these data suggest a general regulatory mechanism by which the coordinated activities of Aurora B and PP1 control mitotic progression.

INTRODUCTION

In mitosis, a cell segregates its duplicated genome into two daughter cells. Reversible protein phosphorylation is an important regulatory mechanism in this process. The opposing activities of protein kinases and protein phosphatases are responsible for establishing the phosphorylation stoichiometry, the relative amounts of phosphorylated and unphosphorylated forms, of mitotic regulatory proteins. Imbalance in either activity can lead to mitotic defects and genomic instability (1).

Entry into mitosis is initiated by the activation of cyclin-dependent kinase 1 (CDK1) (2). CDK1 phosphorylates and activates multiple mitotic substrates including the mitotic protein kinases Aurora A and Aurora B and Polo-like kinase 1 (PLK1). The activation of kinases in the beginning of mitosis results in a dramatic net increase in protein phosphorylation during the early phases of mitosis (35). However, to exit mitosis and achieve the lower amount of mitotic protein phosphorylation that is characteristic of interphase, it is necessary for mitotic phosphoproteins to be dephosphorylated in a timely manner (6).

In vertebrates, most of the dephosphorylation reactions during mitotic exit have been attributed to the phosphoprotein phosphatase family of serine-threonine phosphatases, in particular PP1 (protein phosphatase 1) and PP2A (7, 8). Activation of CDK1 in the G2 phase has been reported to inhibit the activities of these major mitotic protein phosphatases (9). For instance, CDK1 phosphorylation of PP1 at Thr320 inhibits PP1 phosphatase activity during mitosis. After the decline of CDK1 activity in anaphase, PP1 autodephosphorylates Thr320 and regains full activity to drive mitotic exit (10).

PP1 is responsible for the majority of dephosphorylation reactions in eukaryotic cells (11). The catalytic subunit of PP1 is a ubiquitous enzyme that interacts with a diverse set of regulatory proteins that not only target the phosphatase to its substrate but also control its activity (12). More than 200 regulatory proteins of PP1 have been identified, with more predicted to be awaiting identification (13, 14). The binding of the PP1 catalytic subunit to its regulatory proteins to generate PP1 holoenzymes is governed by short sequence motifs (15, 16). Nearly 90% of PP1-binding proteins dock to PP1 through their RVxF motif, [R/K]-X(0,1)-[V/I]-{P}-[F/W], wherein X is any residue and {P} is any residue except proline (1720). RVxF-containing regulatory proteins bind to a hydrophobic region on the catalytic PP1 subunit that is distant from the active site (17, 21). Characterization of the RVxF motif in PP1 interactors reveals an overrepresentation of serine and threonine at the “x” position, with serine occurring in ~21% and threonine in ~18% of known PP1 binding partners (fig. S1) (13). Furthermore, phosphorylation of the serine or threonine residue within the RVxF motif inhibits their binding to PP1 (2225).

During mitosis, PP1 is enriched on chromosomes and at centrosomes (26, 27), and multiple PP1-targeting subunits have been identified at kinetochores, the mitotic spindle, centromeres, the spindle midzone, and the nuclear envelope (2832). One of the key mitotic regulatory proteins of PP1 is the kinetochore protein, kinetochore null 1 (KNL1), also known as cancer susceptibility candidate 5 (22, 28). KNL1 recruits PP1 to the kinetochores through its RVxF motif, in which x is a serine residue. Phosphomimetic mutations of the serine in the PP1-binding RVxF and SILK motifs in KNL1 greatly reduce its binding to PP1 (22, 33). PP1 has been shown to antagonize the activity of Aurora B (34). The balance of Aurora B and PP1 activities is essential for establishing chromosome bi-orientation and for regulating the spindle assembly checkpoint (SAC) (35, 36). During early mitosis, Aurora B localizes to centromeres and chromosomes before relocalizing to the spindle midzone during mitotic exit. Incorrect microtubule-kinetochore attachments or the lack of tension at kinetochores leads to phosphorylation of outer kinetochore proteins by Aurora B and activation of the SAC (37). Once bipolar attachments are established, PP1 dephosphorylates Aurora B substrates at kinetochores to silence the SAC and drive mitotic exit (38, 39).

Here, we identified phosphorylation of RV[S/T]F motifs in known and previously unidentified PP1 regulatory proteins as a cell cycle–dependent event. We show that Aurora B was the primary kinase responsible for this phosphorylation event during mitosis. We propose that Aurora B–dependent phosphorylation of RV[S/T]F motifs is an important regulatory mechanism that prevents PP1 from interacting with its regulatory proteins during mitosis, thereby affecting phosphorylation of a multitude of PP1 substrates and controlling the balance of Aurora B kinase and PP1 phosphatase activities.

RESULTS

PP1 preferentially binds nonphosphorylated RV[S/T]F motifs in vitro

It was previously shown that phosphorylation of the RV[S/T]F motifs in the skeletal muscle glycogen-targeting subunit (GM) and KNL1 negatively regulates their interaction with PP1 (22, 23, 40). To determine whether RV[S/T]F phosphorylation is a general mechanism controlling the interaction of PP1 with its regulatory proteins, we examined the binding of PP1 to nonphosphorylated (unmodified) or phosphorylated versions of RV[S/T]F peptides from different PP1 regulatory proteins (table S1). We tested PP1 binding to these peptides using two independent biochemical experiments—overlays using recombinant human PP1 (Fig. 1A) and in vitro peptide pulldowns (Fig. 1B). In PP1 overlays, the RVRW peptide from the protein YLPM1 (41) was used as a positive control, and the mutated version RARA, which does not bind PP1 (41), was used as a negative control. In both overlay and in vitro peptide pulldowns, PP1 exhibited a clear preference for binding to the unmodified versions of all peptides. The phosphorylated form of each peptide was either not bound by PP1 or showed reduced interaction with PP1 compared to the corresponding nonphosphorylated form (Fig. 1, A and B), suggesting that loss of PP1 binding upon phosphorylation of RV[S/T]F motifs is a general phenomenon.

