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J Biol Chem, Vol. 275, Issue 15, 11529-11537, April 14, 2000
Reversible Phosphorylation at the C-terminal Regulatory Domain of
p21Waf1/Cip1 Modulates Proliferating Cell Nuclear Antigen
Binding*
Mary T.
Scott ,
Nick
Morrice§, and
Kathryn L.
Ball ¶
From the Cancer Research Campaign
Laboratories, University of Dundee Medical School, Dundee DD1 9SY and
§ MRC Protein Phosphorylation Unit, Department of
Biochemistry, University of Dundee,
Dundee DD1 5EH, United Kingdom
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ABSTRACT |
The p53-inducible gene product
p21WAF1/CIP1 plays a critical role in regulating the
rate of tumor incidence, and identifying mechanisms of its
post-translational regulation will define key pathways that link growth
control to p21-dependent tumor suppression. A eukaryotic
cell model system has been developed to determine whether protein
kinase signaling pathways that phosphorylate human p21 exist in
vivo and whether such pathways regulate the binding of p21 to one
of its key target proteins, proliferating cell nuclear antigen (PCNA).
Although human p21 expressed in Sf9 cells is able to
form a complex with human PCNA, the inclusion of cell-permeable phosphatase inhibitors renders p21 protein inactive for PCNA binding. The treatment of this inactive isoform of p21 with alkaline phosphatase restores its binding to PCNA, suggesting that p21 expressed in Sf9 cells is subject to reversible
phosphorylation at a key regulatory site(s). A biochemical approach was
subsequently used to map the phosphorylation sites within p21, whose
modification in vitro can inhibit p21-PCNA complex
formation, to the C-terminal domain at residues Thr145 or
Ser146. A phospho-specific antibody was developed that only
bound to full-length p21 protein after phosphorylation in
vitro at Ser146, and this reagent was further used to
demonstrate that the inactive isoform of p21 recovered from
Sf9 cells treated with phosphatase inhibitors had
been phosphorylated in vivo at Ser146. These
data identify the first phosphorylation site within the C-terminal
regulatory domain of p21 whose modification in vivo modulates p21-PCNA interactions and define a eukaryotic cell model that
can be used to study post-translational signaling pathways that
regulate p21.
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INTRODUCTION |
Cell cycle progression is driven by the
cyclin-dependent protein kinase
(CDK)1 family, which is
tightly regulated by post-translational mechanisms including
phosphorylation, degradation, and the action of small molecular weight
kinase inhibitors. One of these kinase inhibitors the
p21WAF1/CIP1 protein (p21) was originally identified as a
cyclin-dependent kinase and PCNA-binding protein (1) that
was able to inhibit CDK catalytic activity (2) and as a gene whose
expression was induced by the tumor suppressor protein p53 (3). It has
now become clear that p21 is capable of contributing to the regulation of cell division on several different levels. These include mediation of negative growth signals, functions in differentiation and
senescence, and the more recently defined roles for p21 as a modulator
of the apoptotic response (4, 5) and an activator of certain cyclin-CDKs in response to mitogenic signals (6, 7).
The most well defined function of p21 linked to its activity as a
growth inhibitor is as a cyclin-dependent kinase inhibitor (CKI). During the response to DNA damage, p21 levels increase in a
p53-dependent manner leading to the inhibition of Cdk2
catalytic activity (6). The N-terminal half of p21 has been shown to be
sufficient for both cyclin-CDK binding and inhibition as it contains a
cyclin binding motif (aa 16-24) and a CDK interaction site (aa 45-65)
(7-11). A second cyclin binding motif lies at the extreme C terminus
of p21, and although this domain is sufficient to bind and inhibit some
cyclin-CDKs, its function within the full-length protein remains
unclear (12, 13). The mechanism by which p21 inhibits cyclin-CDK
activity is controversial. However, recent developments showing that
p21 is not a general G1-CDK inhibitor but that it can
differentially regulate individual cyclin-CDK combinations begins to
explain some of the discrepancies. Whereas previously it was reported
that p21 could be associated with both active and inactive
G1 cyclin-CDK complexes (14, 15) and that changes in the
stoichiometry of p21 regulated this transition, recent studies have
established that a single molecule of p21 is sufficient to inhibit
completely the catalytic activity of cyclin A-Cdk2 (16). This
correlates with studies showing that all the p21-containing Cdk2
complexes in cells are catalytically inactive (17). In contrast, all
the cyclin D-Cdk4-pRb kinase activity in proliferating cells is in
complex with either p21 or its close relative p27 (18, 19), and at a
molar ratio of 1:1 p21 does not efficiently inhibit cyclin D-Cdk4
activity (18, 20). In fact, it appears from in vitro studies
that p21 can stimulate the assembly of catalytically active cyclin
D-Cdk4 by stabilizing the pre-formed complex (18), and in cells p21
appears to assemble and target the nuclear localization of cyclin
D1-Cdk4 (19). Thus, whereas p21 is a potent inhibitor of
Cdk2-containing complexes, it is a positive modulator of Cdk4 activity.
In addition to a second cyclin-binding site, the C terminus of p21 also
contains a region that interacts with the replication and repair
protein proliferating cell nuclear antigen (PCNA) (aa 144-151), a
putative nuclear localization sequence (aa 140-157), and two cleavage
sites for the apoptosis-associated protease, caspase 3 (21). It was
originally proposed that p21 and PCNA were both components of a
quaternary cyclin D-Cdk4 complex in proliferation cells (1, 14), and it
has subsequently been shown that p21 and PCNA can also bind directly to
each other in the absence of cyclin-CDKs (22). Binding of p21 to PCNA
blocks the ability of PCNA to act as a processivity factor for DNA
polymerase and , modulating the primer template recognition
complex and inhibiting DNA replication in vitro (23).
Although there is clear evidence that p21-PCNA complexes form in
response to DNA damage, it has proved difficult to show a significant
effect of p21 on DNA replication in cells. However, recent data suggest that the interaction with PCNA is important in preventing
endoreduplication (24), inhibiting S-phase progression (25) and
promoting DNA repair (26, 27). The data describing a role for p21 in
nucleotide excision repair (NER) suggests that although p21 can inhibit
PCNA-dependent gap filling activity, it can only do this
when gap filling is uncoupled from incision, and therefore cellular NER
is refractive to inhibition (28). On the other hand, p21-null human
colon cancer cells (HCT116) are defective in their ability to repair certain types of DNA damage, and efficient repair is restored following
expression of exogenous wild type p21 but not a mutant form of p21
missing the PCNA-binding site (27). Other studies have suggested that
p21 is required to aid efficient disassembly of PCNA from repair sites
leading to an increase in the rate at which damaged DNA is repaired
(26). Most recently, PCNA has been shown to play a role in the
regulation of p21 activity by modulating the rate at which p21 is
degraded (29).
To date the majority of studies involving p21 have concentrated on its
transcriptional regulation by p53-dependent and
-independent mechanisms (30). Evidence is now beginning to emerge that
p21 can also be regulated by post-translational mechanisms. The best characterized of these is C-terminal cleavage of p21 by a member of the
caspase family of proteases (21, 31-33). This appears to be an early
event during DNA damage-induced apoptosis that affects both PCNA
binding (31, 33) and cellular localization (32) of p21. In addition,
evidence implicating reversible phosphorylation as a mechanism for
regulating p21 comes from several studies. The strongest data to date,
however, is a study of p21 during cellular differentiation (34).
Stimulation of PC12 cells to differentiate using nerve growth factor
led to loss of epitope binding by a C terminus-specific anti-p21
monoclonal antibody, although there appeared to be no overall change in
p21 protein levels. Phosphatase treatment of the lysates resulted in
recovery of the epitope, suggesting that reversible phosphorylation
within the extreme C-terminal region of p21 occurs in response to nerve growth factor-stimulated signaling pathways. However, potential phosphorylation sites on p21 were not identified in this cell system
nor were possible biochemical effects of this phosphorylation on p21
activity defined. The main difficulty in mapping such regulatory phosphorylation sites on p21 protein is the relatively low level expression of p21 protein in cultured cells that precludes an accurate
biophysical study of post-translational regulatory mechanisms.
In our study, a eukaryotic cell model system was developed using
recombinant human p21 protein expressed in Sf9 cells
to acquire relatively large amounts of p21 in an extensively
phosphorylated state for biochemical characterization. The PCNA binding
activity of p21 protein synthesized in this cell system can be
modulated by protein phosphatase inhibitors or phosphatase treatment,
suggesting that in vivo phosphorylation of p21 can in fact
modulate its activity. A biochemical approach was subsequently used to
map the phosphorylation sites within p21 whose modification in
vitro can inhibit p21-PCNA complex formation to the C-terminal
domain at residue Thr145, Ser146, and
Ser160. An antibody specific for the
phospho-Ser146 p21 epitope was developed and used to
demonstrate that the inactive isoform of p21 recovered from
Sf9 cells treated with phosphatase inhibitors had
been phosphorylated in vivo at Ser146. These
data identify the first phosphorylation site within the C-terminal
regulatory domain of p21 whose modification in vivo modulates p21-PCNA interactions and define a eukaryotic cell model that
can be used to study post-translational signaling pathways that
regulate the p21 protein.
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EXPERIMENTAL PROCEDURES |
Peptides, Proteins, and Antibodies--
All biotinylated
peptides were synthesized by Chiron Mimotopes, Peptide Systems
(Clayton, Australia). Each peptide had a biotin-SGSG spacer at the C
terminus and a free N terminus. The peptides were dissolved in
Me2SO at 5 mg/ml and stored at 20 °C. Untagged human p21 and PCNA were expressed in Escherichia coli using a
pT7-7 expression vector and purified by the methods previously
described (34, 35). PCNA for ELISA was expressed in
Sf9 insect cells infected with baculovirus containing
a human PCNA construct. The cells were harvested 2 days post-infection
by low speed centrifugation, and the pellet was lysed in an equal
volume of extraction buffer containing 50 mM Hepes, pH 7.4, 50 mM NaCl, 1 mM EDTA, 5 mM DTT, 1% (v/v) Nonidet P-40, 10 mM NaF, 10 µg/ml leupeptin, 4 µg/ml aprotonin, 2 µg/ml pepstatin, 1.2 mM benzamidine,
10 µg/ml soybean trypsin inhibitor, and 400 µg/ml Pefabloc before
centrifuging at 14,000 rpm for 15 min. For generation of the
p21-phospho-Ser146 serum, phosphopeptide,
KRRQTS[PO3]MTDFYHSK (synthesized by Dr. G. Bloomberg,
University of Bristol), was conjugated to keyhole limpet hemocyanin and
used to immunize a rabbit by standard methods (36). For affinity
purification of the rabbit sera, the same phosphopeptide,
KRRQTS[PO3]MTDFYHSK, was coupled to Reacti-Gel beads
(Pierce) at a concentration of 0.8 mg of peptide per ml of beads
following the manufacturer's instructions. After coupling excess
reactive groups were blocked by adding 1 M Tris, pH 8.0. The phosphopeptide coupled beads were added to the rabbit sera (250 µl of beads per 10 ml of sera) and rotated for 1 h at 4 °C. The phosphatase inhibitors NaF and okadaic acid had previously been
added to the rabbit sera at concentrations of 50 mM and 50 nM, respectively, to prevent endogenous phosphatases
removing the phosphate group. Following incubation the beads were
pelleted and washed three times with PBS containing 0.1% Tween 20. To
elute the bound antibody, 0.5 ml of 0.1 M glycine, pH 2.5, was added, and the mixture was rotated at 4 °C for 30 min. The beads
were pelleted; the supernatant containing the eluted antibody was
collected, and the pH was neutralized using 0.1 M Tris, pH
8.0.
p21 Phosphorylation--
p21 purified from E. coli (1 µg) was incubated for 20 min at 30 °C in a final volume of 30 µl
of kinase assay buffer (50 mM Hepes, pH 7.4, 10 mM MgCl2, 0.8 mM EDTA, 0.8 mM DTT, 100 µM ATP with
[ -32P]ATP (250 cpm/pmol)) containing 0.5 milliunits of
protein kinase A or 0.1 milliunits of casein kinase 2 or 0.06 milliunits of protein kinase C plus 1 mM CaCl2,
100 µg/ml phosphatidylserine, and 20 µg/ml diacylglycerol.