Fig. 1 PP1 preferentially binds nonphosphorylated RV[S/T]F motifs in vitro.

(A) Phosphorylated (P) or nonphosphorylated (nonP) versions of RV[S/T]F-containing peptides from the indicated proteins were spotted onto nitrocellulose membranes in the indicated amounts. The membranes were overlaid with a mixture of recombinant human PP1 and probed with a PP1-specific antibody. A peptide derived from the PP1-binding protein YLP motif–containing protein 1 (YLPM1) (RVRW) was used as a positive control, and the nonphosphorylable mutant version of this peptide (RARA) was used as the negative control. (B) Activated 5-carboxypentyl–Sepharose 4B N-hydroxysuccinimide ester (CH-Sepharose) beads were coupled to the phosphorylated or nonphosphorylated versions of the indicated RV[S/T]F peptides and incubated with clarified HeLa whole-cell extracts. After washing, proteins bound to the beads were eluted with SDS sample buffer, run on SDS–polyacrylamide gel electrophoresis (PAGE), and immunoblotted for PP1. The position of the 35-kDa mass marker is indicated. Peptides derived from the indicated proteins and sequences are shown in table S1. The data represent one of three independent experiments for both (A) and (B).

RV[S/T]F motifs in PP1-binding proteins are phosphorylated in cells during mitosis

To determine whether phosphorylation of RV[S/T]F PP1-binding motifs occurs in cells and in a manner that depends on the cell cycle, we raised antibodies that specifically recognize the phosphorylated forms of the RV[S/T]F motifs (RVp[S/T]F motifs) of several PP1-binding proteins, including Rap1-interacting factor 1 (RIF1), centrosomal protein of 192 kDa (CEP192), suppressor of fermentation-induced loss of stress resistance 1 (SFI1), breast cancer type 1 susceptibility protein (BRCA1), and cell division cycle–associated 2 (CDCA2; also called Repoman).

To validate these antibodies, we preformed dot blots using different amounts of phosphorylated and nonphosphorylated versions of the antibody epitopes (fig. S2A). Although the phosphorylated forms of the peptides were readily recognized by the antibodies, the nonphosphorylated (unmodified) versions, even at the highest amount (1000 ng), were not. Next, we used these antibodies to investigate the phosphorylation status of RV[S/T]F motifs in RIF1, CEP192, SFI1, BRCA1, and CDCA2 in mitosis and during cell cycle progression. HeLa cells were synchronized in G1/S using a thymidine block, released, and then captured in mitosis with nocodazole, which arrests the cells in prometaphase. The nocodazole was washed out, and the cells were collected at different time points from 0.5 to 22 hours after release from mitotic blockade. We observed an increased phosphorylation of RV[S/T]F motifs of each of the five proteins 30 min after nocodazole washout (Fig. 2A). Cell cycle synchronization was confirmed by immunoblotting with the mitotic marker cyclin B1 (Fig. 2A) and fluorescence-activated cell sorting (FACS) analysis (Fig. 2B). This increase in phosphorylation in mitotic cells was also observed by immunofluorescence staining using antibodies specific for the phosphorylated RVxF epitopes, including phosphorylated CEP192, phosphorylated SFI1, and phosphorylated BRCA1 (fig. S2, B to D).

Fig. 2 RV[S/T]F motifs are phosphorylated in cells during mitosis.

(A) HeLa cells were synchronized using thymidine-nocodazole (T/N) block and released in fresh media thereafter. Samples were collected at the indicated time points, immunoblotted for cyclin B1, and analyzed for phosphorylation within the RV[S/T]F motifs of the indicated proteins using in-house–generated phosphoepitope-specific antibodies. Async, asynchronized cells. Antibodies are characterized in fig. S2, and peptide sequences are shown in table S1. Samples were collected three times with the same synchronization technique, and the data represent one of three independent experiments. Equal loading was confirmed by immunoblotting for tubulin. Mass markers are indicated in kilodaltons. (B) Quantification of cells in each phase of the cell cycle at the indicated time points after synchronization as determined by FACS analysis.

Global analysis of RV[S/T]F motifs shows increased phosphorylation during mitosis

To globally monitor phosphorylation of the ([R/K]-X(0,1)-[V/I]-[S/T]-[F/W]) consensus motif (referred to as the RV[S/T]F motif henceforth) in PP1 binding partners, we generated an antibody specific for RVp[S/T]F, the phosphorylated form of the RV[S/T]F motif present in multiple PP1 binding proteins in the human proteome. We characterized the phospho-specificity and motif selectivity of this antibody on dot blots using different amounts of phosphorylated and nonphosphorylated (unmodified) versions of peptides corresponding to a common version of the RV[S/T]F and RVp[S/T]F motifs of known PP1-interacting proteins, including RIF1 (RVSF and RVpSF), peptides with mutations in RIF1 RVSF motif (KVSW, KVpSW, RISF, RIpSF, RITW, and RIpTW), Ki67 (RVSF and RVpSF), CDCA2 (RVTF and RVpTF), RRP1B (KVTF and KVpTF), BRCA1 (KVTF and KVpTF), and TSC2 (RSVSW and RSVpSW) (fig. S3A) (28, 42, 43). This confirmed that the RVp[S/T]F antibody is phospho-specific and recognizes to some degree related phosphorylated RV[S/T]F motifs in vitro. The phospho-specificity of the antibody was also confirmed by competition with RRVpSFADK, which was used for generating the antibody (fig. S3B). To determine the phosphorylation status of RV[S/T]F motifs in cells, we performed immunoblotting of extracts from HeLa cells synchronized in mitosis as described above. We found a marked increase in phosphorylation of RV[S/T]F motifs in different proteins during mitosis (Fig. 3A).

Fig. 3 Global analysis of RV[S/T]F motif phosphorylation during mitosis.

(A) The phosphoepitope-specific antibody generated using the peptide RRVpSFADK recognizes several proteins in immunoblots of HeLa cell lysates (top). Lysates from synchronized HeLa cells at the indicated times after release from T/N block were probed with this RVp[S/T]F (p-RV[S/T]F)–specific antibody to monitor changes in the phosphorylation status of this motif during the cell cycle. Phosphorylation of PP1 at Thr320 (p-Thr320) was also assessed at these time points. Equal loading was confirmed by immunoblotting for tubulin. Mass markers are indicated in kilodaltons. Three replicates of the p-RV[S/T]F immunoblot were quantified using ImageJ software and normalized to the mitotic (0.5 hours) sample (bottom). Error bars represent means ± SD. (B) Immunofluorescence staining of HeLa cells showing 4′,6-diamidino-2-phenylindole (DAPI), tubulin, and p-RV[S/T]F at different phases of the cell cycle. More than 50 cells were imaged for each condition in four independent experiments. Scale bar, 20 μm. a.u., arbitrary units.

Phosphorylation of PP1 Thr320 by CDK1 during mitotic entry inactivates the enzyme until anaphase when PP1 autodephosphorylates Thr320 and fully activates itself (10, 44). This dephosphorylation occurs within 2 hours of nocodazole release, which corresponds with the observed decrease in phosphorylation of the RV[S/T]F motifs (Fig. 3A). This suggests that in addition to the direct inhibition of the PP1 catalytic subunit by CDK1 phosphorylation, the catalytic activity of PP1 might also be inhibited by phosphorylation within the RV[S/T]F motifs of PP1 regulatory proteins (the regulatory subunits of the PP1 holoenzyme) during mitosis.

The global increase in phosphorylation of RV[S/T]F motifs was also confirmed by immunofluorescence staining using the RVp[S/T]F-specific antibody (Fig. 3B). Compared to interphase cells, metaphase cells showed a dramatic increase in the phosphorylation of RV[S/T]F motifs in the cytoplasm, spindle poles, and along the mitotic spindle. This phosphorylation remains at spindle poles and the central spindle in anaphase and the midbody and telophasic bridge during cytokinesis (Fig. 3B).

Phosphorylation of the RV[S/T]F motifs depends on Aurora B kinase

Next, we wanted to identify the protein kinases responsible for phosphorylation of the RV[S/T]F motifs during mitosis. To do so, we treated HeLa cells with small-molecule inhibitors of the mitotic kinases Aurora A, Aurora B, PLK1, and CDK1, which are activated at mitotic entry and play a role in controlling mitotic progression (4, 6), and monitored the phosphorylation of RV[S/T]F motifs. At low concentration (1 μM), the small molecular inhibitor MLN8054 targets Aurora A, but at high concentration (5 μM), it targets both Aurora A and Aurora B (45). Treatment with a low concentration of MLN8054 only had a modest effect on RV[S/T]F phosphorylation, but treatment with a high concentration markedly reduced RV[S/T]F phosphorylation (Fig. 4A), suggesting that the effect of MLN8054 treatment at high concentration is likely due to inhibition of Aurora B. This is supported by the observation that specific inhibition of Aurora B by ZM447439 or hesperadin showed a marked decrease in the phosphorylation of RV[S/T]F motifs (Fig. 4A). The RV[S/T]F motif is reminiscent of the basophilic consensus motif of Aurora A and Aurora B (4, 46), supporting our observation that Aurora B participates in RV[S/T]F phosphorylation and suggesting that Aurora B may directly phosphorylate RV[S/T]F motifs. The effectiveness and specificity of each inhibitor were determined by investigating the phosphorylation status of known substrates of each protein kinase by Western blotting (Fig. 4B) of HeLa cell extracts. Treatment with the PLK1 inhibitor BI2536 or the CDK1 inhibitor flavopiridol caused only a modest decline in the phosphorylation of the RV[S/T]F motifs in the substrates. Inhibition of CDK1 forces cells out of mitosis, as indicated by the decrease in the mitotic marker H3 phosphorylated on Ser10 (Fig. 4B). To confirm that the RV[S/T]F phosphorylation was Aurora B–dependent, mitotic cells treated with different kinase inhibitors were fixed and stained with the RVp[S/T]F antibody (Fig. 4C). This showed a marked decrease in phosphorylation of the RV[S/T]F motifs upon treatment with Aurora B inhibitor (hesperadin) in cells (Fig. 4C). Mitotic cells treated with CDK1 inhibitor did not show any decrease in phosphorylated RV[S/T]F by immunofluorescence (Fig. 4C).

Fig. 4 Effects of mitotic kinase inhibition on phosphorylation of PP1-binding RV[S/T]F motifs.

(A) After mitotic arrest and treatment with the proteasome inhibitor MG132, HeLa cells were treated with the indicated kinase inhibitors The cells were harvested, and the lysates were separated by SDS-PAGE and immunoblotted for phosphorylated RV[S/T]F (p-RV[S/T]F, top). The blot was quantified using ImageJ software and normalized to the mitotic sample (bottom). MLN8054, Aurora A and Aurora B inhibitor; ZM447439 and hesperadin, Aurora B inhibitors; BI2536, PLK1 inhibitor; flavopiridol, CDK1 inhibitor. n = 3. **P < 0.01, paired Student’s t test. (B) To demonstrate the effectiveness and specificity of each kinase inhibitor, the same samples from (A) were immunoblotted to show the indicated phosphorylated proteins. H3 is phosphorylated on Ser10 by Aurora B; Aurora A is autophosphorylated on Thr288; Aurora B is autophosphorylated on Thr232; PP1 is phosphorylated on Thr320 by CDK1 (arrow); TCTP is phosphorylated on Ser46 by PLK1. n = 3. (C) HeLa cells were treated with inhibitors of Aurora B (hesperadin), Aurora A (Aurora A inhibitor I), CDK1 (roscovitine), or PLK1 (BI2536) for 2 hours before immunostaining for tubulin and phosphorylated RV[S/T]F (p-RV[S/T]F). Nuclei are indicated with DAPI. Control cells were not treated with any inhibitor. More than 50 cells were imaged for each condition in three independent experiments. Scale bar, 20 μm.