Following incubation the reactions were stopped either by (i) removing
a 10-µl sample of the reaction mixture, adding to Laemmli sample
buffer, and subjecting to SDS-PAGE prior to drying and autoradiography
or (ii) by adding a 20-µl sample of the reaction mixture to 0.5 ml of
ice-cold 25% (w/v) trichloroacetic acid and leaving on ice for 1 h to precipitate the p21. The precipitated protein was pelleted at
10,000 rpm for 10 min, and the supernatant was removed. The pellet was
washed twice with 0.5 ml of ice-cold 10% (w/v) trichloroacetic acid
and twice with 0.5 ml of H2O followed by a final rinse with
acetone. The incorporation of radioactivity into the precipitated p21
was determined by Cerenkov counting. Alternatively, p21 phosphorylated at Ser146 in the absence of radiolabel was detected using
p21-phospho-Ser146 IgG by Western blot analysis
following the method of Ball and Lane (37), using the affinity purified
p21-phospho-Ser146 IgG and mAb 118 at 1 µg/ml.
Mapping of p21 Phosphorylation Sites--
p21 was phosphorylated
by either PKA or PKC as described above, and the reactions were stopped
by adding urea to a final concentration of 6 M. After
reducing and alkylating any cysteines (38), the p21 was precipitated
with trichloroacetic acid as described above. The precipitated pellets
were dissolved in 250 mM ammonium bicarbonate containing
1% n-octyl- -glucopyranoside. After reducing the
detergent concentration to 0.25% with 20 mM ammonium
bicarbonate, the phosphorylated p21 was digested by incubating with
either trypsin or Asp-N (1:40, protease:total protein by weight)
overnight at 30 °C. The resulting peptide mixtures were then
separated on a C-18 reverse phase HPLC column with a 0-70%
acetonitrile gradient. The peptide peaks containing radiolabeled
phosphate were collected, and the phosphorylation site(s) for each
enzyme were mapped using a combination of mass spectrometry and solid
phase Edman degradation.
ELISA--
Peptide ELISAs for determination of PCNA binding were
performed as described previously (39) using Sf9 cell
lysates containing human PCNA (see above). Binding of
p21-phospho-Ser146 IgG to immobilized peptides was
determined by ELISA using the method of Craig et al. (45).
To measure the interaction of full-length p21 with PCNA, microtiter
plates were coated for 16 h at 4 °C with 0.5 µg/well purified
recombinant human p21 diluted in 0.1 M
CO3/HCO3, pH 9.0. After extensive washing with
PBS plus 0.2% Tween 20 (PBST), the wells were blocked with 5% non-fat
milk powder in PBST (milk-PBST) for 2 h at room temperature.
Increasing amounts of Sf9 cell lysate from cells
expressing human PCNA diluted in 0.1% milk/PBST was added to the wells
and incubated for 2 h at room temperature. The plates were
incubated with anti-PCNA polyclonal antibody 3009 (37) diluted 1:1000
in 2% milk/PBST for 1 h at room temperature. This was followed by
horseradish peroxidase-conjugated swine anti-rabbit IgG (Dako) diluted
1:1000 in 2% milk/PBST for 1 h at room temperature. Extensive
washing with PBST was carried out between each incubation. Finally,
chromogenic substrate (50 µl) complete 3,3',5,5'-tetramethylbenzidine
(Sigma), prepared in accordance with the manufacturer's instructions,
was added per well. The reaction was stopped by addition of 50 µl/well 1 M H2SO4. The plates
were analyzed using a Dynatech 5000 ELISA plate reader at 450 nm.
BIAcore--
Surface plasmon resonance measurements were
performed using BIAcore. Human PCNA purified from E. coli
(35) was captured on a CM5 sensor chip surface by amine coupling as
described in the manufacturer's instructions (Amersham Pharmacia
Biotech). Full-length purified p21 was passed over the surface of the
chip, and the binding characteristics of different phosphorylated forms of p21 were observed. SPR response was measured in resonance units (RU), for most proteins 1000 RU corresponds to a surface concentration of approximately 1 ng/mm2. HBS (10 mM Hepes, pH
7.6, 150 mM NaCl, 3.4 mM EDTA, 0.05% BIAcore surfactant P20) was used as a buffer in this system at a flow rate of 5 µl/min.
Insect Cell Expression of Human p21--
Sf9
cells grown in Ex-Cell 400 (JRH Bioscience) + 5% FCS were infected
with baculovirus carrying a full-length untagged p21 construct
following the method described by Hupp and Lane (40). After 48 h
the cells were treated with okadaic acid dissolved in ethanol (or
ethanol alone) at a final concentration of 10 nM and
incubated for a further 90 min. The cells were washed in PBS and lysed
on ice in an equal volume of lysis buffer (50 mM Hepes, pH
7.6, containing 0.2% Triton X-100, 0.1 mM EDTA, 2 mM DTT, 2 mM MgCl2, 150 mM NaCl, 10 µg/ml leupeptin, 4 µg/ml aprotonin, 2 µg/ml pepstatin, 1.2 mM benzamidine, 10 µg/ml soybean
trypsin inhibitor, 400 µg/ml Pefabloc, 50 mM NaF, and 1 nM okadaic acid) or under denaturing conditions in an equal
volume of urea buffer (50 mM Hepes, pH 7.6, containing 8 M urea, 1% (v/v) Triton X-100, and 100 mM
DTT), centrifuged at 14,000 rpm for 15 min, and the supernatant removed.