Furthermore, treating cells with the Aurora B inhibitor hesperadin caused a time-dependent reduction in the phosphorylation of RV[S/T]F-containing proteins in cells released from nocodazole arrest (Fig. 5A). Immunofluorescence of cells treated with Aurora B kinase inhibitor was also used to confirm results from Western blotting. The inhibition of Aurora B activity was confirmed by the specific lack of phosphorylation of its substrate H3 at Ser10 (Figs. 4B and 5B) (47). Immunofluorescence staining of Aurora B inhibitor–treated cells revealed a strong reduction of phosphorylated RV[S/T]F staining compared to control cells (Fig. 5C), as quantified in Fig. 5D.

Fig. 5 Aurora B phosphorylates RV[S/T]F motifs during mitosis.

(A) HeLa cells were arrested in mitosis with nocodazole, treated with either dimethyl sulfoxide (−) or the Aurora B inhibitor hesperadin (+) in the presence of the proteasome inhibitor MG132, harvested, and immunoblotted for phosphorylated RV[S/T]F motifs (p-RV[S/T]F). Mass markers are indicated in kilodaltons. (B and C) Immunofluorescence showing nuclei (DAPI), tubulin, and either H3 phosphorylated on Ser10 (p-H3S10, B) or p-RV[S/T]F (C) in mitotically arrested HeLa cells treated with the Aurora B inhibitor hesperadin. More than 15 cells were imaged for three independent replicates. (D) Difference in RVp[S/T]F staining was quantified for each condition, untreated (Control) and Aurora B inhibitor–treated (AurBi), by calculating the total cell fluorescence, using ImageJ. Error bars represent means ± SD. **P < 0.01, paired Student’s t test (n = 15). Scale bars, 20 μm.

Proteomics analysis reveals new candidates phosphorylated by Aurora B on RV[S/T]F motifs

To identify proteins recognized by the antibody specific for RVp[S/T]F, we performed immunoprecipitations with the antibody or control immunoglobulin G (IgG) from mitotically arrested HeLa cells (fig. S4A). This showed a marked enrichment of proteins in the RVp[S/T]F immunoprecipitations compared to control IgG immunoprecipitations in mitotic cells. To determine the identity of these proteins, we precipitated them using trichloroacetic acid and analyzed them by liquid chromatography–coupled tandem mass spectroscopy (LC-MS/MS) (table S2). In total, we analyzed five independent control IgG and five independent RVp[S/T]F immunoprecipitations. The degree of confidence for RVp[S/T]F-specific binding was assessed by a computational tool, significance analysis of interactome (SAINT) (table S3) (48, 49). Using this approach, we identified 421 proteins that specifically bound to RVp[S/T]F antibody (tables S2 and S3).

Next, we investigated whether these proteins bound to the antibody recognizing RVp[S/T]F after Aurora B inhibition. We compared the binding of proteins to the RVp[S/T]F-specific antibody in immunoprecipitates from untreated cells to that of proteins from cells treated with the Aurora B inhibitor hesperadin by label-free intensity-based absolute quantification (iBAQ) (table S2) (50). This revealed that 227 (~54%) of the 421 proteins that bound to the antibody in the absence of Aurora B exhibited no or significantly reduced binding to antibody (P < 0.05) upon Aurora B inhibition (table S2). To determine the functional profile of the proteins specifically enriched in the RVp[S/T]F immunoprecipitates, we performed gene ontology (GO) analysis for these proteins. GO analysis showed an enrichment of proteins involved in mitosis, spindle organization and assembly, and chromosome segregation (table S4). Furthermore, many of the proteins are localized to cellular structures such as the spindle, kinetochore, chromosome, and midbody (table S5). This shows that these RV[S/T]F-containing proteins may potentially regulate the binding of PP1 and the antagonistic activities of PP1 and Aurora B at these structures in mitosis.

Out of the 421 proteins that specifically bound to the antibody recognizing RVp[S/T]F, 37 contained the RV[S/T]F motif and were phosphorylated within this motif during mitosis (table S6). Many of the other proteins specifically bound to the antibody are predicted to be in complex with proteins that contain the RV[S/T]F motif but are not phosphorylated during mitosis. About 68% (25) of the RV[S/T]F-containing proteins failed to bind or exhibited significantly reduced binding to the RVp[S/T]F antibody when the cells were treated with the Aurora B inhibitor hesperadin (table S6). The protein KNL1, a PP1-binding protein that associates with PP1 in a manner that depends on its phosphorylation by Aurora B (22), was identified in our study along with other cell cycle regulatory proteins including RIF1, which controls DNA replication by targeting PP1 to the chromatin (51), CDCA2, which recruits PP1 to anaphase chromosomes to maintain chromosome architecture (52), E3 ubiquitin-protein ligase UBR5 (UBR5), which promotes metaphase to anaphase transition through mediating protein turnover (53), abnormal spindle-like, microcephaly-associated protein (ASPM), which controls spindle positioning and orientation (54), nucleoporin SEH1 (SEH1), which regulates chromosome segregation through controlling Aurora B localization at centromeres (55), and embryonic large molecule derived from yolk sac (ELYS), which recruits PP1 to kinetochores and chromosomes during mitotic exit (56).

Phosphorylation within RV[S/T]F motifs reduces binding to PP1

To validate the results from the mass spectrometry analysis, we preformed reciprocal immunoprecipitations using antibodies that recognize two known PP1-binding proteins: RIF1 and CDCA2 using protein extracts from HeLa cells cultured in the presence and absence of various mitotic kinase inhibitors. Western blot analysis of RIF1 and CDCA2 immunoprecipitations using antibodies specific for the phosphorylated RVSF of RIF1 or the phosphorylated RVTF of CDCA2 confirmed that Aurora B is required for phosphorylation of these motifs (fig. S4B). These experiments also confirmed that phosphorylation of RIF1 in mitosis negatively regulates binding to PP1. PP1-bound microcystin-Sepharose beads were used to pull down proteins from extracts of asynchronous, mitotic, or Aurora B–inhibited cells, and the elution was analyzed for the presence of RIF1. PP1 readily interacted with RIF1 from asynchronous lysates, but this interaction was significantly reduced in mitotic lysates. Inhibition of Aurora B activity partially restored the interaction in mitotic extracts (Fig. 6A).

Fig. 6 Phosphorylation of the RVxF motif by Aurora B inhibits PP1 binding.

(A) Recombinant human PP1α/β/γ coupled to microcystin-Sepharose beads were used to test in vitro binding between PP1 and proteins from asynchronous (Async), mitotic, or Aurora B–inhibited (AurBi) HeLa extracts. After incubating the PP1-coupled beads with cell lysates, the bound proteins were eluted and tested for the presence of RIF1 by immunoblotting (top). Immunoblots were quantified using ImageJ software and normalized relative to RIF1 binding to PP1-coupled beads in extracts from asynchronous cells. Error bars represent means ± SD. *P < 0.05, paired Student’s t test (n = 3 independent experiments). (B) Nonphosphorylated and phosphorylated peptides containing the RV[S/T]F motifs from the indicated proteins coupled to activated CH-Sepharose beads were incubated with HeLa cell extracts. After washing, the bound proteins were eluted with SDS sample buffer and immunoblotted for PP1 (top). The sequences of the peptides are shown in table S1. Three replicates of the experiment were quantified and normalized relative to nonphosphorylated RIF1 peptide (bottom). Error bars represent means ± SD.

To confirm the effect of phosphorylation within RV[S/T]F motifs on PP1 binding, we tested phosphorylated or unmodified versions of RV[S/T]F-containing peptides from proteins identified in our proteomic screen using the Aurora B inhibitors (RIF1, UBR5, ELYS, SEH1, and ASPM) for binding to PP1 in vitro. Whereas the unmodified versions of these peptides bound to PP1, the phosphorylated versions bound considerably less or no PP1 (Fig. 6B), confirming preferential PP1 binding to these peptides in the nonphosphorylated state and supporting the idea that they are true PP1 binders.

DISCUSSION

The substrate specificity of PP1 is controlled by regulatory proteins, most of which use the RVxF binding motif for interaction with the phosphatase. Sequence analysis of this motif from known PP1-binding proteins shows an overrepresentation of either positively charged Arg or Lys residues or phosphorylatable Ser or Thr residues at the x position (fig. S1). The positive charge of the Arg or Lys residue helps the regulatory proteins to bind tightly to the hydrophobic pocket on the surface of PP1, as in the case of the KVRF docking motif in growth arrest and DNA damage–inducible protein GADD34 for example (57). By contrast, a negative charge introduced by phosphorylation of a Ser or Thr residue at the x position provides a regulatory mechanism for the reversible association between the phosphatase and the regulatory protein through the action of protein kinases during specific cellular events. This is consistent with the absence of acidic residues (Asp or Glu) at the x position (fig S1). Phosphorylation within or in close proximity to the PP1 docking site of known regulatory proteins including GM and KNL1 blocks their binding to PP1 (22, 23, 40). Here, we confirmed and extended this observation by identifying additional known and previously unidentified PP1-binding proteins that interact with PP1 through an RV[S/T]F motif in a phosphorylation-dependent manner. Furthermore, we provide evidence that this phosphorylation is a cell cycle–dependent event occurring specifically during mitosis (Figs. 2 and 3).

Among the possible mitotic protein kinases, the RV[S/T]F motif most closely fits the Aurora kinase consensus sequence R-X-S/T-Φ, where X is any amino acid and Φ is a hydrophobic amino acid. We found that Aurora B, but not Aurora A, phosphorylated the Ser or Thr within the binding motif of PP1 in known and potential regulatory proteins of PP1 (Figs. 4 and 5, and table S2). However, not all [R/K][V/I][S/T][F/W] motifs are phosphorylated by Aurora B; therefore, other basophilic kinases including protein kinase A, protein kinase B, calcium/calmodulin-dependent protein kinase II, and CHK2, among others, could play a role in the phosphorylation of these motifs in other cellular events or subcellular compartments in which Aurora B is not involved in regulation of PP1 activity. We also observed a modest decrease in RV[S/T]F phosphorylation upon the inhibition of PLK1, Aurora A, and CDK1 (Fig. 4). The PLK1 consensus motif is characterized by acidic amino acids upstream of and hydrophobic amino acids downstream of the phosphorylation site (4, 35). However, in vitro and in vivo analysis of PLK1 substrates have revealed that PLK1 also phosphorylates [S/T]F motifs (4, 58). Thus, it is possible that PLK1 opposes PP1 function by phosphorylating phenylalanine-containing RV[S/T]F motifs. Our results show that among the proteins that were specifically bound to RVp[S/T]F antibody, 68% were lost or reduced upon inhibition of Aurora B (table S2). The other proteins (32%) enriched in RVp[S/T]F immunoprecipitates that do not change upon Aurora B inhibition might be phosphorylated by other kinases, and we believe that the localization of the specific proteins containing RV[S/T]F motifs dictates the kinase responsible for their phosphorylation. This has been shown previously in the case of CEP192, where the RV[S/T]F motif is targeted by PLK1 (59). The RV[S/T]F motif has almost certainly evolved to regulate PP1 function by controlling its recruitment to binding partners in a phosphorylation-dependent manner in response to specific cellular conditions and at specific cellular locations.