PCNA Binding and Phosphatase Treatment--
The
Sf9 cell supernatant (extracted under non-denaturing
conditions, see above) was diluted 1:10 in lysis buffer containing pure
recombinant PCNA at 5 µg/ml, and immunoprecipitation (41) was carried
out using the anti-p21 monoclonal antibody AB1 (Oncogene Sciences)
linked to protein G. Alternatively, the supernatant was diluted 1:2 in
lysis buffer with and without 0.2 units/ml alkaline phosphatase (Roche
Molecular Biochemicals) and incubated at 30 °C for 10 min. They were
then diluted 1:5 in lysis buffer containing 2.5 µg/ml PCNA, and
immunoprecipitation was carried out with AB1 as above. The
immunoprecipitated complexes were separated by SDS-PAGE (42),
transferred to nitrocellulose, and detected using AB1 (p21) and the
polyclonal serum 3009 (PCNA (37)) following the method described in
Ball and Lane (37).
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RESULTS |
Modulation of p21 Binding Using the Phosphatase Inhibitor Okadaic
Acid--
Although there is increasing evidence to suggest that the
biochemical activity of p21 is regulated at the post-translational level, the sites of modification have not been mapped, and the effect
of modification on the biochemical activity of p21 has not been
determined. We were interested in whether targeting of p21 by protein
kinase signaling pathways had the potential to regulate its activity
and more particularly PCNA binding. Sf9 cells
expressing recombinant human p21 were used as a model system to
determine whether kinase signaling pathways that target p21 exist in
cells. Insect cell-viral expression systems have been previously used
as a unique model to identify novel regulatory phosphorylation sites in
cyclin-dependent protein kinases (43), SV40 viral T-antigen
(44), and the tumor suppressor protein p53 (40, 45). The advantage that
this expression system has in identifying novel signaling pathways that
target a protein of interest is as follows: (i) relatively large
amounts of a target protein can be purified and used for biophysical
study; (ii) the target protein is not degraded, which is a common
problem with cell cycle proteins normally expressed at very low levels;
and (iii) eukaryotic signaling pathways are highly conserved and
functioning in this cell system (46). Various growth conditions were
tested in the p21 expression system, and the majority of the p21
produced in insect cells was competent for binding to E. coli expressed recombinant human PCNA (Fig.
1B, untreated). However, when
the cell-permeable phosphatase inhibitor okadaic acid (OA) was added to
the cell media 90 min prior to harvesting, the p21 was severely compromised in its ability to bind to PCNA (Fig. 1B,
OA treated), despite the fact that 10 nM OA had
no effect on the amount of p21 protein expressed (Fig. 1A).
When the lysates containing p21 from OA-treated cells were incubated
with alkaline phosphatase, PCNA binding to p21 was restored (Fig.
1C). These data suggest that p21 is subject to rapid
reversible phosphorylation and that the addition of OA "traps" p21
in a phosphorylated form that is unable to bind to PCNA. Incubation
with alkaline phosphatase removes the phosphate, relieving inhibition
of binding and allowing p21 to interact with PCNA. Thus, the data
indicate the possible existence of kinase/phosphatase pathways that
target p21 in eukaryotic cells and can modulate PCNA binding.

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Fig. 1.
Sf9 cells as a model to
study p21 regulation. A, human p21 expression levels in
Sf9 cells. Human p21 protein was expressed in
Sf9 insect cells and left untreated or incubated in
the presence of 10 nM OA for 90 min prior to harvesting.
Following lysis the extracts were immunoblotted to quantitate the
levels of p21 protein using the p21-specific mAb 118. B, OA
treatment induces a form of p21 inactive for PCNA binding.
p21-containing lysates from untreated or OA-treated cells were
incubated in buffer containing bacterially expressed human PCNA. The
amount of p21 or PCNA immunoprecipitated with the anti-p21 monoclonal
antibody AB-1 was quantitated using either mAb 118 or 3009, respectively. C, phosphatase (PPase) treatment
restores PCNA binding to OA-treated p21. p21 containing lysate from
OA-treated cells were incubated in the presence or absence of alkaline
phosphatase and then added to buffer containing PCNA. p21-PCNA
complexes were detected by immunoprecipitation as described for
B.
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Phosphorylation of a p21 Peptide Inhibits PCNA
Binding--
Previous studies aimed at determining the structure of
p21, and its close relative p27, have shown that this family of CKIs displays little ordered structure when free in solution and that only
when bound to cyclin-CDKs or PCNA is a more ridged conformation adopted
(47, 48). Given this we reasoned that the best way to regulate the
activity of p21 would be to sterically inhibit protein-protein
interactions by phosphorylation in, or close to, the binding motif,
rather than inducing conformational changes by phosphorylation at a
distant site. Thus, putative phospho-acceptor sites that lie within the
PCNA binding motif on p21 were identified (Fig.
2). A cluster of serine and threonine
residues is present within the C-terminal domain of p21 that binds to
PCNA, and a "motif" search identified three of these residues as
lying within possible consensus phosphorylation sites.

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Fig. 2.
Functional and regulatory domains of
p21. The primary amino acid sequence of human p21 is depicted.
Highlighted are putative kinase phosphorylation consensus
sites, and underlined are the known binding sites for
cyclin, CDK, and PCNA.
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We and others (37, 39) have shown previously that a 20-amino acid
peptide based on residues 140-160 of p21 is sufficient to bind and
form a high affinity interaction with PCNA that can be detected by
peptide precipitation and ELISA. A quantitative ELISA was developed to
compare PCNA binding to p21-derived phosphopeptides with PCNA binding
to the unphosphorylated p21-based peptide. The synthetic peptides
contained the core amino acid sequence
1KRRQTSMTDFYHSKRRLIFSKRKP24, derived from the
sequence of human p21 protein where position 1 is equivalent to
Lys141 and position 24 is Pro164. Increasing
amounts of PCNA-containing lysate was titrated into ELISA wells
pre-coated with the indicated biotinylated synthetic peptide, and the
amount of PCNA bound was quantitated using a polyclonal antibody
specific for the protein (Fig. 3).
Incorporation of a phosphate at positions 5 (Thr145) and 6 (Ser146) decreases PCNA binding more efficiently than
phosphorylation at positions 13 (Ser153) with
phosphorylation at position 20 (Ser160) also giving a
significant decrease in PCNA binding (Fig. 3). This indicates that
phosphorylation at key residues can, as predicted, reduce the stability
of the PCNA-p21 peptide complex.

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Fig. 3.
Phosphorylation of p21-derived peptides
within the C-terminal regulatory domain reduces PCNA binding.
Biotinylated peptides based on the C-terminal domain of p21 (residues
141-164; KRRQTSMTDFYHSKRRLIFSKRKP) were used in an ELISA format (39)
to determine if phosphorylation at Thr145 ( ),
Ser146 ( ), Ser153 ( ), and
Ser160 ( ) affected the ability of the peptide to form a
high affinity interaction with full-length PCNA from
Sf9 cell lysates and were compared with binding to
the unphosphorylated peptide ( ). PCNA binding was detected using the
anti-PCNA sera 3009 (37). The data represent the mean of three
experiments.
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PKA and PKC Phosphorylate p21 Protein--
As phosphorylation of
the PCNA-binding peptide derived from p21 reduced PCNA binding, it was
important to determine whether phosphorylation of full-length p21
within this region also affected PCNA binding. The motif search
suggested that the three serine residues whose phosphorylation reduced
PCNA binding were potential sites for PKA (cAMP-dependent
protein kinase), CK2 (casein kinase 2), and PKC (protein kinase C) (see
Fig. 2), and the ability of these three kinases to phosphorylate
untagged full-length p21 purified from a bacterial expression system
was examined (Fig. 4). Incorporation of
radioactive phosphate into p21 in the presence of each protein kinase
was determined by SDS-PAGE/autoradiography (Fig. 4A) and
quantitated by trichloroacetic acid precipitation assays (Fig.
4B). When p21 was incubated with either PKA or PKC for 20 min at 30 °C in the presence of [ -32P]ATP, the
stoichiometry of phosphorylation was calculated to be 0.5 mol of
phosphate/mol of p21 for PKA and 0.7 mol of phosphate/mol of p21 for
PKC. On the other hand, p21 was not a substrate for CK2 (Fig. 4) under
conditions where p53 was phosphorylated efficiently by this enzyme
(data not shown). These results suggest that full-length p21 could be
phosphorylated with a high stoichiometry by PKA and PKC and prompted us
to map the phosphorylation sites.

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Fig. 4.
Phosphorylation of full-length p21 by PKA and
PKC. The incorporation of [32P]phosphate into
full-length p21 was determined following incubation with PKC, PKA, or
CK2, as indicated. A, an autoradiograph of the samples
analyzed by SDS-PAGE. B, data obtained by scintillation
counting showing the rate of phosphate incorporation (pmol/min/µg
p21) and the stoichiometry defined in moles of phosphate/mol of
protein.
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PKA and PKC Phosphorylation within the C terminus of Full-length
p21 Is Similar but Distinct from That Observed within the p21
Peptide--
Full-length untagged recombinant p21 purified from a
bacterial expression system was phosphorylated by PKA and PKC using
radiolabeled ATP, and phosphorylation sites were mapped by standard
procedures. Urea was used to stop the kinase reactions, and following
reduction and alkylation of the cysteine residues, the reaction
products were precipitated with trichloroacetic acid thus removing
unincorporated [32P]ATP. The resuspended protein was
proteolyzed using either trypsin or Asp-N, and the resultant peptides
were separated by reverse phase HPLC on a C-18 column. The column was
developed with a linear gradient of 0-70% acetonitrile, and those
polypeptide peaks containing radiolabeled phosphate were analyzed by
mass spectrometry and subjected to Edman degradation to identify the
phosphorylated residues. Based on these methods, PKA was found to
phosphorylate full-length p21 at Thr145 (Fig.
5, C and D). In
addition, PKC phosphorylated two sites on full-length p21 at
Ser146 and Ser160 (Fig. 5, A, B, and
D). Interestingly, when similar experiments were performed
using the p21 C-terminal peptide as a substrate (data not shown) the
preferential phosphorylation site for PKA was Ser146 and
not the Thr145 site mapped on the full-length protein. As
it is becoming increasingly clear that many protein kinases require
determinants other than the defined minimal substrate motif for
efficient phosphorylation, this difference suggests that another
region(s) of the full-length protein may influence PKA specificity.
This highlights the importance of using native protein, as well as
peptide substrates when screening for physiologically relevant kinases
during the fractionation of cell lysates.

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Fig. 5.
Mapping the PKA and PKC phosphorylation sites
on full-length p21 protein. p21 was phosphorylated with either PKC
or PKA using [ -32P]ATP and digested with either
trypsin or Asp-N. The resulting peptide mixtures were separated on a
C-18 reverse phase HPLC column using a 0-70% acetonitrile gradient.
The peptide peaks containing radiolabeled phosphate were collected, and
the phosphorylation sites for each enzyme were mapped using a
combination of mass spectrometry and solid phase Edman degradation. Two
radiolabeled peptides were identified after phosphorylation with PKC
(A and B) and one peptide after phosphorylation
with PKA (C). The data from the Edman degradation show the
released of 32P (cpm) per residue, and the sites
phosphorylated by the two enzymes are summarized in the
table (D).
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Phosphorylation of Full-length p21 Protein in Vitro by Either PKA
or PKC Inhibits PCNA Binding--
To determine the effect of
phosphorylating full-length p21 at either residue Thr145 or
Ser146 and Ser160 on PCNA binding, an ELISA was
used to quantitate the binding reaction (Figs.