Using affinity enrichment with a RVp[S/T]F antibody and quantitative proteomics, we identified previously unknown phosphorylation sites for the protein kinase Aurora B within the RV[S/T]F motif of 25 proteins: 6 known [RIF1, antigen identified by monoclonal antibody Ki67 (Ki67), CDCA2, KNL1, BRCA1, and ribosomal RNA processing protein 1 homolog B (RRP1B)] and 19 proteins previously unknown to bind PP1. From this latter group of proteins that interact with PP1 in a phosphorylation- and cell cycle–dependent manner, we validated four proteins with known links to mitotic progression. Peptides containing RV[S/T]F motifs from these proteins preferentially bound to PP1 when the RV[S/T]F motif was not phosphorylated (Fig. 6). These proteins include the E3 ubiquitin ligase UBR5, the microtubule regulator ASPM, the nucleoporin SEH1, and the mitotic exit PP1 scaffold protein ELYS. UBR5 is an HECT (homology to E6AP C terminus) family E3 ubiquitin ligase that has been reported to facilitate anaphase entry by forming complex with the SAC proteins BUBR1 and BUB3 and promoting their turnover by ubiquitination (table S2) (53, 60). Phosphorylation of the “KVTF” sequence in UBR5 by Aurora B might promote PP1 dissociation to keep the SAC activated. Once this motif is dephosphorylated, PP1 could be recruited by UBR5 to contribute to silencing the SAC. ASPM localizes to spindle poles during mitosis and is known to be involved in spindle microtubule organization and cytokinesis (61, 62). Phosphorylation within the “KVSF” motif of ASPM during mitosis has been reported in previous large-scale mass spectrometry studies (4, 63). Our data confirm this phosphorylation during mitosis, and we found this phosphorylation event to be primarily governed by Aurora B kinase. The nucleoporin SEH1 is required for the recruitment of the Nup107-160 nucleoporin complex to kinetochores during mitosis and plays a critical role in establishing correct kinetochore-microtubule attachments (64). ELYS has been reported to recruit the Nup107-160 subcomplex to the kinetochores (65), and it has been shown that the Caenorhabditis elegans homolog of ELYS, MEL-28, recruits PP1 specifically at mitotic exit and plays a crucial role during nuclear reassembly (66). Given the role of Aurora B and PP1 during cytokinesis, these potential PP1 binding partners might be crucial for the recruitment of PP1 and regulation of the Aurora B–PP1 axis during cytokinesis and nuclear envelope reassembly. In budding yeast, RIF1 has been shown to bind PP1, and this interaction has been implicated in replication origin firing (42, 67, 68). Here, we confirmed the RIF1-PP1 interaction in human cells and identified Aurora B–dependent phosphorylation of the RVSF motif of RIF1 during mitosis (fig. S4B). In addition, we also show that phosphorylation within the RVSF of RIF1 reduced PP1 binding, at least in vitro (Fig. 6A).

Collectively, our data reveal that, during mitosis, in addition to inhibitory phosphorylation of PP1 catalytic subunits by CDK1 (10), PP1 function is controlled through a mechanism that relies on PP1-binding regulatory proteins. This dual inhibition mechanism provides on the one hand a fail-safe to limit PP1 activity during mitosis while, on the other hand, allowing for more specific control of the phosphorylation status of select substrates. We propose that the RV[S/T]F motifs phosphorylated by Aurora B during mitosis are dephosphorylated by a yet unknown mitotic phosphatase. After this dephosphorylation event, PP1 can be recruited to its regulatory proteins, which can be themselves PP1 substrates, or target the catalytic subunit to multiple other mitotic phosphorylated substrates (Fig. 7), thus contributing to the global dephosphorylation events that drive mitotic exit. In conclusion, we have identified a previous unknown regulatory mechanism that coordinates the activities of the key mitotic enzymes PP1 and Aurora B for maintaining the kinase-phosphatase balance during mitosis. This balance between the counteracting activities of protein kinases and protein phosphatases is essential to maintain genomic integrity and cell survival.

Fig. 7 Proposed model of PP1 regulation during the cell cycle.

PPI is the catalytic subunit of the PPI holoenzyme, which includes both PP1 and any one of various regulatory proteins that bind to PP1 and control its catalytic activity. PP1 binds to RV[S/T]F motifs in the regulatory proteins during interphase. Upon activation of Aurora B during mitosis, these regulatory proteins are phosphorylated within the RV[S/T]F motifs. This phosphorylation leads to the dissociation of PP1 from the regulatory proteins thereby interfering with targeting of the phosphatase to its substrates. At the end of mitosis, these motifs are dephosphorylated, which regenerates the docking site for PP1, enabling the holoenzyme to target phosphorylated substrates for their dephosphorylation at mitotic exit.

MATERIALS AND METHODS

Cell culture and synchronization

Mycoplasma-free HeLa cells were obtained from American Type Culture Collection and cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and penicillin-streptomycin (100 U ml−1). For cell cycle analysis, cells were arrested with 2 mM thymidine for 17 hours followed by a 7-hour release. After release, cells were blocked in prometaphase with nocodazole (40 ng ml−1). After a 9-hour arrest, the cells were released into fresh media and harvested at different time points within a 24-hour cycle. A part of each sample was fixed in ethanol and stained with propidium iodide for FACS analysis performed at the Flow Cytometry Facility at the University of Calgary.

Antibodies and reagents

The following commercial antibodies were used in this study at the indicated concentrations: PP1 (Santa Cruz Biotechnology, 1:500), RIF1 (Bethyl Laboratories antibodies, 1:500), SFI1 (Proteintech Group Inc., 1:250), BRCA1 (Cell Signaling, 1:1000), CDCA2 (Abcam, 1:1000), cyclin B1 (Santa Cruz Biotechnology, 1:500), tubulin (Sigma-Aldrich, 1:1000), H3 pSer10 (Millipore, 1:1000), p–Aurora A/B/C (Cell Signaling, 1:500), PP1 pThr320 (Cell Signaling, 1:1000), TCTP pSer46 (Cell Signaling, 1:1000), and actin (Cell Signaling, 1:5000). Horseradish peroxidase–conjugated goat anti-mouse and goat anti-rabbit were obtained from Pierce and Thermo Fisher Scientific and were used at 1:5000. The following peptides were used in this study, either unmodified or phosphorylated within RV[S/T]F motif: ZAP (GKKRVRWADLE), ZAPRARA (GKKRARAADLE), RIF1 (KRRVSFADK), CEP192 (SEKHVTFENHK), SFI1 (SRKVTFEGPK), CDCA2 (KRKRVTFGED), TSC2 (QLHRSVSWADSAK), RRP1B (SSKKVTFGLN), MPP10 (KESLKRVTFAL), ORC2 (KTPQKSVSFSLK), BRCA1 (QSPKVTFECEQK), Ki67 (KRRRVSFGGH), UBR5 (VHRVKVTFKDEK), ELYS (RLKETRISFVEEK), SEH1 (KQVWRVSWNIT), and ASPM (SANVSKVSFNEK). The peptides were synthesized with 98% purity at GL Biochem Ltd. The consensus RV[S/T]F logo from known PP1 interactors was generated using WebLogo (69). For the generation of phospho-specific antibodies, the RVp[S/T]F peptides derived from the proteins were coupled to keyhole limpet haemocyanin (KLH) (Imject Maleimide–activated KLH kit, Pierce) and bovine serum albumin (BSA) before injecting them into rabbits. In-house–generated antibodies were affinity-purified on phospho-peptide columns and used in Western blots at the following concentrations: phosphoRIF1 (2 μg ml−1), phosphoCEP192 (2 μg ml−1), phosphoSFI1 (1 μg ml−1), phosphoCDCA2 (5 μg ml−1), and phosphoBRCA1 (5 μg ml−1). NaF (25 mM) and the respective dephospho-peptides (5 μg ml−1) were added to all the phospho-epitope–specific antibody solutions.