6, A and B). The
ELISA wells were coated with either unphosphorylated p21 or with p21
that had been phosphorylated in the presence of either PKA or PKC. The
binding of p21 alone to the ELISA wells and of PCNA to p21 was
quantitated using the anti-p21 monoclonal antibody AB-1 or an
anti-peptide sera to the C-terminal 15 amino acids of PCNA (3009 (37)).
Phosphorylation of p21 by either PKA or PKC did not affect binding of
p21 to the wells (data not shown), whereas incorporation of phosphate
at Thr145 by PKA and dual phosphorylation at
Ser146 and Ser160 by PKC prevents PCNA binding
(Fig. 6, A and B). Although this assay clearly
demonstrates an effect of phosphorylation on the ability of p21 to form
a stable complex with PCNA, it does not determine whether this is
because phosphorylation blocks p21-PCNA complex formation or whether it
destabilizes the complex once it has formed.

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Fig. 6.
Phosphorylation of full-length p21 in
vitro inhibits PCNA binding. The ability of
phosphorylated and unphosphorylated p21 to bind to PCNA was determined
by ELISA (A and B) and by surface plasmon
resonance using BIAcore (C and D). A
and B, p21 incubated in the absence or presence of PKA
(A) or PKC (B) was adsorbed to microtiter wells
and incubated with increasing amounts of PCNA containing
Sf9 cell lysate. The amount of p21 protein bound to
the well was unaffected by phosphorylation (data not shown). PCNA
binding was quantitated using the anti-PCNA sera 3009. The data are the
means ± S.E. of four experiments with the OD being read at 450 nm. C and D, p21 incubated in the absence or
presence of PKA (C) or PKC (D) was passed over
PCNA bound to a sensor chip, and the SPR response was measured in RUs
(resonance units) as a function of time (in seconds).
|
|
To address this problem and determine whether phosphorylation had an
effect on the association rate or the dissociation rate of the complex,
BIAcore was used to measure surface plasmon resonance (SPR) and
determine whether there was a difference in the real time binding of
unphosphorylated and phosphorylated p21 to PCNA. PCNA purified from a
bacterial expression system was captured on a CM5 sensor chip and
either untreated, PKA-phosphorylated p21, or PKC-phosphorylated p21 was
then passed over the surface of the chip. The resulting binding curves
clearly show that phosphorylation of p21 by both PKA and PKC strongly
inhibits real-time binding of the protein to PCNA (Fig. 6, C
and D). In addition, as the dissociation rate of any bound
p21 is unaffected by phosphorylation, the data suggest that
phosphorylation prevents the formation of stable complexes by reducing
the association of phospho-p21 and PCNA. These data also suggest that
the interaction between p21 and PCNA could be regulated in
vivo by protein kinases that modify residues within the PCNA
binding motif of p21 and prompted us to develop reagents that could be
used to determine whether the isoform of p21 we can recover from cell
lysates, which is inactive for PCNA binding, is phosphorylated within
the C-terminal domain.
The Development of a Quantitative Immunochemical Assay to Detect
Ser146 Phosphorylation of p21--
Recent studies have
demonstrated that the conventional method for mapping and quantifying
phosphorylation events in vivo which relies on metabolic
labeling with [32P]orthophosphate can result in DNA
damage and induction of p53-dependent stress-activated
growth arrest pathways (49). The use of immunochemical reagents that
are specific for phosphorylated substrates circumvents these problems
and allows the study of protein phosphorylation under non-invasive
conditions. Thus, we developed -phosphopeptide rabbit sera
( p21-phospho-Ser146) that is specific for the
Ser146 phospho-epitope using both p21-based peptides and
full-length p21. When the C-terminal p21 peptide series was used to
determine the specificity of affinity purified
p21-phospho-Ser146 IgG (Fig.
7A), the IgG bound to the
phospho-Ser146 peptide but failed to bind to both the
unphosphorylated peptide and peptides phosphorylated at position
Thr145, Ser153, and Ser160, showing
absolute specificity under these conditions for the Ser146
phosphopeptide. A titration of PKC-phosphorylated full-length p21
protein was compared with unphosphorylated full-length p21 by Western
blot analysis, where it was demonstrated that the
p21-phospho-Ser146 IgG was at least 100-fold more
efficient at binding to p21 phosphorylated by PKC than to
unphosphorylated protein (Fig. 7B). In addition, to show
that the antibody was specific for phosphorylation at Ser146, the p21-phospho-Ser146 IgG did not
bind to full-length p21 phosphorylated at Thr145 by PKA
(Fig. 7C).

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Fig. 7.
Characterization of the phospho-specific
antibody, p21-phospo-Ser146
IgG. A, binding of p21-phospho-Ser146
IgG to immobilized synthetic peptides was determined by ELISA (45). The
peptide (KRRQTSMTDFYHSKRRLIFSKRKP) was either unphosphorylated ( ) or
phosphorylated at one of the following positions: Thr145
( ), Ser146 ( ), Ser153 ( ), or
Ser160 ( ). B, the affinity of the
p21-phospho-Ser146 sera for bacterially expressed
full-length p21 phosphorylated at Ser146 compared with
unphosphorylated p21 was determined by Western blot analysis. The
upper panel shows p21 that was phosphorylated with PKC, and
the bottom two panels are of unphosphorylated p21. The
anti-p21 monoclonal antibody mAb 118 is used to detect total p21
protein. C, equal amounts of bacterially expressed p21
protein phosphorylated by PKA (lane 1), PKC (lane
2), or unphosphorylated (lane 3) were analyzed by
Western blot analysis. In the bottom panel, total p21
protein was detected using mAb 118, and in the top panel
p21-phospho-Ser146 was shown to be specific for p21
phosphorylated at Ser146.
|
|
The PCNA-binding Inactive Isoform of p21 Expressed in Sf9
Cells Is Phosphorylated at Ser146--
As one of the key
modifications that can inhibit PCNA binding is phosphorylation of p21
at Ser146 (Figs. 3 and 6), we tested the hypothesis that
the inactive isoform of p21 (lysed from Sf9 cells
treated with phosphatase inhibitors) was inactivate for PCNA binding
due to phosphorylation at Ser146. When
Sf9 cells expressing p21 protein were lysed in either
Nonidet P-40 lysis buffer or urea lysis buffer, the PCNA-binding
competent form of p21 (Fig. 1) had a very low level or undetectable
level of Ser146 phosphorylation (Fig.
8, upper panel). Strikingly,
when Sf9 cells expressing p21 protein were pretreated
with phosphatase inhibitors (+ OA, Fig. 8, upper
panel), this PCNA-binding inactive form of p21 (Fig. 1) had
significantly higher levels of Ser146 phosphorylation (Fig.
8, upper panel). As a control, an identical gel was
transferred to nitrocellulose and probed with the p21-specific monoclonal antibody 118 to show that the increase in Ser146
phosphorylation observed in the presence of OA occurred without an
increase in p21 protein levels (Fig. 8, lower panel).
Although we cannot rule out the possibility that other in
vivo phosphorylation events contribute to the inactivation of p21
for PCNA binding (for example at Thr145), there is a strict
correlation between the loss of PCNA binding activity and an increase
in Ser146 phosphorylation of p21. Thus, we have
demonstrated that phosphorylation at Ser146 can be
stabilized by OA and contributes to the loss of the PCNA binding
function of p21. In addition, the data show that signaling pathways
that target Ser146 of p21 protein exist in eukaryotic
cells.

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Fig. 8.
Ser146 of p21 is phosphorylated
in vivo. Sf9 cells expressing
human p21 were incubated in the absence or presence of the phosphatase
inhibitor OA (as indicated) for 90 min prior to harvesting. Control and
treated cells were extracted in lysis buffer containing Nonidet P-40
and phosphatase inhibitors (see under "Experimental Procedures") or
under denaturing conditions using urea buffer. The lysates were
subjected to Western blot analysis with bacterially expressed
full-length p21 phosphorylated with PKC (lane 1) or
unphosphorylated p21 (lanes 2 and 3) being
included as controls. The bottom panel shows total p21
protein detected by the anti-p21 mAb 118, and the upper
panel shows Ser146 phosphorylated p21 detected using
p21-phospho-Ser146 IgG.
|
|
 |
DISCUSSION |
Recent studies have made it apparent that the absolute levels of
the cyclin-dependent kinase inhibitor protein p21 are
important in determining the rate of tumor incidence (50, 51) and that levels of p21 protein can determine the sensitivity of cells within a
solid phase tumor to radiation-induced damage (52). Thus, enzymes that
modify the specific activity of p21 as a growth suppressor may be
expected to impact on growth control mechanisms and the rate of
tumorigenesis. We have initiated studies to determine if
post-translational mechanisms contribute to the control of p21 activity
as a PCNA-binding protein.
p21-PCNA protein complexes form in cells in response to DNA damage (53)
and appear to be involved in multiple damage responses. First, although
it has previously proven difficult to demonstrate that p21 inhibits DNA
replication in cells, two recent studies suggest that p21 inhibits
S-phase progression and DNA synthesis in a PCNA-dependent
manner (25, 54). Second, p21 appears to stimulate
PCNA-dependent NER, and p21-deficient cells are unable to
repair efficiently certain types of damaged DNA (26, 27). Third, it has
been proposed that the ability of p21 to arrest cells in the
G2 phase of the cell cycle (54-57) is also a
PCNA-dependent process, at least in some cell types (54).
Finally, steady state levels of p21 are regulated by both its rate of
protein synthesis and degradation, with recent studies demonstrating
that PCNA plays a critical role in determining the rate of p21
turnover. When p21 is bound to PCNA it is degraded more slowly leading
to a decrease in its rate of turnover. This is in contrast to
cyclin-CDK binding which increases the rate of p21 degradation
(29).
By using a human cell line we observed that p21 and PCNA could form a
complex after very low doses of UVC, and the interaction occurred in
the absence of protein synthesis, implicating a post-translational mechanism for regulating p21-PCNA complex
assembly.2 However, human
cell lines express relatively small amounts of p21, and we have found
that the protein is associated with a number of different protein
complexes making quantitative immunoprecipitation difficult. In
addition, given that (i) many regulatory post-translational modifications might be short lived in cells and (ii) labeling with
[32P]orthophosphate leads to activation of
p53-dependent pathways (49), it is difficult to dissect
accurately post-translational signaling to p21 in mammalian cells using
conventional methods. In the current study these difficulties have been
overcome by first developing a eukaryotic cell system to study
post-translational regulation of p21 protein and second by generating
immunochemical reagents to study p21 phosphorylation, bypassing the
requirement for metabolic labeling with 32P.
The evolutionary conservation of signaling pathways that regulate key
cell cycle and checkpoint proteins in Sf9 cells is
now well documented. Examples of how such cells can be utilized to study post-translational modification are provided by elegant studies
on the regulation of p53 and cyclin-CDKs by reversible phosphorylation.
Insect cells expressing human p53 have revealed a UV- and
serum-dependent signaling pathway that induces
phosphorylation of p53 within the C-terminal negative regulatory domain
(40), and most recently, novel regulatory phosphorylation sites within the Mdm2-binding site of p53 have been identified in this system (45).
In both cases subsequent research has shown that these pathways also
exist in human cells (58, 59). In addition, studies on the regulation
of human cyclin-CDK catalytic activity in insect cell lysates lead to
the discovery of the cyclin-dependent kinase activating
kinase (43), an essential activator of the cell cycle-regulated CDKs.