PP1-binding assays

For the peptide pulldowns, the RV[S/T]F-containing peptides (either unmodified or phosphorylated within the RV[S/T]F motif) derived from different proteins were coupled to activated CNBr-Sepharose beads (GE Healthcare) using the manufacturer’s protocol. Peptide-coupled beads were incubated with HeLa whole-cell extracts for 3 hours at 4°C. The beads were washed with tris buffer (pH 7.5) plus 500 mM NaCl and 0.5% NP-40, and the bound proteins were eluted and analyzed for the presence of PP1 by immunoblotting.

For PP1 overlays, recombinant PP1 was expressed in Escherichia coli BL21 and affinity-purified using microcystin-Sepharose beads as described previously (70). RV[S/T]F-containing peptides were coupled to BSA using glutaraldehyde (G5882, Sigma-Aldrich) as the coupling agent. These peptides were spotted onto nitrocellulose membrane in different amounts and overlaid with a mixture of recombinant human PP1(α/β/γ) (1 μg ml−1). Phosphatase inhibitors (25 mM NaF and 0.5 μM microcystin-LR) were included at all steps. PP1 binding was analyzed by immunoblotting.

Kinase inhibitor assays

HeLa cells were treated with 2 mM thymidine for 17 hours and released for 7 hours followed by treatment with nocodazole (100 ng ml−1) or 100 nM taxol for 15 hours for inducing prometaphase arrest. MLN8054 (a gift from S. Gerber, Dartmouth College, used at 1 μM to inhibit Aurora A and at 5 μM to inhibit both Aurora A and Aurora B), Aurora A inhibitor I (100 nM, Selleckchem), ZM447439 (5 μM, Tocris), hesperadin (100 nM, Selleckchem), BI2536 (100 nM, Selleckchem), flavopiridol (2 μM, Selleckchem), or roscovitine (50 μM, Millipore) was added for 45 min. The cells were treated with MG132 (10 μM, Millipore) for 30 min before adding the kinase inhibitors.

Immunoprecipitation

Nocodazole-treated (100 ng ml−1) HeLa mitotic cells with or without 1-hour hesperadin treatment (100 nM) were collected by mitotic shake-off and released for 30 min in the presence or absence of hesperadin. The cells were lysed using nucleosome preparation buffer [10 mM Hepes (pH 7.9), 10 mM KCl, 1 mM CaCl2, 1.5 mM MgCl2, 0.34 M sucrose, 10% glycerol, 0.1% Triton X-100 with micrococcal nuclease (100 U ml−1), and TurboNuclease (100 U ml−1)]. After a 10-min incubation at 37°C, an equal volume of high-salt buffer (600 mM NaCl with 2% Triton X-100) was added followed by sonication and clearing of extract at 10,000 rpm for 10 min. All the buffers were supplemented with protease inhibitors (EDTA-free protease inhibitor cocktail tablets, S8830, Sigma-Aldrich) and phosphatase inhibitors (25 mM NaF and 0.5 μM microcystin-LR). The protein concentration was determined using Bradford reagent and BSA as standard. Before the immunoprecipitation, lysate was precleared with CL-4B Sepharose beads (1/10 lysate volume).

For immunoprecipitations, the phosphoRV[S/T]F IgG and the control IgG were coupled to protein A–Sepharose beads using dimethyl pimelimidate before incubation with the cell extracts. The beads were washed three times with high-salt wash buffer [400 mM NaCl with 0.5% NP-40 in phosphate-buffered saline (PBS)] followed by two washes with low-salt wash buffer (150 mM NaCl with 0.2% NP-40 in PBS). The beads were washed two times with PBS before release with the elution buffer [1% SDS, 15% glycerol, 50 mM tris-HCl (pH 8.7), and 150 mM NaCl].