The advantage of the insect cell expression system for studying p21
modification is that relatively large amounts of full-length p21
protein can be produced in a soluble form for biophysical study. Our
initial data using this system suggested that agents that inhibit
protein phosphatase activity could be used to modulate the PCNA binding
activity of p21; however, whether this reflected the direct
modification of p21 or an indirect mechanism was unclear. The approach
taken to address this issue was to identify putative in
vitro phosphorylation sites with the potential to disrupt the high
affinity interaction normally observed between p21 and PCNA (22, 37,
39). By using this approach we identified three putative
phosphorylation sites within the C-terminal domain of p21 which
significantly decreased its ability to bind to PCNA by steric
hindrance. In order to determine if these sites were phosphorylated in Sf9 cells and if phosphorylation
was increased by the addition of phosphatase inhibitors, we chose to
make antisera to synthetic phosphopeptides representing the C-terminal
phosphorylation sites. Rabbit sera produced to a
Ser146-phosphorylated peptide had a strict requirement for
phosphorylation at Ser146 of full-length p21 with the
affinity purified IgG failing to bind to unphosphorylated p21 or p21
phosphorylated at Thr145. By using this reagent, it was
demonstrated that the effect OA had on PCNA binding activity of p21 was
accompanied by stabilization of Ser146 phosphorylation
within the C terminus of p21. A site that we also showed could strongly
inhibit PCNA binding.
In addition to the fact that this immunochemical approach allowed us to
study p21 modification in the absence of DNA-damaging radioisotopes, it
has also provided a valuable reagent that can be used to develop a
site-specific assay for the Ser146 kinase using purified
full-length p21 as a substrate. Although in the current study PKC and
PKA were used as tools to phosphorylate p21 in vitro for
biochemical analysis, there is no evidence that these kinases are
relevant to the physiological regulation of p21 in cells. Thus, we are
currently using the p21-phospho-Ser146 IgG to develop a
sensitive ELISA-based assay to screen for endogenous kinase activity
during fractionation of cell lysates by column chromatography.
The region of p21 involved in binding to PCNA is found within the
C-terminal domain of p21 with residues 140-160 being sufficient to
form a stable interaction with PCNA (37, 39, 60) and to inhibit its
function in DNA replication (39). The crystal structure of human PCNA
complexes with a C-terminal peptide containing the PCNA binding motif
has been solved (60). The structure shows that p21 interacts with the
interdomain connector loop of PCNA and is therefore likely to prevent
the interaction of PCNA with other replication factors. p21 appears to
be anchored to PCNA via hydrogen bonds. In addition, an anti-parallel
-strand structure is formed with the connector, and basic regions of
the peptide form electrostatic interactions with PCNA, and hydrophobic
residues in two regions of the peptide lie in complementary hydrophobic cavities on the surface of PCNA. If the residues that we have identified as phosphorylation sites on p21 are compared with the structure of the PCNA-p21 peptide complex, it is possible to see why
phosphorylation is able to disrupt the interaction of p21 with PCNA, as
all three of the residues are involved in direct interactions with
PCNA. The hydroxyl group of Ser146 contributes to an
intramolecular hydrogen bond stabilizing a 310 helix, and
this amino acid is also part of a hydrophobic cluster that fits into a
corresponding hydrophobic pocket on PCNA. Thus, phosphorylation at this
residue would interfere with secondary structure as well as introducing
a negative charge into a hydrophobic region. Phosphorylation at
Thr145 would similarly disrupt the formation of an
intermolecular hydrogen bond with Pro253 of PCNA, whereas
the hydroxyl group of Ser160 is involved in hydrogen bonds
with both Gly69 and Met119 of PCNA.
Our current data suggest a model where post-translational mechanisms
may contribute to the regulation of p21 by preventing formation of some
complexes and promoting others. Thus, in dividing cells we suggest that
phosphorylation of p21 may suppress formation of a linear complex
between p21 and PCNA and that following exposure to damaging agents
dephosphorylation of the C-terminal regulatory domain would be required
to promote a complex between these two proteins. Additional properties
of p21 that could potentially be subject to regulation by C-terminal
phosphorylation include steady state levels, nuclear localization, and
Cdk4 targeting. As the rate of p21 protein degradation can be
influenced by PCNA binding, C-terminal phosphorylation may be expected
to decrease the absolute level of p21 protein in a cell. The nuclear
localization of p21 and its ability to target cyclin D-Cdk4 complexes
to the nucleus both require an intact C-terminal regulatory domain. A putative bipartite nuclear localization sequence lies between residues
140 and 157, and the C-terminal domain of p21 has been shown by LaBaer
et al. (18) to be essential for the nuclear localization of
cyclin D-Cdk4. Truncation mutants missing the extreme C terminus
disperse throughout the cell, whereas N-terminal deletion constructs
that retain the nuclear localization sequence show strong nuclear
staining (25). Recent reports highlight the importance of p21
subcellular localization for physiological outcome following DNA
damage. Thus, localization of p21 could determine the response to
apoptotic signals with cytoplasmic accumulation of full-length p21
providing protection against apoptotic cell death (4).
 |
ACKNOWLEDGEMENT |
We thank Eleanor Ramsay for valuable technical assistance.
 |
FOOTNOTES |
*
This work was supported by the Cancer Research Campaign.The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
¶
Cancer Research Campaign Senior Cancer Research Fellow. To
whom correspondence should be addressed. Tel.: 44-1382-425582; Fax:
44-1382-669993; E-mail: k.l.ball@dundee.ac.uk.
2
M. T. Scott and K. L. Ball, manuscript
in preparation.
 |
ABBREVIATIONS |
The abbreviations used are:
CDK, cyclin-dependent protein kinase;
PCNA, proliferating cell
nuclear antigen;
aa, amino acid;
NER, nucleotide excision repair;
ELISA, enzyme-linked immunosorbent assay;
DTT, dithiothreitol;
SPR, surface plasmon resonance;
RU, resonance units;
PBS, phosphate-buffered
saline;
PAGE, polyacrylamide gel electrophoresis;
OA, okadaic acid;
HPLC, high pressure liquid chromatography;
PKC, protein kinase C;
PKA, cAMP-dependent protein kinase.
 |
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