Mass spectrometry analysis

Immunoprecipitations were trichloroacetic acid–precipitated and digested in solution with trypsin in 50 mM ammonium bicarbonate. Reactions were quenched by the addition of 50% acetonitrile/5% formic acid and dried. Peptides were analyzed on a Q-Exactive Plus mass spectrometer (Thermo Fisher Scientific) equipped with an Easy-nLC 1000 (Thermo Fisher Scientific) as previously reported (8). Peptides were resuspended in 5% methanol/1% formic acid and loaded on to a trap column [1 cm length, 100 μm inner diameter, ReproSil, C18 AQ 5-μm, 120 Å pore (A. Maisch)] vented to waste via a micro-tee and eluted across a fritless analytical resolving column (35 cm length, 100 μm inner diameter, ReproSil, C18 AQ 3-μm, 120 Å pore) pulled in-house (Sutter P-2000, Sutter Instruments) with a 60-min gradient of 5 to 30% LC-MS buffer B [LC-MS buffer A, 0.0625% formic acid, 3% acetonitrile (ACN); LC-MS buffer B, 0.0625% formic acid, 95% ACN]. The Q-Exactive Plus was set to perform an Orbitrap MS1 scan (R = 70 K; automatic gain control (AGC) target = 3 × 106] from 350 to 1500 Thomson, followed by higher energy collisional dissociation (HCD) MS2 spectra on the 10 most abundant precursor ions detected by Orbitrap scanning (R = 17.5 K; AGC target = 1 × 105; max ion time = 75 ms) before repeating the cycle. Precursor ions were isolated for HCD by quadrupole isolation at width = 0.8 Thomson and HCD fragmentation at 26 normalized collision energy. Charge state 2, 3, and 4 ions were selected for MS2. Precursor ions were added to a dynamic exclusion list ± 20 parts per million for 20 s. The resulting data files were searched using Comet (release version 2014.01) in high-resolution mode (71) against a target-decoy (reversed) (72) version of the human proteome sequence database (UniProt; downloaded February 2013, 40,482 entries of forward and reverse protein sequences) with a precursor mass tolerance of ±1 Da and a fragment ion mass tolerance of 0.02 Da, and requiring fully tryptic peptides with up to three miscleavages. Carbamidomethylcysteine was enabled as a fixed modification, and oxidized methionine was enabled as variable modification. The resulting peptide spectral matches were filtered to <1% false discovery rate based on reverse-hit counting (73). Peptide quantification was performed using MassChroQ (74). Protein quantification was performed by iBAQ (50).

Data analysis

Total peptide counts from −RVp[S/T]F and control immunoprecipitations from mitotically arrested HeLa cells were input into SAINT (49) using the CRAPome interface (48). For a protein to be considered specific to the RVp[S/T]F immunoprecipitations, we required the interaction to have an AvgP score in the SAINT analysis of 0.9 or above in at least two of the five replicates. Changes in RVp[S/T]F binding upon Aurora B kinase inhibitor addition were determined by Student’s t test. Proteins not quantified in immunoprecipitations upon Aurora kinase B inhibitor addition were called “lost”; proteins quantified in four or five out of five replicates of control immunoprecipitations and only one out of five replicates of immunoprecipitations upon Aurora kinase inhibitor addition [P value, not defined (nd)] were called lost; proteins quantified in two or three out of five replicates of control immunoprecipitations and only one out of five replicates of immunoprecipitations upon Aurora kinase inhibitor addition (P value: nd) with a decrease of twofold or more were called lost; proteins quantified in immunoprecipitations in the presence or absence of Aurora kinase inhibitor with a P < 0.05 and a fold-change decrease of twofold or more were called “reduced”; protein quantified in immunoprecipitations in the presence or absence of Aurora B inhibitor with a P > 0.05 or P value: nd were called “change not significant.” GO annotations were performed in Cytoscape using BiNGO to test for ontology enrichment. To determine significance of enrichment of terms, a Bonferroni-corrected P value cutoff of 0.05 was used.

Immunofluorescence staining and microscopy

For immunofluorescence studies, HeLa cells were grown on poly-lysine–coated coverslips, fixed with 3.7% formaldehyde, permeabilized with 0.5% Triton X-100, and blocked in 1% BSA/PBS. The coverslips were then incubated with primary antibodies for 2 hours followed by Alexa Fluor 488–conjugated goat anti-rabbit and Alexa Fluor 594– conjugated goat anti-mouse secondary antibodies (Molecular Probes, Thermo Fisher Scientific) for 1 hour. Nuclei were counterstained with DAPI (1 μg ml−1; Sigma-Aldrich), and images were acquired using a Leica DMIRE2 microscope as described above. RVp[S/T]F staining in control and Aurora B inhibitor–treated cells was quantified using ImageJ as described in (75). Total corrected cellular fluorescence (TCCF) was calculated using TCCF = integrated density – (area of selected cell × mean fluorescence of background readings), where a neighboring interphase cell was used as the background fluorescence intensity.

SUPPLEMENTARY MATERIALS

www.sciencesignaling.org/cgi/content/full/11/530/eaai8669/DC1

Fig. S1. Consensus RV[S/T]F motif in PP1-interacting proteins.

Fig. S2. Validation of phospho-specific antibodies by dot blots and immunofluorescence.

Fig. S3. Validation and characterization of the RVp[S/T]F antibody.

Fig. S4. Phosphorylation within RVS/TF motifs during mitosis.

Table S1. List of peptide sequences used in this study.

Table S2. List of proteins specifically bound to p-RV[S/T]F antibody and their binding behavior upon Aurora B inhibition.

Table S3. Table containing SAINT analysis of the proteins enriched in the p-RV[S/T]F immunoprecipitations.

Table S4. Table containing GO analysis based on biological processes for proteins enriched in p-RV[S/T]F immunoprecipitations.

Table S5. Table containing GO analysis based on cellular component localization for proteins enriched in p-RV[S/T]F immunoprecipitations.

Table S6. List of proteins containing “RV[S/T]F” motifs specifically enriched in the p-RV[S/T]F immunoprecipitation and their Aurora B sensitivity.

REFERENCES AND NOTES

Acknowledgments: We thank P. Douglas and S. Lees-Miller for help with microscopy and S. Gerber for MLN8054 inhibitor. Funding: Funding for this work was provided by the Cancer Research Society of Canada (to G.B.M.); Alberta Cancer Foundation, Eyes High International Doctoral Scholarship, and Faculty of Graduate Studies Doctoral Scholarship from University of Calgary (to I.N.); and American Cancer Society Research Grant (IRG-82-003-30) and the National Institute of General Medical Sciences (R35GM119455) (to A.N.K.). Author contributions: I.N., G.B.M., and A.N.K. conceived the study. I.N., G.B.M., and S.F.R. performed the experiments. I.N., G.B.M., and A.N.K. wrote the paper. Competing interests: The authors declare that they have no competing financial interests. Data and materials availability: The MS data have been deposited to ProteomeXchange Consortium (76), http://proteomexchange.org, with accession number PXD009369. All other data needed to evaluate the conclusions are present in the article or in the Supplementary Materials.
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